• Discovery of predictive biomarkers for cancer therapy through computational approaches.
  Wang X, Nguyen J, Nader K, Miihkinen M, Wall P, Singhal A, Bedard PL, Ideker T, Aittokallio T, Haibe-Kains B.Nat Rev Clin Oncol. 2026 Jan 6. doi: 10.1038/s41571-025-01109-8. Online ahead of print. PMID: 41495240 Review.

• Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D. Chowdhury B, Zhu K, Li C, Alsing J, Luebeck J, Stefanova ME, Chapman OS, Kraft K, Zhang S, Lim JYS, Xie Y, Kim YJ, Wu S, Chavez L, Nir G, Henssen AG, Mischel PS, Chang HY, Bafna V.Nat Commun. 2025 Dec 20. doi: 10.1038/s41467-025-67614-7. Online ahead of print. PMID: 41422275 Free article.

• Widespread Epistasis between Cancer Driver Mutations and Allele-Specific Copy Number Variations. Merzliakov S, Dong G, Castro A, Bihie M, Nichols-Evans Y, Carter H, Huang KL.bioRxiv [Preprint]. 2025 Dec 14:2025.12.11.693698. doi: 10.64898/2025.12.11.693698. PMID: 41415395 Free PMC article.

• Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations. Cao Y, Patel L, Alcoser L, Mendenhall E, Benner C, Heinz S, Goren A.Genome Res. 2026 Jan 5;36(1):129-141. doi: 10.1101/gr.281320.125. PMID: 41386983

Discovery of predictive biomarkers for cancer therapy through computational approaches. Wang X, Nguyen J, Nader K, Miihkinen M, Wall P, Singhal A, Bedard PL, Ideker T, Aittokallio T, Haibe-Kains B.Nat Rev Clin Oncol. 2026 Jan 6. doi: 10.1038/s41571-025-01109-8. Online ahead of print.PMID: 41495240 Review.

Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D. Chowdhury B, Zhu K, Li C, Alsing J, Luebeck J, Stefanova ME, Chapman OS, Kraft K, Zhang S, Lim JYS, Xie Y, Kim YJ, Wu S, Chavez L, Nir G, Henssen AG, Mischel PS, Chang HY, Bafna V.Nat Commun. 2025 Dec 20. doi: 10.1038/s41467-025-67614-7. Online ahead of print.PMID: 41422275 Free article.

Widespread Epistasis between Cancer Driver Mutations and Allele-Specific Copy Number Variations. Merzliakov S, Dong G, Castro A, Bihie M, Nichols-Evans Y, Carter H, Huang KL.bioRxiv [Preprint]. 2025 Dec 14:2025.12.11.693698. doi: 10.64898/2025.12.11.693698.PMID: 41415395 Free PMC article. Preprint.

 

Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations. Cao Y, Patel L, Alcoser L, Mendenhall E, Benner C, Heinz S, Goren A. Genome Res. 2026 Jan 5;36(1):129-141. doi: 10.1101/gr.281320.125.PMID: 41386983

Germline Pathogenic Variants Among Women Without a History of Breast Cancer: A Secondary Analysis of the WISDOM Randomized Clinical Trial. Fergus KB, Ross KS, Scheuner MT, Blanco AM, Tice JA, Ziv E, Shieh Y, van 't Veer L, Olopade OI, Goodman DL, Tong BS, Harvey H, DeRosa D, Risty L, Silver E, Kaster A, Fiscalini AS, Blum K, Heise R, Sabacan L, Heditsian D, Brain S, Petruse A, Eklund M, Hiatt RA, Borowsky AD, Naeim A, Park HL, LaCroix AZ, Parker BA, Lancaster R, Esserman J, Wenger N, Arasu V, Anton-Culver H, Esserman LJ, Madlensky L.JAMA Intern Med. 2025 Dec 12:e257323. doi: 10.1001/jamainternmed.2025.7323. Online ahead of print.PMID: 41385723

Risk-Based vs Annual Breast Cancer Screening: The WISDOM Randomized Clinical Trial. Esserman LJ, Fiscalini AS, Naeim A, Van't Veer LJ, Kaster A, Scheuner MT, LaCroix AZ, Borowsky AD, Anton-Culver H, Olopade OI, Esserman J, Lancaster R, Madlensky L, Blanco AM, Ross KS, Goodman DL, Tong BS, Hogarth M, Heditsian D, Brain S, Lee V, Blum K, Kim MO, Sabacan LP, Fergus KB, Yau C, Park HL, Parker BA, Kaplan C, Rhoads KF, Eder S, Adduci K, Matthews JB, Wenger NS, Shieh Y, Hiatt RA, Ziv E, Tice JA, Eklund M.JAMA. 2025 Dec 12:e2524784. doi: 10.1001/jama.2025.24784. Online ahead of print.PMID: 41385349

Chromothripsis and ecDNA initiated by N4BP2 nuclease fragmentation of cytoplasm-exposed chromosomes. Krupina K, Goginashvili A, Baughn MW, Moore S, Steele CD, Nguyen AT, Zhang DL, Koeppel J, Trivedi P, Malhotra A, Jenkins D, Shiau AK, Miyake Y, Koga T, Miki S, Furnari FB, Campbell PJ, Alexandrov LB, Cleveland DW.Science. 2025 Dec 11;390(6778):1156-1163. doi: 10.1126/science.ado0977. Epub 2025 Dec 11.PMID: 41379955

Modeling nonlinear and interaction effects of spatiotemporal and other non-genetic factors improves phenotypic prediction for complex traits. DeVito R, Gymrek M.medRxiv [Preprint]. 2025 Nov 28:2025.11.26.25341090. doi: 10.1101/2025.11.26.25341090.PMID: 41358300 Free PMC article. Preprint.

Unifying proteomic technologies with ProteinProjector. Schaffer LV, Jain M, Nasser R, Sharan R, Ideker T. Bioinform Adv. 2025 Oct 22;5(1):vbaf266. doi: 10.1093/bioadv/vbaf266. eCollection 2025.PMID: 41357305 Free PMC article.

Genome-wide selection inference at short tandem repeats. Huang B, Durvasula A, Mousavi N, Ziaei-Jam H, Maksimov M, Lohmueller KE, Gymrek M.PLoS Genet. 2025 Dec 1;21(12):e1011959. doi: 10.1371/journal.pgen.1011959. eCollection 2025 Dec.PMID: 41325473 Free PMC article.

igv-reports: Embedding interactive genomic visualizations in HTML reports to aid variant review. Robinson JT, Thorvaldsdottir H, Mesirov JP. bioRxiv [Preprint]. 2025 Nov 10:2025.10.29.685397. doi: 10.1101/2025.10.29.685397. PMID: 41278691 

 Tulp3 quantitative alleles titrate requirements for viability, brain development, and kidney homeostasis but do not suppress Zfp423 mutations in mice. McCoy CA, Concepcion D, Mezody MG, Lara RZ, Deshpande O, Liang C, Long R, Hamilton BA.PLoS Genet. 2025 Oct 15;21(10):e1011911. doi: 10.1371/journal.pgen.1011911. eCollection 2025 Oct.PMID: 41091799 Free PMC article.

Nonequivalence of Zfp423 premature termination codons in mice. Concepcion D, Liang C, Kim D, Hamilton BA.Genetics. 2025 Oct 8;231(2):iyaf164. doi: 10.1093/genetics/iyaf164.PMID: 40825037 Free PMC article.

Interferon Restores Antigen Presentation and Sensitizes Medulloblastoma to T Cell Killing. Eisemann T, Masihi MB, Tzaridis T, Pister V, Youm I, Chambers KR, Dutta A, Wenzel AT, Chin K, Pomeroy SL, Mesirov JP, Fraenkel E, Bagchi A, Chavez L, Wechsler-Reya RJ. bioRxiv [Preprint]. 2025 Oct 2:2025.09.30.679624. doi: 10.1101/2025.09.30.679624. PMID: 41256535 

Extrachromosomal DNA associates with poor survival across a broad spectrum of childhood solid tumors. Chapman OS, Sridhar S, Chow EY, Kenkre R, Kirkland J, Dutta A, Wang S, Zhang W, Brown M, Luebeck J, Lo YY, Rodriguez-Fos E, Henssen AG, Okonechnikov K, Ghasemi DR, Pajtler KW, Kawauchi D, Bafna V, Paul M, Yip K, Mesirov JP, Chavez L. medRxiv [Preprint]. 2025 Aug 7:2025.07.22.24308163. doi: 10.1101/2025.07.22.24308163. PMID: 40778132 

A Systematic Review with a Demonstrative Case of KIT and DOG-1 Expressing Gastrointestinal Stromal Tumors Harboring ETV6-NTRK3 Fusions. Ranjbarian T, Antkowiak M, Mallory RJ, Doherty TM, Hosseini M, Mesirov JP, Fanta PT, Sicklick JK. Clin Cancer Res. 2025 May 15;31(10):2056-2061. doi: 10.1158/1078-0432.CCR-24-3203. PMID: 39992648 

Inactivation of Histone Chaperone HIRA Unmasks a Link Between Normal Embryonic Development of Melanoblasts and Maintenance of Adult Melanocyte Stem Cells. Jaber-Hijazi F, Arnold R, Swaminathan K, Gilroy K, Wenzel AT, Lagnado A, Kirschner K, Robertson N, Reid C, Fullarton N, Pawlikowski J, Rai TS, Baranyk I, Shi CH, Yip KY, Blyth K, Mesirov JP, Harris ML, Passos JF, Machesky LM, Adams PD. Aging Cell. 2025 Jul;24(7):e70070. doi: 10.1111/acel.70070. Epub 2025 May 14. PMID: 40669469 

 Genomics to Notebook (g2nb): Extending the Electronic Notebook to Address the Challenges of Bioinformatics Analysis. Reich M, Tabor T, Liefeld T, Joshi J, Kim F, Huang E, Thorvaldsdottir H, Blankenberg D, Mesirov JP. J Bioinform Syst Biol. 2025;8(1):1-7. doi: 10.26502/jbsb.5107096. Epub 2025 Jan 27. PMID: 40191160 

Osgood NRB, Zawalick NM, Sawyer CB, Cowan QT, Gu S, Mawson SJ, Ranzau BL, Li L, Gymrek M, Goren A, Komor AC. Genome editing with programmable base editors in human cells. (2025) Methods Enzymol.

Faraji F, Ramirez SI, Clubb LM, Sato K, Burghi V, Hoang TS, Officer A, Anguiano Quiroz PY, Galloway WMG, Mikulski Z, Medetgul-Ernar K, Marangoni P, Jones KB, Cao Y, Molinolo AA, Kim K, Sakaguchi K, Califano JA 3rd, Smith Q, Goren A, Klein OD, Tamayo P, Gutkind JS. YAP-driven malignant reprogramming of oral epithelial stem cells at single cell resolution. (2025) Nat Commun. [link]

 Stevens I, Pacia D, Hansen JN, Parker J, Payne-Foster P, Ideker T, Bélisle-Pipon JC, Ravitsky V. Towards the ethical development of functional genomics research. Trends Biotechnol. 2025 Oct 30:S0167-7799(25)00443-3. doi: 10.1016/j.tibtech.2025.10.015. Online ahead of print. PMID: 41173722 [PubMed] [PDF]

Leah V Schaffer, Mayank Jain, Rami Nasser, Roded Sharan, Trey Ideker. Unifying proteomic technologies with ProteinProjector. Bioinformatics Advances, vbaf266, https://doi.org/10.1093/bioadv/vbaf266. 22 October 2025. [PubMed] [PDF]

Datasets: ProteinProjector is available as part of the Cell Mapping Toolkit at https://github.com/idekerlab/cellmaps_coembedding

Campos AD, Shepard RM, Ortega Z, Heumann I, Wilke AE, Nam A, Cable C, Kouhmareh K, Klemke R, Mattson NM, Ideker T, De Arruda Saldanha C, Heinz S, Weaver V, Von Schalscha T, Wettersten HI, Weis SM, Cheresh DA. A STAT3/integrin axis accelerates pancreatic cancer initiation and progression. Cell Rep. 2025 Aug 26;44(8):116010. doi: 10.1016/j.celrep.2025.116010. Epub 2025 Jul 22. PMID: 40701148 [PubMed] [PDF]  

Noller K, Botsis T, Camara PG, Ciotti L, Cooper LA, Goecks J, Griffith M, Haas BJ, Ideker T, Karchin R, Kontos D, Lai J, Marcus D, Meyer CA, Naegle K, Pati S, Peters B, Pratt D, Raphael BJ, Reich M, Savova GK, Wright C, Fertig EJ, Bakas S. Informatics at the Frontier of Cancer Research. Cancer Res. 2025 Aug 15;85(16):2967-2986. doi: 10.1158/0008-5472.CAN-24-2829. PMID: 40600473 [PubMed] [PDF]

Ono K, Fong D, Gao C, Churas C, Pillich R, Lenkiewicz J, Pratt D, Pico AR, Hanspers K, Xin Y, Morris J, Kucera M, Franz M, Lopes C, Bader G, Ideker T, Chen J.  Cytoscape Web: bringing network biology to the browser. Nucleic Acids Res. 2025 Jul 7;53(W1):W203-W212. doi: 10.1093/nar/gkaf365. PMID: 40308211 [PubMed] [PDF] 

Zhao H, Ideker T, Wong STC. Artificial Intelligence-Powered Insights into Polyclonality and Tumor Evolution. Research (Wash D C). 2025 Jul 2;8:0765. doi: 10.34133/research.0765. eCollection 2025. PMID: 40607324  [PubMed] [PDF]

Kim H, Bae B, Park M, Shin Y, Ideker T, Nam H. A genotype-to-drug diffusion model for generation of tailored anti-cancer small molecules. Nat Commun. 2025 Jul 1;16(1):5628. doi: 10.1038/s41467-025-60763-9. PMID: 40593549 [PubMed] [PDF]

Yin X, Pu Y, Yuan S, Pache L, Churas C, Weston S, Riva L, Simons LM, Cisneros WJ, Clausen T, Biddle G, Doss-Gollin S, Deming M, De Jesus PD, Kim HN, Fuentes D, Whitelock JM, Esko JD, Lord MS, Mena I, García-Sastre A, Hultquist JF, Frieman MB, Ideker T, Pratt D, Martin-Sancho L, Chanda SK. Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection. PLoS Biol. 2025 Jun 12;23(6):e3002738. doi: 10.1371/journal.pbio.3002738. eCollection 2025 Jun. PMID: 40504864 [PubMed] [PDF]

Lenkiewicz J† , Churas C† , Hu M, Qian G, Jain M, Levinson MA, Al Manir S, Qin Y, Fong D, Ono K, Chen J, Gao C, Pratt D, Parker JA, Clark T, Ideker T*, Schaffer LV*. Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization. Bioinformatics. 2025 Jun 2;41(6):btaf205. doi: 10.1093/bioinformatics/btaf205. PMID: 40489639 [PubMed] [PDF] †Equal contribution *Corresponding authors [PubMed] [PDF] 

Baron M, Tagore M, Wall P, Zheng F, Barkley D, Yanai I, Yang J, Kiuru M, White RM, Ideker T. Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation. Nat Genet. 2025 May;57(5):1179-1188. doi: 10.1038/s41588-025-02163-9. Epub 2025 Apr 16. PMID: 40240879 [PubMed] [PDF] 

Lee I, Wallace ZS, Wang Y, Park S, Nam H, Majithia AR, Ideker T. A genotype-phenotype transformer to assess and explain polygenic risk. bioRxiv [Preprint]. 2025 Apr 11:2024.10.23.619940. doi: 10.1101/2024.10.23.619940. PMID: 40291728 [PubMed] [PDF]

Schaffer LV, Hu M, Qian G, Moon KM, Pal A, Soni N, Latham AP, Pontano Vaites L, Tsai D, Mattson NM, Licon K, Bachelder R, Cesnik A, Gaur I, Le T, Leineweber W, Palar A, Pulido E, Qin Y, Zhao X, Churas C, Lenkiewicz J, Chen J, Ono K, Pratt D, Zage P, Echeverria I, Sali A, Harper JW, Gygi SP, Foster LJ, Huttlin EL, Lundberg E, Ideker T. Multimodal cell maps as a foundation for structural and functional genomics. Nature. 2025 Apr 9. doi: 10.1038/s41586-025-08878-3. Online ahead of print. PMID: 40205054 [PubMed] [PDF] [Published Erratum]

Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. Nat Aging. 2025 Apr;5(4):709-719. doi: 10.1038/s43587-024-00794-x. Epub 2025 Jan 13. PMID: 39806003 [PubMed] [PDF]

Kumar V, Hevener AL, Ruby JG, Sebastiani P, Kuchel GA; Participants of the NIA Heterogeneity and Successful Aging Workshop. Workshop Report-Heterogeneity and Successful Aging Part II: Approaches to Investigate Heterogeneity in Aging Research. J Gerontol A Biol Sci Med Sci. 2025 Apr 7;80(5):glaf021. doi: 10.1093/gerona/glaf021. PMID: 40257451 [PubMed] [PDF] 

MICAL2 Promotes Pancreatic Cancer Growth and Metastasis. Garg B, Khan S, Courelli AS, Panneerpandian P, Sheik Pran Babu D, Mose ES, Gulay KCM, Sharma S, Sood D, Wenzel AT, Martsinkovskiy A, Rajbhandari N, Patel J, Jaquish D, Esparza E, Jaque K, Aggarwal N, Lambies G, D'Ippolito A, Austgen K, Johnston B, Orlando DA, Jang GH, Gallinger S, Goodfellow E, Brodt P, Commisso C, Tamayo P, Mesirov JP, Tiriac H, Lowy AM. Cancer Res. 2025 Mar 14;85(6):1049-1063. doi: 10.1158/0008-5472.CAN-24-0744. PMID: 39745352

Mei Y, Gosztyla ML, Tan X, Dozier LE, Wilkinson B, McKetney J, Lee J, Chen M, Tsai D, Kopalle H, Gritsenko MA, Hartel N, Graham NA, Flores I, Gilmore-Hall SK, Xu S, Marquez CA, Liu SN, Fong D, Chen J, Licon K, Hong D, Wright SN, Kreisberg JF, Nott A, Smith RD, Qian WJ, Swaney DL, Iakoucheva LM, Krogan NJ, Patrick GN, Zhou Y, Feng G, Coba MP, Yeo GW, Ideker T. Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders. Cell Syst. 2025 Mar 3:101204. doi: 10.1016/j.cels.2025.101204. Online ahead of print. PMID: 40054464 [PubMed] [PDF]

Begzati A, Godinez-Macias KP, Long T, Watrous JD, Moranchel R, Kantz ED, Tuomilehto J, Havulinna AS, Niiranen TJ, Jousilahti P, Salomaa V, Yu B, Norby F, Rebholz CM, Selvin E, Winzeler EA, Cheng S, Alotaibi M, Goyal R, Ideker T, Jain M, Majithia AR. Plasma Lipid Metabolites, Clinical Glycemic Predictors, and Incident Type 2 Diabetes. Diabetes Care. 2025 Mar 1;48(3):473-480. doi: 10.2337/dc24-2266. PMID: 39761415 [PubMed] [PDF]

Turnham RE, Pitea A, Jang GM, Xu Z, Lim HC, Choi AL, Von Dollen J, Levin RS, Webber JT, McCarthy E, Hu J, Li X, Che L, Singh A, Yoon A, Chan GKL, Kelley RK, Swaney DL, Zhang W, Bandyopadhyay S, Theis FJ, Eckhardt M, Chen X, Shokat KM, Ideker T, Krogan NJ, Gordan JD. HBV Remodels PP2A Complexes to Rewire Kinase Signaling in Hepatocellular Carcinoma. Cancer Res. 2025 Feb 17;85(4):660-674. doi: 10.1158/0008-5472.CAN-24-0456. PMID: 39652575 [PubMed] [PDF]

Singhal A, Zhao X, Wall P, So E, Calderini G, Partin A, Koussa N, Vasanthakumari P, Narykov O, Zhu Y, Jones SE, Abbas-Aghababazadeh F, Kadambat Nair S, Bélisle-Pipon JC, Jayaram A, Parker BA, Yeung KT, Griffiths JI, Weil R, Nath A, Haibe-Kains B, Ideker T. The Hallmarks of Predictive Oncology. Cancer Discovery. 2025 Feb 7;15(2):271-285. doi: 10.1158/2159-8290.CD-24-0760. PMID: 39760657 [PubMed] [PDF] (Review)

Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. State of the interactomes: an evaluation of molecular networks for generating biological insights. Mol Syst Biol. 2025 Jan;21(1):1-29. doi: 10.1038/s44320-024-00077-y. Epub 2024 Dec 9. PMID: 39653848 [PubMed] [PDF]  

Garg B, Khan S, Courelli AS, Panneerpandian P, Sheik Pran Babu D, Mose ES, Gulay KCM, Sharma S, Sood D, Wenzel AT, Martsinkovskiy A, Rajbhandari N, Patel J, Jaquish D, Esparza E, Jaque K, Aggarwal N, Lambies G, D'Ippolito A, Austgen K, Johnston B, Orlando DA, Jang GH, Gallinger S, Goodfellow E, Brodt P, Commisso C, Tamayo P, Mesirov JP, Tiriac H, Lowy AM. MICAL2 Promotes Pancreatic Cancer Growth and Metastasis. Cancer Res. 2025 Jan 2. doi: 10.1158/0008-5472.CAN-24-0744. Epub ahead of print. PMID: 39745352.

Matteo D'Antonio, Wilfredo G Gonzalez Rivera, Robert A Greenes, Melissa Gymrek, Kelly A Frazer. (2025) A highly accurate risk factor-based XGBoost multiethnic model for identifying patients with skin cancer. Nature Communications. [Article]

Ibra Lujumba, Yagoub Adam, Helyaneh Ziaei Jam, Itunuoluwa Isewon, Nomakhosazana Monnakgotla, Yang Li, Blessing Onyido, Kakembo Fredrick, Faith Adegoke, Jerry Emmanuel, Jumoke Adeyemi, Olajumoke Ibitoye, Samuel Owusu-Ansah, Matthew Boladele Akanle, Habi Joseph, Mike Nsubuga, Ronald Galiwango, Martin Okitwi, Namuswe Magdalene, Odur Walter, Zama Mngadi, Marion Adebiyi, Jelili Oyelade, Melissa Nel, Daudi Jjingo, Melissa Gymrek, Ezekiel Adebiyi. (2025) A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools. Nat Protoc. [Article]

Nicola R B Osgood, Natalie M Zawalick, Courtney B Sawyer, Quinn T Cowan, Sifeng Gu, S J Mawson, Brodie L Ranzau, Lehan Li, Melissa Gymrek, Alon Goren, Alexis C Komor. (2025) Genome editing with programmable base editors in human cells. Methods Enzymol. [Article]

Matteo D'Antonio, Timothy D Arthur, Wilfredo G Gonzalez Rivera, Ximei Wu, Jennifer P Nguyen, Melissa Gymrek, Park Woo-Yeong, Kelly A Frazer. (2025) Genetic analysis of elevated levels of creatinine and cystatin C biomarkers reveals novel genetic loci associated with kidney function. Hum Mol Genet. [Article ]

 

2024

Talwar JV, Klie A, Pagadala MS, Carter H. GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies. Bioinformatics. 2024 Aug;40(8).

Ozturk K, Panwala R, Sheen J, Ford K, Jayne N, Portell A, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P. Interface-guided phenotyping of coding variants in the transcription factor RUNX1. Cell Reports. 2024 Jul 23;43(7).

Jado JC, Dow M, Carolino K, Klie A, Fonseca GJ, Ideker T, Carter H, Winzeler EA. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Scientific Reports. 2024 Jun 18;14(1):13989.

Mah CK, Ahmed N, Lopez NA, Lam DC, Pong A, Monell A, Kern C, Han Y, Prasad G, Cesnik AJ, Lundberg E. Bento: a toolkit for subcellular analysis of spatial transcriptomics data. Genome Biology. 2024 Apr 2;25(1):82.

Sears TJ, Pagadala MS, Castro A, Lee K, Kong JH, Tanaka K, Lippman S, Zanetti M, Carter H. Integrated germline and somatic features reveal divergent immune pathways driving ICB response. Cancer Immunology Research. 2024 Sep 10.

Patel LA, Cao Y, Mendenhall EM, Benner C^#, Goren A^# The Wild West of spike-in normalization. (2024) Nat Biotechnol. [link]

Aarushi Sehgal, Helyaneh Ziaei Jam, Andrew Shen, Melissa Gymrek. (2024) Genome-wide detection of somatic mosaicism at short tandem repeats. Bioinformatics. [Article] [github]

Helyaneh Ziaei Jam, Justin M Zook, Sara Javadzadeh, Jonghun Park, Aarushi Sehgal, Melissa Gymrek. (2024) LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads. Genome Biology. [Article] [github]

Michael Lamkin, Melissa Gymrek. (2024) The emerging role of tandem repeats in complex traits. Nature Reviews Genetics. [Article] (Comment)

Adam C English, Egor Dolzhenko, Helyaneh Ziaei Jam, Sean K McKenzie, Nathan D Olson, Wouter De Coster, Jonghun Park, Bida Gu, Justin Wagner, Michael A Eberle, Melissa Gymrek, Mark J P Chaisson, Justin M Zook, Fritz J Sedlazeck. (2024) Analysis and benchmarking of small and large genomic variants across tandem repeats. Nature Biotechnology. [Article]

Fong SH. A blueprint to discovering synthetic lethal gene interactions for precision oncology. Nature Genetics. 2024 Dec 3. https://doi.org/10.1038/s41588-024-02024-x [PDF] (Research Briefing to accompany Fong, et al. Nature Genetics. 2024 Nov) 

Hu M, Alkhairy S, Lee I, Pillich RT, Fong D, Smith K, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. Nat Methods. 2024 Nov 28. doi: 10.1038/s41592-024-02525-x. Online ahead of print. PMID: 39609565 [PubMed] [PDF]

Fong SH, Kuenzi BM, Mattson NM, Lee J, Sanchez K, Bojorquez-Gomez A, Ford K, Munson BP, Licon K, Bergendahl S, Shen JP, Kreisberg JF, Mali P, Hager JH, White MA, Ideker T. A multilineage screen identifies actionable synthetic lethal interactions in human cancers. Nature Genetics. 2024 Nov 18. doi: 10.1038/s41588-024-01971-9. Online ahead of print. PMID: 39558023 [PubMed] [PDF] [Published Erratum] 

Hu M, Ideker T. Putting proteins in context. Cell Systems.  2024 Nov 28. doi: 10.1038/s41592-024-02525-x. Online ahead of print. PMID: 39609565 [PubMed] [PDF] (Review)

Kong J, Zhao X, Singhal A, Park S, Bachelder R, Shen J, Zhang H, Moon J, Ahn C, Ock CY, Carter H, Ideker T. Prediction of immunotherapy response using mutations to cancer protein assemblies. Science Advances. 2024 Sep 20;10(38):eado9746. doi: 10.1126/sciadv.ado9746. Epub 2024 Sep 20. PMID: 39303028 [PubMed] [PDF] 

Nasser R, Schaffer LV, Ideker T, Sharan R. Multi-modal contrastive learning of subcellular organization using DICE. Bioinformatics. 2024 Sep 1;40(Suppl 2):ii105-ii110. doi: 10.1093/bioinformatics/btae387. PMID: 39230695  [PubMed] [PDF]

Megagiannis P*, Mei Y*, Yan RE, Yuan L, Wilde JJ, Eckersberg H, Suresh R, Tan X, Chen H, Farmer WT, Cha K, Le PU, Catoire H, Rochefort D, Kwan T, Yee BA, Dion P, Krishnaswamy A, Cloutier JF, Stifani S, Petrecca K, Yeo GW, Murai KK, Feng G, Rouleau GA, Ideker T, Sanjana NE, Zhou Y. Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes. Cell Reports. 2024 Aug 27;43(8):114637. doi: 10.1016/j.celrep.2024.114637. Epub 2024 Aug 17. PMID: 39154337  [PubMed] [PDF] *Equal Contribution

Cesnik A*, Schaffer LV*, Gaur I, Jain M, Ideker T, Lundberg E. Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes. Annu Rev Biomed Data Sci. 2024 Aug;7(1):369-389. doi: 10.1146/annurev-biodatasci-102423-113534. Epub 2024 Jul 24. PMID: 38748859 *Equal Contribution [PubMed] [PDF] (Review)

Ozturk K, Panwala R, Sheen J, Ford K, Jayne N, Portell A, Zhang DE, Hutter S, Haferlach T, Ideker T, Mali P, Carter H. Interface-guided phenotyping of coding variants in the transcription factor RUNX1. Cell Reports. 2024 Jul 4;43(7):114436. doi: 10.1016/j.celrep.2024.114436. Online ahead of print. PMID: 38968069 [PubMed] [PDF]

Yin X, Pu Y, Yuan S, Pache L, Churas C, Weston S, Riva L, Simons LM, Cisneros WJ, Clausen T, De Jesus PD, Kim HN, Fuentes D, Whitelock J, Esko J, Lord M, Mena I, García-Sastre A, Hultquist JF, Frieman MB, Ideker T, Pratt D, Martin-Sancho L, Chanda SK. Global siRNA Screen Reveals Critical Human Host Factors of SARS-CoV-2 Multicycle Replication. bioRxiv [Preprint]. 2024 Jul 10:2024.07.10.602835. doi: 10.1101/2024.07.10.602835. PMID: 39026801 [PubMed]

Park S*, Silva E*, Singhal A*, Kelly MR, Licon K, Panagiotou I, Fogg C, Fong S, Lee JJY, Zhao X, Bachelder R, Parker BA, Yeung KT, Ideker T. A deep learning model of tumor cell architecture elucidates response and resistance to CDK4/6 inhibitors. Nat Cancer. 2024 Jul;5(7):996-1009. doi: 10.1038/s43018-024-00740-1. Epub 2024 Mar 5. PMID: 38443662; PMCID: PMC11286358. *Equal Contribution [PubMed] [PDF]

Wall P, Ideker T. Representing mutations for predicting cancer drug response. Bioinformatics. 2024 Jun 28;40(Supplement_1):i160-i168. doi: 10.1093/bioinformatics/btae209. PMID: 38940147 [PubMed] [PDF]

Leger BS, Meredith JJ, Ideker T, Sanchez-Roige S, Palmer AA. Rare and common variants associated with alcohol consumption identify a conserved molecular network. Alcohol, Clinical and Experimental Research.  21 June 2024 https://doi.org/10.1111/acer.15399 [PubMed] [PDF]

Jado JC*, Dow M*, Carolino K, Klie A, Fonseca GJ, Ideker T, Carter H, Winzeler EA. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. Sci Rep. 2024 Jun 18;14(1):13989. doi: 10.1038/s41598-024-63943-7. PMID: 38886371 *Equal Contribution [PubMed] [PDF]

Clark T†, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S†, Bélisle-Pipon JC, Brandt C†, Chen J†, Ding Y†, Fodeh S†, Krogan N†, Lundberg E†, Mali P†, Payne-Foster P†, Ratcliffe S†, Ravitsky V†, Sali A†, Schulz W†, Ideker T. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv [Preprint]. 2024 May 24:2024.05.21.589311. doi: 10.1101/2024.05.21.589311. PMID: 38826258 †Co-Corresponding Authors [bioRxiv] [PDF] (Preprint)

Munson BP, Chen M, Bogosian A, Kreisberg JF, Licon K, Abagyan R, Kuenzi BM, Ideker T. De novo generation of multi-target compounds using deep generative chemistry. Nat Commun. 2024 May 6;15(1):3636. doi: 10.1038/s41467-024-47120-y. PMID: 38710699  [PubMed] [PDF]

Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. State of the Interactomes: an evaluation of molecular networks for generating biological insights. bioRxiv [Preprint]. 2024 Apr 29:2024.04.26.587073. doi: 10.1101/2024.04.26.587073. PMID: 38746239. [PubMed] [PDF] (Preprint) 

Hu M, Alkhairy S, Lee I, Pillich RT, Fong D, Smith K, Bachelder R, Ideker T, Pratt D. Evaluation of large language models for discovery of gene set function. ArXiv [Preprint]. 2024 Apr 1:arXiv:2309.04019v2. PMID: 37731657 [PubMed] [PDF](Preprint) 

Zhao X*, Singhal A*, Park S, Kong J, Bachelder R, Ideker T. Cancer mutations converge on a collection of protein assemblies to predict resistance to replication stress. Cancer Discovery. 2024 Mar 1;14(3):508-523. doi: 10.1158/2159-8290.CD-23-0641. PMID: 38236062  *Equal Contribution [PubMed] [PDF]

Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv [Preprint]. 2024 Feb 8:2023.12.03.569805. doi: 10.1101/2023.12.03.569805. PMID: 38076945 [PubMed] [PDF] (Preprint)

Sen SK, Green ED, Hutter CM, Craven M, Ideker T, Di Francesco V. Opportunities for basic, clinical, and bioethics research at the intersection of machine learning and genomics. Cell Genomics. 2024 Jan 10;4(1):100466. doi: 10.1016/j.xgen.2023.100466. Epub 2023 Dec 15. PMID: 38190108 [PubMed] [PDF] (Review)

Hu M, Zhang X, Latham A, Šali A, Ideker T, Lundberg E. Tools for assembling the cell: Towards the era of cell structural bioinformatics. Pac Symp Biocomput. 2024;29:661-665. PMID: 38160316. [PubMed] [PDF]

Klemm JD, Singer DS, Mesirov JP. Transforming Cancer Research through Informatics. Cancer Discov. 2024 Oct 4;14(10):1779-1782. doi: 10.1158/2159-8290.CD-24-0604. PMID: 39363746; PMCID: PMC11463720.

Panda A, Suvakov M, Thorvaldsdottir H, Mesirov JP, Robinson JT, Abyzov A. Genome-wide analysis and visualization of copy number with CNVpytor in igv.js. Bioinformatics. 2024 Aug 2;40(8):btae453. doi: 10.1093/bioinformatics/btae453. PMID: 39018173; PMCID: PMC11303504.

Garg B, Khan S, Babu DS, Mose E, Gulay K, Sharma S, Sood D, Wenzel AT, Martsinkovskiy A, Patel J, Jaquish D, Lambies G, D'Ippolito A, Austgen K, Johnston B, Orlando D, Jang GH, Gallinger S, Goodfellow E, Brodt P, Commisso C, Tamayo P, Mesirov JP, Tiriac H, Lowy AM. MICAL2 Is a Super Enhancer Associated Gene that Promotes Pancreatic Cancer Growth and Metastasis. bioRxiv [Preprint]. 2024 Jun 30:2024.06.26.600548. doi: 10.1101/2024.06.26.600548. PMID: 38979336; PMCID: PMC11230455.

Gold MP, Ong W, Masteller AM, Ghasemi DR, Galindo JA, Park NR, Huynh NC, Donde A, Pister V, Saurez RA, Vladoiu MC, Hwang GH, Eisemann T, Donovan LK, Walker AD, Benetatos J, Dufour C, Garzia L, Segal RA, Wechsler-Reya RJ, Mesirov JP, Korshunov A, Pajtler KW, Pomeroy SL, Ayrault O, Davidson SM, Cotter JA, Taylor MD, Fraenkel E. Developmental basis of SHH medulloblastoma heterogeneity. Nat Commun. 2024 Jan 8;15(1):270. doi: 10.1038/s41467-023-44300-0. PMID: 38191555; PMCID: PMC10774283.

2023

Klie A, Laub D, Talwar JV, Stites H, Jores T, Solvason JJ, Farley EK, Carter H. Predictive analyses of regulatory sequences with EUGENe. Nature Computational Science. 2023 Nov;3(11):946-56.

Pagadala M, Sears T, Wu VH, Perez-Guijarro E, Kim H, Castro A, Talwar J, Gonzalez-Colin C, Cao S, Schmiedel B, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harsimendy H, Patel SP, Alexandrov L, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind SJ, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nature Communications. 2023 May 12;14(1):2744. PMID: 37173324

Castro A, Goodman A, Rane Z, Talwar J, Frampton G, Morris G, Lippman S, Zhang X, Kurzrock R, Carter H Autoimmune HLA Alleles and Neoepitope Presentation Predict Post-Allogenic Transplant Relapse. Journal of Immunotherapy and Precision Oncology. 2023 May 15. PMID: 37637234

Talwar JV, Laub D, Pagadala MS, Castro A, Lewis M, Luebeck GE, Gorman BR, Pan C, Dong FN, Markianos K, Teerlink CC, Lynch J, Hauger R, Pyarajan S, Tsao PS, Morris GP, Salem RM, Thompson WK, Curtius K, Zanetti M, Carter H. Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility. Am J Hum Genet. 2023 Jul 6;110(7):1138-1161. doi: 10.1016/j.ajhg.2023.05.013. Epub 2023 Jun 19. PMID: 37339630

Prasad Trivedi, Christopher D Steele, Franco K C Au, Ludmil B Alexandrov, Don W Cleveland. Mitotic tethering enables inheritance of shattered micronuclear chromosomes. Nature. 2023 Jun;618(7967):1049-1056. DOI: 10.1038/s41586-023-06216-z.  Epub 2023 Jun 14. PMID: 37316668

Li JSZ, Abbasi A, Kim DH, Lippman SM, Alexandrov LB, Cleveland DW. Chromosomal fragile site breakage by EBV-encoded EBNA1 at clustered repeats. Nature. 2023 Apr;616(7957):504-509. DOI: 10.1038/s41586-023-05923-x. Epub 2023 Apr 12. PMID: 37046091

McMahon MA, Rahdar M, Mukhopadhyay S, Bui HH, Hart C, Damle S, Courtney M, Baughn MW, Cleveland DW, Bennett CF. GOLGA8 increases bulk antisense oligonucleotide uptake and activity in mammalian cells. Mol Ther Nucleic Acids. 2023 Mar 27;32:289-301. DOI: 10.1016/j.omtn.2023.03.017. PMID: 37096163; PMCID: PMC10122063

Baughn MW, Melamed Z, López-Erauskin J, Beccari MS, Ling K, Zuberi A, Presa M, Gonzalo-Gil E, Maimon R, Vazquez-Sanchez S, Chaturvedi S, Bravo-Hernández M, Taupin V, Moore S, Artates JW, Acks E, Ndayambaje IS, Agra de Almeida Quadros AR, Jafar-Nejad P, Rigo F, Bennett CF, Lutz C, Lagier-Tourenne C, Cleveland DW. Mechanism of STMN2 cryptic splice-polyadenylation and its correction for TDP-43 proteinopathies. Science. 2023 Mar 17;379(6637):1140-1149. DOI: 10.1126/science.abq5622. Epub 2023 Mar 16. PMID: 36927019.

Margoliash J, Fuchs S, Li Y, Zhang X, Massarat A, Goren A^# & Melissa Gymrek^#.
Polymorphic short tandem repeats make widespread contributions to blood and serum traits. (2023) Cell Genom. [link]; Accompanying perspective [link]

Maksimov MO, Wu C, Ashbrook DG, Villani F, Colonna V, Mousavi N, Ma N, Lu L, Pritchard JK, Goren A, Williams RW, Palmer AA, Gymrek M. A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice. (2023) Genome Res. [link]; Cover Image highlighting this study [link]

Jonathan Margoliash, Shai Fuchs, Yang Li, Xuan Zhang, Arya Massarat, Alon Goren, Melissa Gymrek. (2023) Polymorphic short tandem repeats make widespread contributions to blood and serum traits. Cell Genomics. [Article] [Accompanying perspective]

Helyaneh Ziaei Jam, Yang Li, Ross DeVito, Nima Mousavi, Nichole Ma, Ibra Lujumba, Yagoub Adam, Mikhail Maksimov, Bonnie Huang, Egor Dolzhenko, Yunjiang Qiu, Fredrick Elishama Kakembo, Habi Joseph, Blessing Onyido, Jumoke Adeyemi, Mehrdad Bakhtiari, Jonghun Park, Sara Javadzadeh, Daudi Jjingo, Ezekiel Adebiyi, Vineet Bafna, Melissa Gymrek. (2023) A deep population reference panel of tandem repeat variation. Nature Communications. [Aricle]

Oxana Sachenkova Lundström, Max Adriaan Verbiest, Feifei Xia, Helyaneh Ziaei Jam, Inti Zlobec, Maria Anisimova, Melissa Gymrek. (2023) WebSTR: A Population-wide Database of Short Tandem Repeat Variation in Humans. J Mol Biol. [Article]

Arya Massarat, Melissa Gymrek, Brian McStay, Hákon Jónsson. (2023) Human pangenome supports analysis of complex genomic regions. Nature. [] (Perspective)

Mikhail O Maksimov, Cynthia Wu, David G Ashbrook, Flavia Villani, Vincenza Colonna, Nima Mousavi, Nichole Ma, Lu Lu, Jonathan K Pritchard, Alon Goren, Robert W Williams, Abraham A Palmer, Melissa Gymrek. (2023) A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice. Genome Research. [Article ] [Cover image!]

Arya R Massarat, Michael Lamkin, Ciara Reeve, Amy L Williams, Matteo D'Antonio, Melissa Gymrek. (2023) Haptools: a toolkit for admixture and haplotype analysis. Bioinformatics. [Article] [Github]

An Zheng, Zeyang Shen, Christopher K Glass, Melissa Gymrek. (2023) Deep learning predicts the impact of regulatory variants on cell-type-specific enhancers in the brain. Bioinform Adv. [Article]

Max Verbiest, Mikhail Maksimov, Ye Jin, Maria Anisimova, Melissa Gymrek, Tugce Bilgin Sonay. (2024) Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species. J Evol Biol. [Article]

Koch Z, Li A, Evans DS, Cummings S, Ideker T. Somatic mutation as an explanation for epigenetic aging. bioRxiv. 2023 Dec 9:2023.12.08.569638. doi: 10.1101/2023.12.08.569638. PMID: 38106096; PMCID: PMC10723383. (Preprint) [PubMed]

Baron M, Tagore M, Wall P, Zheng F, Barkley D, Yanai I, Yang J, Kiuru M, White RM, Ideker T. Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation. bioRxiv. 2023 Sep 22:2023.09.19.558457. doi: 10.1101/2023.09.19.558457. PMID: 37786690; PMCID: PMC10541613. (Preprint) [PubMed]

Tagore M, Hergenreder E, Perlee SC, Cruz NM, Menocal L, Suresh S, Chan E, Baron M, Melendez S, Dave A, Chatila WK, Nsengimana J, Koche RP, Hollmann TJ, Ideker T, Studer L, Schietinger A, White RM. GABA Regulates Electrical Activity and Tumor Initiation in Melanoma. Cancer Discov. 2023 Oct 5;13(10):2270-2291. doi: 10.1158/2159-8290.CD-23-0389. PMID: 37553760 [PubMed] [PDF]

Wright SN, Leger BS, Rosenthal SB, Liu SN, Jia T, Chitre AS, Polesskaya O, Holl K, Gao J, Cheng R, Garcia Martinez A, George A, Gileta AF, Han W, Netzley AH, King CP, Lamparelli A, Martin C, St Pierre CL, Wang T, Bimschleger H, Richards J, Ishiwari K, Chen H, Flagel SB, Meyer P, Robinson TE, Solberg Woods LC, Kreisberg JF, Ideker T, Palmer AA. Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks. Cell Reports. 2023 Aug 29;42(8):112873. doi: 10.1016/j.celrep.2023.112873. Epub 2023 Jul 31. PMID: 37527041 [PubMed] [PDF] [Published Erratum]

Carlin DE, Larsen SJ, Sirupurapu V, Cho MH, Silverman EK, Baumbach J, Ideker T. Hierarchical association of COPD to principal genetic components of biological systems. PLoS One. 2023 May 25;18(5):e0286064. doi: 10.1371/journal.pone.0286064. eCollection 2023. PMID: 37228113 [PubMed] [PDF]

Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst. 2023 May 16:S2405-4712(23)00116-3. doi: 10.1016/j.cels.2023.04.007. 22 May 2023. PMID: 37220749 [PubMed] [PDF]

Ford K*, Munson BP*, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep. 2023 May 11;13(1):7678. doi: 10.1038/s41598-023-33329-2. PMID: 37169829 *Equal Contribution [PubMed] [PDF]

Pillich RT, Chen J, Churas C, Fong D, Gyori BM, Ideker T, Karis K, Liu SN, Ono K, Pico A, Pratt D. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinformatics. 2023 Mar 1;39(3):btad118. doi: 10.1093/bioinformatics/btad118. PMID: 36882166 [PubMed][PDF]

Rosenthal SB, Wright SN, Liu S, Churas C, Chilin-Fuentes D, Chen CH, Fisch KM, Pratt D, Kreisberg JF, Ideker T. Mapping the common gene networks that underlie related diseases. Nat Protoc. 2023 Jun;18(6):1745-1759. doi: 10.1038/s41596-022-00797-1. Epub 2023 Jan 18. PMID: 36653526 [PubMed] [PDF] (Review)

Ma JY, Ting S, Tam B, Pham T, Reich M, Mesvirov J, Tamayo P, Kim W. Deciphering the Functional Roles of Individual Cancer Alleles Across Comprehensive Cancer Genomic Studies. bioRxiv [Preprint]. 2023 Nov 16:2023.11.14.567106. doi: 10.1101/2023.11.14.567106. PMID: 38014215; PMCID: PMC10680728.

Johnson JAI, Tsang AP, Mitchell JT, Zhou DL, Bowden J, Davis-Marcisak E, Sherman T, Liefeld T, Loth M, Goff LA, Zimmerman JW, Kinny-Köster B, Jaffee EM, Tamayo P, Mesirov JP, Reich M, Fertig EJ, Stein-O'Brien GL. Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS. Nat Protoc. 2023 Dec;18(12):3690-3731. doi: 10.1038/s41596-023-00892-x. Epub 2023 Nov 21. PMID: 37989764; PMCID: PMC10961825.

Chapman OS, Luebeck J, Sridhar S, Wong IT, Dixit D, Wang S, Prasad G, Rajkumar U, Pagadala MS, Larson JD, He BJ, Hung KL, Lange JT, Dehkordi SR, Chandran S, Adam M, Morgan L, Wani S, Tiwari A, Guccione C, Lin Y, Dutta A, Lo YY, Juarez E, Robinson JT, Korshunov A, Michaels JA, Cho YJ, Malicki DM, Coufal NG, Levy ML, Hobbs C, Scheuermann RH, Crawford JR, Pomeroy SL, Rich JN, Zhang X, Chang HY, Dixon JR, Bagchi A, Deshpande AJ, Carter H, Fraenkel E, Mischel PS, Wechsler-Reya RJ, Bafna V, Mesirov JP, Chavez L. Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma. Nat Genet. 2023 Dec;55(12):2189-2199. doi: 10.1038/s41588-023-01551-3. Epub 2023 Nov 9. PMID: 37945900; PMCID: PMC10703696.

Castanza AS, Recla JM, Eby D, Thorvaldsdóttir H, Bult CJ, Mesirov JP. Extending support for mouse data in the Molecular Signatures Database (MSigDB). Nat Methods. 2023 Nov;20(11):1619-1620. doi: 10.1038/s41592-023-02014-7. PMID: 37704782.

Liefeld T, Huang E, Wenzel AT, Yoshimoto K, Sharma AK, Sicklick JK, Mesirov JP, Reich M. NMFClustering: Accessible NMF-based clustering utilizing GPU acceleration. bioRxiv [Preprint]. 2023 Jun 27:2023.06.16.545370. doi: 10.1101/2023.06.16.545370. Update in: J Bioinform Syst Biol. 2023;6(4):379-383. doi: 10.26502/jbsb.5107072. PMID: 37398372; PMCID: PMC10312797.

Wu VH, Yung BS, Faraji F, Saddawi-Konefka R, Wang Z, Wenzel AT, Song MJ, Pagadala MS, Clubb LM, Chiou J, Sinha S, Matic M, Raimondi F, Hoang TS, Berdeaux R, Vignali DAA, Iglesias-Bartolome R, Carter H, Ruppin E, Mesirov JP, Gutkind JS. The GPCR-Gαs-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure. Nat Immunol. 2023 Aug;24(8):1318-1330. doi: 10.1038/s41590-023-01529-7. Epub 2023 Jun 12. PMID: 37308665; PMCID: PMC10735169.

Pagadala M, Sears TJ, Wu VH, Pérez-Guijarro E, Kim H, Castro A, Talwar JV, Gonzalez-Colin C, Cao S, Schmiedel BJ, Goudarzi S, Kirani D, Au J, Zhang T, Landi T, Salem RM, Morris GP, Harismendy O, Patel SP, Alexandrov LB, Mesirov JP, Zanetti M, Day CP, Fan CC, Thompson WK, Merlino G, Gutkind JS, Vijayanand P, Carter H. Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. Nat Commun. 2023 May 12;14(1):2744. doi: 10.1038/s41467-023-38271-5. PMID: 37173324; PMCID: PMC10182072.

Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. 3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma. Nat Commun. 2023 Apr 21;14(1):2300. doi: 10.1038/s41467-023-38044-0. PMID: 37085539; PMCID: PMC10121654.

Reich M, Tabor T, Liefeld J, Joshi J, Kim F, Thorvaldsdottir H, Blankenberg D, Mesirov JP. Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis. bioRxiv [Preprint]. 2023 Apr 6:2023.04.04.535621. doi: 10.1101/2023.04.04.535621. PMID: 37066251; PMCID: PMC10104038.

Liefeld T, Huang E, Wenzel AT, Yoshimoto K, Sharma AK, Sicklick JK, Mesirov JP, Reich M. NMF Clustering: Accessible NMF-based Clustering Utilizing GPU Acceleration. J Bioinform Syst Biol. 2023;6(4):379-383. doi: 10.26502/jbsb.5107072. Epub 2023 Dec 21. PMID: 38390437; PMCID: PMC10883375.

Robinson JT, Thorvaldsdottir H, Turner D, Mesirov JP. igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics. 2023 Jan 1;39(1):btac830. doi: 10.1093/bioinformatics/btac830. PMID: 36562559; PMCID: PMC9825295.

2022

Castro A, Kaabinejadian S, Hildebrand W, Zanetti M, Carter H. Immunogenic potential of neopeptides depends on parent protein subcellular location. The EMBO Journal. 2022 Dec 15:e111071. PMID: 36314681

Deichaite I, Hopper A, Krockenberger L, Sears TJ, Sutton L, Ray X, Sharabi A, Navon A, Sanghvi P, Carter H, Moiseenko V. Germline Genetic Biomarkers to Stratify Patients for Personalized Radiation Treatment. Journal of Translational Medicine. Dec;20(1):1-3. PMID: 35962345

Pagadala MS, Linscott JA, Talwar JV, Seibert TM, Rose B, Lynch J, Panizzon M, Hauger R, Hansen MH, Sammon JD, Hayn MH, Kader K, Carter H, Ryan ST. PRState: Incorporating genetic ancestry in prostate cancer risk scores for men of African ancestry. BMC cancer. 2022 Dec;22(1):1-1. PMID: 36494783

Gandhi S, Mitterhoff R, Rapoport R, Farago M, Greenberg A, Hodge L, Eden S, Benner C, Goren A, Simon I.
Mitotic H3K9ac is controlled by phase-specific activity of HDAC2, HDAC3, and SIRT1. (2022) Life Sci Alliance. [link]

 McDaniel S, Komor A^#, Goren A^#. The use of base editing technology to characterize single nucleotide variants. (2022) Comput Struct Biotechnol J. [link]

Martin F Orth, Didier Surdez, Tobias Faehling, Anna C Ehlers, Aruna Marchetto, Sandrine Grossetête, Richard Volckmann, Danny A Zwijnenburg, Julia S Gerke, Sakina Zaidi, Javier Alonso, Ana Sastre, Sylvain Baulande, Martin Sill, Florencia Cidre-Aranaz, Shunya Ohmura, Thomas Kirchner, Stefanie M Hauck, Eva Reischl, Melissa Gymrek, Stefan M Pfister, Konstantin Strauch, Jan Koster, Olivier Delattre, Thomas G P Grünewald. (2022) Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation. Cell Rep. [Article]

Milad Mortazavi, Yangsu Ren, Shubham Saini, Danny Antaki, Celine L St Pierre, April Williams, Abhishek Sohni, Miles F Wilkinson, Melissa Gymrek, Jonathan Sebat, Abraham A Palmer. (2022) SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains. Cell Genomics. [Article]

Schantell M, Taylor BK, Spooner RK, May PE, O’Neill J, Morsey BM, Wang T, Ideker T, Bares SH, Fox HS, Wilson TW. Epigenetic aging is associated with aberrant neural oscillatory dynamics serving visuospatial processing in people with HIV. Aging (Albany NY). 2022 Dec 15;14(24):9818-9831. doi: 10.18632/aging.204437. Epub 2022 Dec 15. PMID: 36534452 [PubMed] [PDF]

Van Oss SB, Parikh SB, Castilho Coelho N, Wacholder A, Belashov I, Zdancewicz S, Michaca M, Xu J, Kang YP, Ward NP, Yoon SJ, McCourt KM, McKee J, Ideker T, VanDemark AP, DeNicola GM, Carvunis AR. On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur, thanks to the previously uncharacterized homocysteine synthase Yll058w. J Biol Chem. 2022 Dec;298(12):102697. doi: 10.1016/j.jbc.2022.102697. Epub 2022 Nov 13. PMID: 36379252 [PubMed] [PDF]

Li A, Koch Z, Ideker T. Epigenetic aging: Biological age prediction and informing a mechanistic theory of aging. J Intern Med. 2022 Nov;292(5):733-744. doi: 10.1111/joim.13533. Epub 2022 Jun 20. PMID: 35726002 [PubMed] [PDF] (Review)

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. Understudied proteins: opportunities and challenges for functional proteomics. Nat Methods. 2022 Jul;19(7):774-779. doi: 10.1038/s41592-022-01454-x. PMID: 35534633 [PubMed] [PDF]

Kustatscher G, Collins T, Gingras AC, Guo T, Hermjakob H, Ideker T, Lilley KS, Lundberg E, Marcotte EM, Ralser M, Rappsilber J. An open invitation to the Understudied Proteins Initiative. Nat Biotechnol. 2022 Jun;40(6):815-817. doi: 10.1038/s41587-022-01316-z. PMID: 35534555 [PubMed ][PDF]

Ottilie S*, Luth MR*, Hellemann E*, Goldgof GM*, Vigil E, Kumar P, Cheung AL, Song M, Godinez-Macias KP, Carolino K, Yang J, Lopez G, Abraham M, Tarsio M, LeBlanc E, Whitesell L, Schenken J, Gunawan F, Patel R, Smith J, Love MS, Williams RM, McNamara CW, Gerwick WH, Ideker T, Suzuki Y, Wirth DF, Lukens AK, Kane PM, Cowen LE, Durrant JD, Winzeler EA. Adaptive laboratory evolution in S. cerevisiae highlights role of transcription factors in fungal xenobiotic resistance. Commun Biol. 2022 Feb 11;5(1):128. doi: 10.1038/s42003-022-03076-7. PMID: 35149760 *Equal Contribution [PubMed] [PDF]

Konno N, Kijima Y*, Watano K*, Ishiguro S*, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W, Yachie N. Deep distributed computing to reconstruct extremely large lineage trees. Nat Biotechnol. 2022 Apr;40(4):566-575. doi: 10.1038/s41587-021-01111-2. Epub 2022 Jan 6. PMID: 34992246 *Equal Contribution [PubMed] [PDF]

Leskoske KL, Garcia-Mansfield K, Sharma R, Krishnan A, Rusert JM, Mesirov JP, Wechsler-Reya RJ, Pirrotte P. Subgroup-Enriched Pathways and Kinase Signatures in Medulloblastoma Patient-Derived Xenografts. J Proteome Res. 2022 Sep 2;21(9):2124-2136. doi: 10.1021/acs.jproteome.2c00203. Epub 2022 Aug 17. PMID: 35977718 PMCID: PMC9442791

Wenzel AT, Champa D, Venkatesh H, Sun S, Tsai CY, Mesirov JP, Bui JD, Howell SB, Harismendy O. Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer. NPJ Syst Biol Appl. 2022 Jun 17;8(1):20. doi: 10.1038/s41540-022-00230-z. PMID: 35715421 PMCID: PMC9206019

Saddawi-Konefka R, O'Farrell A, Faraji F, Clubb L, Allevato MM, Jensen SM, Yung BS, Wang Z, Wu VH, Anang NA, Msari RA, Schokrpur S, Pietryga IF, Molinolo AA, Mesirov JP, Simon AB, Fox BA, Bui JD, Sharabi A, Cohen EEW, Califano JA, Gutkind JS. Lymphatic-preserving treatment sequencing with immune checkpoint inhibition unleashes cDC1-dependent antitumor immunity in HNSCC. Nat Comm. 2022 Jul 25;13(1):4298. doi: 10.1038/s41467-022-31941-w. PMID: 35879302 PMCID: PMC9314425

Do M, Wu CCN, Sonavane PR, Juarez EF, Adams SR, Ross J, Rodriguez YBA, Patel C, Mesirov JP, Carson DA, Advani SJ, Willert K. A FZD7-specific Antibody-Drug Conjugate Induces Ovarian Tumor Regression in Preclinical Models. Mol Cancer Ther. 2022;21(1):113-24. Epub 20211019. doi: 10.1158/1535-7163.MCT-21-0548. PubMed PMID: 34667113; PMCID: PMC8742765.

2021

Xian S, Dosset M, Almanza G, Searles S, Sahani P, Waller TC, Jepsen K, Carter H, Zanetti M. The unfolded protein response links tumor aneuploidy to local immune dysregulation. EMBO reports. Dec 6;22(12):e52509. PMID: 34698427

Ozturk K, Carter H. Predicting functional consequences of mutations using molecular interaction network features. Human Genetics. Aug 25:1-6. PMID: 34432150

Zhang P, Kitchen-Smith I, Xiong L, Stracquadanio G, Brown K, Richter P, Wallace M, Bond E, Sahgal N, Moore S, Nornes S, De Val S, Surakhy M, Sims D, Wang X, Bell DA, Zeron-Medina J, Jiang Y, Ryan A, Selfe J, Shipley J, Kar S, Pharoah P, Loveday C, Jansen R, Grochola LF, Palles C, Protheroe A, Millar V, Ebner D, Pagadala M, Blagden SP, Maughan T, Domingo E, Tomlinson I, Turnbull C, Carter H, Bond G. Germline and somatic genetic variants in the p53 pathway interact to affect cancer risk, progression and drug response. Cancer Research. PMID: 33558336

Chen K, Ozturk K, Contreras RL, Simon J, McCann S, Chen WJ, Carter H, Fraley SI. Phenotypically supervised single-cell sequencing parses within-cell-type heterogeneity. Iscience. Jan 22;24(1):101991. (2021) PMID: 33490901

Castro A, Ozturk K, Zanetti M, Carter H ** In silico analysis suggests less effective MHC-II presentation of SARS-CoV-2 RBM peptides: Implication for neutralizing antibody responses. Plos one. Feb 11;16(2):e0246731. PMID: 33571241

Gymrek M^#, Goren A^#. Missing heritability may be hiding in repeats. (2021) Science [link]

Zheng A, Lamkin M, Qiu Y, Ren K, Goren A^# & Melissa Gymrek^#.
A flexible simulation toolkit for designing and evaluating ChIP-sequencing experiments. (2021) BMC Bioinformatics [link]

Melissa Gymrek, Alon Goren. (2021) Missing heritability may be hiding in repeats. Science. [Article] (Perspective)

Marten A Hoeksema, Zeyang Shen, Inge R Holtman, An Zheng, Nathan J Spann, Isidoro Cobo, Melissa Gymrek, Christopher K Glass. (2021) Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4. Science Advances. [Article]

Mel Lina Pinsach-Abuin, Bernat Del Olmo, Adrian Pérez-Agustin, Jesus Mates, Catarina Allegue, Anna Iglesias, Qi Ma, Daria Merkurjev, Sergiy Konovalov, Jing Zhang, Farah Sheikh, Amalio Telenti, Josep Brugada, Ramon Brugada, Melissa Gymrek, Julia di Iulio, Ivan Garcia-Bassets, Sara Pagans. (2021) Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants. Cell Rep Med. [Article]

An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren, Melissa Gymrek. (2021) A flexible ChIP-sequencing simulation toolkit . BMC Bioinformatics. [preprint] [chips package]

Mehrdad Bakhtiari, Jonghun Park, Yuan-Chun Ding, Sharona Shleizer-Burko, Susan L Neuhausen, Bjarni V Halldórsson, Kári Stefánsson, Melissa Gymrek, Vineet Bafna. (2021) Variable number tandem repeats mediate the expression of proximal genes. Nature Communications. [Article]

Ileena Mitra, Bonnie Huang, Nima Mousavi, Nichole Ma, Michael Lamkin, Richard Yanicky, Sharona Shleizer-Burko, Kirk E. Lohmueller, Melissa Gymrek. (2021) Patterns of de novo tandem repeat mutations and their role in autism. Nature. [ Article ] [ Nature news summary ] [ Blog lay summary ]

An Zheng, Michael Lamkin, Hanqing Zhao, Cynthia Wu, Hao Su, Melissa Gymrek. (2021) Deep neural networks identify context-specific determinants of transcription factor binding affinity. Nature Machine Intelligence. [DOI] [github]

Fong SH, Munson BP, Ideker T. Uncovering Tumorigenesis Circuitry with Combinatorial CRISPR. Cancer Res. 2021 Dec 15;81(24):6078-6079. doi: 10.1158/0008-5472.CAN-21-3672. PMID: 34911780 [PubMed] [PDF]

Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. A multi-scale map of cell structure fusing protein images and interactions. Nature. 2021 Nov 24. doi: 10.1038/s41586-021-04115-9. Online ahead of print. PMID: 34819669 [PubMed] [PDF]

• Related press: “We Might Not Know Half of What’s in Our Cells, New AI Technique Reveals,” features Trey Ideker, PhD, and Yue Qin, grad student. See also GEN, SciTech Daily, ScienceDaily, The Medical News, Neuroscience News, Science Blog, Laboratory Equipment, La Jolla Light, Times of San Diego and Patch

Zheng F*, Kelly MR*, Ramms DJ, Heintschel ML, Tao K, Tutuncuoglu B, Lee JJ, Ono K, Foussard H, Chen M, Herrington KA, Silva E, Liu SN, Chen J, Churas C, Wilson N, Kratz A, Pillich RT, Patel DN, Park J, Kuenzi B, Yu MK, Licon K, Pratt D, Kreisberg JF, Kim M, Swaney DL, Nan X, Fraley SI, Gutkind JS, Krogan NJ†, Ideker T†. Interpretation of cancer mutations using a multiscale map of protein systems. Science. 2021 Oct;374(6563):eabf3067. doi: 10.1126/science.abf3067. Epub 2021 Oct 1. PMID: 34591613 *Equal Contribution, †Co-Corresponding Authors [PubMed] [PDF] 

• Related press: “Looking Beyond DNA to See Cancer with New Clarity,” features Trey Ideker, PhD. See also FierceBiotech, MSN, San Francisco Chronicle and Times of San Diego.

Swaney DL, Ramms DJ, Wang Z, Park J, Goto Y, Soucheray M, Bhola N, Kim K, Zheng F, Zeng Y, McGregor M, Herrington KA, O’Keefe R, Jin N, VanLandingham NK, Foussard H, Von Dollen J, Bouhaddou M, Jimenez-Morales D, Obernier K, Kreisberg JF, Kim M, Johnson DE, Jura N, Grandis JR, Gutkind JS, Ideker T†, Krogan NJ†. A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Science. 2021 Oct;374(6563):eabf2911. doi: 10.1126/science.abf2911. Epub 2021 Oct 1. PMID: 34591642 †Co-Corresponding Authors [PubMed] [PDF] 

Kim M, Park J, Bouhaddou M, Kim K, Rojc A, Modak M, Soucheray M, McGregor MJ, O’Leary P, Wolf D, Stevenson E, Foo TK, Mitchell D, Herrington KA, Muñoz DP, Tutuncuoglu B, Chen KH, Zheng F, Kreisberg JF, Diolaiti ME, Gordan JD, Coppé JP, Swaney DL, Xia B, van ‘t Veer L, Ashworth A, Ideker T†, Krogan NJ†. A protein interaction landscape of breast cancer. Science. 2021 Oct;374(6563):eabf3066. doi: 10.1126/science.abf3066. Epub 2021 Oct 1. PMID: 34591612 †Co-Corresponding Authors [PubMed] [PDF] 

Martin-Sancho L, Tripathi S, Rodriguez-Frandsen A, Pache L, Sanchez-Aparicio M, McGregor MJ, Haas KM, Swaney DL, Nguyen TT, Mamede JI, Churas C, Pratt D, Rosenthal SB, Riva L, Nguyen C, Beltran-Raygoza N, Soonthornvacharin S, Wang G, Jimenez-Morales D, De Jesus PD, Moulton HM, Stein DA, Chang MW, Benner C, Ideker T, Albrecht RA, Hultquist JF, Krogan NJ, García-Sastre A, Chanda SK. Restriction factor compendium for influenza A virus reveals a mechanism for evasion of autophagy. Nat Microbiol. 2021 Oct;6(10):1319-1333. doi: 10.1038/s41564-021-00964-2. Epub 2021 Sep 23. PMID: 34556855 [PubMed] [PDF] 

Tanaka H, Kreisberg JF†, Ideker T†. Genetic dissection of complex traits using hierarchical biological knowledge. PLoS Comput Biol. 2021 Sep 17;17(9):e1009373. doi: 10.1371/journal.pcbi.1009373. eCollection 2021 Sep. PMID: 34534210 †Co-Corresponding Authors [PubMed] [PDF] 

Karlsson Linnér R, Mallard TT, Barr PB, Sanchez-Roige S, Madole JW, Driver MN, Poore HE, de Vlaming R, Grotzinger AD, Tielbeek JJ, Johnson EC, Liu M, Rosenthal SB, Ideker T, Zhou H, Kember RL, Pasman JA, Verweij KJH, Liu DJ, Vrieze S; COGA Collaborators, Kranzler HR, Gelernter J, Harris KM, Tucker-Drob EM, Waldman ID, Palmer AA, Harden KP, Koellinger PD, Dick DM. Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction. Nat Neurosci. 2021 Oct;24(10):1367-1376. doi: 10.1038/s41593-021-00908-3. Epub 2021 Aug 26. PMID: 34446935 [PubMed] [Original PDF | Correction PDF] **Author Correction: Nat Neurosci. . 2025 Jan;28(1):213. doi: 10.1038/s41593-024-01853-7.

Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T. A convergent molecular network underlying autism and congenital heart disease. Cell Systems. 2021 Aug 13:S2405-4712(21)00287-8. doi: 10.1016/j.cels.2021.07.009. Online ahead of print. PMID: 34411509 [PubMed] [PDF] 

Spooner RK, Taylor BK, L’Heureux E, Schantell M, Arif Y, May PE, Morsey B, Wang T, Ideker T, Fox HS, Wilson TW. Stress-induced aberrations in sensory processing predict worse cognitive outcomes in healthy aging adults. Aging (Albany NY). 2021 Aug 18;13(16):19996-20015. doi: 10.18632/aging.203433. Epub 2021 Aug 18. PMID: 34410999 [PubMed] [PDF] 

Ma J, Fong SH, Luo Y., Bakkenist CJ, Shen JP, Mourragui S, Wessels LFA, Hafner M, Sharan R, Peng J, Ideker T.  Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. Nat Cancer. 2021 Feb;2(2):233-244. doi: 10.1038/s43018-020-00169-2. Epub 2021 Jan 25. PMID: 34223192 [PubMed] [PDF] (Analysis)

Zhang Q, Carlin D, Zhu F, Cattaneo P, Ideker T, Evans SM, Bloomekatz J, Chi NC. Unveiling Complexity and Multipotentiality of Early Heart Fields. Circulation Research. 2021 Aug 6;129(4):474-487. doi: 10.1161/CIRCRESAHA.121.318943. Epub 2021 Jun 24. PMID: 34162224 [PubMed] [PDF] 

Schaffer LV, Ideker T. Mapping the multiscale structure of biological systems. Cell Systems. 2021 Jun 16;12(6):622-635. doi: 10.1016/j.cels.2021.05.012. PMID: 34139169 [PubMed] [PDF] (Review)

Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O’Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional Landscape of SARS-CoV-2 Cellular Restriction. Molecular Cell. 2021 Jun 17;81(12):2656-2668.e8. doi: 10.1016/j.molcel.2021.04.008. Epub 2021 Apr 13. PMID: 33930332 [PubMed] [PDF] 

J Lew B, Schantell MD, O’Neill J, Morsey B, Wang T, Ideker T, Swindells S, S Fox H, Wilson TW. Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging. Cereb Cortex. 2021 Jul 5;31(8):3752-3763. doi: 10.1093/cercor/bhab045. PMID: 33822880 [PubMed] [PDF] 

Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. HiDeF: identifying persistent structures in multiscale ‘omics data. Genome Biol. 2021 Jan 7;22(1):21. doi: 10.1186/s13059-020-02228-4. PMID: 33413539; PMCID: PMC7789082. [PubMed] [PDF] 

Sharma AK, de la Torre J, NS IJ, Sutton TL, Zhao B, Khan TM, Banerjee S, Cui C, Nguyen V, Alkhuziem M, Snaebjornsson P, van Boven H, Bruining A, Tang CM, Yoon H, De la Fuente A, Kato S, Patel H, Heinrich MC, Corless CL, Horgan S, Burgoyne AM, Fanta P, Mesirov JP, Blakely AM, Davis JL, Mayo SC, van Houdt WJ, Steeghs N, Sicklick JK. Location of Gastrointestinal Stromal Tumor (GIST) in the Stomach Predicts Tumor Mutation Profile and Drug Sensitivity. Clin Cancer Res. 2021. Epub 20210729. doi: 10.1158/1078-0432.CCR-21-1221. PubMed PMID: 34326133.

Richelle A, Kellman BP, Wenzel AT, Chiang AWT, Reagan T, Gutierrez JM, Joshi C, Li S, Liu JK, Masson H, Lee J, Li Z, Heirendt L, Trefois C, Juarez EF, Bath T, Borland D, Mesirov JP, Robasky K, Lewis NE. Model-based assessment of mammalian cell metabolic functionalities using omics data. Cell Rep Methods. 2021;1(3). Epub 20210630. doi: 10.1016/j.crmeth.2021.100040. PubMed PMID: 34761247; PMCID: PMC8577426.

Maynard RE, Poore B, Hanaford AR, Pham K, James M, Alt J, Park Y, Slusher BS, Tamayo P, Mesirov J, Archer TC, Pomeroy SL, Eberhart CG, Raabe EH. TORC1/2 kinase inhibition depletes glutathione and synergizes with carboplatin to suppress the growth of MYC-driven medulloblastoma. Cancer Lett. 2021;504:137-45. Epub 20210208. doi: 10.1016/j.canlet.2021.02.001. PubMed PMID: 33571541.

Chen K, Ozturk K, Liefeld T, Reich M, Mesirov JP, Carter H, Fraley SI. A phenotypically supervised single-cell analysis protocol to study within-cell-type heterogeneity of cultured mammalian cells. STAR Protoc. 2021;2(2):100561. Epub 20210525. doi: 10.1016/j.xpro.2021.100561. PubMed PMID: 34095869; PMCID: PMC8165572.

Banerjee S, Yoon H, Ting S, Tang CM, Yebra M, Wenzel AT, Yeerna H, Mesirov JP, Wechsler-Reya RJ, Tamayo P, Sicklick JK. KIT(low) Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor. Mol Cancer Ther. 2021;20(10):2035-48. Epub 20210810. doi: 10.1158/1535-7163.MCT-20-0973. PubMed PMID: 34376580; PMCID: PMC8492542.

Benitez JA, Finlay D, Castanza A, Parisian AD, Ma J, Longobardi C, Campos A, Vadla R, Izurieta A, Scerra G, Koga T, Long T, Chavez L, Mesirov JP, Vuori K, Furnari F. Pten Deficiency Leads To Proteasome Addiction, A Novel Vulnerability In Glioblastoma. Neuro-oncology. 2021. Epub 2021/01/12. doi: 10.1093/neuonc/noab001. PubMed PMID: 33428749.

Naviaux, RK. Metabolic and behavioral features of acute hyperpurinergia and the maternal immune
activation mouse model of autism spectrum disorder. PLoS One. March 18, 2021, PMID: 33735311 (PDF).

2020

Castro A, Pyke RM, Zhang X, Thompson WK, Day CP, Alexandrov LB, Zanetti M, Carter H Strength of immune selection in tumors varies with sex and age. Nat Commun 11, 4128 PMID: 32807809

Goodman AM, Castro A, Pyke RM, Okamura R, Kato S, Riviere P, Frampton G, Sokol E, Zhang X, Ball ED, Carter H, Kurzrock R. MHC-I genotype and tumor mutational burden predict response to immunotherapy. Genome Med. May 19;12(1):45. PMID: 32430031

Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek. (2020) TRTools: a toolkit for genome-wide analysis of tandem repeats. Bioinformatics. [pubmed] [TRTools package]

Martin W Breuss, Danny Antaki, Renee D George, Morgan Kleiber, Kiely N James, Laurel L Ball, Oanh Hong, Ileena Mitra, Xiaoxu Yang, Sara A Wirth, Jing Gu, Camila A B Garcia, Madhusudan Gujral, William M Brandler, Damir Musaev, An Nguyen, Jennifer McEvoy-Venneri, Renatta Knox, Evan Sticca, Martha Cristina Cancino Botello, Javiera Uribe Fenner, Maria Cárcel Pérez, Maria Arranz, Andrea B Moffitt, Zihua Wang, Amaia Hervás, Orrin Devinsky, Melissa Gymrek, Jonathan Sebat, Joseph G Gleeson. (2020) Autism risk in offspring can be assessed through quantification of male sperm mosaicism. Nature Medicine. [pubmed]

Kuenzi BM, Park J, Fong SH, Sanchez KS, Lee J, Kreisberg JF, Ma J, Ideker T. Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. Cancer Cell (2020), https://doi.org/10.1016/j.ccell.2020.09.014. PMID: 33096023. [PubMed] [PDF] 

• Related Press: UCSD Health, AZoLifeSciences, Med India, Health IT Analytics and ScienceDaily. 

Singhal A*, Cao S*, Churas C*, Pratt D, Fortunato S, Zheng F, Ideker T. Multiscale community detection in Cytoscape. PLoS Comput Biol. 2020 Oct 23;16(10):e1008239. doi: 10.1371/journal.pcbi.1008239. eCollection 2020 Oct. PMID: 33095781 *Equal Contribution [PDF] [PubMed]

Gordon DE*, Hiatt J*, Bouhaddou M*, Rezelj VV*, Ulferts S*, Braberg H*, Jureka AS*, Obernier K*, Guo JZ*, Batra J*, Kaake RM*, Weckstein AR*, Owens TW*, Gupta M*, Pourmal S*, Titus EW*, Cakir M*,… García-Sastre A†, Rassen JA†, Grosse R†, Rosenberg OS†, Verba KA†, Basler CF†, Vignuzzi M†, Peden AA†, Beltrao P†, Krogan NJ†. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science. 2020 Oct 15:eabe9403. doi: 10.1126/science.abe9403. Online ahead of print. PMID: 33060197 *Equal Contribution, †Co-Corresponding Authors [PDF] [PubMed] 

Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O’Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Functional Landscape of SARS-CoV-2 Cellular Restriction. bioRxiv. 2020 Sep 30:2020.09.29.319566. doi: 10.1101/2020.09.29.319566. PMID: 33024967 [PDF] [PubMed] (Preprint)

Proskovec AL, Rezich MT, O’Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Association of Epigenetic Metrics of Biological Age With Cortical Thickness. JAMA Netw Open. 2020 Sep 1;3(9):e2015428. doi: 10.1001/jamanetworkopen.2020.15428. PMID: 32926115 [PDF] [PubMed]

Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, Callejas-Valera JL, Allevato M, Gilardi M, Santos J, Fukusumi T, Sakai A, Ando M, Sadat S, Liu C, Xu G, Fisch KM, Wang Z, Molinolo AA, Gutkind JS, Ideker T, Koch WM, Califano JA. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. 2020 Oct;39(40):6327-6339. doi: 10.1038/s41388-020-01431-8. Epub 2020 Aug 26. PMID: 32848210 [PDF] [PubMed]

Ochsner, S.A., Pillich, R.T. & McKenna, N.J. Consensus transcriptional regulatory networks of coronavirus-infected human cells. Sci Data 7, 314 (2020). https://doi.org/10.1038/s41597-020-00628-6 [PDF] [PubMed] 

Silva E, Michaca M, Munson B, Bean GJ, Jaeger PA, Licon K, Winzeler EA, Ideker T. Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. G3 (Bethesda). 2020 Sep 2;10(9):2981-2988. doi: 10.1534/g3.120.401417. PMID: 32732306 [PDF] [PubMed]

Tina Wang, Jianzhu Ma, Andrew N. Hogan, Samson Fong, Katherine Licon, Brian Tsui, Jason F. Kreisberg, Peter D. Adams, Anne-Ruxandra Carvunis, Danika L. Bannasch, Elaine A. Ostrander, Trey Ideker. Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome. Cell Systems. 2020 Aug 26;11(2):176-185.e6. doi: 10.1016/j.cels.2020.06.006. Epub 2020 Jul 2. PMID: 32619550 [PDF] [PubMed] *Cover Article

• Related Press: Scientific American, BBC, NPR, Washington Post, Discover Magazine, Smithsonian, New York Post, (and more!) 

Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. Decoding of persistent multiscale structures in complex biological networks. Version 2. bioRxiv. 2020 Jun 18:2020.06.16.151555. doi: 10.1101/2020.06.16.151555. Preprint. PMID: 32587977 [PDF] [PubMed]

Gordon DE*, Jang GM*, Bouhaddou M*, Xu J*, Obernier K*, White KM*, O’Meara MJ*, Rezelj VV*,… Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020 Jul;583(7816):459-468. doi: 10.1038/s41586-020-2286-9. Epub 2020 Apr 30. PMID: 32353859 *Equal Contribution [PDF] [PubMed] 

Sun SM*, Batté A*, Tittel-Elmer M, van der Horst S, van Welsem T, Bean G, Ideker T, van Leeuwen F, van Attikum H. A genetic interaction map centered on cohesin reveals auxiliary factors in sister chromatid cohesion in S. cerevisiae. J Cell Sci. 2020 May 22;133(10):jcs237628. doi: 10.1242/jcs.237628. PMID: 32299836 *Equal Contribution [PDF] [PubMed]

Jia T, Munson B, Lango Allen H, Ideker T, Majithia AR. Thousands of missing variants in the UK Biobank are recoverable by genome realignment. Ann Hum Genet. 2020 May;84(3):214-220. doi: 10.1111/ahg.12383. Epub 2020 Mar 31. PMID: 32232836 [PDF] [PubMed]

Kreisberg, J.F., Ideker, T., Meric-Bernstam, F. et al. Prospecting whole cancer genomes. Nature Cancer. 1, 273–275. 20 Mar 2020. doi: https://doi.org/10.1038/s43018-020-0045-3. [PDF]

Wiesman AI, Rezich MT, O’Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Epigenetic Markers of Aging Predict the Neural Oscillations Serving Selective Attention. Cereb Cortex. 2020 Mar 14;30(3):1234-1243. doi: 10.1093/cercor/bhz162. PMID: 31504270. [PDF] [PubMed]

Kuenzi BM, Ideker T. A census of pathway maps in cancer systems biology. Nat Rev Cancer. 2020 Apr;20(4):233-246. doi: 10.1038/s41568-020-0240-7. Epub 2020 Feb 17. PMID: 32066900 [PDF] [PubMed] (Review)

Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW 2nd, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O’Donnell AF, Ideker T, Carvunis AR. De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. Nat Commun. 2020 Feb 7;11(1):781. doi: 10.1038/s41467-020-14500-z. PMID: 32034123. PMCID: PMC7005711 [PDF] [PubMed]

Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 Jan 17;9. pii: e51461. doi: 10.7554/eLife.51461. PMID: 31951200. PMCID: PMC7030789. [PDF] [PubMed]

Rusert JM, Juarez EF, Brabetz S, Jensen J, Garancher A, Chau LQ, Tacheva-Grigorova SK, Wahab S, Udaka YT, Finlay D, Seker-Cin H, Reardon B, Grobner S, Serrano J, Ecker J, Qi L, Kogiso M, Du Y, Baxter PA, Henderson JJ, Berens ME, Vuori K, Milde T, Cho YJ, Li XN, Olson JM, Reyes I, Snuderl M, Wong TC, Dimmock DP, Nahas SA, Malicki D, Crawford JR, Levy ML, Van Allen EM, Pfister SM, Tamayo P, Kool M, Mesirov JP, Wechsler-Reya RJ. Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer research. 2020;80(23):5393-407. Epub 2020/10/14. doi: 10.1158/0008-5472.CAN-20-1655. PubMed PMID: 33046443; PMCID: PMC7718387.

Gevaert O, Nabian M, Bakr S, Everaert C, Shinde J, Manukyan A, Liefeld T, Tabor T, Xu J, Lupberger J, Haas BJ, Baumert TF, Hernaez M, Reich M, Quintana FJ, Uhlmann EJ, Krichevsky AM, Mesirov JP, Carey V, Pochet N. Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes. JCO clinical cancer informatics. 2020;4:421-35. Epub 2020/05/10. doi: 10.1200/CCI.19.00125. PubMed PMID: 32383980; PMCID: PMC7265792.

Wu VH, Wenzel A, Yung B, Wang Z, Mesirov JP, Gutkind JS. Illuminating the onco-GPCRome: targeting the prostaglandin receptor-Gαs signaling axis as a novel immune checkpoint in cancer. The Journal of Immunology. 2020;204(1 Supplement):165.37-.37

Naviaux, RK. Human Herpesvirus-6 Reactivation, Mitochondrial Fragmentation, and the Coordination of Antiviral and Metabolic Phenotypes in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. ImmunoHorizons, epub ahead of print, 2020 (PDF).

Naviaux, RK. Cell Danger Response Biology—The new science that connects environmental health with mitochondria and the rising tide of chronic illness. Mitochondrion 2020;51:40-45. (PDF).

2019

Castro A, Ozturk K, Pyke RM, Xian Su, Zanetti M, Carter H. Elevated neoantigen levels in tumors with somatic mutations to B2M and HLA. BMC medical genomics 12 (6), 107. PMID: 31345234

Marty R, Gfeller D, Genolet R, Harari A, Carter H ****Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survival Pac Symp Biocomput. 2019;24:148-159. PMID: 30864318

Tsui B, Dow M, Skola D, Carter H ****Extracting allelic read counts from 250,000 human sequencing runs in Sequence. Read Archive Pac Symp Biocomput. 2019;24:196-207. PMID: 30864322

Fotsing S, Margoliash J, Wang C, Saini S, Shleizer-Burko S, Goren A^# & Melissa Gymrek^#.
The impact of short tandem repeat variation on gene expression. (2019) Nat Genet. [pubmed]

 Ben-Yair R, Butty VL, Busby M, Qiu Y, Levine SS, Goren A^#, Boyer LA^#, Burns CG^# & Burns CE^#.
H3K27me3-mediated silencing of structural genes is required for zebrafish heart regeneration. (2019) Development. [pubmed]

Etchegaray JP^#, Zhong L, Li C, Henriques T, Ablondi E, Nakadai T, Van Rechem C, Ferrer C, Ross KN, Choi JE, Samarakkody A, Ji F, Chang A, Sadreyev RI, Ramaswamy S, Nechaev S, Whetstine JR, Roeder RG, Adelman K, Goren A^# & Mostoslavsky R^#. The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing. (2019) Molecular Cell [pubmed]

Stephanie Feupe Fotsing, Jonathan Margoliash, Catherine Wang, Shubham Saini, Sharona Shleizer-Burko, Alon Goren, Melissa Gymrek. (2019) The impact of short tandem repeat variation on gene expression. Nature Genetics. [pubmed] [Data]

Nima Mousavi, Sharona Shleizer-Burko, Richard Yanicky, Melissa Gymrek. (2019) Profiling the genome-wide landscape of tandem repeat expansions. Nucleic Acids Research. [pubmed] [github]

Jonathan Flint, Trey Ideker. The great hairball gambit. PLOS Genetics 15(11): e1008519. 2019 Nov 25. https://doi.org/10.1371/journal.pgen.1008519. PMID: 31770365. [PDF] [PubMed] (Opinion Piece)

Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations.  Genome Biol. 2019 Nov 25;20(1):249. doi: 10.1186/s13059-019-1824-y. PMID: 31767039. [PDF] [PubMed] (Review)

Licon K, Shen JP, Munson BP, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T.  Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. 11 October 2019. In: Oliver S., Castrillo J. (eds) Yeast Systems Biology. Methods in Molecular Biology, vol 2049. Humana, New York, NY. 2019;2049:73-85. doi: 10.1007/978-1-4939-9736-7_4. PMID: 31602605. [PDF] [PubMed] (eBook PDF) (Book chapter)

Otasek D, Morris JH, Bouças J, Pico AR, Demchak B. Cytoscape Automation: empowering workflow-based network analysis. Genome Biol. 2019 Sep 2;20(1):185. doi: 10.1186/s13059-019-1758-4. PMID: 31477170 [PDF] [PubMed]

Chatterjee N, Pazarentzos E, Mayekar MK, Gui P, Allegakoen DV, Hrustanovic G, Olivas V, Lin L, Verschueren E, Johnson JR, Hofree M, Yan JJ, Newton BW, Dollen JV, Earnshaw CH, Flanagan J, Chan E, Asthana S, Ideker T, Wu W, Suzuki J, Barad BA, Kirichok Y, Fraser JS, Weiss WA, Krogan NJ, Tulpule A, Sabnis AJ, Bivona TG. Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Cell Rep. 2019 Aug 27;28(9):2317-2330.e8. doi: 10.1016/j.celrep.2019.07.063. PMID: 31461649 [PDF] [PubMed]

Bouhaddou M, Eckhardt M, Chi Naing ZZ, Kim M, Ideker T, Krogan NJ. Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Curr Opin Genet Dev. 2019 Jul 6;54:110-117. doi: 10.1016/j.gde.2019.04.005. [Epub ahead of print] . PMID: 31288129 [PDF] [PubMed] (Review)

Carlin DE, Fong SH, Qin Y, Jia T, Huang JK, Bao B, Zhang C, Ideker T. A Fast and Flexible Framework for Network-Assisted Genomic Association. iScience. 2019 May 24;16:155-161. doi: 10.1016/j.isci.2019.05.025. [Epub ahead of print] PMID: 31174177 [PDF] [PubMed]

van de Haar J, Canisius S, Yu MK, Voest EE, Wessels LFA, Ideker T. Identifying Epistasis in Cancer Genomes: A Delicate Affair. Cell. 2019 May 30;177(6):1375-1383. doi: 10.1016/j.cell.2019.05.005. PMID: 31150618 [PDF] [PubMed] (Review)

Buckley AR, Ideker T, Carter H, Schork NJ. Rare variant phasing using paired tumor:normal sequence data. BMC Bioinformatics. 2019 May 27;20(1):265. doi: 10.1186/s12859-019-2753-1. PMID: 31132991 [PDF] [PubMed]

Silva E, Ideker T. Transcriptional responses to DNA damage. DNA Repair (Amst). 2019 Jul;79:40-49. doi: 10.1016/j.dnarep.2019.05.002. Epub 2019 May 7. PMID: 31102970 [PDF] [PubMed] (Review)

Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Erratum in: Nat Commun. 2019 May 29;10(1):2415. PMID: 31097695  [PDF] [PubMed]

Fong SH, Carlin DE, Ozturk K; 2018 UCSD Network Biology Class, Ideker T. Strategies for Network GWAS Evaluated Using Classroom Crowd Science. Cell Syst. 2019 Apr 24;8(4):275-280. doi: 10.1016/j.cels.2019.03.013. PMID: 31022372 [PDF] [PubMed] (Corrected Author List, 23 Oct 2019)

Lytle NK, Ferguson LP, Rajbhandari N, Gilroy K, Fox RG, Deshpande A, Schürch CM, Hamilton M, Robertson N, Lin W, Noel P, Wartenberg M, Zlobec I, Eichmann M, Galván JA, Karamitopoulou E, Gilderman T, Esparza LA, Shima Y, Spahn P, French R, Lewis NE, Fisch KM, Sasik R, Rosenthal SB, Kritzik M, Von Hoff D, Han H, Ideker T, Deshpande AJ, Lowy AM, Adams PD, Reya T. A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma. Cell. 2019 Mar 29. pii: S0092-8674(19)30272-7. doi:10.1016/j.cell.2019.03.010. [Epub ahead of print] PMID: 30955884 [PDF] [PubMed]

Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Syst. 2019 Mar 27;8(3):267-273.e3. doi: 10.1016/j.cels.2019.02.003. Epub 2019 Mar 13. PMID: 30878356 [PDF] [PubMed]

Wallace ZS, Rosenthal SB, Fisch KM, Ideker T, Sasik R. On entropy and information in gene interaction networks. Bioinformatics. 2019 Mar 1;35(5):815-822. doi: 10.1093/bioinformatics/bty691. PMID: 30102349 [PDF] [PubMed]

Ideker T, Hood L. A Blueprint for Systems Biology. Clin Chem. 2019 Feb;65(2):342-344. doi: 10.1373/clinchem.2018.291062. Epub 2018 Dec 28. Review. PMID: 30593465 [PDF] [PubMed] (Review)

Banerjee S, Wei T, Wang J, Lee JJ, Gutierrez HL, Chapman O, Wiley SE, Mayfield JE, Tandon V, Juarez EF, Chavez L, Liang R, Sah RL, Costello C, Mesirov JP, de la Vega L, Cooper KL, Dixon JE, Xiao J, Lei X. Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression. Proc Natl Acad Sci U S A. 2019 Dec 3;116(49):24881-24891. doi: 10.1073/pnas.1912033116. Epub 2019 Nov 21. PubMed PMID: 31754034; PubMed Central PMCID: PMC6900511.

Tokita MJ, Nahas S, Briggs B, Malicki DM, Mesirov JP, Reyes IAC, Farnaes L, Levy ML, Kingsmore SF, Dimmock D, Crawford JR, Wechsler-Reya RJ. Biallelic loss of GNAS in a patient with pediatric medulloblastoma. Cold Spring Harb Mol Case Stud. 2019 Oct;5(5). doi: 10.1101/mcs.a004572. Print 2019 Oct. PubMed PMID: 31624069; PubMed Central PMCID: PMC6824258.

Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA, Mani DR. A Curated Resource for Phosphosite-specific Signature Analysis. Mol Cell Proteomics. 2019 Mar;18(3):576-593. doi: 10.1074/mcp.TIR118.000943. Epub 2018 Dec 18. PubMed PMID: 30563849; PubMed Central PMCID: PMC6398202.

Brenner SE, Bulyk M, Crawford DC, Mesirov JP, Morgan AA, Radivojac P. Precision Medicine: Improving health through high-resolution analysis of personal data. Pac Symp Biocomput. 2019;24:220-223. PubMed PMID: 30864324; NIHMSID:NIHMS1024185.M

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P Jr, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2019 Jan;565(7738):E5-E6. doi: 10.1038/s41586-018-0722-x. PubMed PMID: 30559381.

2018

Dow M, Marty R, Tsui B, Alexandrov LB, Nakagawa H, Taniguchi K, Ekihiro S, Harismendy O, Shalapour S, Karin M, Carter H, Font-Burgada J Integrative genomic analysis of mouse and human hepatocellular carcinoma PNAS Oct 16;115(42):E9879-88. PMID: 30287485

Pyke RM, Thomson WK, Salem RM, Font-Burgada J, Zanetti M, Carter H Evolutionary pressure against MHC class II binding cancer mutations Cell Oct 4;175(2):416-28. PMID: 30245014

Greenfield R, Tabib A, Keshet I, Moss J, Sabag O, Goren A & Cedar H. Role of transcription complexes in the formation of the basal methylation pattern in early development. (2018) PNAS. [pubmed]

 Javasky E, Shamir I, Gandhi S, Egri S, Sandler O, Rothbart SB, Kaplan N, Jaffe JD, Goren A^# & Simon I^#.
Study of the mitotic chromatin shows involvement of histone modifications in bookmarking and reveals nucleosome deposition patterns. (2018) Genome Res. [pubmed]

Reizel Y, Sabag O, Skversky Y, Spiro A, Steinberg B, Bernstein D, Wang A, Kieckhaefer J, Li C, Pikarsky E, Levin-Klein R, Goren A, Rajewsky K, Kaestner KH, Cedar H. Postnatal DNA demethylation and its role in tissue maturation. (2018) Nature Commun. [pubmed]

Shubham Saini, Ileena Mitra, Nima Mousavi, Stephanie Feupe Fotsing, Melissa Gymrek. (2018) A reference haplotype panel for genome-wide imputation of short tandem repeats. Nature Communications. [pubmed] [Data]

Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna (2018) Targeted Genotyping of Variable Number Tandem Repeats with adVNTR. Genome Research. [pubmed]

Arfon M. Smith, Kyle E. Niemeyer, Daniel S. Katz, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn D. Huff, Christopher R. Madan, Abigail Cabunoc Mayes, Kevin M. Moerman, Pjotr Prins, Karthik Ram, Ariel Rokem, Tracy K. Teal, Roman Valls Guimera, Jacob T. Vanderplas. (2018) Journal of Open Source Software (JOSS): design and first-year review. PeerJ [PeerJ]

Joanna Kaplanis, Assaf Gordon, Tal Shor, Omer Weissbrod, Dan Geiger, Mary Wahl, Michael Gershovits, Barak Markus, Mona Sheikh, Melissa Gymrek, Gaurav Bhatia, Daniel. G. MacArthur, Alkes L. Price, Yaniv Erlich. (2018) Quantitative analysis of population-scale family trees with millions of relatives. Science [pubmed]

van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F. Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Res. 2018 Nov 30;46(21):11251-11261. doi: 10.1093/nar/gky801. PMID: 30203048 [PDF][PubMed]

Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. Typing tumors using pathways selected by somatic evolution. Nat Commun. 2018 Oct 8;9(1):4159. doi: 10.1038/s41467-018-06464-y. PMID: 30297789 [PDF][PubMed]

Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD. DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell. 2018 Sep 20;71(6):882-895. doi: 10.1016/j.molcel.2018.08.008. Review. PMID: 30241605 [PDF][PubMed] (Review)

Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass. Special Issue: Theory and Application of Network Biology Toward Precision Medicine.* Journal of Molecular Biology. Volume 430, Issue 18, Part A, Pages 2873-3028 (14 September 2018)  [PDF][PubMed] [Flyer] (Review)

• *Special Issue, Edited by Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass.
• *Cover art by Kivilcim Ozturk, Michelle Dow and Hannah Carter.

Kivilcim Ozturk, Michelle Dow, Daniel E. Carlin, Rafael Bejar and Hannah Carter. The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. Journal of Molecular Biology. Volume 430, Issue 18, Part A, Pages 2875–2899 (14 September 2018) [PDF] [PubMed] [Flyer] (Review)*Special Issue, Edited by Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass.

• *Cover art by Kivilcim Ozturk, Michelle Dow and Hannah Carter.

Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. Journal of Molecular Biology. Volume 430, Issue 18, Part A, Pages 2900–2912 (14 September 2018).  [Epub ahead of print: 2018 Jun 19] doi: 10.1016/j.jmb.2018.06.026. PMID: 29932943 [PDF] [PubMed] (Review)

• *Special Issue, Edited by Barry Demchak, Jason F. Kreisberg, Juan I. Fuxman Bass.
• *Cover art by Kivilcim Ozturk, Michelle Dow and Hannah Carter. 

Buckley AR, Ideker T, Carter H, Harismendy O, Schork NJ. Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. Genome Med. 2018 Sep 14;10(1):69. doi: 10.1186/s13073-018-0579-5. PMID: 30217226 [PDF] [PubMed]

Eckhardt M*, Zhang W*, Gross AM, Von Dollen J, Johnson JR, Franks-Skiba KE, Swaney DL, Johnson TL, Jang GM, Shah PS, Brand TM, Archambault J, Kreisberg JF, Grandis JR, Ideker T†, Krogan NJ†. Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Cancer Discov. 2018 Nov;8(11):1474-1489. doi: 10.1158/2159-8290.CD-17-1018. Epub 2018 Sep 12. PMID: 30209081 *Equal Contribution, †Co-Corresponding Authors [PDF] [PubMed]

Ang CS*, Shen JP*, Hardy-Abeloos CJ, Huang JK, Ross JS, Miller VA, Jacobs MT, Chen IL, Xu D, Ali SM, Baumgartner J, Lowy A, Fanta P, Ideker T, Millis SZ, Harismendy O. Genomic Landscape of Appendiceal Neoplasms. JCO Precis Oncol. 2018 Aug 8;2:PO.17.00302. doi: 10.1200/PO.17.00302. eCollection 2018. PMID: 32913983 *Equal Contribution [PDF] [PubMed]

Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell. 2018 Jul 26;174(3):505-520. doi: 10.1016/j.cell.2018.06.016. Review. PMID: 30053424 [PDF] [PubMed] (Review)

Zhang W, Ma J, Ideker T. Classifying tumors by supervised network propagation. Bioinformatics. 2018 Jul 1;34(13):i484-i493. doi: 10.1093/bioinformatics/bty247. Erratum in: Bioinformatics. 2019 Feb 4;35(14):2528. PMID: 29949979 [PDF] [PubMed]  

Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collection. F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. PMID: 29983926 [PDF] [PubMed] (Review)

Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T. Visible Machine Learning for Biomedicine. CELL. Volume 173, Issue 7, 14 June 2018, Pages 1562–1565. doi: https://doi.org/10.1016/j.cell.2018.05.056 [PDF] [PubMed] (Review)

Zhang W*, Bojorquez-Gomez A*, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nat Genet. 2018 Apr 2. doi: 10.1038/s41588-018-0091-2. PMID: 29610481 *Equal Contribution [PDF] [PubMed]

• Press: Even DNA that Doesn’t Encode Genes Can Drive Cancer
• Press: Researchers Identify Hundreds of Mutations outside of Coding Genes that Influence Tumor Gene Expression

Bui N*, Huang JK*, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP†, Kreisberg JF†, Ideker T†. Disruption of NSD1 in head and neck cancer promotes favorable chemotherapeutic responses linked to hypomethylation. Mol Cancer Ther. 2018 Jul;17(7):1585-1594. doi: 10.1158/1535-7163.MCT-17-0937. Epub 2018 Apr 10. PMID: 29636367 *Equal Contribution, †Co-Corresponding Authors  [PDF] [PubMed]

Huang JK, Jia T, Carlin DE, Ideker T. pyNBS: A Python implementation for network-based stratification of tumor mutations. Bioinformatics. 2018 Mar 28. doi: 10.1093/bioinformatics/bty186. PMID: 29608663 [PDF] [PubMed]

Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Cell Syst. 2018 Mar 26. pii: S2405-4712(18)30095-4. doi: 10.1016/j.cels.2018.03.001. PMID: 29605183 [PDF] [PubMed]

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell. Nat Methods. 2018 Mar 5. doi: 10.1038/nmeth.4627. PMID: 29505029 [PDF] [PubMed] *Cover Article

• Cover Art: Nature Methods “About the Cover”
• Press: Cracking Open the Black Box of AI with Cell Biology
• Press: How a Yeast Cell Helps Crack Open the “Black Box” Behind Artificial Intelligence
• Press: Deep Learning-Based Cell Model May Predict Patient Tumor Cell Growth Someday

Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Mol Cell. 2018 Feb 15;69(4):699-708.e7. doi: 10.1016/j.molcel.2018.01.017. PMID: 29452643 [PDF] [PubMed]

Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F. ndexr-an R package to interface with the network data exchange. Bioinformatics. 2018 Feb 15;34(4):716-717. doi: 10.1093/bioinformatics/btx683. PMID: 29087446 [PDF] [PubMed]

Jaeger PA, Ornelas L, McElfresh C, Wong LR, Hampton RY, Ideker T. Systematic Gene-to-Phenotype Arrays: A High-Throughput Technique for Molecular Phenotyping. Mol Cell. 2018 Jan 18;69(2):321-333.e3. doi: 10.1016/j.molcel.2017.12.016. PMID: 29351850 [PDF] [PubMed]

Neal S, Jaeger PA, Duttke SH, Benner C, Glass CK, Ideker T, Hampton RY. The Dfm1 Derlin Is Required for ERAD Retrotranslocation of Integral Membrane Proteins. Mol Cell. 2018 Jan 18;69(2):306-320.e4. doi: 10.1016/j.molcel.2017.12.012. PMID: 29351849 [PDF] [PubMed]

Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA, Mani DR. A curated resource for phosphosite-specific signature analysis. Mol Cell Proteomics. 2018 Dec 18. pii: mcp.TIR118.000943. doi: 10.1074/mcp.TIR118.000943. [Epub ahead of print] PubMed PMID: 30563849.

Mah CK, Tabor T and Mesirov JP. An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data [version 1; referees: 2 approved with reservations]. F1000Research 2018, 7:1306 (https://doi.org/10.12688/f1000research.15830.1)

Carlin DE, Kim F, Ideker T and Mesirov JP. A unified GenomeSpace recipe to identify essential genes and associated subnetworks from Genome-Scale CRISPR-Cas9 knockout screens [version 1; referees: awaiting peer review]. F1000Research 2018, 7:1636

Archer TC, Ehrenberger T, Mundt F, Gold MP, Krug K, Mah CK, Mahoney EL, Daniel CJ, LeNail A, Ramamoorthy D, Mertins P, Mani DR, Zhang H, Gillette MA, Clauser K, Noble M, Tang LC, Pierre-François J, Silterra J, Jensen J, Tamayo P, Korshunov A, Pfister SM, Kool M, Northcott PA, Sears RC, Lipton JO, Carr SA, Mesirov JP, Pomeroy SL, Fraenkel E. Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2018 Sep 10;34(3):396-410.e8. doi: 10.1016/j.ccell.2018.08.004. PubMed PMID: 30205044.

Li T, Kim A, Rosenbluh J, Horn H, Greenfeld L, An D, Zimmer A, Liberzon A, Bistline J, Natoli T, Li Y, Tsherniak A, Narayan R, Subramanian A, Liefeld T, Wong B, Thompson D, Calvo S, Carr S, Boehm J, Jaffe J, Mesirov J, Hacohen N, Regev A, Lage K. GeNets: a unified web platform for network-based genomic analyses. Nature methods. 2018; 15(7):543-546. PubMed PMID: 29915188

Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, Aiden EL. Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell systems. 2018; 6(2):256-258.e1. NIHMSID: NIHMS949176 PubMed PMID:29428417, PMCID: PMC6047755.

Naviaux RK. Metabolic features and regulation of the healing cycle—A new model for chronic disease pathogenesis and treatment. Mitochondrion, ePub ahead of print, 2018 (PDF).

2017

Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H ****MHC-I genotype restricts the oncogenic mutational landscape Cell Nov 30;171(6):1272-83. PMID: 29107334

Engin B, Carlin D, Pratt D, Carter H ****Modeling of RAS Complexes Supports Roles in Cancer for Less Studied Partners BMC Biophysics Aug 11;10(1):5. PMID: 28815022

Carter H, Marty R, Hofree M, Gross A, Jensen J, Fisch K, Wu X, DeBoever C, Van Nostrand E, Song Y, Wheeler E, Kreisberg J, Lippman S, Yeo G, Gutkind S, Ideker T Interaction landscape of inherited polymorphisms with somatic events in cancer Cancer Discovery Apr 1;7(4):410-23. PMID: 28188128

Vardi O, Shamir I, Javasky E, Goren A, Simon I. Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences. (2017) PloS one. [pubmed]

Melissa Gymrek, Thomas Willems, David Reich, Yaniv Erlich. (2017) Interpreting short tandem repeat variations in humans using mutational constraint. Nature Genetics. [pubmed]

Victor Rusu, Eitan Hoch, Josep M. Mercader, Danielle E. Tenen, Melissa Gymrek, Christina R. Hartigan, Michael DeRan, Marcin von Grotthuss, Pierre Fontanillas, Alexandra Spooner, Gaelen Guzman, Amy A. Deik, Kerry A. Pierce, Courtney Dennis, Clary B. Clish, Steven A. Carr, Bridget K. Wagner, Monica Schenone, Maggie C.Y. Ng, Brian H. Chen, MEDIA Consortium, SIGMA T2D Consortium , Federico Centeno-Cruz, Carlos Zerrweck, Lorena Orozco, David M. Altshuler, Stuart L. Schreiber, Jose C. Florez, Suzanne B.R. Jacobs, Eric S. Lander. (2017) Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms. Cell [pubmed]

Thomas Willems, Dina Zielinski, Assaf Gordon, Melissa Gymrek, Yaniv Erlich. (2017) Genome-wide profiling of heritable and de novo STR variations. Nature Methods. [pubmed]

Melissa Gymrek (2017) A genomic view of short tandem repeats. Curr Opin Genet Dev. [pubmed]

Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI. Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. Nat Commun. 2017 Nov 1;8(1):1238. doi: 10.1038/s41467-017-01439-x. PMID: 29089570 [PDF] [PubMed]

Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Cancer Res. 2017 Nov 1;77(21):e58-e61. doi: 10.1158/0008-5472.CAN-17-0606. PMID: 29092941 [PDF] [PubMed] (Review)

Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell. 2017 October 26. DOI: http://dx.doi.org/10.1016/j.cell.2017.09.050. PMID: 29107334 [PDF] [PubMed]

Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. PLoS Comput Biol. 2017 Oct 12;13(10):e1005598. doi: 10.1371/journal.pcbi.1005598. PMID: 29023449; PMCID: PMC5638226. [PDF] [PubMed]

Ideker T, Nussinov R. Network approaches and applications in biology. PLoS Comput Biol. 2017 Oct 12;13(10):e1005771. doi: 10.1371/journal.pcbi.1005771. PMID: 29023447; PMCID: PMC5638228 [PDF] [PubMed] (Editorial)

Farré JC, Kramer M, Ideker T, Subramani S. Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes. Autophagy. 2017 Jul 3;13(7):1248-1249. doi: 10.1080/15548627.2017.1313946. Epub 2017 May 9. PMID: 28486053 [PDF] [PubMed] (Review)

Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods. 2017 Jun;14(6):577-580. doi: 10.1038/nmeth.4286. Epub 2017 May 8. PMID: 28481362 [PDF] [PubMed]

Buckley AR, Standish KA, Bhutani K, Ideker T, Lasken RS, Carter H, Harismendy O, Schork NJ. Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. BMC Genomics. 2017 Jun 12;18(1):458. doi: 10.1186/s12864-017-3770-y. PMID: 28606096 [PDF] [PubMed]

Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. Nat Rev Genet. 2017 Sep;18(9):551-562. doi: 10.1038/nrg.2017.38. Epub 2017 Jun 12. PMID: 28607512. [PDF] [PubMed] (Review)

Carlin D, Kosnicki K, Garamszegi S et al. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Res. 2017 Jun 6;6:784. doi: 10.12688/f1000research.11616.2. PMID: 29487738; PMCID: PMC5806050. [PDF] [PubMed]

Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G. Systems biology guided by XCMS Online metabolomics. Nat Methods. 2017 Apr 27;14(5):461-462. doi: 10.1038/nmeth.4260. PMID: 28448069 [PDF] [PubMed] (Review)

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biology. 2017 Mar 28;18(1):57. doi: 10.1186/s13059-017-1186-2. PMID: 28351423; PMCID: PMC5371228. [PDF] [PubMed]

• Data: [Dataset] [GitHub]

Cole JJ, Robertson NA, Rather MI, Thomson JP, McBryan T, Sproul D, Wang T, Brock C, Clark W, Ideker T, Meehan RR, Miller RA, Brown-Borg HM, Adams PD. Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol. 2017 Mar 28;18(1):58. doi: 10.1186/s13059-017-1185-3. PMID: 28351383; PMCID: PMC5370462. [PDF] [PubMed]

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods. 2017 Jun;14(6):573-576. doi: 10.1038/nmeth.4225. Epub 2017 Mar 20. PMID: 28319113; PMCID: PMC5449203. [PDF] [PubMed]

• Networks and visualizations: 293T_SyntheticLethal; A549_SyntheticLethal; HeLa_SyntheticLethal
• Source code: http://idekerlab.ucsd.edu/papers/rsasik2017/dual_crispr_pipeline.zip

Carter H, Ideker T. Common genetic variation in the germline influences where and how tumors develop. Mol Cell Oncol. 2017 Mar 10;4(3):e1302905. doi: 10.1080/23723556.2017.1302905. eCollection 2017. PMID: 28616579 [PDF] [PubMed] (Review)

Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discovery. 2017 Feb 10. doi: 10.1158/2159-8290.CD-16-1045. PMID: 28188128 [PDF] [PubMed] *Cover article

• Cover Art: About the Cover
• Data generated by the TCGA Research Network: http://cancergenome.nih.gov/

Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy. Molecular Cell. 2017 Feb 16;65(4):761-774.e5. doi: 10.1016/j.molcel.2016.12.024. PMID: 28132844 [PDF] [PubMed]

• See [Datasets]

Pillich RT, Chen J, Rynkov V, Welker D, Pratt D. NDEx: A Community Resource for Sharing and Publishing of Biological Networks. Methods Mol Biol. 2017 02 Feb;1558:271-301. doi: 10.1007/978-1-4939-6783-4_13. PMID: 28150243. Book chapter. [PDF] [PubMed]

Hachigian LJ, Carmona V, Fenster RJ, Kulicke R, Heilbut A, Sittler A, Pereira de Almeida L, Mesirov JP, Gao F, Kolaczyk ED, Heiman M. Control of Huntington's Disease-Associated Phenotypes by the Striatum-Enriched Transcription Factor Foxp2. Cell Rep. 2017 Dec 5;21(10):2688-2695. doi: 10.1016/j.celrep.2017.11.018. PubMed PMID: 29212017.

Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant Review with the Integrative Genomics Viewer. Cancer Res. 2017 Nov 1;77(21):e31-e34. doi: 10.1158/0008-5472.CAN-17-0337. PubMed PMID: 29092934; PubMed Central PMCID: PMC5678989.

Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M, Amin-Mansour A, Rabasha B, Bahl S, Mullane SA, Robinson BD, Aldubayan S, Khani F, Karir B, Kim E, Chimene-Weiss J, Hofree M, Romanel A, Osborne JR, Kim JW, Azabdaftari G, Woloszynska-Read A, Sfanos K, De Marzo AM, Demichelis F, Gabriel S, Van Allen EM, Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA. Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer Discov. 2017 Sep;7(9):973-983. doi: 10.1158/2159-8290.CD-16-0960. Epub 2017 May 17. PubMed PMID: 28515055.

Kim JW, Abudayyeh OO, Yeerna H, Yeang CH, Stewart M, Jenkins RW, Kitajima S, Konieczkowski DJ, Medetgul-Ernar K, Cavazos T, Mah C, Ting S, Van Allen EM, Cohen O, Mcdermott J, Damato E, Aguirre AJ, Liang J, Liberzon A, Alexe G, Doench J, Ghandi M, Vazquez F, Weir BA, Tsherniak A, Subramanian A, Meneses-Cime K, Park J, Clemons P, Garraway LA, Thomas D, Boehm JS, Barbie DA, Hahn WC, Mesirov JP, Tamayo P. Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst. 2017 Aug 23;5(2):105-118.e9. doi: 10.1016/j.cels.2017.08.002. PubMed PMID: 28837809.

Reich M, Tabor T, Liefeld T, Thorvaldsdóttir H, Hill B, Tamayo P, Mesirov JP. The GenePattern Notebook Environment. Cell Syst. 2017 Aug 23;5(2):149-151.e1. doi: 10.1016/j.cels.2017.07.003. Epub 2017 Aug 16. PubMed PMID: 28822753; PubMed Central PMCID: PMC5572818.

Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B,Kaffenberger SD, Eaton JK, Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV, Javaid S, Huang C, Wu X, Tseng YY, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA, Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF, Clemons PA, Stockwell BR, Schreiber SL. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017 Jul 27;547(7664):453-457. doi: 10.1038/nature23007. Epub 2017 Jul 5. PubMed PMID: 28678785.

Carlin D, Kosnicki K, Garamszegi S et al. A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression. F1000Research 2017, 6:784 (doi: 10.12688/f1000research.11616.1)

Boulay G, Awad ME, Riggi N, Archer TC, Iyer S, Boonseng WE, Rossetti NE, Naigles B, Rengarajan S, Volorio A, Kim JC, Mesirov JP, Tamayo P, Pomeroy SL, Aryee MJ, Rivera MN. OTX2 Activity at Distal Regulatory Elements Shapes the Chromatin Landscape of Group 3 Medulloblastoma. Cancer Discov. 2017 Mar;7(3):288-301. doi: 10.1158/2159-8290.CD-16-0844. Epub 2017 Feb 17. PubMed PMID: 28213356; PubMed Central PMCID: PMC5340587.

Silterra J, Gillette MA, Lanaspa M, Pellé KG, Valim C, Ahmad R, Acácio S, Almendinger KD, Tan Y, Madrid L, Alonso PL, Carr SA, Wiegand RC, Bassat Q, Mesirov JP, Milner DA Jr, Wirth DF. Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas. J Infect Dis. 2017 Jan 15;215(2):312-320. doi: 10.1093/infdis/jiw531. PubMed PMID: 27837008.

Naviaux RK. Antipurinergic therapy for autism—an in-depth review. Mitochondrion, ePub ahead of print, 2017 (PDF).

Robert K. Naviaux; Brooke Curtis; Kefeng Li; Jane C. Naviaux; A. Taylor Bright; Gail E. Reiner; Marissa Westerfield; Suzanne Goh; William A. Alaynick; Lin Wang; Edmund V. Capparelli; Cynthia Adams; Ji Sun; Sonia Jain; Feng He; Deyna A. Arellano; Lisa E. Mash; Leanne Chukoskie; Alan Lincoln; Jeanne Townsend. Low-dose suramin in autism spectrum disorder: a small, phase I/II, randomized clinical trial. Annals of Clinical and Translational Neurology, May 26, 2017. (PDF)

2016

Engin B, Kreisberg J, Carter H ****Structure-based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces PLoS One Apr 4;11(4):e0152929. PMID: 27043210

Levy E, Marty R, Garate-Calderon V, Woo B, Dow M, Armisen R, Carter H, Harismendy O Immune DNA signature of T-Cell infiltration in breast tumor exomes Scientific Reports 6, Article number: 30064. PMID: 27452728

Busby M, Xue C, Li C, Farjoun Y, Gienger E, Yofe I, Gladden A, Epstein CB, Cornett EM, Rothbart SB, Nusbaum C & Goren A.
Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq. (2016) Epigenetics & chromatin. [pubmed]

Bandopadhayay P, Ramkissoon LA, Jain P, Bergthold G, Wala J, Zeid R, Schumacher SE, Urbanski L, O'Rourke R, Gibson WJ, Pelton K, Ramkissoon SH, Han HJ, Zhu Y, Choudhari N, Silva A, Boucher K, Henn RE, Kang YJ, Knoff D, Paolella BR, Gladden-Young A, Varlet P, Pages M, Horowitz PM, Federation A, Malkin H, Tracy AA, Seepo S, Ducar M, Van Hummelen P, Santi M, Buccoliero AM, Scagnet M, Bowers DC, Giannini C, Puget S, Hawkins C, Tabori U, Klekner A, Bognar L, Burger PC, Eberhart C, Rodriguez FJ, Hill DA, Mueller S Haas-Kogan DA, Phillips JJ, Santagata S, Stiles CD, Bradner JE, Jabado N, Goren A, Grill J, Ligon AH, Goumnerova L, Waanders AJ, Storm PB, Kieran MW, Ligon KL, Beroukhim R, Resnick AC.
MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. (2016) Nat Genet. [pubmed]

Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D.
Oct1 and OCA-B are selectively required for CD4 memory T cell function. (2015) J Exp Med. [pubmed]

Rotem, A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA and Bernstein BE.
Single-cell chromatin profiles reveal a spectrum of stem cell epigenetic states. (2015) Nature Biotechnol. [pubmed]

Swapan Mallick, Heng Li, Mark Lipson, Iain Mathieson, Melissa Gymrek, Fernando Racimo, Mengyao Zhao, Niru Chennagiri, Susanne Nordenfelt, Arti Tandon, Pontus Skoglund, Iosif Lazaridis, Sriram Sankararaman, Qiaomei Fu, Nadin Rohland, Gabriel Renaud, Yaniv Erlich, Thomas Willems, Carla Gallo, Jeffrey P. Spence, Yun S. Song, Giovanni Poletti, Francois Balloux, George van Driem, Peter de Knijff, Irene Gallego Romero, Aashish R. Jha, Doron M. Behar, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Andres Moreno-Estrada, Olga L. Posukh, Elena Balanovska, Oleg Balanovsky, Sena Karachanak-Yankova, Hovhannes Sahakyan, Draga Toncheva, Levon Yepiskoposyan, Chris Tyler-Smith, Yali Xue, M. Syafiq Abdullah, Andres Ruiz-Linares, Cynthia M. Beall, Anna Di Rienzo, Choongwon Jeong, Elena B. Starikovskaya, Ene Metspalu, Jüri Parik, Richard Villems, Brenna M. Henn, Ugur Hodoglugil, Robert Mahley, Antti Sajantila, George Stamatoyannopoulos, Joseph T. S. Wee, Rita Khusainova, Elza Khusnutdinova, Sergey Litvinov, George Ayodo, David Comas, Michael F. Hammer, Toomas Kivisild, William Klitz, Cheryl A. Winkler, Damian Labuda, Michael Bamshad, Lynn B. Jorde, Sarah A. Tishkoff, W. Scott Watkins, Mait Metspalu, Stanislav Dryomov, Rem Sukernik, Lalji Singh, Kumarasamy Thangaraj, Svante Pääbo, Janet Kelso, Nick Patterson, David Reich (2016) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. [pubmed]

Melissa Gymrek, Yossi Farjoun. (2016) Recommendations for open data science. Gigascience. [pubmed]

Thomas Willems, Melissa Gymrek, G David Poznik, Chris Tyler-Smith, 1000 Genomes Project Chromosome Y Group, Yaniv Erlich. (2016) Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet. [pubmed]

G David Poznik, Yali Xue, Fernando L Mendez, Thomas F Willems, Andrea Massaia, Melissa A Wilson Sayres, Qasim Ayub, Shane A McCarthy, Apurva Narechania, Seva Kashin, Yuan Chen, Ruby Banerjee, Juan L Rodriguez-Flores, Maria Cerezo, Haojing Shao, Melissa Gymrek, Ankit Malhotra, Sandra Louzada, Rob Desalle, Graham R S Ritchie, Eliza Cerveira, Tomas W Fitzgerald, Erik Garrison, Anthony Marcketta, David Mittelman, Mallory Romanovitch, Chengsheng Zhang, Xiangqun Zheng-Bradley, Gonçalo R Abecasis, Steven A McCarroll, Paul Flicek, Peter A Underhill, Lachlan Coin, Daniel R Zerbino, Fengtang Yang, Charles Lee, Laura Clarke, Adam Auton, Yaniv Erlich, Robert E Handsaker, The 1000 Genomes Project Consortium, Carlos D Bustamante, Chris Tyler-Smith. (2016) Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics. [pubmed]

Javier Quilez, Audrey Guilmatre, Paras Garg, Gareth Highnam, Melissa Gymrek, Yaniv Erlich, Ricky S. Joshi, David Mittelman, Andrew J. Sharp. (2016) Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans. Nucleic Acids Research. [pubmed]

Melissa Gymrek, Thomas Willems, Haoyang Zeng, Barak Markus, Mark J Daly, Alkes L Price, Jonathan Pritchard, Yaniv Erlich. (2016) Abundant contribution of short tandem repeats to gene expression variation in humans. Nature Genetics. [pubmed]

Ideker T. The Real Value of an Atlas. NIH Biomedical Informatics Blog. 31 Oct 2016. [PDF] (Review)

Saito R, Rocanin-Arjo A, You YH, Darshi M, Van Espen B, Miyamoto S, Pham J, Pu M, Romoli S, Natarajan L, Ju W, Kretzler M, Nelson R, Ono K, Thomasova D, Mulay SR, Ideker T, D’Agati V, Beyret E, Belmonte JC, Anders HJ, Sharma K. Systems biology analysis reveals role of MDM2 in diabetic nephropathy. JCI Insight. 2016 Oct 20;1(17):e87877. doi: 10.1172/jci.insight.87877. PMID: 27777973. [PDF] [PubMed]

Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10750-8. doi: 10.1073/pnas.1608077113. Epub 2016 Sep 16. PubMed PMID: 27638202; PubMed Central PMCID: PMC5047191. [PDF] [PubMed]

Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Molecular Cell. 2016 Jul 19. pii: S1097-2765(16)30280-5. doi: 10.1016/j.molcel.2016.06.022. PMID: 27453043. [PDF] [PubMed]

Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exomesequencing data. Nat Commun. 2016 Jul 15;7:12096. doi: 10.1038/ncomms12096. PMID: 27417679; PMCID: PMC4947162. [PDF] [PubMed]

• Get positive and negative datasets [Click to download ZIP file] 

Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. Int J Cancer. 2016 Jul 15;139(2):373-82. doi: 10.1002/ijc.30081. Epub 2016 Mar 30. PMID: 26949921; PMCID: PMC5579720. [PDF][PubMed]

Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hofree M, Huang R, Johns H, Karydas A, Knopman DS, Loboda A, Masliah E, Narasimhan R, Petersen RC, Podtelezhnikov A, Pradhan S, Rademakers R, Sun CH, Younkin SG, Miller BL, Ideker T, Wyss-Coray T. Network-driven plasma proteomics expose molecular changes in the Alzheimer’s brain. Mol Neurodegener. 2016 Apr 26;11:31. doi: 10.1186/s13024-016-0095-2. Erratum in: Mol Neurodegener. 2016 May 23;11(1):42. doi: 10.1186/s13024-016-0105-4. PMID: 27112350; PMCID: PMC4845325. [PDF] [PubMed]

Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS,Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell. 2016 Apr 21;62(2):157-168. doi: 10.1016/j.molcel.2016.03.019. PMID: 27105112; PMCID: PMC4995115. [PDF] [PubMed]

• Tutorial for implementing Hannum, et al., MOL CELL (2013): GitHub Source Code
• Meet the Author: Interview with Andy Gross
• Press: NPR Health: People Who Are HIV-Positive May Be Aging Faster Than Their Peers
• Press: NIH Science News: Biomarker Tracks Accelerated HIV-Associated Aging
• Press: UCSD Health: HIV Infection Prematurely Ages People by an Average of Five Years

Ono, Kei. Technical aspects of “Panama Papers” analysis. Newsweek Japan, 12 April 2016. [PDF] (Review)

Yu M, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng C, Krogan N, Sharan R, Ideker T. Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. Cell Syst. 2016 Feb 24;2(2):77-88. doi: 10.1016/j.cels.2016.02.003. PMID: 26949740; PMCID: PMC4772745. [PDF][PubMed] *Cover article

• Cover Art: Artwork by first author Michael Yu
• Press: Just the FAQs: Connecting Connecting Genotype to Phenotype with “Ontotype”

Liss MA, DeConde R, Caovan D, Hofler J, Gabe M, Palazzi KL, Patel ND, Lee HJ, Ideker T, Van Poppel H, Karow D, Aertsen M, Casola G, Derweesh IH. Parenchymal Volumetric Assessment as a Predictive Tool to Determine Renal Function Benefit of Nephron-Sparing Surgery Compared with Radical Nephrectomy. J Endourol. 2016 Jan;30(1):114-21. doi: 10.1089/end.2015.0411. Epub 2015 Sep 25. PMID: 26192380; PMCID: PMC4841003. [PDF] [PubMed]

Qu K*, Garamszegi S*, Wu F*, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. PMID: 26780094; PMCID: PMC4767623. *Equal Contribution [PDF] [PubMed]

Spira A, Disis ML, Schiller JT, Vilar E, Rebbeck TR, Bejar R, Ideker T, Arts J, Yurgelun MB, Mesirov JP, Rao A, Garber J, Jaffee EM, Lippman SM. Leveraging premalignant biology for immune-based cancer prevention. Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10750-8. doi: 10.1073/pnas.1608077113. Epub 2016 Sep 16. PubMed PMID: 27638202; PubMed Central PMCID: PMC5047191.

Hanaford AR, Archer TC, Price A, Kahlert UD, Maciaczyk J, Nikkhah G, Kim JW, Ehrenberger T, Clemons PA, Dančík V, Seashore-Ludlow B, Viswanathan V, Stewart ML, Rees MG, Shamji A, Schreiber S, Fraenkel E, Pomeroy SL, Mesirov JP, Tamayo P, Eberhart CG, Raabe EH. DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets. Clin Cancer Res. 2016 Aug 1;22(15):3903-14. Doi: 10.1158/1078-0432.CCR-15-3011. Epub 2016 Mar 24. PubMed PMID: 27012813; PubMed Central PMCID: PMC5055054.

D'Antonio M, Tamayo P, Mesirov JP, Frazer KA. Kataegis Expression Signature in Breast Cancer Is Associated with Late Onset, Better Prognosis, and Higher HER2 Levels. Cell Rep. 2016 Jul 19;16(3):672-83. doi: 10.1016/j.celrep.2016.06.026. Epub 2016 Jun 30. PubMed PMID: 27373164; PubMed Central PMCID: PMC4972030.

Durand NC, Robinson JT, Shamim MS, Machol I, Mesirov JP, Lander ES, Aiden EL. Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst. 2016 Jul;3(1):99-101. doi: 10.1016/j.cels.2015.07.012. PubMed PMID: 27467250; PubMed Central PMCID: PMC5596920.

Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016 May 19;165(5):1267-1279. doi: 10.1016/j.cell.2016.04.028. Epub 2016 May 12. PubMed PMID: 27180905; PubMed Central PMCID: PMC5029792.

Kim JW, Botvinnik OB, Abudayyeh O, Birger C, Rosenbluh J, Shrestha Y, Abazeed ME, Hammerman PS, DiCara D, Konieczkowski DJ, Johannessen CM, Liberzon A, Alizad-Rahvar AR, Alexe G, Aguirre A, Ghandi M, Greulich H, Vazquez F, Weir BA, Van Allen EM, Tsherniak A, Shao DD, Zack TI, Noble M, Getz G, Beroukhim R, Garraway LA, Ardakani M, Romualdi C, Sales G, Barbie DA, Boehm JS, Hahn WC, Mesirov JP, Tamayo P. Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 May;34(5):539-46. doi: 10.1038/nbt.3527. Epub 2016 Apr 18. PubMed PMID: 27088724; PubMed Central PMCID: PMC4868596.

Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Mar;13(3):245-247. doi: 10.1038/nmeth.3732. Epub 2016 Jan 18. PubMed PMID: 26780094; PubMed Central PMCID: PMC4767623.

Valim C, Ahmad R, Lanaspa M, Tan Y, Acácio S, Gillette MA, Almendinger KD, Milner DA Jr, Madrid L, Pellé K, Harezlak J, Silterra J, Alonso PL, Carr SA, Mesirov JP, Wirth DF, Wiegand RC, Bassat Q. Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia. Am J Respir Crit Care Med. 2016 Feb 15;193(4):448-59. doi: 10.1164/rccm.201506-1100OC. PubMed PMID: 26469764; PubMed Central PMCID: PMC5440057.

Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity. 2016 Jan 19;44(1):194-206. doi: 10.1016/j.immuni.2015.12.006. Epub 2016 Jan 12. PubMed PMID: 26795250; PubMed Central PMCID: PMC5330663.

Zhu X, Girardo D, Govek EE, John K, Mellén M, Tamayo P, Mesirov JP, Hatten ME. Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit Formation. Neuron. 2016 Jan 6;89(1):100-12. doi: 10.1016/j.neuron.2015.11.030. Epub 2015 Dec 17. PubMed PMID: 26711116; PubMed Central PMCID: PMC4707072.

Metabolic features of chronic fatigue syndrome. Naviaux RK, Naviaux JC, Li K, Bright AT, Alaynick WA, Wang L, Baxter A, Nathan N, Anderson W, Gordon E. Proc Natl Acad Sci U S A. 2016 Aug 29. PMID: N/A (PDF)

Neurometabolic Disorders: Potentially Treatable Abnormalities in Patients With Treatment-Refractory Depression and Suicidal Behavior. Pan LA, Martin P, Zimmer T, Segreti AM, Kassiff S, McKain BW, Baca CA, Rengasamy M, Hyland K, Walano N, Steinfeld R, Hughes M, Dobrowolski SK, Pasquino M, Diler R, Perel J, Finegold DN, Peters DG, Naviaux RK, Brent DA, Vockley J. Am J Psychiatry. 2016 Aug 13. PMID: 27523499

2015

Engin B, Hofree M**,** Carter H ****Identifying Mutation-Specific Cancer Pathways Using a Structurally Resolved Protein Interaction Network Pac Symp Biocomput. 84-95. PMID: 25592571

Etchegaray JP^#, Chavez L, Huang Y, Ross KN, Choi J, Martinez-Pastor B, Walsh RM, Sommer CA, Lienhard M, Kugel S, Gladden A, Silberman DM, Ramaswamy S, Mostoslavsky G, Hochedlinger G, Goren A^#, Rao A and Mostoslavsky R^#. The Histone Deacetylase Sirt6 Controls Embryonic Stem Cell Fate Via Tet-Mediated Production of 5-Hydroxymethylcytosine. (2015) Nature Cell Biol. [pubmed]

Shakya A, Callister C, Goren A, Yosef N, Garg N, Khoddami V, Nix D, Regev A, Tantin D.
Pluripotency transcription factor oct4 mediates stepwise nucleosome demethylation and depletion. (2015) Mol Cell Biol. [pubmed]

Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y and Meissner A.Dissecting neural differentiation regulatory networks through epigenetic footprinting. (2015) Nature [pubmed]

1000 Genomes Project Consortium. (2015) A global reference for human genetic variation. Nature. [pubmed]

Carvunis A, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. Evidence for a common evolutionary rate in metazoan transcriptional networks. Elife. 2015 Dec 18;4:e11615. doi: 10.7554/eLife.11615. PMID: 26682651; PMCID: PMC4764585. [PDF] [PubMed]

Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS. Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues. Journal of Proteome Research. 2015 Dec 4;14(12):4995-5006. doi: 10.1021/acs.jproteome.5b00827. Epub 2015 Oct 20. [PDF] [PubMed]

Gross AM, Kreisberg JF, Ideker T. Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types. PLoS One. 2015 Nov 10;10(11):e0142618. doi: 10.1371/journal.pone.0142618. PMID: 26555223; PMCID: PMC4640835. [PDF] [PubMed]

Lau E, Sedy J, Sander C, Shaw MA, Feng Y, Scortegagna M, Claps G, Robinson S, Cheng P, Srivas R, Soonthornvacharin S, Ideker T, Bosenberg M, Gonzalez R, Robinson W, Chanda SK, Ware C, Dummer R, Hoon D, Kirkwood JM, Ronai ZA. Transcriptional repression of IFNβ1 by ATF2 confers melanoma resistance to therapy. Oncogene. 2015 Nov 12;34(46):5739-48. doi: 10.1038/onc.2015.22. Epub 2015 Mar 2. PMID: 25728676; PMCID: PMC4558399. [PDF] [PubMed]

Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T. NDEx, the Network Data Exchange. Cell Syst. 2015 Oct 28;1(4):302-305. doi: 10.1016/j.cels.2015.10.001. PMID: 26594663; PMCID: PMC4649937. [PDF] [PubMed]

Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, Sobol RW, Ideker T. Chemogentic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. 2015 Nov 3;6(34):35755-69. doi: 10.18632/oncotarget.5928. PMID: 26437225; PMCID: PMC4742139. [PDF] [PubMed]

Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B. cyNeo4j: connecting Neo4j and Cytoscape. Bioinformatics. 2015 Dec 1;31(23):3868-9. doi: 10.1093/bioinformatics/btv460. Epub 2015 Aug 12. PMID: 26272981; PMCID: PMC4653389. [PDF] [PubMed]

Till A, Saito R, Merkurjev D, Liu JJ, Syed GH, Kolnik M, Siddiqui A, Glas M, Scheffler B, Ideker T, Subramani S. Evolutionary trends and functional anatomy of the human expanded autophagy network. Autophagy. 2015;11(9):1652-67. doi: 10.1080/15548627.2015.1059558. PMID: 26103419; PMCID: PMC4590607. [PDF] [PubMed]

Jaeger PA, McElfresh C, Wong LR, Ideker T. Beyond Agar: Gel Substrates with Improved Optical Clarity and Drug Efficiency and Reduced Autofluorescence for Microbial Growth Experiments. Appl Environ Microbiol. 2015 Aug 15;81(16):5639-49. doi: 10.1128/AEM.01327-15. Epub 2015 Jun 12. PMID: 26070672; PMCID: PMC4510171. [PDF] [PubMed]

Ono K, Muetze T, Kolishovski, G, Shannon P, Demchak B. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000Res. 2015 Aug 5;4:478. doi: 10.12688/f1000research.6767.1. PMID: 26672762; PMCID: PMC4670004. [PDF] [PubMed]

Gross AM, Ideker T. Molecular networks in context. Nat Biotechnol. 2015 Jul;33(7):720-1. doi: 10.1038/nbt.3283. PMID: 26154012. [PDF] [PubMed] (Review)

Choueiri MB, Shen JP, Gross AM, Huang JK, Ideker T, Fanta P. ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer. PLoS One. 2015 Jun 17;10(6):e0126898. doi: 10.1371/journal.pone.0126898. PMID: 26083491; PMCID: PMC4470586. [PDF] [PubMed]

Roosing S, Hofree M, Kim S, Scott E, Copeland B, Romani M, Silhavy JL, Rosti RO, Schroth J, Mazza T, Miccinilli E, Zaki MS, Swoboda KJ, Milisa-Drautz J, Dobyns WB, Mikati MA, İncecik F, Azam M, Borgatti R, Romaniello R, Boustany RM, Clericuzio CL, D’Arrigo S, Strømme P, Boltshauser E, Stanzial F, Mirabelli-Badenier M, Moroni I, Bertini E, Emma F, Steinlin M, Hildebrandt F, Johnson CA, Freilinger M, Vaux KK, Gabriel SB, Aza-Blanc P, Heynen-Genel S, Ideker T, Dynlacht BD, Lee JE, Valente EM, Kim J, Gleeson JG. Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome. Elife. 2015 May 30;4:e06602. doi: 10.7554/eLife.06602. PMID: 26026149; PMCID: PMC4477441. [PDF] [PubMed]

Krogan NJ, Lippman S, Agard DA, Ashworth A, Ideker T. The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell. 2015 May 21;58(4):690-8. doi: 10.1016/j.molcel.2015.05.008. PMID: 26000852; PMCID: PMC5359018.[PDF] [PubMed] (Review)

Raju SC, Hauff SJ, Lemieux AJ, Orosco RK, Gross AM, Nguyen LT, Savariar E, Moss W, Whitney M, Cohen EE, Lippman SM, Tsien RY, Ideker T, Advani SJ, Nguyen QT. Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma. Oral Oncol. 2015 May;51(5):470-5. doi: 10.1016/j.oraloncology.2015.01.014. Epub 2015 Feb 27. PMID: 25735654; PMCID: PMC4427339. [PDF] [PubMed]

Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM. Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Mol Cell. 2015 Jan 22;57(2):273-89. doi: 10.1016/j.molcel.2014.11.016. Epub 2014 Dec 18. PMID: 25533186; PMCID: PMC5706562. [PDF] [PubMed] 

Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015 Dec 23;1(6):417-425. PubMed PMID: 26771021; PubMed Central PMCID: PMC4707969.

Katz Y, Wang ET, Silterra J, Schwartz S, Wong B, Thorvaldsdóttir H, Robinson JT, Mesirov JP, Airoldi EM, Burge CB. Quantitative visualization of alternative exon expression from RNA-seq data. Bioinformatics. 2015 Jul 15;31(14):2400-2. doi: 10.1093/bioinformatics/btv034. Epub 2015 Jan 22. PubMed PMID: 25617416; PubMed Central PMCID: PMC4542614.

Wilson FH, Johannessen CM, Piccioni F, Tamayo P, Kim JW, Van Allen EM, Corsello SM, Capelletti M, Calles A, Butaney M, Sharifnia T, Gabriel SB, Mesirov JP, Hahn WC, Engelman JA, Meyerson M, Root DE, Jänne PA, Garraway LA. A functional landscape of resistance to ALK inhibition in lung cancer. Cancer Cell. 2015 Mar 9;27(3):397-408. doi: 10.1016/j.ccell.2015.02.005. PubMed PMID: 25759024; PubMed Central PMCID: PMC4398996.

Thorvaldsdóttir H, Robinson JT, Turner D, Mesirov JP. A genomic data viewer for iPad. Genome Biol. 2015 Feb 26;16:46. doi: 10.1186/s13059-015-0595-3. PubMed PMID: 25723152; PubMed Central PMCID: PMC4342165.

Tan Y, Wu F, Tamayo P, Haining WN, Mesirov JP. Constellation Map: Downstream visualization and interpretation of gene set enrichment results. F1000Res. 2015 Jun 24;4:167. doi: 10.12688/f1000research.6644.1. eCollection 2015. PubMed PMID: 26594333; PubMed Central PMCID: PMC4648224.

Papageorgiou A, Rapley J, Mesirov JP, Tamayo P, Avruch J. A genome-wide siRNA screen in mammalian cells for regulators of S6 phosphorylation. PLoS One. 2015 Mar 19;10(3):e0116096. doi: 10.1371/journal.pone.0116096. eCollection 2015. PubMed PMID: 25790369; PubMed Central PMCID: PMC4366019.

High-fat diet and FGF21 cooperatively promote aerobic thermogenesis in mtDNA mutator mice. Wall CE, Whyte J, Suh JM, Fan W, Collins B, Liddle C, Yu RT, Atkins AR, Naviaux JC, Li K, Bright AT, Alaynick WA, Downes M, Naviaux RK, Evans RM. Proc Natl Acad Sci U S A. 2015 Jul 14;112(28):8714-9. PMID: 26124126

Antipurinergic therapy corrects the autism-like features in the Fragile X (Fmr1 knockout) mouse model. Naviaux JC, Wang L, Li K, Bright AT, Alaynick WA, Williams KR, Powell SB, Naviaux RK. Mol Autism. 2015 Jan 13;6:1. doi: 10.1186/2040-2392-6-1. eCollection 2015. PMID: 25705365

2014

Krebs W, Schmidt SV, Goren A, De Nardo D, Labzin L, Bovier A, Ulas T, Theis H, Kraut M, Latz E, Beyer M, Schultze JL.
Optimization of transcription factor binding map accuracy utilizing knockout mouse models. (2014) Nuc. Acids Research. [pubmed]

Nicolo Riggi, Birgit Knoechel, Shawn M. Gillespie, Esther Rheinbay, Gaylor Boulay, Mario Suva, Nikki E. Rosetti, Wannaporn E. Boonseng, Ozgur Oksuz, Edward B. Cook, Aurelie Formey, Anoop Patel, Melissa Gymrek, Vishal Thapar, Vikram Deshpande, David T. King, Francis J. Hornicek, Petur Nielsen, Ivan Stamenkovic, Martin J. Aryee, Bradley E. Bernstein, Miguel N. Rivera. (2014) EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma. Cancer Cell [pubmed]

Melissa Gymrek. (2014) PyBamView: a browser based application for viewing short read alignments. Bioinformatics. [pubmed]

Thomas F. Willems, Melissa Gymrek, Gareth Highnam, The 1000 Genomes Project, David Mittelman, Yaniv Erlich. (2014) The Landscape of Human STR Variation. Genome Res. [pubmed]

Dina Zielinski, Barak Markus, Mona Sheikh, Melissa Gymrek, Clement Chu, Marta Zaks, Balaji Srinivasan, Jodi D. Hoffman, Dror Aizenbud, Yaniv Erlich. (2014) OTX2 Duplication Is Implicated in Hemifacial Microsomia. PLoS One. 9(5):e96788 [pubmed]

Cancer Genome Atlas Research Network. Under a Creative Commons license. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23;159(3):676-90. doi: 10.1016/j.cell.2014.09.050. PMID: 25417114; PMCID: PMC4243044. [PDF] [PubMed]

Wilkinson DS, Jariwala JS, Anderson E, Mitra K, Meisenhelder J, Chang JT, Ideker T, Hunter T, Nizet V, Dillin A, Hansen M. Phosphorylation of LC3 by the Hippo kinases STK3/STK4 is essential for autophagy. Mol Cell. 2015 Jan 8;57(1):55-68. doi: 10.1016/j.molcel.2014.11.019. Epub 2014 Dec 24. PMID: 25544559; PMCID: PMC4373083. [PDF] [PubMed]

Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 2014 Jul 1;3:151. doi: 10.12688/f1000research.4492.2. PMID: 25165537; PMCID: PMC4133763. [PDF] [PubMed] 

Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. Version 2. F1000Res. 2014 Jul 1;3:143. doi: 10.12688/f1000research.4510.2. PMID: 25520778; PMCID: PMC4264639. [PDF] [PubMed]

Welker D, Demchak B. Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000Res. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. PMID: 25075307; PMCID: PMC4103495. eCollection 2014. [PDF] [PubMed]

Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. The Cytoscape app article collection. F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. PMID: 25580224; PMCID: PMC4288400. eCollection 2014. [PDF] [PubMed]

Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with Cytoscape 3. Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-24. doi: 10.1002/0471250953.bi0813s47. PMID: 25199793; PMCID: PMC4174321. [PDF] [PubMed]

Shaughnessy DT, McAllister K, Worth L, Haugen AC, Meyer JN, Domann FE, Van Houten B, Mostoslavsky R, Bultman SJ, Baccarelli AA, Begley TJ, Sobol RW, Hirschey MD, Ideker T, Santos JH, Copeland WC, Tice RR, Balshaw DM, Tyson FL. Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress. Environ Health Perspect. 2014 Dec;122(12):1271-8. doi: 10.1289/ehp.1408418. Epub 2014 Aug 15. PMID: 25127496; PMCID: PMC4256704. [PDF] [PubMed] [TI: Provided data analysis.] (Review)

Hauff SJ, Raju SC, Orosco RK, Gross AM, Diaz-Perez JA, Savariar E, Nashi N, Hasselman J, Whitney M, Myers JN, Lippman SM, Tsien RY, Ideker T, Nguyen QT. Matrix-Metalloproteinases in Head and Neck Carcinoma-Cancer Genome Atlas Analysis and Fluorescence Imaging in Mice. Otolaryngol Head Neck Surg. 2014 Oct;151(4):612-8. doi: 10.1177/0194599814545083. Epub 2014 Aug 4. PMID: 25091190; PMCID: PMC4469264. [PDF] [PubMed]

Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss. Nat Genet. 2014 Sep;46(9):939-43. doi: 10.1038/ng.3051. Epub 2014 Aug 3. PMID: 25086664; PMCID: PMC4146706. [PDF] [PubMed]

Lee K, Sung MK, Kim J, Kim K, Byun J, Paik H, Kim B, Huh WK, Ideker T. Proteome-wide remodeling of protein location and function by stress. Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):E3157-66. doi: 10.1073/pnas.1318881111. Epub 2014 Jul 15. PMID: 25028499; PMCID: PMC4121818. [PDF] [PubMed]

Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics. 2014 Jun 15;30(12):i34-42. doi: 10.1093/bioinformatics/btu282. PMID: 24932003; PMCID: PMC4058954.[PDF] [PubMed]

Emig-Agius D, Olivieri K, Pache L, Shih HL, Pustovalova O, Bessarabova M, Young JA, Chanda SK, Ideker T. An integrated map of HIV-human protein complexes that facilitate viral infection. PLoS One. 2014 May 9;9(5):e96687. doi: 10.1371/journal.pone.0096687. PMID: 24817247; PMCID: PMC4016004. [PDF] [PubMed]

Joshi S, Singh AR, Zulcic M, Bao L, Messer K, Ideker T, Dutkowski J, Durden DL. Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PLoS One. 2014 Apr 25;9(4):e95893. doi: 10.1371/journal.pone.0095893. PMID: 24770346; PMCID: PMC4000195. [PDF] [PubMed]

Carvunis AR, Ideker T. Siri of the cell: what biology could learn from the iPhone. Cell. 2014 Apr 24;157(3):534-8. doi: 10.1016/j.cell.2014.03.009. PMID: 24766803; PMCID: PMC4154484. [PDF] [PubMed]

Novarino G*, Fenstermaker AG*, Zaki MS*, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel-Salam GM, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben-Omran T, Mojahedi F, Mahmoud IG, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al-Allawi N, Bindu PS, Azam M, Gunel M, Caglayan A, Bilguvar K, Tolun A, Issa MY, Schroth J, Spencer EG, Rosti RO, Akizu N, Vaux KK, Johansen A, Koh AA, Megahed H, Durr A, Brice A, Stevanin G, Gabriel SB, Ideker T, Gleeson JG. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014 Jan 31;343(6170):506-511. doi: 10.1126/science.1247363. PMID: 24482476; PMCID: PMC4157572. *Equal Contribution [PDF][PubMed]

Bean GJ, Jaeger PA, Bahr S, Ideker T. Development of ultra-high-density screening tools for microbial “omics.”. PLoS One. 2014 Jan 21;9(1):e85177. doi: 10.1371/journal.pone.0085177. PMID: 24465499; PMCID: PMC3897414. [PDF] [PubMed]

Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 2014 Jan;42(Database issue):D1269-74. doi: 10.1093/nar/gkt1192. Epub 2013 Nov 23. PMID: 24271398; PMCID: PMC3965056. [PDF] [PubMed]

Reversal of autism-like behaviors and metabolism in adult mice with single-dose antipurinergic therapy. Naviaux JC, Schuchbauer MA, Li K, Wang L, Risbrough VB, Powell SB, Naviaux RK. Transl Psychiatry. 2014 Jun 17;4:e400. doi: 10.1038/tp.2014.33. PMID: 24937094

A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent. McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM. Biotechnol Bioeng. 2014 Apr;111(4):803-15. PMID: 24249002

2013

Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M.
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. (2013)Science [pubmed]

Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A.
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. (2013) Nature [pubmed]

Michal Breker, Melissa Gymrek, Ofer Moldavski, Maya Schuldiner. (2013) LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast. Nucleic Acids Res. [pubmed]

Melissa Gymrek, Yaniv Erlich. (2013) Profiling short tandem repeats from short reads. Methods Mol Biol. [pubmed]

Michal Breker, Melissa Gymrek, Maya Schuldiner. (2013) A novel single-cell screening platform reveals proteome plasticity during yeast stress responses. J Cell Biol. [pubmed]

Melissa Gymrek, Amy McGuire, David Golan, Eran Halperin, Yaniv Erlich. (2013) Identifying personal genomes by surname inference. Science. [pubmed]

Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T. A UV-Induced Genetic Network Links the RSC Complex to Nucleotide Excision Repair and Shows Dose-Dependent Rewiring. Cell Rep. 2013 Dec 26;5(6):1714-24. doi: 10.1016/j.celrep.2013.11.035. Epub 2013 Dec 19. PMID: 24360959; PMCID: PMC4136507. [PDF] [PubMed]

• Yeast UV-induced genetic network (Differential Score) [Data]
• Yeast UV-induced genetic network (Static Score) [Data]

Potts MB, Kim HS, Fisher KW, Hu Y, Carrasco YP, Bulut GB, Ou YH, Herrera-Herrera ML, Cubillos F, Mendiratta S, Xiao G, Hofree M, Ideker T, Xie Y, Huang LJ, Lewis RE, Macmillan JB, White MA. Using Functional Signature Ontology (FUSION) to identify mechanisms of action for natural products. Sci Signal. 2013 Oct 15;6(297):ra90. doi: 10.1126/scisignal.2004657. PMID: 24129700; PMCID: PMC4075427. [PDF] [PubMed]

Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations.  Nat Methods. 2013 Nov;10(11):1108-15. doi: 10.1038/nmeth.2651. Epub 2013 Sep 15. PMID: 24037242; PMCID: PMC3866081. [PDF] [PubMed]

Sharma K, Karl B, Mathew AV, Gangoiti JA, Wassel CL, Saito R, Pu M, Sharma S, You YH, Wang L, Diamond-Stanic M, Lindenmeyer MT, Forsblom C, Wu W, Ix JH, Ideker T, Kopp JB, Nigam SK, Cohen CD, Groop PH, Barshop BA, Natarajan L, Nyhan WL, Naviaux RK. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol. 2013 Nov;24(11):1901-12. doi: 10.1681/ASN.2013020126. Epub 2013 Oct 10. PMID: 23949796; PMCID: PMC3810086. [PDF] [PubMed]

Jaehnig EJ, Kuo D, Hombauer H, Ideker TG, Kolodner RD. Checkpoint kinases regulate a global network of transcription factors in response to DNA damage. Cell Rep. 2013 Jul 11;4(1):174-88. doi: 10.1016/j.celrep.2013.05.041. Epub 2013 Jun 27. PMID: 23810556; PMCID: PMC3855057. [PDF] [PubMed]

Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR. Temporal transcription response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013 Jun 11;2:e00675. doi: 10.7554/eLife.00675. PMID: 23795294; PMCID: PMC3679525. [PDF] [PubMed]

Fukuyama H, Verdier Y, Guan Y, Makino-Okamura C, Shilova V, Liu X, Maksoud E, Matsubayashi J, Haddad I, Spirohn K, Ono K, Hetru C, Rossier J, Ideker T, Boutros M, Vinh J, Hoffmann JA. Landscape of protein-protein interactions in Drosophila immune deficiency signaling during bacterial challenge. Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10717-22. doi: 10.1073/pnas.1304380110. Epub 2013 Jun 7. PMID: 23749869; PMCID: PMC3696746.[PDF] [PubMed]

Lee K, Byun K, Hong W, Chuang HY, Pack CG, Bayarsaikhan E, Paek SH, Kim H, Shin HY, Ideker T, Lee B. Proteome-wide discovery of mislocated proteins in cancer. Genome Res. 2013 Aug;23(8):1283-94. doi: 10.1101/gr.155499.113. Epub 2013 May 14. PMID: 23674306; PMCID: PMC3730102. [PDF] [PubMed]

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol. 2013;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9. PMID: 23671412; PMCID: PMC3649990. [PDF] [PubMed]

Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, Wu SL, Hancock WS. Genome wide proteomics of ERBB2 and EGRF and other oncogenic pathways in inflammatory breast cancer. J Proteome Res. 2013 Jun 7;12(6):2805-17. doi: 10.1021/pr4001527. Epub 2013 May 22. PMID: 23647160; PMCID: PMC4142215. [PDF] [PubMed]

Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 31, 38–45 (2013). doi: 10.1038/nbt.2463. [PDF] [PubMed] *Cover article

• Cover Art: About the cover
• Data: Quantitative genetic interaction profiles [Data]

Chen M, Licon K, Otsuka R, Pillus L, Ideker T. Decoupling Epigenetic and Genetic Effects through Systematic Analysis of Gene Position. Cell Rep. 2013 Jan 31;3(1):128-37. doi: 10.1016/j.celrep.2012.12.003. Epub 2013 Jan 3. PMID: 23291096; PMCID: PMC3563736. [PDF] [PubMed]

Data included are RNA-Seq data for 4 heterozygous diploid yeast strains and diploid wild-type. There are three replicates for each heterozygous strain, and six replicates for wild-type. [GEO data set]

Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. The Anatomy of Successful Computational Biology Software. Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. PMID: 24104757; PMCID: PMC4166496. [PDF] [PubMed] 

Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Curr Opin Genet Dev. 2013 Dec;23(6):611-21. doi: 10.1016/j.gde.2013.10.003. Epub 2013 Nov 14. PMID: 24238873; PMCID: PMC3866044. [PDF] [PubMed] (Review)

Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biology networks. Nat Rev Genet. 2013 Oct;14(10):719-32. doi: 10.1038/nrg3552. PMID: 24045689; PMCID: PMC3940161. [PDF] [PubMed] (Review) 

Hannum G*, Guinney J*, Zhao L*, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T†, Zhang K†. Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol Cell. 2013 Jan 24;49(2):359-367. doi: 10.1016/j.molcel.2012.10.016. Epub 2012 Nov 21. PMID: 23177740; PMCID: PMC3780611 *Equal Contribution, †Co-Corresponding Authors [PDF] [PubMed] 

• Tutorial for implementing Hannum, et al., MOL CELL (2013): https://github.com/theandygross/HIV_Methylation Data sets: http://idekerlab.ucsd.edu/papers/ghannum2013/paper.pdf 
• Bisulphite converted DNA from the 656 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. GEO Data Set: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279

Metabolic features of the cell danger response. Naviaux RK. Mitochondrion. 2014 May;16:7-17. doi: 10.1016/j.mito.2013.08.006. Epub 2013 Aug 24. Review. PMID: 23981537 (PDF)

AMPK dysregulation promotes diabetes-related reduction of superoxide and mitochondrial function. Dugan LL, You YH, Ali SS, Diamond-Stanic M, Miyamoto S, DeCleves AE, Andreyev A, Quach T, Ly S, Shekhtman G, Nguyen W, Chepetan A, Le TP, Wang L, Xu M, Paik KP, Fogo A, Viollet B, Murphy A, Brosius F, Naviaux RK, Sharma K. J Clin Invest. 2013 Nov;123(11):4888-99. PMID: 24135141

Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. Sharma K, Karl B, Mathew AV, Gangoiti JA, Wassel CL, Saito R, Pu M, Sharma S, You YH, Wang L, Diamond-Stanic M, Lindenmeyer MT, Forsblom C, Wu W, Ix JH, Ideker T, Kopp JB, Nigam SK, Cohen CD, Groop PH, Barshop BA, Natarajan L, et al. J Am Soc Nephrol. 2013 Nov;24(11):1901-12. PMID: 23949796

AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder. Akizu N, Cantagrel V, Schroth J, Cai N, Vaux K, McCloskey D, Naviaux RK, Van Vleet J, Fenstermaker AG, Silhavy JL, Scheliga JS, Toyama K, Morisaki H, Sonmez FM, Celep F, Oraby A, Zaki MS, Al-Baradie R, Faqeih EA, Saleh MA, Spencer E, Rosti RO, et al. Cell. 2013 Aug 1;154(3):505-17. PMID: 23911318

Antipurinergic therapy corrects the autism-like features in the poly(IC) mouse model. Naviaux RK, Zolkipli Z, Wang L, Nakayama T, Naviaux JC, Le TP, Schuchbauer MA, Rogac M, Tang Q, Dugan LL, Powell SB. PLoS One. 2013;8(3):e57380. PMID: 23516405

Alpers-Huttenlocher syndrome. Saneto RP, Cohen BH, Copeland WC, Naviaux RK. Pediatr Neurol. 2013 Mar;48(3):167-78. PMID: 23419467

2012

Sebastian C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, MacDonald AI, McGlynn L, Maxwell F, Edwards J, Giacosa S, Guccione E, Weissleder R, Bernstein BE, Regev A, Shiels PG, Lombard DB, Mostoslavsky R.
The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. (2012) Cell [pubmed]

ENCODE Project Consortium.
An integrated encyclopedia of DNA elements in the human genome. (2012) Nature [pubmed]

Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I.
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. (2012) Mol Cell. [pubmed]

Dina Zielinski, Melissa Gymrek, Yaniv Erlich. (2012) Back to the family: a renewed approach to rare variant studies. Genome Med. [pubmed]

Carlos Sebastian, Bernadette Zwaans, Dafne Silberman, Melissa Gymrek, Alon Goren, Lei Zhong, Oren Ram, Jessica Truelove, Alexander Guimaraes, Debra Toiber, Claudia Cosentino, Joel Greenson, Alasdair MacDonald, Liane McGlynn, Fraser Maxwell, Joanne Edwards, Sofia Giacosa, Ernesto Guccione, Ralph Weissleder, Bradley Bernstein, Aviv Regev, Paul Shiels, David Lombard, Raul Mostoslavsky. (2012) The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. [pubmed]

Michal Nadler-Holly, Michal Breker, Ranit Gruber, Ariel Azia, Melissa Gymrek, Miriam Eisenstein, Keith Willison, Maya Schuldiner, Amnon Horovitz. (2012) Interactions of subunit CCT3 in the yeast chaperonin CCT/TRiC with Q/N-rich proteins revealed by high-throughput microscopy analysis. Proc Natl Acad Sci U S A. [pubmed]

Melissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich. (2012) lobSTR: A short tandem repeat profiler for personal genomes. Genome Res. [pubmed]

Melissa Gymrek, Yaniv Erlich. (2012) Using DNA sequencers as stethoscopes. Genome Med. [pubmed]

Jaeger P, Doherty C, Ideker T. Modeling Transcriptome Dynamics in a Complex World, Cell, Volume 151, Issue 6, 1161-1162, 7 December 2012. [PDF] [PubMed] (Review Article)

Bean GJ, Ideker T. Differential analysis of high-throughput quantitative genetic interaction data. Genome Biol. 2012 Dec 26;13(12):R123. [PDF] [PubMed]

Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. A travel guide to Cytoscape plugins. Nature Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6. [PDF] [PubMed] (Review Article)

Choi S, Srivas R, Fu KY, Hood BL, Dost B, Gibson GA, Watkins SC, Van Houten B, Bandeira N, Conrads TP, Ideker T, Bakkenist CJ. Quantitative Proteomics Reveal ATM Kinase-dependent Exchange in DNA Damage Response Complexes. J Proteome Res. 2012 Oct 5;11(10):4983-91. doi: 10.1021/pr3005524. Epub 2012 Sep 18. [PDF] [PubMed]

Califano A, Butte AJ, Friend S, Ideker T, Schadt E. Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nature Genetics. 2012 Jul 27;44(8):841-7. doi: 10.1038/ng.2355. [PDF] [PubMed] (Review Article)

Chuang HY, Rassenti L, Salcedo M, Licon K, Kohlmann A, Haferlach T, Foà R, Ideker T*, Kipps TJ*. Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. Blood. 2012 Sep 27;120(13):2639-49. Epub 2012 Jul 26. *Corresponding authors [PDF] [PubMed] 

• Supplemental Figures, Methods and Data [Suppl. Data]
• Expression data from untreated CLL patients [GEO Data Set]

Ryan CJ, Roguev A, Patrick K, Xu J, Jahari H, Tong Z, Beltrao P, Shales M, Qu H, Collins SR, Kliegman JI, Jiang L, Kuo D, Tosti E, Kim HS, Edelmann W, Keogh MC, Greene D, Tang C, Cunningham P, Shokat KM, Cagney G, Svensson JP, Guthrie C, Espenshade PJ, Ideker T, Krogan NJ Hierarchical modularity and the evolution of genetic interactomes across species. Mol Cell. 2012 Jun 8;46(5):691-704. [PDF] [PubMed]

Bark SJ, Wegrzyn J, Taupenot L, Ziegler M, O’Connor DT, Ma Q, Smoot M, Ideker T, Hook V. The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. PLoS One. 2012;7(8):e41134. doi: 10.1371/journal.pone.0041134. Epub 2012 Aug 16. [PDF] [PubMed]

Travesa A, Kuo D, de Bruin RA, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR 3rd, Ideker T, Wittenberg C. DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO Journal. 2012 Feb 14;31(7):1811-22. doi: 10.1038/emboj.2012.28. [PDF] [PubMed]

Lau E, Kluger H, Varsano T, Lee K, Scheffler I, Rimm DL, Ideker T, Ronai ZA. PKCe promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell. 2012 Feb 3;148(3):543-55. [PDF] [PubMed]

Ideker T, Krogan NJ. Differential network biology. Molecular Systems Biology. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. [PDF] [PubMed] (Review Article)

Zhang L, Lim SL, Du H, Zhang M, Kozak I, Hannum G, Wang X, Ouyang H, Hughes G, Zhao L, Zhu X, Lee C, Su Z, Zhou X, Shaw R, Geum D, Wei X, Zhu J, Ideker T, Oka C, Wang N, Yang Z, Shaw PX, Zhang K. High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-ß family member growth differentiation factor 6. J Biol Chem. 2012 Jan 6;287(2):1520-6. Epub 2011 Nov 2. [PDF] [PubMed]

Lesch-Nyhan variant syndrome: real-time rt-PCR for mRNA quantification in variable presentation in three affected family members. Nguyen KV, Naviaux RK, Paik KK, Nakayama T, Nyhan WL. Nucleosides Nucleotides Nucleic Acids. 2012;31(8):616-29. PMID: 22908952

Lesch-Nyhan syndrome: mRNA expression of HPRT in patients with enzyme proven deficiency of HPRT and normal HPRT coding region of the DNA. Nguyen KV, Naviaux RK, Paik KK, Nyhan WL. Mol Genet Metab. 2012 Aug;106(4):498-501. PMID: 22766437

Oxidative shielding or oxidative stress? Naviaux RK. J Pharmacol Exp Ther. 2012 Sep;342(3):608-18. PMID: 22700427 (PDF)

2011

Ram O*, Goren A*, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, Bernstein BE.
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. (2011) Cell [pubmed]

Zhou VW*, Goren A*, Bernstein BE.
Charting histone modifications and the functional organization of mammalian genomes. (2011) Nat Rev Genet. [pubmed]

Oren Ram, Alon Goren, Ido Amit, Noam Shoresh, Nir Yosef, Jason Ernst, Manolis Kellis, Melissa Gymrek, Robbyn Issner, Michael Coyne, Timothy Durham, Xiaolan Zhang, Julie Donaghey, Charles Epstein, Aviv Regev, Bradley Bernstein. (2011) Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. [pubmed]Guénolé A, Srivas R, Vreeken K, Wang ZZ, Wang S, Krogan NJ*, Ideker T*, van Attikum H*., Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps. Mol Cell. 2012 Dec 22. doi:pii: S1097-2765(12)00980-X. 10.1016/j.molcel.2012.11.023. [PDF] [PubMed] *Corresponding authors

• Yeast DNA damage response (Static Score) [Data]
• Yeast DNA damage response (Differential Score) [Data]

Atwood A*, DeConde R*, Wang SS, Mockler TC, Sabir JS, Ideker T, Kay SA. Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18560-5. doi: 10.1073/pnas.1115753108. Epub 2011 Oct 31. PMID: 22042857; PMCID: PMC3215069. *Equal Contribution [PDF] [PubMed]

Dutkowski J., Ideker T. Protein networks as logic functions in development and cancer. PLoS Comput Biol. 2011 Sep;7(9):e1002180. doi: 10.1371/journal.pcbi.1002180. Epub 2011 Sep 29. PMID: 21980275; PMCID: PMC3182870. [PDF][PubMed]

Mercer EM, Lin YC, Benner C, Jhunjhunwala S, Dutkowski J, Flores M, Sigvardsson M, Ideker T, Glass CK, Murre C. Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity. 2011 Sep 23;35(3):413-25. doi: 10.1016/j.immuni.2011.06.013. Epub 2011 Sep 8. PMID: 21903424; PMCID: PMC3183365. [PDF] [PubMed]

Srivas R, Hannum G, Ruscheinski J, Ono K, Wang PL, Smoot M, Ideker T. Assembling global maps of cellular function through integrative analysis of physical and genetic networks. Nat Protoc. 2011 Aug 11;6(9):1308-23. doi: 10.1038/nprot.2011.368. PMID: 21886098; PMCID: PMC3383003. [PDF] [PubMed]

Smoot ME, Ono K, Ideker T. Maere, S. PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics. 2011 Apr 1;27(7):1030-1. doi: 10.1093/bioinformatics/btr045. Epub 2011 Jan 28. PMID: 21278188; PMCID: PMC3065683. [PDF] [PubMed]

Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011 Feb 1;27(3):431-2. doi: 10.1093/bioinformatics/btq675. Epub 2010 Dec 12. PMID: 21149340; PMCID: PMC3031041. [PDF] [PubMed]

Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. 2011 Mar 18;144(6):860-3. doi: 10.1016/j.cell.2011.03.007. PMID: 21414478; PMCID: PMC3102020. [PDF] [PubMed] (Review)

Friend SH, Ideker T. Point: Are we prepared for the future doctor visit?. Nat Biotechnol. 2011 Mar;29(3):215-8. doi: 10.1038/nbt.1794. PMID: 21390021. [PDF] [PubMed] (Comment)

Novel mutations in the human HPRT gene. Nguyen KV, Naviaux RK, Paik KK, Nyhan WL. Nucleosides Nucleotides Nucleic Acids. 2011 Jun;30(6):440-5. PMID: 21780909

Fibroblast immuno-diagnosis of cytochrome oxidase (COX) deficiency in mitochondrial disease. Du A, Naviaux RK, Le T, Xu C, Sommer SS, Haas RH. Mitochondrion. 2011 May;11(3):430-6. PMID: 21187165

Novel mutations in the human MCCA and MCCB gene causing methylcrotonylglycinuria. Nguyen KV, Naviaux RK, Patra S, Barshop BA, Nyhan WL. Mol Genet Metab. 2011 Feb;102(2):218-21. PMID: 21071250

2010

Ozsolak F*, Goren A*, Gymrek M*, Guttman M, Regev A, Bernstein BE, Milos PM.
Digital transcriptome profiling from attomole-level RNA samples. (2010) Genome Res. [pubmed]

Goren A*, Ozsolak F*, Shoresh N*, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE.
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.(2010) Nat Methods [pubmed]

Kristen Naegle, Melissa Gymrek, Brian Joughin, Joel Wagner, Roy Welsch, Michael Yaffe, Douglas Lauffenburger, Forest White. (2010) PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies. Mol Cell Proteomics. [pubmed]

Fatih Ozsolak, Alon Goren, Melissa Gymrek, Mitchell Guttman, Aviv Regev, Bradley Bernstein, Patrice Milos. (2010) Digital transcriptome profiling from attomole-level RNA samples. Genome Res. [pubmed]

Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller D, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science. 2010 Dec 3;330(6009):1385-9. doi: 10.1126/science.1195618. Erratum in: Science. 2011 Jan 21;331(6015):284. PMID: 21127252; PMCID: PMC3006187. [PDF] [PubMed]

• Supplemental Data: Supporting Online Material for Rewiring of Genetic Networks in Response to DNA Damage
• Differential epistasis mapping (dE-MAP) [Data]

Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K†, Ideker T†. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res. 2010 Dec;20(12):1672-8. doi: 10.1101/gr.111765.110. Epub 2010 Oct 26. PMID: 20978140; PMCID: PMC2989993. †Co-Corresponding Authors [PDF] [PubMed]

Cannistraci CV, Ravasi T, Montevecchi FM, Ideker T, Alessio M. Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes. Bioinformatics. 2010 Sep 15;26(18):i531-9. doi: 10.1093/bioinformatics/btq376. PMID: 20823318; PMCID: PMC2935424. [PDF] [PubMed]

Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nat Methods. 2010 Oct;7(10):801-5. doi: 10.1038/nmeth.1506. PMID: 20936779; PMCID: PMC2967489. [PDF] [PubMed] 

• Core MAPK Y2H [Data]
• Full MAPK Y2H [Data]

Pentchev K*, Ono K*, Herwig R, Ideker T, Kamburov A. Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. Bioinformatics. 2010 Nov 1;26(21):2796-7. doi: 10.1093/bioinformatics/btq522. Epub 2010 Sep 16. PMID: 20847220; PMCID: PMC2958747. *Equal Contribution  [PDF] [PubMed]

Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol. 2010;11(7):R77. doi: 10.1186/gb-2010-11-7-r77. Epub 2010 Jul 23. PMID: 20653936; PMCID: PMC2926788. [PDF] [PubMed]

• Expression profiles of three yeast species after exposure to fluconazole. [Data]

Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, Ideker T, Glass CK, Murre C. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010 Jul;11(7):635-43. doi: 10.1038/ni.1891. Epub 2010 Jun 13. PMID: 20543837; PMCID: PMC2896911. [PDF] [PubMed]

Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, Ideker T, Aza-Blanc P, Gleeson JG. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature. 2010 Apr 15;464(7291):1048-51. doi: 10.1038/nature08895. PMID: 20393563; PMCID: PMC2929961. [PDF] [PubMed]

Lee, K., Thorneycoft, D., Achuthan, P., Hermjakob, H., Ideker, T. Mapping Plant Interactomes Using Literature Curated and Predicted Protein-Protein Interaction Datasets. Plant Cell. 2010 Apr;22(4):997-1005. doi: 10.1105/tpc.109.072736. Epub 2010 Apr 6. PMID: 20371643; PMCID: PMC2879763. [PDF] [PubMed]

• Protein sub-cellular localization in A. taliana [Data]

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 2010 Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. PMID: 20211142; PMCID: PMC2836267. [PDF] [Pubmed]

• Human TF interactions [Data]
• Mouse TF interactions [Data]

König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, García-Sastre A, Young JA, Palese P, Shaw ML, Chanda SK. Human Host Factors Required for Influenza Virus Replication. Nature. 2010 Feb 11;463(7282):813-7. doi: 10.1038/nature08699. PMID: 20027183; PMCID: PMC2862546. [PDF] [PubMed]

van Steensel B*, Braunschweig U*, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Res. 2010 Feb;20(2):190-200. doi: 10.1101/gr.098822.109. Epub 2009 Dec 9. PMID: 20007327; PMCID: PMC2813475. *Equal Contribution [PDF] [PubMed]

• Targeting Interactions in Chromatin. [Data]

Bandyopadhyay, S. and Ideker T. Integrative systems biology. Nature Genetics 42(12) (2010). [Poster] (Review)

Chuang HY, Hofree M, Ideker T. A decade of systems biology. Annu Rev Cell Dev Biol. 2010;26:721-44. doi: 10.1146/annurev-cellbio-100109-104122. PMID: 20604711; PMCID: PMC3371392. [PDF] [PubMed] (Review)

Polymerase gamma disease through the ages. Saneto RP, Naviaux RK. Dev Disabil Res Rev. 2010;16(2):163-74. PMID: 20818731

Role of reactive oxygen species in hyperadrenergic hypertension: biochemical, physiological, and pharmacological evidence from targeted ablation of the chromogranin a (Chga) gene. Gayen JR, Zhang K, RamachandraRao SP, Mahata M, Chen Y, Kim HS, Naviaux RK, Sharma K, Mahata SK, O'Connor DT. Circ Cardiovasc Genet. 2010 Oct;3(5):414-25. PMID: 20729505

The clinical diagnosis of POLG disease and other mitochondrial DNA depletion disorders. Cohen BH, Naviaux RK. Methods. 2010 Aug;51(4):364-73. PMID: 20558295

POLG DNA testing as an emerging standard of care before instituting valproic acid therapy for pediatric seizure disorders. Saneto RP, Lee IC, Koenig MK, Bao X, Weng SW, Naviaux RK, Wong LJ. Seizure. 2010 Apr;19(3):140-6. PMID: 20138553

2009

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A.
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. (2009) Science [pubmed]

Alon Goren, Fatih Ozsolak, Noam Shoresh, Manching Ku, Mazhar Adli, Chris Hart, Melissa Gymrek, Or Zuk, Aviv Regev, Patrice Milos, Bradley Bernstein. (2009) Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. [pubmed]

Hannum G*, Srivas R*, Guénolé A, van Attikum H, Krogan NJ, Karp RM, Ideker T. Genome-wide association data reveal a global map of genetic interactions among protein complexes. PLoS Genet. 2009 Dec;5(12):e1000782. doi: 10.1371/journal.pgen.1000782. Epub 2009 Dec 24. PMID: 20041197; PMCID: PMC2788232. *Equal Contribution [PDF] [PubMed]

Gersten M, Alirezaei M, Marcondes MC, Flynn C, Ravasi T, Ideker T, Fox HS. An integrated systems analysis implicates EGR1 downregulation in SIVE-induced neural dysfunction. J Neurosci. 2009 Oct 7;29(40):12467-76. doi: 10.1523/JNEUROSCI.3180-09.2009. PMID: 19812322; PMCID: PMC2802851. [PDF] [PubMed]

RNA from duplicate hippocampal samples taken from nine control monkeys and nine monkeys with evidence of SIV encephalitis were hybridized to Affymetrix arrays. [Data Set]

Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J. Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog. 2009 Sep;5(9):e1000570. doi: 10.1371/journal.ppat.1000570. Epub 2009 Sep 4. PMID: 19730696; PMCID: PMC2731838. [PDF] [PubMed]

Kelley R, Ideker T. Genome-wide fitness and expression profiling implicate Mga2 in adaptation to hydrogen peroxide. PLoS Genet. 2009 May;5(5):e1000488. doi: 10.1371/journal.pgen.1000488. Epub 2009 May 29. PMID: 19503593; PMCID: PMC2676504. [PDF] [PubMed]

• Enrichment Summary: Differentially expressed or sensitive members of each significantly over-represented condition or transcription factor target set mentioned in the study. [Data Set]
• Expression Table: Log ratios and p-values for all micro-array expression profiling experiments conducted in this study. [Data Set]
• Fitness Table: P-values for acute and adaptive screens conducted in this study. [Data Set]
• TFs Table: Table containing all of the transcription factor target sets used in this study. [Data Set]

Bushman FD, Malani N, Fernandes J, D’Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May;5(5):e1000437. doi: 10.1371/journal.ppat.1000437. Epub 2009 May 29. PMID: 19478882; PMCID: PMC2682202. [PDF] [PubMed]

Moxley JF*, Jewett MC*, Antoniewicz MR*, Villas-Boas SG*, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G. Special Feature: Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6477-82. doi: 10.1073/pnas.0811091106. Epub 2009 Apr 3. PMID: 19346491; PMCID: PMC2672541. *Equal Contribution [PDF] [PubMed]

Mak HC, Pillus L, Ideker T. Dynamic reprogramming of transcription factors to and from the subtelomere. Genome Res. 2009 Jun;19(6):1014-25. doi: 10.1101/gr.084178.108. Epub 2009 Apr 16. PMID: 19372386; PMCID: PMC2694488. [PDF] [PubMed]

Schwartz AS, Yu J, Gardenour KR, Finley RL Jr, Ideker T. Cost-effective strategies for completing the interactome. Nat Methods. 2009 Jan;6(1):55-61. doi: 10.1038/nmeth.1283. Epub 2008 Dec 14. PMID: 19079254; PMCID: PMC2613168. [PDF] [PubMed]

Ideker T. Book Review: “Wetware: A Computer in Every Living Cell” by Dennis Bray. Cell 138: 820-821 (2009) (Review)

The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. Angly FE, Willner D, Prieto-Dav A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, et al. PLoS Comput Biol. 2009 Dec;5(12):e1000593. PMID: 20011103

Determination of DNA mutation load in human tissues using denaturing HPLC-based heteroduplex analysis. Lim KS, Naviaux RK, Haas RH. Methods Mol Biol. 2009;554:287-99. PMID: 19513681

De novo mutation in POLG leads to haplotype insufficiency and Alpers syndrome. Chan SS, Naviaux RK, Basinger AA, Casas KA, Copeland WC. Mitochondrion. 2009 Sep;9(5):340-5. PMID: 19501198

Monitoring phosphorylation of the pyruvate dehydrogenase complex. Rardin MJ, Wiley SE, Naviaux RK, Murphy AN, Dixon JE. Anal Biochem. 2009 Jun 15;389(2):157-64. PMID: 19341700

Retained features of embryonic metabolism in the adult MRL mouse. Naviaux RK, Le TP, Bedelbaeva K, Leferovich J, Gourevitch D, Sachadyn P, Zhang XM, Clark L, Heber-Katz E. Mol Genet Metab. 2009 Mar;96(3):133-44. PMID: 19131261

2008

Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, Yakhini Z, Simon I.
Global organization of replication time zones of the mouse genome.(2008) Genome Res. [pubmed]

Goren A, Tabib A, Hecht M, Cedar H.
DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin. (2008) Genes Dev. [pubmed]

Naturally occurring mitochondrial DNA heteroplasmy in the MRL mouse. Sachadyn P, Zhang XM, Clark LD, Naviaux RK, Heber-Katz E. Mitochondrion. 2008 Dec;8(5-6):358-66. PMID: 18761428

Mitochondrial control of epigenetics. Naviaux RK. Cancer Biol Ther. 2008 Aug;7(8):1191-3.PMID: 18719362

Molecular and clinical genetics of mitochondrial diseases due to POLG mutations. Wong LJ, Naviaux RK, Brunetti-Pierri N, Zhang Q, Schmitt ES, Truong C, Milone M, Cohen BH, Wical B, Ganesh J, Basinger AA, Burton BK, Swoboda K, Gilbert DL, Vanderver A, Saneto RP, Maranda B, Arnold G, Abdenur JE, Waters PJ, Copeland WC. Hum Mutat. 2008 Sep;29(9):E150-72. PMID: 18546365

Impact of nucleoside reverse transcriptase inhibitors on mitochondrial DNA and RNA in human skeletal muscle cells. Saitoh A, Haas RH, Naviaux RK, Salva NG, Wong JK, Spector SA. Antimicrob Agents Chemother. 2008 Aug;52(8):2825-30. PMID: 18541728

The in-depth evaluation of suspected mitochondrial disease. Mitochondrial Medicine Society's Committee on Diagnosis, Haas RH, Parikh S, Falk MJ, Saneto RP, Wolf NI, Darin N, Wong LJ, Cohen BH, Naviaux RK. Mol Genet Metab. 2008 May;94(1):16-37. PMID: 18243024

Pitfalls in the denaturing high-performance liquid chromatography analysis of mitochondrial DNA mutation. Lim KS, Naviaux RK, Wong S, Haas RH. J Mol Diagn. 2008 Jan;10(1):102-8. PMID: 18165269

2007

2006

Goren A, Simchen G, Fibach E, Szabo PE, Tanimoto K, Chakalova L, Pfeifer GP, Fraser PJ, Engel JD, Cedar H.
Fine tuning of globin gene expression by DNA methylation. (2006) PLoS One. [pubmed]

Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics, San Diego, CA, USA; December 2-4, 2005, Revised Selected Papers. Lecture Notes in Computer Science, Springer Berlin / Heidelberg, Volume 4023/2006, 0302-9743 (Print) 1611-3349 (Online May 16 2007). [PDF]

Bandyopadhyay S, Kelley R, Ideker T. Discovering Regulated Networks During HIV-1 Latency and Reactivation. Pac Symp Biocomput. 2006:354-66. PMID: 17094252; PMCID: PMC5224933. [PDF] [PubMed]

Suthram S, Shlomi T, Ruppin E, Sharan R, Ideker T. A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics. 2006 Jul 26;7:360. doi: 10.1186/1471-2105-7-360. PMID: 16872496; PMCID: PMC1550431. [PDF] [PubMed]

Reguly T*, Breitkreutz A*, Boucher L*, Breitkreutz BJ*, Hon GC, Myers CL, Parsons A, Friesen H, Oughtred R, Tong A, Stark C, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya OG, Ideker T, Dolinski K, Batada NN*, Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol. 2006;5(4):11. doi: 10.1186/jbiol36. Epub 2006 Jun 8. PMID: 16762047; PMCID: PMC1561585. *Equal Contribution [PDF] [PubMed]

Beyer A, Workman C, Hollunder J, Radke D, Möller U, Wilhelm T, Ideker T. Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol. 2006 Jun 16;2(6):e70. doi: 10.1371/journal.pcbi.0020070. Epub 2006 Jun 16. PMID: 16789814; PMCID: PMC1479087. [PDF] [PubMed]

Workman CT, Mak HC, McCuine S, Tagne JB, Agarwal M, Ozier O, Begley TJ, Samson LD, Ideker T. A Systems Approach to Mapping DNA Damage Response Pathways. Science. 2006 May 19;312(5776):1054-9. doi: 10.1126/science.1122088. PMID: 16709784; PMCID: PMC2811083. [PDF] [PubMed]

Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol. 2006 Mar;13(2):133-44. doi: 10.1089/cmb.2006.13.133. PMID: 16597231. [PDF] [PubMed]

Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 2006 Mar;16(3):428-35. doi: 10.1101/gr.4526006. PMID: 16510899; PMCID: PMC1415213. [PDF] [PubMed] *Cover Article

Feist AM†, Scholten JC†, Palsson BØ, Brockman FJ, Ideker T. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri. Mol Syst Biol. 2006;2:2006.0004. doi: 10.1038/msb4100046. Epub 2006 Jan 31. PMID: 16738551; PMCID: PMC1681478. †Co-Corresponding Authors [PDF] [PubMed]

Ideker T, Valencia A. Bioinformatics in the human interactome project. Bioinformatics. 2006 Dec 15;22(24):2973-4. doi: 10.1093/bioinformatics/btl579. PMID: 17142816. [PDF] [PubMed]

Ideker T, Winslow LR, Lauffenburger DA. Bioengineering and systems biology. Ann Biomed Eng. 2006 Jul;34(7):1226-33. doi: 10.1007/s10439-006-9119-3. PMID: 16929563. [PDF] [PubMed] (Review)

Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol. 2006 Apr;24(4):427-33. doi: 10.1038/nbt1196. PMID: 16601728.[PDF] [PubMed] (Review)

Warner GJ, Adeleye YA, Ideker T. Interactome networks: the state of the science. Genome Biol. 2006;7(1):301. doi: 10.1186/gb-2006-7-1-301. Epub 2006 Jan 23. PMID: 16515723; PMCID: PMC1431712. [PDF] [PubMed]

Molecular diagnosis of Alpers syndrome. Nguyen KV, Sharief FS, Chan SS, Copeland WC, Naviaux RK. J Hepatol. 2006 Jul;45(1):108-16.PMID: 16545482

2005

Suthram S, Sittler T, Ideker T. The Plasmodium protein network diverges from those of other eukaryotes. Nature. 2005 Nov 3;438(7064):108-12. doi: 10.1038/nature04135. PMID: 16267557; PMCID: PMC2830740.[PDF] [PubMed]

• Supplemental Information: The Plasmodium protein network diverges from those of other eukaryotes 

Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol. 2005 Jul-Aug;12(6):835-46. doi: 10.1089/cmb.2005.12.835. PMID: 16108720.[PDF] [PubMed]

Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biol. 2005;6(7):R62. doi: 10.1186/gb-2005-6-7-r62. Epub 2005 Jul 1. PMID: 15998451; PMCID: PMC1175993. [PDF] [PubMed]

• Supplemental Information: Internal validation for 17 out of 24 restricted network models.

Hsiao A, Ideker T, Olefsky JM, Subramaniam S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W627-32. doi: 10.1093/nar/gki443. PMID: 15980550; PMCID: PMC1160204. [PDF] [PubMed]

Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV. enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W389-92. doi: 10.1093/nar/gki439. PMID: 15980495; PMCID: PMC1160200.[PDF] [PubMed]

Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005). [PDF] [PubMed]

Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1974-9. doi: 10.1073/pnas.0409522102. Epub 2005 Feb 1. PMID: 15687504; PMCID: PMC548573. [PDF] [PubMed] *Cover Article

Scott J, Ideker T, Karp RM, Sharan R. Efficient algorithms for detecting protein signaling pathways in protein interaction networks. Proceedings of the Ninth Annual International Conference on Research in Computational Biology (RECOMB) (2005). J Comput Biol. 2006 Mar;13(2):133-44. doi: 10.1089/cmb.2006.13.133. PMID: 16597231. [PDF] [PubMed]

Ideker, T. “Data collection and analysis in systems biology.” Wiley Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, Dunn, M.J., Jorde, L.B., Little, P.F.R., Subramaniam, S. (Eds). 0-470-84974-6 (2005) [Book]

Ideker, T., Tan, K., Uetz, P. “Visualization and Integration of Protein Interaction Networks”,  in Protein-Protein Interactions Second Edition: A Molecular Cloning Manual, E. Golemis and P. Adams eds. CSHL Press, Cold Spring Harbor, N.Y. 7(42):839-856 (2005) [Book chapter]

Sand DNA - a genetic library of life at the water's edge Naviaux RK, Good B, McPherson JD, Steffen DL, Markusic D, Ransom B, Coreil J. Marine Ecology Progress Series. 2005;301:9-22. PMID: 0

Ultrafast nanolaser flow device for detecting cancer in single cells. Gourley PL, Hendricks JK, McDonald AE, Copeland RG, Barrett KE, Gourley CR, Naviaux RK. Biomed Microdevices. 2005 Dec;7(4):331-9.PMID: 16404511

Mitochondrial correlation microscopy and nanolaser spectroscopy - new tools for biophotonic detection of cancer in single cells. Gourley PL, Hendricks JK, McDonald AE, Copeland RG, Barrett KE, Gourley CR, Singh KK, Naviaux RK. Technol Cancer Res Treat. 2005 Dec;4(6):585-92.PMID: 16292878

Mitochondrial correlation as a biophotonic marker for detecting cancer in a single cell Gourley PL, Hendricks JK, McDonald AE, Copeland RG, Barrett KE, Gourley CR, Naviaux RK. Biomedical Optics. 2005, Mar 29;pp. 461-472.PMID: 0

Optical phenotyping of human mitochondria in a biocavity laser Gourley PL, Naviaux RK. IEEE Journal of Selected Topics in Quantum Electronics. 2005;11:818-826.PMID: 0

Mono-allelic POLG expression resulting from nonsense-mediated decay and alternative splicing in a patient with Alpers syndrome. Chan SS, Longley MJ, Naviaux RK, Copeland WC. DNA Repair (Amst). 2005 Dec 8;4(12):1381-9.PMID: 16181814

POLG mutations in Alpers syndrome. Nguyen KV, stergaard E, Ravn SH, Balslev T, Danielsen ER, Vardag A, McKiernan PJ, Gray G, Naviaux RK. Neurology. 2005 Nov 8;65(9):1493-5.PMID: 16177225

POLG mutations associated with Alpers syndrome and mitochondrial DNA depletion. Naviaux RK, Nguyen KV. Ann Neurol. 2005 Sep;58(3):491.PMID: 16130100

2004 AND PRIOR

Lande-Diner L, Zhang J, Hashimshony T, Goren A, Keshet I, Cedar H.
Gene repression paradigms in animal cells. (2004) Cold Spring Harbor Symp Quant Biol. [pubmed]

Goren A, Cedar H.
Replicating by the clock. (2003) Nat Rev Mol Cell Biol. [pubmed]