News and Announcements

• A commentary co-authored by Jill Mesirov, PhD., the Deputy Director of NCI, and the Director of the ITCR program at NCI was published October 1, 2024 in Cancer Discover:  Transforming Cancer Research through Informatics. 

• Alon Goren, PhD. published a study in Nature Biotechnology: “The Wild West of spike-in normalization” and highlighted in UC San Diego Today, “Technique to Study How Proteins Bind to DNA is Easily Misused; New Study Offers Solution.”  This work shows that a large number of studies quantifying the interactions between proteins and DNA were done using improper normalization, thus leading to inaccurate conclusions. The paper provides guidelines to avoid such issues.

• Trey Ideker, PhD. and Hannah Carter, PhD. published a study in Scientific Reports: In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells. In this study they used forward evolution to study how cancer cells acquire resistance to commonly used chemotherapies. Understanding resistance mechanisms is critical to anticipate and counter them.

• Robert Naviaux, MD, PhD, published a paper: Metabolic network analysis of pre-ASD
  newborns and 5-year-old children with autism spectrum disorder in UCSan Diego Today:
  Metabolism of Autism Reveals Developmental Origins and Newsweek: Scientists Reveal How
  Autism Develops in Kids.  Dr. Naviaux also did a Q&A with the N of One Foundation: https://www.nofone.org/dr-robert-naviaux-bloodspot-qa.

• Trey Ideker, PhD., and his team authored a study published in Cancer Discovery that uses artificial intelligence to predict the best treatment for cancer patients.  This groundbreaking study was highlighted in UC San Diego Today, “AI Harnesses Tumor Genetics to Predict Treatment Response” and by CBS 8 news “UC San Diego School of Medicine uses AI to predict which drugs to use to treat cancer patients”.

• Lukas Chavez, PhD, received funding from NCI's The Childhood Cancer Data Initiative (CCDI) for his reasearch “Unlocking the Potential of Extrachromosomal Circular DNA (eccDNA) as Prognostic Markers in Childhood and Adolescents and Young Adults (AYA) Cancers”.

• Hannah Carter, PhD, was published in Nature Computational Science November 16, 2023: Predicative analysis of regulatory sequences with EUGENe and highlighted in UC San Diego Today, Introducing EUGENe: An Easy-to-Use Deep Learning Genomics Software.

• Jill Mesirov, PhD, Lukas Chavez, PhD, and Hannah Carter, PhD, were published in Nature Genetics November 9, 2023:  Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.

• Congratulations to Hanna Carter, PhD, winner of the Moores Cancer Center 2023 Jawsome Shark Tank (JST) – Multidisciplinary Pilot Project Program

• Short tandem repeats (STRs) are a widespread yet routinely understudied class of genetic variants which account for ~10% of the genetic differences between any pair of humans. This week the Gymrek and Goren labs from the Department of Medicine published a study in Cell Genomics led by PhD student Jonathan Margoliash, which demonstrates that 5.2-7.6% of previously identified genetic signals for human blood traits may actually be driven STRs, and highlights specific STRs as likely driving some of the strongest genetic effects on the platelet counts of healthy adults. The accompanying perspective article called the STR study "a technical tour de force" that heralds "the beginning of a stream of discoveries to come [from] STR association studies".

• Lukas Chavez, PhD and Jill Mesirov PhD: A study of newly created databases of medulloblastoma has found that patients with tumors containing circular extrachromosomal DNA -- loops of DNA found outside of regular chromosomes -- are twice as likely to relapse and three times as likely to die within five years of diagnosis: “DNA loops” in pediatric brain tumors double relapse risk.

• Lukas Chavez, PhD, received $3.2 million from the National Institutes of Health to study how unique DNA circles found in cancer cells drive deadly pediatric brain tumors.

• Lukas Chavez, PhD, is leveraging the latest technology to take a never before-seen-look at ependymoma, one of the deadliest pediatric brain tumors.

• Congratulations to Jill Mesirov, PhD. Her article, “Extending support for mouse data in the Molecular Signature Database (MSigDB)” was published in the high impact journal, Springer Nature. 

• Vanguard Award: Congratulations to Dr. Robert Naviaux, MD, PhD, who received the 2023 United Mitochondrial Disease Foundation’s prestigious Vanguard Award for his pioneering work and dedication in the field of Mitochondrial Medicine -- the highest award given in the field! 

•  Melissa Gymrek, PhD and Alon Goren, PhD are co-PIs with Dr. Alexis Komor from Chemistry on an award that was selected for funding on the first round of the DISC0 CIRM awards. 
  CIRM recently announced the second round of the DISC0 awards, and Dr. Alon Goren’s proposal was selected for funding.

•  UC San Diego Ranked 8th Globally For Most Influential Researchers  Trey Ideker, PhD is listed among the 2022 Highly Cited Researchers in the world.  The Highly Cited Researchers list identifies and celebrates exceptional researchers who are having a significant impact on the research community as evidenced by the rate at which their peers are citing their work.  

•  3D Genomics reveals target for aggressive childhood cancers  Using a combination of deep sequencing approaches and three-dimensional genomics, Lukas Chavez, PhD and an international team of scientists identified new disease mechanisms and drug targets in RELA and PFA ependymomas. 2022. 

•  UC San Diego Joins NIH ‘Bridge to Artificial Intelligence’ Program. The NIH Common Fund’s initiative will expand the use of artificial intelligence to solve pressing challenges in human health.  Trey Ideker, PhD, will serve as principal investigator of a Data Generation Project called Cell Maps for AI. 2022. 

•  Jill Mesirov, Ph.D. awarded a Chan-Zuckerberg grant for the project Gene Set Enrichment Analysis for Single-Cell Data (scGSEA)