HIV Transmission Networks Mapped to Reduce Infection Rate

Researchers at the University of California, San Diego School of Medicine have mapped the transmission network of human immunodeficiency virus (HIV) in San Diego. The mapping of HIV infections, which used genetic sequencing, allowed researchers to predictively model the likelihood of new HIV transmissions and identify persons at greatest risk for transmitting the virus. … Read the full story from the UC San Diego Newsroom

Toward a New Model of the Cell

Everything You Always Wanted to Know About Genes

Turning vast amounts of genomic data into meaningful information about the cell is the great challenge of bioinformatics, with major implications for human biology and medicine. Researchers at the University of California, San Diego School of Medicine and colleagues have proposed a new method that creates a computational model of the cell from large networks of gene and protein interactions, discovering how genes and proteins connect to form higher-level cellular machinery. …Read the full story from the UCSD Newsroom


Trey Ideker, PhDThe new approach comes from the medical genetics laboratory of Trey Ideker, PhD, in the departments of bioengineering and medicine. Postdoctoral fellow Janusz Dutkowski, PhD, is lead author and Michael Kramer, PhD, a coauthor of the study report in Nature Biotechnology.

Ideker, senior author, is professor of bioengineering and medicine and chief of the Division of Medical Genetics in the Department of Medicine.

Citation for the report:  Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nature Biotechnology (2012) doi:10.1038/nbt.2463. Published online 16 December 2012  Read the abstract

Biomarking Time

Methylome modifications offer new measure of our “biological” age

Women live longer than men. Individuals can appear or feel years younger – or older – than their chronological age. Diseases can affect our aging process. When it comes to biology, our clocks clearly tick differently.

In a new study, researchers at the University of California, San Diego School of Medicine, with colleagues elsewhere, describe markers and a model that quantify how aging occurs at the level of genes and molecules, providing not just a more precise way to determine how old someone is, but also perhaps anticipate or treat ailments and diseases that come with the passage of time. … Read the full story from the UCSD Newsroom


Trey Ideker, PhDTrey Ideker, PhD, is co-senior author of the study report. He is professor of medicine and chief of the Division of Medical Genetics, professor of bioengineering and faculty investigator in the UCSD Institute for Genomic Medicine.The overall goal of Ideker’s work is to map and model molecular networks of cellular processes in health and disease, particularly in cancer and the response to genotoxic stress.

Coauthors of the study report include Rob DeConde, a graduate student in Ideker’s laboratory.

Read the abstract of the study report in PubMed

Citation: Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan J-B, 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. Molecular cell doi:10.1016/j.molcel.2012.10.016. PMID: 23177740

Testing Antioxidant Drugs is Transparent

A study using genetically modified zebrafish to visualize early events involved in development of human atherosclerosis describes an efficient model – one that the researchers say offers many applications for testing the potential effectiveness of new antioxidant and dietary therapies. …Read the full story from the UCSD Newsroom

Laboratory test tubes

Leader of the research team is Yury Miller, MD, PhD, associate professor of medicine in the Division of Endocrinology and Metabolism. His Department of Medicine coauthors include Joseph L. Witztum, MD, professor in the same division; and Sotirios “Sam” Tsimikas, MD, FACC, professor in the Division of Cardiology.   |   Read the article online in the Journal of Clinical Investigation.

New Center Looks at How Human Systems Function or Fail

A new center called the National Resource for Network Biology (NRNB), based at the University of California, San Diego School of Medicine, will help clinicians analyze an ever-growing wealth of complex biological data and apply that knowledge to real problems and diseases… Read the full story from the UCSD Newsroom

Dr. Trey Ideker

Lead investigator of the study is Trey Ideker, Ph.D., Professor and Chief of the Division of Medical Genetics in the Department of Medicine and Professor of Bioengineering (pictured above).

Among the Department of Medicine project collaborators is James H. Fowler, Ph.D., Professor of Medicine and Political Science.

Read the abstract of the project.

A Boon for Hepatitis C Research: Dr. Martina Buck Develops First Tissue Culture Model

Dr. Martina Buck, faculty researcher in the Division of Gastroenterology, has developed the first tissue culture system for the Hepatitis C virus. The system offers a model in which investigators can more easily test potential treatments for Hepatitis C.

Her report of the system is published in PLoS ONE.

Martina Buck, Ph.D., is Assistant Professor of Medicine in the Division of Gastroenterology and a researcher in the Tumor Growth, Invasion and Metastasis Program at the Moores UCSD Cancer Center.

Read the full story from
UC San Diego Health Sciences Communications

Citation for the report: Buck M (2008) Direct Infection and Replication of Naturally Occurring Hepatitis C Virus Genotypes 1, 2, 3 and 4 in Normal Human Hepatocyte Cultures. PLoS ONE 3(7): e2660. doi:10.1371/journal.pone.0002660  |  Read the report (free full text)

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