GuanLab achieved top performance in 2013 DREAM (Dialogue for Reverse Engineering Assessments and Methods) - breast cancer network inference challenge

News & Announcements

Zach Wright and Dattatreya Mellacheruvu
An international consortium led by Alexey Nesvizhskii lab publishes a new computational resource for scoring protein-protein interaction data, the Contaminant Repository for Affinity Purification (CRAPome), in Nature Methods. Congratulations to Dattatreya Mellacheruvu and Zach Wright, the primary developers of this new resource.

Jeffrey Kidd, Ph.D.
"More than 7 billion people live on this planet – members of a single species that originated in one place and migrated all over the Earth over tens of thousands of years. But even though we all trace our family lineage to a few common ancestors, scientists still don’t know exactly when and how those few ancestors started to give rise to the incredible diversity of today’s population. A brand-new finding, made using advanced analysis of DNA from all over the world, sheds new light on this mystery. By studying the DNA sequence of Y chromosomes of men from many different populations, scientists have determined that their male most recent common ancestor (MRCA) lived sometime between 120,000 and 156,000 years ago. It’s the first time the human ancestry has been traced back through the male line by sequencing the DNA of many entire Y chromosomes. And, it agrees reasonably well with previous findings about our female most recent common ancestor, made by studying DNA carried down through the human race’s female line. Such studies used DNA from mitochrondria -- structures inside cells – and placed that time of the most recent common ancestor between 99,000 and 148,000 years ago. That agreement makes the new finding especially significant: The research was done by a team of scientists from Stanford University, the University of Michigan Medical School, Stony Brook University, and their colleagues, and is published in the journal Science. The team hopes their work will lead to further research on Y chromosomes as vehicles for studying human history – and tracing male lineages back to the common “Adam” ancestors. Jeffrey Kidd, Ph.D., an assistant professor in U-M's departments of Human Genetics and Computational Medicine & Bioinformatics who worked on the new study, notes that only recently has it become possible to sequence Y chromosomes, because of technical limitations of previous approaches. The new paper details how the team was able to make reliable measurements of the sequence variation along the Y chromosome – which is handed down only from father to son without exchanging, or recombining, genetic material with other chromosomes. Kidd notes that this initial paper on Y chromosome sequence diversity provides important first evidence that the male most recent common ancestor did not live more recently than the female most recent common ancestor. “We’re interested in understanding the historical relationships between many different human populations, and the migration patterns that have led to the peopling of the world,” he says. “We hope that others will make use of this approach and sequence additional chromosomes of interest that are related to the peopling of specific places.” The study involved Y chromosomes obtained through the Human Genome Diversity Project, and from other sources. It included chromosomes from 69 men in several populations in sub-Saharan Africa, and from Siberia, Cambodia, Pakistan, Algeria and Mexico. The great migrations of our ancestors out of Africa, across Asia and Europe and into the Americas all helped shape today’s populations – as did more recent forces related to colonialism and ever-growing global mobility. Genetic studies such as this one may help anthropologists understand those migrations – and their timing – even better by giving them a genetic “clock” to use when studying today’s humans, or potentially DNA extracted from ancient bones. It may also help scientists understand the great genetic diversity seen across Africa, and the evolution process that led to modern humans. The reconciliation of the timing of ancestors some might call “Adam” and “Eve”, however, may be this study’s most important immediate implication. “This has been a conundrum in human genetics for a long time,” said Carlos D. Bustamante, Ph.D., a professor of genetics at Stanford and senior author of the study. “Previous research has indicated that the male MRCA lived much more recently than the female MRCA. But now our research shows that there’s no discrepancy. In fact, if anything, the Y chromosome may be a bit older.” In addition to Kidd and Bustamante, the research team includes U-M’s Elzbieta Sliwerska, Stanford’s G. David Poznik, Brenna M. Henn, Muh-Ching Yee, Ghia M. Euskirchen, Alice A. Lin, Michael Snyder, and Peter A. Underhill, and Lluis Quintana-Murci from Institut Pasteur in Paris. Reference: Science 2 August 2013: Vol. 341 no. 6145 pp. 562-565 DOI: 10.1126/science.1237619 Funding: National Library of Medicine LM-07033, National Science Foundation DGE-1147470; National Institutes of Health 3R01HG003229 and DP5OD009154; Institut Pasteur, CNRS MIE, Foundation Simone et Cino del Duca."

John V. Moran
"The American Society of Human Genetics (ASHG) has named John V. Moran, Ph.D., Professor of Human Genetics and Professor of Internal Medicine in the Department of Internal Medicine at the University of Michigan, as the 2013 recipient of the Curt Stern Award. This annual award, named in honor of the late pioneering geneticist Curt Stern, Ph.D., recognizes researchers who have made significant scientific contributions during the past decade. ASHG will present the award, which will include a crystal plaque and cash prize, on Saturday, October 26, during the organization’s 63rd annual meeting in Boston. Dr. Moran, a Howard Hughes Medical Institute Investigator, has been a leader in research on genome instability and the biology of DNA sequences that can change their position in the genome, creating or reversing mutations and altering the genome’s size. Among his accomplishments is the discovery that processed pseudogenes are formed in the genome by the reverse transcriptase enzyme for the mobile DNA element referred to as L1. He developed the cell culture assay used in this research. His finding that the L1 insertion can lead to deletions in the genome has been confirmed by human genome analysis as well as numerous other studies, demonstrating the importance of retrotransposition in shaping the human genome through evolutionary time, and showing that these L1 insertions occur much more frequently than previously thought. The Curt Stern Award also recognizes Dr. Moran’s mentorship of graduate students and postdoctoral researchers as well ask his stalwart support of and service to ASHG."

Brian Athey and Gil Omenn
"Yesterday in Washington, the White House shone a spotlight on free exchange of scientific information – a concept called “open science” that aims to accelerate the development of new treatments and technologies, and is a priority for federal research sponsors. A U-M Medical School leaders who has led open science initiatives for many years took part. Brian Athey, Ph.D., who chairs the Department of Computational Medicine & Bioinformatics, exhibited information about a new open science initiative at the White House event hosted by the Office of Science and Technology Policy. He was joined by Gilbert S. Omenn, M.D., Ph.D., director of the U-M Center for Computational Biomedicine and Informatics. At the White House event, Dr. Athey (center) and U-M's Dr. Gilbert S. Omenn presented information about tranSMART. They are with Dr. Cristoph Brockel, Senior Director, Translational & Bioinformatics at Pfizer. Athey’s open science experience includes his leadership of the National Library of Medicine’s Next-Generation Internet Visible Human Project, which created complete three-dimensional digital representations of the normal male and female human bodies, and the DARPA Virtual Soldier Project, which creates interpretable medical representations of soldiers’ physiology to guide combat medical treatment. He has also led the National Center for Integrative Biomedical Informatics (NCIBI), which is funded by the National Institutes of Health and based at U-M. He has also served as an advisor to the chief information officer of the NIH. Athey is co-CEO of the new tranSMART Foundation, a nonprofit, global open-source public-private partnership. Omenn is chair of the foundation’s board of directors. The foundation is working to create an informatics-based analysis and data-sharing cloud platform for clinical and translational research. It will allow scientists at universities, companies and agencies around the world to share pre-competitive data in a way that saves money and time in translating research findings into cures and diagnostic tools. transSMART offers tools originally developed by the NCIBI. The drive for open science was accelerated this year by the OSTP director’s mandate that all federal agencies that fund research take steps to make the results of that research openly available within a year of publication. “The reasons for sharing are many,” says Athey, “starting with the government funding of the production of the data in the first place. But beyond just making data available, we need to find ways to bring together heterogeneous kinds of data, from molecular and clinical studies, that will let us see the relationships that are important for diseases. And we have to bring it together in a standardized way that people will adopt widely.” The tranSMART approach seeks to do this, he notes."

Jeffrey Kidd
"Jeffrey Kidd, Ph.D., an assistant professor at the U-M Medical School, has been named one of only 22 Pew Scholars in the United States for 2013. It’s an honor given by The Pew Charitable Trusts to some of the most promising early-career biomedical scientists. He is the 18th Pew Scholar on the U-M faculty and will receive a four-year, $240,000 unrestricted research grant. Kidd – who holds faculty positions in both the Department of Human Genetics and the Department of Computational Medicine and Bioinformatics -- straddles the worlds of DNA research and bioinformatics, a field that develops techniques to analyze and glean new knowledge from large amounts of biomedical data. He and his team will use the Pew funding to develop a new approach that measures the DNA differences that exist within each individual human."

Mallory Freeberg
The NSF IGERT grant has helped fund Mallory’s research; this year she’s representing the Univ. of MI in the IGERT annual online video and poster competition.

PNAS paper published by Jun Li, Assistant Professor, Human Genetics and Assistant Research Professor, Computational Medicine and Bioinformatics and colleagues, on circadian rhythm disruption in depression
PNAS paper published by Jun Li, Assistant Professor, Human Genetics and Assistant Research Professor, Computational Medicine and Bioinformatics and colleagues, on circadian rhythm disruption in depression. "Every cell in our bodies runs on a 24-hour clock, tuned to the night-day, light-dark cycles that have ruled us since the dawn of humanity. The brain acts as timekeeper, keeping the cellular clock in sync with the outside world so that it can govern our appetites, sleep, moods and much more. But new research shows that the clock may be broken in the brains of people with depression -- even at the level of the gene activity inside their brain cells. It’s the first direct evidence of altered circadian rhythms in the brain of people with depression, and shows that they operate out of sync with the usual ingrained daily cycle. The findings, in the Proceedings of the National Academy of Sciences, come from scientists from the University of Michigan Medical School and other institutions."

"This book is great for people who have basic knowledge of programming, network analysis, and Cytoscape usage but would like to visualize and explore some network data. Readers are expected to know the basic concepts of network data, and be capable of using text editing software to edit tabular data which is imported into Cytoscape. Optionally, the user should understand network clustering and command line tools such as R." "Instant Cytoscape Complex Network Analysis How-to" is currently available on

Dr. Arul Chinnaiyan
"Arul Chinnaiyan The award honors faculty who have made important and lasting contributions to society by developing novel ideas and insights through their research, and then translating them to practice. Chinnaiyan is the S.P. Hicks Endowed Professor of Pathology, professor of urology, director of the Michigan Center for Translational Pathology, and a Howard Hughes Medical Institute investigator. He is being honored for his work as a researcher, innovator, and entrepreneur in the field of molecular pathology. “Arul Chinnaiyan’s work shows how critical university research is to the development of new ways to diagnose and treat disease,” said Vice President for Research Steve Forrest. “It also highlights the key role of technology licensing and entrepreneurship in moving new ideas quickly and effectively from the laboratory to practice.” An internationally recognized scholar, Chinnaiyan found in 2005 that a majority of prostate cancers harbor gene fusions or translocations, shedding new light on our understanding of the molecular basis of prostate cancer and laying the groundwork for new diagnostic tests and therapies. Since that landmark discovery, gene fusions also have been discovered in lung cancer, colon cancer, breast cancer and others. Chinnaiyan’s work has led to 75 new invention disclosures resulting in 12 patents, and six license and option agreements. Products arising from these licenses already are reaching the marketplace in the form of new diagnostic tests for prostate cancer. In addition to licensing technology, Chinnaiyan has founded three companies. Compendia Biosciences, founded in 2006, was based on a cancer genomics research database now used by a range of pharmaceutical and biotechnology companies. More recently, he formed Armune Bioscience Inc. to develop and commercialize new diagnostic tests for prostate, lung, and breast cancers. And in 2012 he joined with Shaomeng Wang, Warner-Lambert/Parke-Davis Professor of Medicine, and professor of internal medicine, pharmacology, medicinal chemistry, to found OncoFusion Therapeutics Inc., a company that aims to develop personalized cancer therapies based on the specific driving genetic mutations in an individual’s tumor. Established in 2007, the Distinguished University Innovator Award recipient is chosen by the vice president for research on the recommendation of a faculty selection committee, which reviews a pool of nominees each year. The recipient is honored in a public ceremony and delivers a lecture focusing on the innovative work that led to the award. This year’s award ceremony and lecture will take place at 4 p.m. April 30 in the Ford Amphitheater at University Hospital with a reception to follow in the Ford Lobby." - The University Record