GuanLab achieved top performance in 2013 DREAM (Dialogue for Reverse Engineering Assessments and Methods) - breast cancer network inference challenge
DCM&B Chair, Brian D. Athey, Ph.D., elected as fellow of the American College of Medical Informatics (ACMI)

News & Announcements

Cristen Willer
" A global hunt for genes that influence heart disease risk has uncovered 157 changes in human DNA that alter the levels of cholesterol and other blood fats – a discovery that could lead to new medications. The huge scan of genetic variations linked to blood lipid levels used an advanced device called a Metabochip. Each of the changes points to genes that can modify levels of cholesterol and other blood fats and are potential drug targets. Many of the changes point to genes not previously linked to blood fats, also called lipids. A surprising number of the variations were also associated with coronary artery disease, type 2 diabetes, obesity, and high blood pressure. The research also reveals that triglycerides – another type of blood lipid – play a larger role in heart disease risk than previously thought. The results, published in a paper and a letter appearing simultaneously in the journal Nature Genetics, come from the Global Lipids Genetics Consortium -- a worldwide team of scientists who pooled genetic and clinical information from more than 188,000 people from many countries and heritages. The analysis of the combined data was led by a team from the University of Michigan Medical School and School of Public Health. They used sophisticated computing and statistical techniques to search for genetic variations that modify blood lipid levels. The results increase by more than a third the total number of genetic variants linked to blood lipids. All but one of the variants associated with blood lipids are near stretches of DNA that encode proteins. “These results give us 62 new clues about lipid biology, and more places to look than we had before,” says Cristen Willer, Ph.D., the lead author of one paper and an assistant professor of Internal Medicine, Human Genetics and Computational Medicine & Bioinformatics at the U-M Medical School. “Once we take the time to truly understand these clues, we’ll have a better understanding of lipid biology and cardiovascular disease -- and potentially new targets for treatment.” But, cautions senior author and U-M School of Public Health Professor Gonçalo Abecasis, Ph.D., it will take much further work to study the implicated genes and to find and test potential drugs that could target them. The consortium’s “open science” approach will include publishing further detail online for other researchers to use freely toward this goal. A further analysis of the dataset, published as a letter with lead author Ron Do, Ph.D. and senior author Sekar Kathiresan, M.D. from the Broad Institute and Massachusetts General Hospital, suggests triglyceride levels have more impact on coronary artery disease risk than previously thought."

tranSMART 1.1 Screen Shot
The tranSMART Foundation Announces New Version of the tranSMART Open Source Data Sharing Platform for the Life Sciences Community Open Platform Enables Scientists Around the Globe to More Quickly Advance their Research Wakefield, Massachusetts – September 16, 2013 – The tranSMART Foundation, a non-profit organization providing a global, open-source knowledge management platform for scientists to share their pre-competitive data, today announced the release of tranSMART version 1.1.  Originally developed as an internal project by Johnson & Johnson, this new version of the cloud-based data sharing solution eliminates the need for user organizations to purchase commercial software and integrates significant new contributions by the developer community over the past year into one new release.  “Scientists at universities, non-profit research organizations, and pharmaceutical and biotechnology companies are struggling to effectively leverage the massive amounts of high-quality research data available to advance their studies,” said tranSMART Foundation co-CEO Brian Athey, Ph.D., also with the University of Michigan. “To date, we have more than 25 life science organizations utilizing the tranSMART platform to link research data with clinical data in a central repository.  We envision that through this platform scientists will have the ability to effectively collaborate using pre-competitive data – facilitating quicker and more cost-effective translational medicine research.”  The Foundation’s co-CEO, Michael Braxenthaler, Ph.D., who also holds positions with Roche and the Pistoia Alliance, added, “Our goal is to create a collaborative translational research community.  Our development community is focused on the Foundation’s three C’s: code, community and content.  With the open tranSMART platform, we are limiting dependency on commercial software products and leveraging the expertise of the entire user community.  We have an aggressive product roadmap to develop the next generation of the platform to include new interfaces and analytical functionality as well as a more modern information architecture.”    The tranSMART Foundation is a partnership between the Pistoia Alliance, the University of Michigan and the Imperial College London with the mission to enable effective sharing, integration, standardization, and analysis of heterogeneous data from collaborative translational research by mobilizing the tranSMART open-source and open-data community.  As an open source solution, several leading U.S. and European-based academic, pharmaceutical and service provider organizations have contributed to this release through code development, quality assurance, testing, scientific data contribution, and hosting services for “demo” instances. Please visit: for access to release notes, documentation, source code, and other resources.  Training and support for the user community is provided by the tranSMART Foundation, as well its network of service providers.   

DCM&B faculty member Yang Zhang awarded 2013 Dean’s Award for Basic Science Research. This award recognizes a scientist or group of scientists identified as having made outstanding contributions to the Medical School in basic biomedical science research.

Kraig Stevenson
Gene expression is a critical step in translating information from DNA sequences into living cells. The first step of this process involves the transcription of DNA into RNA. Quantifying the abundance of RNA within an an organism thus provides important readout of cellular function. In recent years, advances in high-throughput sequencing have provided new ways to make these measurements. Importantly, they allow not only the total abundance of RNA within a sample to be determined, but also the relative proportion of RNA molecules from a particular gene that come from the maternal and paternal alleles. Unfortunately, with the most common computational methods used to analyze these data, measurements of allele-specific expression often show a systematic bias favoring detection of one allele over the other. In a new paper published by Bioinformatics graduate student Kraig Stevenson, postdoc Joseph Coolon, and CCMB faculty member Patricia Wittkopp, the sources of this systematic bias (as well as sources of other erroneous measures of allele-specific expression) are identified. By identifying the causes of these problems, this work paves the way for improving computational methods used to study allele-specific gene expression.

Alex Kip (Writer/Actor)
Ora Pescovitz, M.D., Norman Hogikyan, M.D., and Joel D. Howell, M.D., to participate in “talk-back” sessions after performances. James Cavalcoli, Ph.D., featured in production. Two years after graduating from the University of Michigan, an event that was immediately preceded by a terrifying diagnosis of cancer that threatened to end his career, actor and playwright Alex Kip has penned a play inspired by his experience. My Other Voice will premiere in Ann Arbor at the Arthur Miller Theatre at U-M Thursdays – Sundays from Aug.15-Sept. A special Aug. 25 performance will feature a “talk-back” session hosted by U-M EVPMA/UMHS CEO Ora Pescovitz, M.D. The session will allow audience members to speak openly about challenges of the physician’s role in cancer care and will also encourage physicians to dialogue with patients. Norman Hogikyan, M.D., professor and chief of Laryngology, Rhinology and General Otolaryngology will host a talk-back session with patients and audience members on Aug. 30 about specific vocal-related issues and health. Additional talk-back sessions will be announced for the Medical Arts Program, coordinated by Joel D. Howell, M.D., Ph.D., professor of Internal Medicine, Health Management and Policy, and History. In May, Pescovitz described Alex as “the epitome of courage” and praised his ability to “reinvent himself as a person and artist” on her blog, Medicine that Speaks. “It can be easy to give up and become a victim of circumstance.” says Pescovitz. “It is not easy to confront and surmount obstacles that get in the way of your dreams. Yet, that’s what Alex has done.” Kip, 25, a native of Columbus, Ohio, received his BFA in musical theatre from U-M and is also a graduate of the London Dramatic Academy. He was given a 15-30 percent chance of survival after being diagnosed with non-Hodgkins lymphoma as a senior at U-M. During subsequent treatment at the U-M Medical Center, Kip lost his voice. “No longer able to speak or sing,” he says, “I had to find a new identity.” Now in complete remission, Kip wrote “My Other Voice” with the goal of providing inspiration and hope to other cancer patients, particularly young adults, whose survival rate for cancer has not improved at the same rate as other age groups. James Cavalcoli, Ph.D., assistant professor of Computational Medicine and Bioinformatics, will play the role of Dr. Foster in the performance. “My hope is that this play will spread awareness of the unique difficulties young adults experience when diagnosed with cancer, while also giving patients hope for the future,” says Kip. “It will also be used as a teaching tool for doctors in training, or help this underserved group secure the age-appropriate resources they need. I want it to act as a patient advocate for young adult cancer victims.” Prior to the play’s upcoming premiere, it received several readings with industry professionals in New York City and had a staged reading in Columbus, Ohio. The Ann Arbor production will feature U-M faculty, students and other industry professionals both on stage and behind the scenes. For more information, visit . Watch a promo video for the play here:

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."