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Attractor Metagenes - DREAM7

Team Attractor Metagenes receives its award at the DREAM7 Conference. Gustavo Stolovitzky (IBM Research), Adam Margolis (Sage Bionetworks), Dimitris Anastassiou, Tai-Hsien Ou Yang, Wei-Yi Cheng, Stephen Friend (Sage Bionetworks), Erhan Bilal (IBM Research)

The team of Professor Dimitris Anastassiou and graduate students Wei-Yi Cheng and Tai-Hsien Ou Yang has been recognized as the best performer in the Sage Bionetworks – DREAM Breast Cancer Prognosis Challenge. This challenge, one of four organized as part of the seventh Dialogue for Reverse Engineering Assessments and Methods (DREAM7), was designed to assess the ability of participants’ computational models to predict breast cancer survival using patient clinical information and molecular profiling data. As a reward for this accomplishment, the journal Science Translational Medicine has just published a paper from the Anastassiou lab describing their model. It is also the journal’s cover theme for this issue, which includes a second article describing the Challenge.

The Columbia University researchers based their DREAM entry on previous work to identify what they call “attractor metagenes,” sets of strongly co-expressed genes that they have found to be present with very little variation in many cancer types. Moreover, these metagenes appear to be associated with specific attributes of cancer including chromosomal instability, epithelial-mesenchymal transition, and a lymphocyte-specific immune response. As Wei-Yi Cheng comments in Sage Synapse, “We like to think of these three main attractor metagenes as representing three key ‘bioinformatic hallmarks of cancer,’ reflecting the ability of cancer cells to divide uncontrollably and invade surrounding tissues, and the ability of the organism to recruit a particular type of immune response to fight the disease.”

Barry Honig, Professor of Biochemistry & Molecular Biophysics, Howard Hughes Medical Institute investigator, and Director of the Center for Computational Biology and Bioinformatics, was honored by The Protein Society with the Christian B. Anfinsen Award. The award, sponsored by The Aviv Family Foundation, recognizes significant technical achievements in the field of protein science. The following is an excerpt from the award citation: Dr. Honig is the recipient of the 2012 award for his contributions to our understanding of the electrostatic properties of proteins and the development of DelPhi and GRASP, which are among the most widely used programs in structural biology. These and other computational tools from his group have enabled numerous discoveries related to protein molecular recognition, protein-membrane interactions, and protein structural stability. Honig's own recent discoveries related to cell-cell adhesion and sequence-dependent protein-DNA recognition are outstanding examples.

Barry Honig, Professor of Biochemistry & Molecular Biophysics, Howard Hughes Medical Institute investigator, and Director of the Center for Computational Biology and Bioinformatics, was honored by The American Society for Biochemistry and Molecular Biology with the DeLano Award for Computational Biosciences for his work in macromolecular interactions in biology. The award is given to a scientist for innovative and accessible development or application of computer technology to enhance research in the life sciences at the molecular level. Dr. Honig's software tools and their underlying conceptual basis are widely used by the general biological research community to analyze the role of electrostatics in macromolecular interactions.

The John Simon Guggenheim Foundation has named Harmen Bussemaker, Associate Professor in Columbia's Department of Biological Sciences, as one of its 2010 Fellows. The award supports a project titled "Deciphering the language of gene expression regulation," in which Dr. Bussemaker will combine methods from biophysics and genetics in order to predict the behavior of gene regulatory networks, and test these predictions using wet lab experiments. Guggenheim Fellows are appointed on the basis of impressive achievement in the past and exceptional promise for future accomplishment. Click here to learn more.

Harmen Bussemaker, Associate Professor in Columbia's Department of Biological Sciences, was one of this year's recipients of the Lenfest Distinguished Columbia Faculty Award. The awards are given annually to faculty of unusual merit across a range of professorial activities — including scholarship, University citizenship, and professional involvement — with a primary emphasis on the instruction and mentoring of undergraduate and graduate students. Click here to learn more.

Andrea Califano, Professor of Biomedical Informatics, co-Director of the Center for Computational Biology and Bioinformatics, and Director of the National Center for the Multiscale Analysis of Genetic and Cellular Networks has been appointed for a 5 year term to the National Cancer Institute (NCI) Board of Scientific Advisors. The NCI Board of Scientific Advisors provide scientific advice on a wide variety of matters concerning scientific program policy, progress and future direction of the NCI’s extramural research programs, and concept review of extramural program initiatives.

At the 2008 Annual Meeting of the cancer Biomedical Informatics Grid (caBIG™) initiative, members of the C2B2 software development team were recognized with awards for their technical achievements and contributions to the program, including their work in defining standards for the execution of bioinformatics workflows on caGrid (the grid infrastructure of caBIG) and in interfacing caGrid with TeraGrid, one of the largest national computational grid networks.

Barry Honig, PhD, professor of biochemistry & molecular biophysics and Director of C2B2, was inducted into the American Academy of Arts & Sciences in an October 6 ceremony in Cambridge, Massachusetts. The Academy is an independent research center conducting multidisciplinary studies of problems in science, technology, and global security; social policy and American institutions; the humanities and culture; and education.

Dana Pe'er has been presented with the 2007 NIH Director's New Innovator Award (http://www.nih.gov/news/pr/sep2007/od-18a.htm). Part of an NIH Roadmap for Medical Research initiative, this award recognizes outstanding scientists who are "well-positioned to make significant — and potentially transformative — discoveries in a variety of areas.”

This award, proposed by NIH Director, Elias A. Zerhoni, MD was created to help new scientists fund highly innovative approaches to major research challenges that could lead to significant medical advances.

Dr. Pe'er is assistant professor of biological sciences at Columbia University, a member of the Center for Computational Biology and Bioinformatics and an investigator at the MAGNet Center. She utilizes computational and biotechnology approaches to understand how a cell’s regulatory network processes signals and how the signal processing goes wrong in cancer.

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