Tracking the H1N1 pandemic virus (October 16 2009)
The recent outbreak and sudden spread of a novel H1N1 influenza virus has caused a worldwide concern and has tested our ability to respond to major public health challenges. Significant scientific resources have been marshaled to discover the best possible responses against this novel swine origin influenza virus. A group led by Raul Rabadan at the Center for Computational Biology and the Department of Biomedical Informatics at Columbia University has been studying the evolution of influenza viruses and the origins of flu pandemics by analyzing large data sets that contain genomic information. After the first news of the outbreak in April 2009, the group worked intensely to decipher the origins, the diversification, and the spread of the pandemic virus, and investigated the factors that could contribute to its virulence. The results of these studies are published in major scientific journals including the New England Journal of Medicine, Eurosurveillance, PLoS, etc., and have received special attention from the media, including:- CNN
- Reuters International
- Associated Press and ABC News
- China Radio International
The Rabadan lab was also the subject of the cover story in the Fall 2009 issue of the Columbia Magazine.
Portion of this work was performed in close collaboration with Gustavo Palacios and Ian Lipkin at Columbia University and the researchers at the Institute for Advanced Study in Princeton, New Jersey.
3rd Annual DREAM Conference (November 3 2008)
The 3rd Annual DREAM (Dialogue for Reverse Engineering Assessments and Methods) Conference was held at the Broad Institute in Boston from October 29th to November 2nd 2008, jointly with the 5th Annual RECOMB Satellite Conference on Regulatory Genomics and the 4th Annual RECOMB Satellite Conference on Systems Biology. The meeting was organized by the Broad Institute of MIT and Harvard, and the MIT Computer Science and Artificial Intelligence Lab (CSAIL).
The meeting brought together computational and experimental scientists in the area of regulatory genomics, to discuss current research directions, latest findings, and establish new collaborations towards a systems-level understanding of gene regulation. The program comprised 16 keynote presentations, 93 oral presentations selected from submitted manuscripts and 1-page abstracts, and 160 posters in four poster sessions. More than 500 participants registered attended the joint meeting, of which the vast majority attended all three meetings.
Conference Chairs: Manolis Kellis (MIT), Andrea Califano Columbia University, Gustavo Stolovitzky (IBM).
Organizing Commitee: Eleazar Eskin, Nir Friedman, Leroy Hood, Trey Ideker, Douglas Lauffenburger, Satoru Miyano, Eran Segal, Ron Shamir. Partner journal editors: Hillary Sussman, CSHL (Genome Research), Thomas Lemberger, EMBO (Nature MSB), Sorin Istrail, Brown University (Journal of Computational Biology).
For more information please visit the http://compbio.mit.edu/recombsat/ conference website.
Andrea Califano appointed to the NCI Board of Scientific Advisors (September 26 2008)
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.C2B2 receives technical achievements awards (June 25 2008)
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.C2B2 awarded caBIG Knowledge Center (June 2 2008)
The Center for Computational Biology and Bioinformatics (C2B2), in collaboration with the Broad Institute of MIT and Harvard, has a received a 3-year award from the National Cancer Institute to establish and operate the Molecular Analysis Tools Knowledge Center of the cancer Biomedical Informatics Grid (caBIG™) initiative. The mission of the Knowledge Center is to promote the adoption of caBIG™ technologies aiming to facilitate the discovery of the next generation of cancer diagnostics and therapeutics which will help realize the vision of molecular and personalized medicine. geWorkbench, the bioinformatics platform of the MAGNet Center, will be one of the tools supported by the Knowledge Center.
The caBIG™ initiative, overseen by the NCI Center for Biomedical Informatics and Information Technology, was conceived to advance basic and clinical research on cancer and improve clinical outcomes for patients. Information such as patient registries, tissue management data, and study results can be uploaded to the grid-based system.
Dana Pe'er Receives 2007 NIH Director’s New Innovator Award (September 19 2007)
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, M.D. 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.
2nd Annual DREAM Conference (September 19 2007)
The 2nd Annual DREAM ( Dialogue for Reverse Engineering Assessments and Methods ) conference has been announced and will be held December 3 and 4, 2007 at the New York Academy of Sciences in New York, NY.The conference will feature several speakers including: Tim Gardner, Ravi Iyengar, Fritz Roth, Chris Sander, Ron Shamir, Ilya Shmulevich, Mike Snyder, Peter Sorger, Ioannis Xenarios; as well as a presentation of accepted papers.
Also to be discussed will be the DREAM Challenge, which consists of 5 separate challenges composed of one or more datasets which participants used to generate predictions as to the best possible network from which the data originated. All predictions and results will be disclosed at the conference.
For more information please visit the DREAM Conference Website.
2007 C2B2/MAGNet Annual Retreat (June 4 2007)
The 2007 annual C2B2/MAGNet Center retreat took place on April 6, at Wave Hill (http://wavehill.org) in New York city. Several of the Center's faculty members had the opportunity topresent and inform the C2B2/MAGNet community about the ongoing research in their laboratories. Presentations from the meeting are available online at: http://magnet.c2b2.columbia.edu/retreats/07/.geWorkbench wins award (February 8 2007)
geWorkbench, the bioinformatics platform of the MAGNet Center, was recognized with an excellence award during the 2007 annual meeting of the cancer Biomedical Informatics Grid (caBIG) initiative. The geWorkbench project team was sited for "excellence in the design, planning and implementation of one of the first unrestricted open-source software projects from integrative genomics analysis".DREAM Conference eBriefing (January 25 2007)
Meeting notes and presentations from the September 2006 DIMACS Workshop on the Dialogue on Reverse Engineering Assessment Methods (DREAM) are now available as an eBriefing on the New York Academy of Sciences web site.Second DREAM Initiative Meeting (September 7 2006)
The MAGNet Center and the IBM Computational Biology Center (CBC) are jointly hosting the second meeting on the DREAM initiative (Dialogue on Reverse Engineering Assessment and Methods). The meeting will be held in New York, at the Wave Hill Conference Center. Program and registration details are available here. DREAM aims at the creation of a yearly workshop and database for the comparative analysis of systems biology methods and algorithms, specifically in the area of reverse engineering.This will be the second in a series of planning workshops. The first one took place on March 2006 at the New York Academy of Sciences. A meeting report as well as the presentations from this 2 day event are now available at the Academy's web site.
geWorkbench version 1.0 released (May 31 2006)
Version 1.0 of geWorkbench, the Center's bioinformatics platform, is now available for download from the projects's web site at geworkbench.org. The site provides detailed documentation for end-users as well as programers interested in developing components for geWorkbench. A companion GForge site has also been setup to support collaborative development.First annual retreat presentations available online. (May 25 2006)
The presentations from the first annual MAGNet cetner retreat (March 2 2006, at Wave Hill [http://wavehill.org/] ) are now available online at: http://magnet.c2b2.columbia.edu/retreats/06/.GeneTegrate project site released (May 18 2006)
The GeneTegrate project provides a computational platform and a unifying semantic modeling layer to enrich, simplify and accelerate the analyses of distributed heterogeneous biological data. The project's web site is available at: http://www.genetegrate.org/DREAM Initiative Planning Workshop (March 9 2006)
The National Center for Biomedical Computing at Columbia University (MAGNet), in collaboration with the IBM Computational Biology Center (CBC), is starting a new initiative to create a yearly workshop and database for the comparative analysis of systems biology methods and algorithms, specifically in the area of reverse engineering. A small planning workshop has been organized, which will be hosted in March by the New York Academy of Sciences in the context of their Systems Biology SIG. The meeting will convene a small number of colleagues to further explore and define the details and formats of this initiative. The goal of this planning workshop is to explore the scientific community consensus and potential interest in creating a community-driven database called DREAM (Database for Reverse Engineering Analysis and Methods) and an associated recurring workshop that will use this database for the quantitative and systematic comparison of systems biology methods and algorithms.More information on this initiative is available here.
First Annual MAGNet Retreat (March 2 2006)
The first annual MAGNet cetner retreat took place on March 2nd, at Wave Hill (http://wavehill.org) in New York city. The one day event (see agenda) provided an opportunity for the Core I, II and III investigators to present results of ongoing research related to the Center's activities. All presentations were recorded and will be soon made available as downloadable movie files from this web site.Center tools used in mRNA stability study in yeast (December 6 2005)
In a paper published in the Proceedings of the National Academy of Sciences, Columbia University researchers and their colleagues report results of studying the genome-wide regulation of mRNA stability in yeast. Using MatrixREDUCE (a variant of the REDUCE algorithm developed by the Bussemaker lab) they managed to identify and computationally characterize the binding sites for six mRNA stability regulators in Saccharomyces cerevisiae, which include two members of the Pumilio-homology domain (Puf) family of RNA-binding proteins, Puf3p and Puf4p. Data and supporting material for the PNAS paper are available here.MAGNet Press Release (September 30 2005)
A press release announcing the formation of MAGNet is now available.