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Bioinformatics and Systems Biology
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$77 million NIH grant launches new HIV/AIDS vaccine center
Adam Godzik, Ph.D. manages the massive amounts of valuable information generated by the Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery, established in 2012.
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Seeing is believing
Dr. Dorit Hanein’s laboratory is developing an imaging technique that allows them to peer into a cell and see what’s going on—which proteins are doing what, when and with whom – in real time.
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Some like it sweet
Dr. Andrei Osterman and his team use computer models to reconstruct and predict metabolic pathways in the bacteria T. maritime and S. oneidensis, which may have potential industrial applications to produce biohydrogen or clean up nuclear waste.
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Studying bioinformatics and systems biology
The Bioinformatics and Systems Biology Program is helping to develop a new paradigm of research—one that shifts focus from traditional studies of single genes or processes to unified systems views on biological processes. This approach combines data-mining from large-scale, technology-driven projects, such as human genome or structural genomics projects, with traditional hypothesis-driven experimental work.
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The explosive growth of biological research in the last decade has led to an exponential increase in the amount of information available about important biological systems. With new developments, such as sequencing entire genomes of many organisms, this increase is likely to continue. Not only the amount of data will increase, but also new types of data—such as exact timing of various steps in regulatory pathways—will become available. These developments necessitate a system-wide appreciation of what’s happening in a cell or organism and the computing and organizational power to make sense of it all. The Bioinformatics and Systems Biology Program is helping to develop this new paradigm both by creating new bioinformatics tools and at the same time, in collaboration with other research groups at the Institute, applying new tools and new ways of thinking to specific research projects.
How our research helps improve health
With the genome now completed, the sequences of all ~20-25,000 human genes are now known. The function or even the speculated function of more than half of these genes, however, is still unknown, leaving a large gaps in our understanding of human genetics, development, health, and disease. The next phase of genomics will be dedicated to deciphering gene function, from which will come the targets for future drug discovery.
Research - Infectious and Inflammatory Disease - Bioinformatics and
Systems Biology: How Our Research Helps |
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Evolution of the animal apoptosis network.
Zmasek CM, Godzik A.
Cold Spring Harb Perspect Biol. 2013 Mar 1;5(3). doi:pii: a008649. 10.1101/cshperspect.a008649.
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Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.
Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA.
BMC Genomics. 2013 Feb 12;14:94. doi: 10.1186/1471-2164-14-94.
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Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.
Kazanov MD, Li X, Gelfand MS, Osterman AL, Rodionov DA.
Nucleic Acids Res. 2013 Jan;41(2):790-803. doi: 10.1093/nar/gks1184. Epub 2012 Dec 2.
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This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes.
Zmasek CM, Godzik A.
PLoS Comput Biol. 2012;8(11):e1002701. doi: 10.1371/journal.pcbi.1002701. Epub 2012 Nov 15.
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Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.
Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS.
J Bacteriol. 2013 Jan;195(1):29-38. doi: 10.1128/JB.01977-12. Epub 2012 Oct 19.
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A Blueprint for HIV Vaccine Discovery.
Burton DR, Ahmed R, Barouch DH, Butera ST, Crotty S, Godzik A, Kaufmann DE, McElrath MJ, Nussenzweig MC, Pulendran B, Scanlan CN, Schief WR, Silvestri G, Streeck H, Walker BD, Walker LM, Ward AB, Wilson IA, Wyatt R.
Cell Host Microbe. 2012 Oct 18;12(4):396-407. doi: 10.1016/j.chom.2012.09.008. Review.
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Research - Infectious and Inflammatory Disease - Bioinformatics and
Systems Biology: Recent Publications |
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A Blueprint for HIV Vaccine Discovery.
Burton DR, Ahmed R, Barouch DH, Butera ST, Crotty S, Godzik A, Kaufmann DE, McElrath MJ, Nussenzweig MC, Pulendran B, Scanlan CN, Schief WR, Silvestri G, Streeck H, Walker BD, Walker LM, Ward AB, Wilson IA, Wyatt R
Cell Host Microbe. 2012 Oct 18;12(4):396-407
Structure of a novel winged-helix like domain from human NFRKB protein.
Kumar A, Möcklinghoff S, Yumoto F, Jaroszewski L, Farr CL, Grzechnik A, Nguyen P, Weichenberger CX, Chiu HJ, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Conklin BR, Fletterick RJ, Wilson IA
PLoS One. 2012;7(9):e43761
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