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  • Tavazoie Lab
    observations into a new type of knowledge From this perspective the goal of our research is to understand the organizing principles behind the function and evolution of biological networks At one scale we use large scale global observations to reveal the nuts and bolts of these networks and to understand how they come together to orchestrate biological behavior At the other extreme we aim to achieve a holistic understanding of

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/ (2013-05-27)
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  • Research - Tavazoie Lab
    predictive understanding of biological behavior in terms of how these components come together interact and orchestrate adaptive processes Are there universal organizing principles that underlie function and evolution in the underlying networks It is becoming increasingly clear that this systems level understanding requires a revolutionary change in how we think about and conduct biology both in terms of making the appropriate observations but also in the conceptual frameworks required to turn these observations into a new type of knowledge From this perspective the goal of our research is to understand the organizing principles behind the function and evolution of biological networks At one scale we use large scale global observations to reveal the nuts and bolts of these networks and to understand how they come together to orchestrate biological behavior At the other extreme we aim to achieve a holistic understanding of function by considering the native ecological context in which these networks have evolved At the highest level we aim to understand how these networks embody an internal representation of the world outside We have focused on these problems in the context of transcriptional regulatory and genetic networks of organisms ranging from bacteria to human In addition to using

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/research/ (2013-05-27)
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  • Publications - Tavazoie Lab
    Syst Biol 2010 Jun 8 6 378 PDF Goodarzi H Bennett BD Amini S Reaves ML Hottes AK Rabinowitz JD Tavazoie S Revealing global regulatory perturbations across human cancers Molecular Cell 2009 Dec 11 36 900 911 PDF Goodarzi H Elemento O Tavazoie S Preview in same issue A FIRE y PAGE in computational analysis of cancer profiles by Prensner JR Chinnaiyan AM PDF Global protein occupancy landscape of a bacterial genome Molecular Cell 2009 Jul 31 35 2 247 53 PDF Vora T Hottes AK Tavazoie S Global discovery of adaptive mutations Nature Methods 2009 Aug 6 8 581 3 PDF Goodarzi H Hottes AK Tavazoie S Coupling of zygotic transcription to mitotic control at the Drosophila mid blastula transition Development 2009 Jun 136 12 2101 10 PDF Lu X Li JM Elemento O Tavazoie S Wieschaus EF Genetic architecture of intrinsic antibiotic susceptibility PLoS ONE 2009 May 20 4 5 e5629 PDF Girgis HS Hottes AK Tavazoie S Genetic dissection of an exogenously induced biofilm in laboratory and clinical isolates of E coli PLoS Pathog 2009 May 5 5 e1000432 Epub 2009 May 15 PDF Amini S Goodarzi H Tavazoie S Microarray profiling of phage display selections for rapid mapping of transcription factor DNA interactions PLoS Genet 2009 Apr 5 4 e1000449 Epub 2009 Apr 10 PDF Freckleton G Lippman SI Broach JR Tavazoie S let 7 Overexpression leads to an increased fraction of cells in G2 M direct down regulation of Cdc34 and stabilization of Wee1 kinase in primary fibroblasts J Biol Chem 2009 Mar 13 284 11 6605 9 Epub 2009 Jan 6 PDF Legesse Miller A Elemento O Pfau SJ Forman JJ Tavazoie S Coller HA Predictive behavior within microbial genetic networks Science 2008 320 1313 1317 Epub 2008 May 8 PDF Tagkopoulos I Liu Y Tavazoie S A universal framework for regulatory element discovery across all genomes and data types Molecular Cell 2007 28 2 337 50 PDF Elemento O Slonim N Tavazoie S Highlight in Nature Reviews Genetics 8 908 909 PDF A comprehensive genetic characterization of bacterial motility PLoS Genetics 2007 3 9 e154 PDF Girgis H Liu Y Ryu W Tavazoie S Highlight in Nature Reviews Genetics 8 653 653 PDF Unmasking the zygotic genome using chromosome deletion in the Drosophila embryo PLoS Biology 2007 5 5 e117 PDF De Renzis S Elemento O Tavazoie S Wieschaus EF Fastcompare A non alignment approach for genome scale discovery of DNA and mRNA regulatory elements using network level conservation Methods in Mol Biol Comparative Genomics 2007 Elemento O Tavazoie S Role of transcription factor Kar4 in regulating downstream events in the Saccharomyces cerevisiae pheromone response pathway Mol Cell Biol 2006 Nov 13 Epub PDF Lahav R Gammie A Tavazoie S Rose MD Ab initio genotype phenotype association reveals the intrinsic modularity of genetic networks Molecular Systems Biology 2006 2 2006 0005 Epub 2006 Jan 31 PDF Slonim N Elemento O equal contribution and Tavazoie S Revealing posttranscriptional regulatory elements through network level conservation

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/publications/ (2013-05-27)
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  • Tools - Tavazoie Lab
    485 264 268 FIRE a motif discovery and characterization program based on mutual information Molecular Cell 2007 28 2 337 50 EVE a simulation framework for microbial populations in complex dynamic environments Science 2008 320 5881 1313 1317 iPAGE a functional and categorical enrichment program based on mutual information Molecular Cell 2009 36 5 900 911 FIRE pro a motif discovery and characterization program for proteins based on mutual information

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/tools/ (2013-05-27)
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  • Personnel - Tavazoie Lab
    Department of Biomedical Engineering The Institute for Computational Medicine Johns Hopkins University mbeer jhu edu Noam Slonim IBM Research Haifa Israel noams il ibm com Tiffany Vora Moshe Pritsker Editor in Chief Journal of Visualized Experiments Kendra Harris MD PhD student Tri institutional Program Cornell Medical School Chang Chan Assistant Professor of Medicine UMDNJ Robert Wood Johnson Medical School Gordon Freckleton Research Scientist ImClone Systems Hany Girgis Postdoctoral Fellow Mootha

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/personnel/ (2013-05-27)
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  • PI: Saeed - Tavazoie Lab
    1992 Professional history 2011 present Professor Department of Biochemistry and Molecular Biophysics Columbia University 2000 2011 Member Lewis Sigler Institute for Integrative Genomics Princeton University 2009 2011 Professor Department of Molecular Biology Princeton University 2005 2009 Associate Professor Department of Molecular Biology Princeton University 2000 2005 Assistant Professor Department of Molecular Biology Princeton University 1999 2000 Postdoctoral Fellow Computational Genomics Harvard Medical School 1993 1999 Graduate student Dept of Genetics

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/pi-saeed/ (2013-05-27)
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  • Contact - Tavazoie Lab
    Personnel PI Saeed Contact Contact Principal Investigator Saeed Tavazoie Biochemistry and Molecular Biophysics Columbia University Russ Berrie Pavilion Room 405A 1150 St Nicholas Ave New York NY 10032 st2744 columbia

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/contact/ (2013-05-27)
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  • Predicting gene expression from sequence - Tavazoie Lab
    novel predicted regulatory elements This framework allowed us for the first time to predict expression patterns of 70 of yeast genes from their local regulatory sequences A universal framework for regulatory element discovery A major focus of on going work is to extract mammalian regulatory programs from the rapidly increasing flood of expression data encompassing tissue specific gene expression in normal and disease states e g cancer and highly structured expression patterns in organs like the brain However regulatory element discovery in mammalian genomes poses unique challenges such as large inter genic regions distal regulatory elements local and large scale chromosomal composition trends a vast diversity of cell types and highly complex expression programs To deal with these challenges we have rephrased the problem in an information theoretic framework which has freed us from making any assumptions about the structure of the underlying sequence or the specific model by which the sequence affects gene expression This has led to a versatile framework for regulatory element discovery across all genomes and data types with exceptional sensitivity and near zero false positive rates Elemento et al Molecular Cell 2007 28 337 Our approach named FIRE for Finding Informative Regulatory Elements is available to the public both as standalone software and through a user friendly web interface iget c2b2 columbia edu Global regulatory perturbations in disease states Our computational methods have led the way in pathway and regulatory network analysis of microarray expression data in the context of human disease We have developed an information theoretic framework that addresses the challenging and largely unsolved problem of 1 discovering perturbed pathways from microarray expression studies and 2 revealing the underlying transcriptional and post transcriptional regulatory processes through which the observed pathway perturbations are orchestrated In a major recent study we focused on the analysis of a compendium of cancer microarray expression data existing in the public domain Across this extensive and diverse dataset we discovered a large number of known and novel pathway perturbations and then went on to identify the local DNA and RNA regulatory elements that mediate these changes in gene expression This ab initio approach yields the vast majority of previously known cancer pathways along with their associated transcription factor binding sites The majority of pathways and regulatory elements are novel In fact a surprisingly large fraction of cis regulatory elements reside within 3 UTR regions and most do not correspond to microRNA targeting sequences This represents a vastly unexplored role for post transcriptional processes in cancer Our framework connects these putative regulatory elements to specific pathways providing a powerful starting point for understanding their biology and mechanisms of action We are encouraged by the high sensitivity with which our approach rediscovers the components of classical tumor promoting and tumor suppressing pathways e g MAPK WNT P53 CREB TNF ERK JNK VEGF etc These pathways and their gene regulatory consequences were worked out over the course of 20 years of labor intensive genetics and biochemistry across hundreds of laboratories Our rediscovery

    Original URL path: https://tavazoielab.c2b2.columbia.edu/lab/research/gene-exp-from-seq/ (2013-05-27)
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