We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data. by Simon Kasif, Richard J Roberts

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To supplement or not to supplement: a metabolic network framework for human nutritional supplements. by Christopher D Nogiec, Simon Kasif

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Probabilistic protein function prediction from heterogeneous genome-wide data. by Naoki Nariai, Eric D Kolaczyk, Simon Kasif

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Segmentally variable genes: a new perspective on adaptation. by Yu Zheng, Richard J Roberts, Simon Kasif

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Quantitative analysis of single nucleotide polymorphisms within copy number variation. by Soohyun Lee, Simon Kasif, Zhiping Weng, Charles R Cantor

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Biological process linkage networks. by Dikla Dotan-Cohen, Stan Letovsky, Avraham A Melkman, Simon Kasif

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A predictive phosphorylation signature of lung cancer. by Chang-Jiun Wu, Tianxi Cai, Klarisa Rikova, David Merberg, Simon Kasif, Martin Steffen

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Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes by Christopher Nogiec, Alison Burkart, Jonathan M. Dreyfuss, Carles Lerin, Simon Kasif, Mary-Elizabeth Patti

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Membrane metallo-endopeptidase (Neprilysin) regulates inflammatory response and insulin signaling in white preadipocytes by Alfred K. Ramirez, Simon Dankel, Weikang Cai, Masaji Sakaguchi, Simon Kasif, C. Ronald Kahn

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Network-based analysis of affected biological processes in type 2 diabetes models. by Manway Liu, Arthur Liberzon, Sek Won Kong, Weil R Lai, Peter J Park, Isaac S Kohane, Simon Kasif

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. by Jeremiah J Faith, Boris Hayete, Joshua T Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J Collins, Timothy S Gardner

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Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes by Alfred K. Ramirez, Matthew D. Lynes, Farnaz Shamsi, Ruidan Xue, Yu-Hua Tseng, C. Ronald Kahn, Simon Kasif, Jonathan M. Dreyfuss

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Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity by Alfred K. Ramirez, Simon N. Dankel, Bashir Rastegarpanah, Weikang Cai, Ruidan Xue, Mark Crovella, Yu-Hua Tseng, C. Ronald Kahn, Simon Kasif

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One for all and all for One: Improving replication of genetic studies through network diffusion. by Daniel Lancour, Adam Naj, Richard Mayeux, Jonathan L Haines, Margaret A Pericak-Vance, Gerard D Schellenberg, Mark Crovella, Lindsay A Farrer, Simon Kasif

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Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease by Daniel Lancour, Josée Dupuis, Richard Mayeux, Jonathan L. Haines, Margaret A. Pericak-Vance, Gerard C. Schellenberg, Mark Crovella, Lindsay A. Farrer, Simon Kasif

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Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. by Han-Pil Choi, Silvia Juarez, Sergio Ciordia, Marisol Fernandez, Rafael Bargiela, Juan P Albar, Varun Mazumdar, Brian P Anton, Simon Kasif, Manuel Ferrer, Martin Steffen

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An Aberrant Transcription Factor Network Essential for Wnt Signaling and Stem Cell Maintenance in Glioblastoma by Esther Rheinbay, Mario L. Suvà, Shawn M. Gillespie, Hiroaki Wakimoto, Anoop P. Patel, Mohammad Shahid, Ozgur Oksuz, Samuel D. Rabkin, Robert L. Martuza, Miguel N. Rivera, David N. Louis, Simon Kasif, Andrew S. Chi, Bradley E. Bernstein

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Deep sequencing of the oral microbiome reveals signatures of periodontal disease. by Bo Liu, Lina L Faller, Niels Klitgord, Varun Mazumdar, Mohammad Ghodsi, Daniel D Sommer, Theodore R Gibbons, Todd J Treangen, Yi-Chien Chang, Shan Li, O Colin Stine, Hatice Hasturk, Simon Kasif, Daniel Segrè, Mihai Pop, Salomon Amar

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Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. by Manching Ku, Richard P Koche, Esther Rheinbay, Eric M Mendenhall, Mitsuhiro Endoh, Tarjei S Mikkelsen, Aviva Presser, Chad Nusbaum, Xiaohui Xie, Andrew S Chi, Mazhar Adli, Simon Kasif, Leon M Ptaszek, Chad A Cowan, Eric S Lander, Haruhiko Koseki, Bradley E Bernstein

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High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control by Jonathan M. Dreyfuss, Yixing Yuchi, Xuehong Dong, Vissarion Efthymiou, Hui Pan, Donald C. Simonson, Ashley Vernon, Florencia Halperin, Pratik Aryal, Anish Konkar, Yinong Sebastian, Brandon W. Higgs, Joseph Grimsby, Cristina M. Rondinone, Simon Kasif, Barbara B. Kahn, Kathleen Foster, Randy Seeley, Allison Goldfine, Vera Djordjilović, Mary Elizabeth Patti

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