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
Published 2020-11-01

To supplement or not to supplement: a metabolic network framework for human nutritional supplements.

by Christopher D Nogiec, Simon Kasif
Published 2013-01-01

Probabilistic protein function prediction from heterogeneous genome-wide data.

by Naoki Nariai, Eric D Kolaczyk, Simon Kasif
Published 2007-03-01

Segmentally variable genes: a new perspective on adaptation.

by Yu Zheng, Richard J Roberts, Simon Kasif
Published 2004-04-01

Quantitative analysis of single nucleotide polymorphisms within copy number variation.

by Soohyun Lee, Simon Kasif, Zhiping Weng, Charles R Cantor
Published 2008-01-01

Biological process linkage networks.

by Dikla Dotan-Cohen, Stan Letovsky, Avraham A Melkman, Simon Kasif
Published 2009-01-01

A predictive phosphorylation signature of lung cancer.

by Chang-Jiun Wu, Tianxi Cai, Klarisa Rikova, David Merberg, Simon Kasif, Martin Steffen
Published 2009-11-01

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
Published 2019-04-01

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
Published 2015-03-01

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
Published 2007-06-01

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
Published 2007-01-01

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
Published 2017-12-01

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
Published 2020-04-01

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
Published 2020-09-01

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
Published 2018-04-01

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
Published 2013-01-01

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
Published 2013-05-01

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
Published 2012-01-01

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
Published 2008-10-01

Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism

by Carles Lerin, Allison B. Goldfine, Tanner Boes, Manway Liu, Simon Kasif, Jonathan M. Dreyfuss, Ana Luisa De Sousa-Coelho, Grace Daher, Irini Manoli, Justin R. Sysol, Elvira Isganaitis, Niels Jessen, Laurie J. Goodyear, Kirk Beebe, Walt Gall, Charles P. Venditti, Mary-Elizabeth Patti
Published 2016-10-01