G
Gary D. Bader
Researcher at University of Toronto
Publications - 350
Citations - 68394
Gary D. Bader is an academic researcher from University of Toronto. The author has contributed to research in topics: Biology & Stem cell. The author has an hindex of 94, co-authored 315 publications receiving 55824 citations. Previous affiliations of Gary D. Bader include University of Washington & Lunenfeld-Tanenbaum Research Institute.
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Journal ArticleDOI
An automated method for finding molecular complexes in large protein interaction networks.
TL;DR: A novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes is described.
Journal ArticleDOI
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
Yuen Ho,Albrecht Gruhler,Adrian Heilbut,Gary D. Bader,Gary D. Bader,Lynda Moore,Sally-Lin Adams,Anna Millar,Paul J. Taylor,Keiryn L. Bennett,Kelly Boutilier,Lingyun Yang,Cheryl Wolting,Ian Donaldson,Søren Schandorff,Juanita Shewnarane,Mai Vo,Joanne Taggart,Marilyn Goudreault,Brenda Muskat,Cris Alfarano,Danielle Dewar,Zhen Lin,Katerina Michalickova,Katerina Michalickova,Andrew Willems,Andrew Willems,Holly Sassi,Peter A Nielsen,Karina Juhl Rasmussen,Jens R. Andersen,Lene E. Johansen,Lykke Haastrup Hansen,Hans Jespersen,Alexandre V. Podtelejnikov,Eva Nielsen,Janne S. Crawford,Vibeke Poulsen,Birgitte D Sørensen,Jesper Matthiesen,Ronald C. Hendrickson,Frank Gleeson,Tony Pawson,Tony Pawson,Michael Moran,Daniel Durocher,Daniel Durocher,Matthias Mann,Christopher W. V. Hogue,Christopher W. V. Hogue,Daniel Figeys,Mike Tyers,Mike Tyers +52 more
TL;DR: Comparison of the HMS-PCI data set with interactions reported in the literature revealed an average threefold higher success rate in detection of known complexes compared with large-scale two-hybrid studies.
Journal ArticleDOI
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.
David Warde-Farley,Sylva L. Donaldson,Ovi Comes,Khalid Zuberi,Rashad Badrawi,Pauline Chao,Max Franz,Chris Grouios,Farzana Kazi,Christian Lopes,Anson Maitland,Sara Mostafavi,Jason Montojo,Quentin Shao,George Wright,Gary D. Bader,Quaid Morris +16 more
TL;DR: The high accuracy of the GeneMANIA prediction algorithm, an intuitive user interface and large database make Gene MANIA a useful tool for any biologist.
Journal ArticleDOI
Integration of biological networks and gene expression data using Cytoscape
Melissa S. Cline,Michael E. Smoot,Ethan Cerami,Allan Kuchinsky,Nerius Landys,Christopher T. Workman,Rowan H. Christmas,Iliana Avila-Campilo,Iliana Avila-Campilo,Michael L. Creech,Benjamin Gross,Kristina Hanspers,Ruth Isserlin,Ryan Kelley,Sarah Killcoyne,Samad Lotia,Steven Maere,John H. Morris,Keiichiro Ono,Vuk Pavlovic,Alexander R. Pico,Aditya Vailaya,Peng-Liang Wang,Annette M. Adler,Bruce R. Conklin,Leroy Hood,Martin Kuiper,Chris Sander,Ilya Schmulevich,Benno Schwikowski,Guy J. Warner,Trey Ideker,Gary D. Bader +32 more
TL;DR: This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Journal ArticleDOI
The genetic landscape of a cell.
Michael Costanzo,Anastasia Baryshnikova,Jeremy Bellay,Yungil Kim,Eric D. Spear,Carolyn S. Sevier,Huiming Ding,Judice L. Y. Koh,Kiana Toufighi,Sara Mostafavi,Jeany Prinz,Robert P. St.Onge,Benjamin VanderSluis,Taras Makhnevych,Franco J. Vizeacoumar,Solmaz Alizadeh,Sondra Bahr,Renee L. Brost,Yiqun Chen,Murat Cokol,Raamesh Deshpande,Zhijian Li,Zhen Yuan Lin,Wendy Liang,Michaela Marback,Jadine Paw,Bryan Joseph San Luis,Ermira Shuteriqi,Amy Hin Yan Tong,Nydia Van Dyk,Iain M. Wallace,Joseph Whitney,Matthew T. Weirauch,Guoqing Zhong,Hongwei Zhu,Walid A. Houry,Michael Brudno,Sasan Ragibizadeh,Balázs Papp,Csaba Pál,Frederick P. Roth,Guri Giaever,Corey Nislow,Olga G. Troyanskaya,Howard Bussey,Gary D. Bader,Anne-Claude Gingras,Quaid Morris,Philip M. Kim,Chris A. Kaiser,Chad L. Myers,Brenda J. Andrews,Charles Boone +52 more
TL;DR: A network based on genetic interaction profiles reveals a functional map of the cell in which genes of similar biological processes cluster together in coherent subsets, and highly correlated profiles delineate specific pathways to define gene function.