Evan Paull

Evan Paull

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Evan Paull

Evan Paull

Publications by authors named "Evan Paull"

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SJARACNe: a scalable software tool for gene network reverse engineering from big data.

Bioinformatics 2019 Jun;35(12):2165-2166

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6581437PMC
June 2019

The number of titrated microRNA species dictates ceRNA regulation.

Nucleic Acids Res 2018 05;46(9):4354-4369

Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.

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http://dx.doi.org/10.1093/nar/gky286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961349PMC
May 2018

Prophetic Granger Causality to infer gene regulatory networks.

PLoS One 2017 6;12(12):e0170340. Epub 2017 Dec 6.

University of California Santa Cruz, Department of Biomolecular Engineering, Santa Cruz, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170340PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718405PMC
January 2018

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

Nat Commun 2017 10 30;8(1):1186. Epub 2017 Oct 30.

HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1038/s41467-017-01383-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662764PMC
October 2017

ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES.

Pac Symp Biocomput 2016 ;21:405-16

Department of Biomolecular Engineering, University of California Santa Cruz, USA,

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856035PMC
October 2016

Pathway-Based Genomics Prediction using Generalized Elastic Net.

PLoS Comput Biol 2016 Mar 9;12(3):e1004790. Epub 2016 Mar 9.

Department of Biomolecular Engineering and Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1004790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784899PMC
March 2016

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

Authors:
Daniel J Brat Roel G W Verhaak Kenneth D Aldape W K Alfred Yung Sofie R Salama Lee A D Cooper Esther Rheinbay C Ryan Miller Mark Vitucci Olena Morozova A Gordon Robertson Houtan Noushmehr Peter W Laird Andrew D Cherniack Rehan Akbani Jason T Huse Giovanni Ciriello Laila M Poisson Jill S Barnholtz-Sloan Mitchel S Berger Cameron Brennan Rivka R Colen Howard Colman Adam E Flanders Caterina Giannini Mia Grifford Antonio Iavarone Rajan Jain Isaac Joseph Jaegil Kim Katayoon Kasaian Tom Mikkelsen Bradley A Murray Brian Patrick O'Neill Lior Pachter Donald W Parsons Carrie Sougnez Erik P Sulman Scott R Vandenberg Erwin G Van Meir Andreas von Deimling Hailei Zhang Daniel Crain Kevin Lau David Mallery Scott Morris Joseph Paulauskis Robert Penny Troy Shelton Mark Sherman Peggy Yena Aaron Black Jay Bowen Katie Dicostanzo Julie Gastier-Foster Kristen M Leraas Tara M Lichtenberg Christopher R Pierson Nilsa C Ramirez Cynthia Taylor Stephanie Weaver Lisa Wise Erik Zmuda Tanja Davidsen John A Demchok Greg Eley Martin L Ferguson Carolyn M Hutter Kenna R Mills Shaw Bradley A Ozenberger Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean Claude Zenklusen Brenda Ayala Julien Baboud Sudha Chudamani Mark A Jensen Jia Liu Todd Pihl Rohini Raman Yunhu Wan Ye Wu Adrian Ally J Todd Auman Miruna Balasundaram Saianand Balu Stephen B Baylin Rameen Beroukhim Moiz S Bootwalla Reanne Bowlby Christopher A Bristow Denise Brooks Yaron Butterfield Rebecca Carlsen Scott Carter Lynda Chin Andy Chu Eric Chuah Kristian Cibulskis Amanda Clarke Simon G Coetzee Noreen Dhalla Tim Fennell Sheila Fisher Stacey Gabriel Gad Getz Richard Gibbs Ranabir Guin Angela Hadjipanayis D Neil Hayes Toshinori Hinoue Katherine Hoadley Robert A Holt Alan P Hoyle Stuart R Jefferys Steven Jones Corbin D Jones Raju Kucherlapati Phillip H Lai Eric Lander Semin Lee Lee Lichtenstein Yussanne Ma Dennis T Maglinte Harshad S Mahadeshwar Marco A Marra Michael Mayo Shaowu Meng Matthew L Meyerson Piotr A Mieczkowski Richard A Moore Lisle E Mose Andrew J Mungall Angeliki Pantazi Michael Parfenov Peter J Park Joel S Parker Charles M Perou Alexei Protopopov Xiaojia Ren Jeffrey Roach Thaís S Sabedot Jacqueline Schein Steven E Schumacher Jonathan G Seidman Sahil Seth Hui Shen Janae V Simons Payal Sipahimalani Matthew G Soloway Xingzhi Song Huandong Sun Barbara Tabak Angela Tam Donghui Tan Jiabin Tang Nina Thiessen Timothy Triche David J Van Den Berg Umadevi Veluvolu Scot Waring Daniel J Weisenberger Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Andrew W Xu Lixing Yang Travis I Zack Jianhua Zhang B Arman Aksoy Harindra Arachchi Chris Benz Brady Bernard Daniel Carlin Juok Cho Daniel DiCara Scott Frazer Gregory N Fuller JianJiong Gao Nils Gehlenborg David Haussler David I Heiman Lisa Iype Anders Jacobsen Zhenlin Ju Sol Katzman Hoon Kim Theo Knijnenburg Richard Bailey Kreisberg Michael S Lawrence William Lee Kalle Leinonen Pei Lin Shiyun Ling Wenbin Liu Yingchun Liu Yuexin Liu Yiling Lu Gordon Mills Sam Ng Michael S Noble Evan Paull Arvind Rao Sheila Reynolds Gordon Saksena Zack Sanborn Chris Sander Nikolaus Schultz Yasin Senbabaoglu Ronglai Shen Ilya Shmulevich Rileen Sinha Josh Stuart S Onur Sumer Yichao Sun Natalie Tasman Barry S Taylor Doug Voet Nils Weinhold John N Weinstein Da Yang Kosuke Yoshihara Siyuan Zheng Wei Zhang Lihua Zou Ty Abel Sara Sadeghi Mark L Cohen Jenny Eschbacher Eyas M Hattab Aditya Raghunathan Matthew J Schniederjan Dina Aziz Gene Barnett Wendi Barrett Darell D Bigner Lori Boice Cathy Brewer Chiara Calatozzolo Benito Campos Carlos Gilberto Carlotti Timothy A Chan Lucia Cuppini Erin Curley Stefania Cuzzubbo Karen Devine Francesco DiMeco Rebecca Duell J Bradley Elder Ashley Fehrenbach Gaetano Finocchiaro William Friedman Jordonna Fulop Johanna Gardner Beth Hermes Christel Herold-Mende Christine Jungk Ady Kendler Norman L Lehman Eric Lipp Ouida Liu Randy Mandt Mary McGraw Roger Mclendon Christopher McPherson Luciano Neder Phuong Nguyen Ardene Noss Raffaele Nunziata Quinn T Ostrom Cheryl Palmer Alessandro Perin Bianca Pollo Alexander Potapov Olga Potapova W Kimryn Rathmell Daniil Rotin Lisa Scarpace Cathy Schilero Kelly Senecal Kristen Shimmel Vsevolod Shurkhay Suzanne Sifri Rosy Singh Andrew E Sloan Kathy Smolenski Susan M Staugaitis Ruth Steele Leigh Thorne Daniela P C Tirapelli Andreas Unterberg Mahitha Vallurupalli Yun Wang Ronald Warnick Felicia Williams Yingli Wolinsky Sue Bell Mara Rosenberg Chip Stewart Franklin Huang Jonna L Grimsby Amie J Radenbaugh Jianan Zhang
June 2015

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

Bioinformatics 2013 Nov 27;29(21):2757-64. Epub 2013 Aug 27.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, Department of Systems Biology, HMS LINCS Center, Harvard Medical School, Boston, MA 02115 and Howard Hughes Medical Institute, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799471PMC
November 2013

Molecular pathways: extracting medical knowledge from high-throughput genomic data.

Clin Cancer Res 2013 Jun 21;19(12):3114-20. Epub 2013 Feb 21.

Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-12-2093DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686839PMC
June 2013