Anurag Sethi

Anurag Sethi

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Anurag Sethi

Anurag Sethi

Publications by authors named "Anurag Sethi"

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The promise and reality of therapeutic discovery from large cohorts.

J Clin Invest 2020 Feb;130(2):575-581

Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1172/JCI129196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6994121PMC
February 2020

Using the Seven Bridges Cancer Genomics Cloud to Access and Analyze Petabytes of Cancer Data.

Curr Protoc Bioinformatics 2017 12 8;60:11.16.1-11.16.32. Epub 2017 Dec 8.

Seven Bridges Genomics Inc., Cambridge, Massachusetts.

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http://dx.doi.org/10.1002/cpbi.39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726550PMC
December 2017

Identifying Allosteric Hotspots with Dynamics: Application to Inter- and Intra-species Conservation.

Structure 2016 05 7;24(5):826-837. Epub 2016 Apr 7.

Program in Computational Biology and Bioinformatics, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT 06520, USA; Department of Computer Science, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT 06520, USA. Electronic address:

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http://www.cell.com/structure/pdf/S0969-2126(16)00086-1.pdf
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http://dx.doi.org/10.1016/j.str.2016.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883016PMC
May 2016

Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.

Cell Syst 2016 Mar;2(3):147-157

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Department of Computer Science, Yale University, New Haven, CT 06520.

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http://dx.doi.org/10.1016/j.cels.2016.02.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817108PMC
March 2016

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma.

Authors:
W Marston Linehan Paul T Spellman Christopher J Ricketts Chad J Creighton Suzanne S Fei Caleb Davis David A Wheeler Bradley A Murray Laura Schmidt Cathy D Vocke Myron Peto Abu Amar M Al Mamun Eve Shinbrot Anurag Sethi Samira Brooks W Kimryn Rathmell Angela N Brooks Katherine A Hoadley A Gordon Robertson Denise Brooks Reanne Bowlby Sara Sadeghi Hui Shen Daniel J Weisenberger Moiz Bootwalla Stephen B Baylin Peter W Laird Andrew D Cherniack Gordon Saksena Scott Haake Jun Li Han Liang Yiling Lu Gordon B Mills Rehan Akbani Mark D M Leiserson Benjamin J Raphael Pavana Anur Donald Bottaro Laurence Albiges Nandita Barnabas Toni K Choueiri Bogdan Czerniak Andrew K Godwin A Ari Hakimi Thai H Ho James Hsieh Michael Ittmann William Y Kim Bhavani Krishnan Maria J Merino Kenna R Mills Shaw Victor E Reuter Ed Reznik Carl S Shelley Brian Shuch Sabina Signoretti Ramaprasad Srinivasan Pheroze Tamboli George Thomas Satish Tickoo Kenneth Burnett Daniel Crain Johanna Gardner Kevin Lau David Mallery Scott Morris Joseph D Paulauskis Robert J Penny Candace Shelton W Troy Shelton Mark Sherman Eric Thompson Peggy Yena Melissa T Avedon Jay Bowen Julie M Gastier-Foster Mark Gerken Kristen M Leraas Tara M Lichtenberg Nilsa C Ramirez Tracie Santos Lisa Wise Erik Zmuda John A Demchok Ina Felau Carolyn M Hutter Margi Sheth Heidi J Sofia Roy Tarnuzzer Zhining Wang Liming Yang Jean C Zenklusen Jiashan Zhang Brenda Ayala Julien Baboud Sudha Chudamani Jia Liu Laxmi Lolla Rashi Naresh Todd Pihl Qiang Sun Yunhu Wan Ye Wu Adrian Ally Miruna Balasundaram Saianand Balu Rameen Beroukhim Tom Bodenheimer Christian Buhay Yaron S N Butterfield Rebecca Carlsen Scott L Carter Hsu Chao Eric Chuah Amanda Clarke Kyle R Covington Mahmoud Dahdouli Ninad Dewal Noreen Dhalla Harsha V Doddapaneni Jennifer A Drummond Stacey B Gabriel Richard A Gibbs Ranabir Guin Walker Hale Alicia Hawes D Neil Hayes Robert A Holt Alan P Hoyle Stuart R Jefferys Steven J M Jones Corbin D Jones Divya Kalra Christie Kovar Lora Lewis Jie Li Yussanne Ma Marco A Marra Michael Mayo Shaowu Meng Matthew Meyerson Piotr A Mieczkowski Richard A Moore Donna Morton Lisle E Mose Andrew J Mungall Donna Muzny Joel S Parker Charles M Perou Jeffrey Roach Jacqueline E Schein Steven E Schumacher Yan Shi Janae V Simons Payal Sipahimalani Tara Skelly Matthew G Soloway Carrie Sougnez Angela Tam Donghui Tan Nina Thiessen Umadevi Veluvolu Min Wang Matthew D Wilkerson Tina Wong Junyuan Wu Liu Xi Jane Zhou Jason Bedford Fengju Chen Yao Fu Mark Gerstein David Haussler Katayoon Kasaian Phillip Lai Shiyun Ling Amie Radenbaugh David Van Den Berg John N Weinstein Jingchun Zhu Monique Albert Iakovina Alexopoulou Jeremiah J Andersen J Todd Auman John Bartlett Sheldon Bastacky Julie Bergsten Michael L Blute Lori Boice Roni J Bollag Jeff Boyd Erik Castle Ying-Bei Chen John C Cheville Erin Curley Benjamin Davies April DeVolk Rajiv Dhir Laura Dike John Eckman Jay Engel Jodi Harr Ronald Hrebinko Mei Huang Lori Huelsenbeck-Dill Mary Iacocca Bruce Jacobs Michael Lobis Jodi K Maranchie Scott McMeekin Jerome Myers Joel Nelson Jeremy Parfitt Anil Parwani Nicholas Petrelli Brenda Rabeno Somak Roy Andrew L Salner Joel Slaton Melissa Stanton R Houston Thompson Leigh Thorne Kelinda Tucker Paul M Weinberger Cynthia Winemiller Leigh Anne Zach Rosemary Zuna

Reads meet rotamers: structural biology in the age of deep sequencing.

Curr Opin Struct Biol 2015 Dec 1;35:125-34. Epub 2015 Dec 1.

Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2015.11.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751031PMC
December 2015

Membrane-mediated regulation of the intrinsically disordered CD3ϵ cytoplasmic tail of the TCR.

Biophys J 2015 May;108(10):2481-2491

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico; New Mexico Consortium, Los Alamos, New Mexico. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2015.03.059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457001PMC
May 2015

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.

PLoS Comput Biol 2013 16;9(5):e1003046. Epub 2013 May 16.

Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1003046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656115PMC
March 2014

Binding and movement of individual Cel7A cellobiohydrolases on crystalline cellulose surfaces revealed by single-molecule fluorescence imaging.

J Biol Chem 2013 Aug 1;288(33):24164-72. Epub 2013 Jul 1.

Material Physics and Applications, Los Alamos National Laboratory, Los Alamos, New Mexico 87544, USA.

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http://dx.doi.org/10.1074/jbc.M113.455758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3745362PMC
August 2013

Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics.

Chem Phys 2013 Aug;422

Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA ; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA.

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http://dx.doi.org/10.1016/j.chemphys.2013.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810979PMC
August 2013

Increased enzyme binding to substrate is not necessary for more efficient cellulose hydrolysis.

Proc Natl Acad Sci U S A 2013 Jul 19;110(27):10922-7. Epub 2013 Jun 19.

Biomass Conversion Research Laboratory (BCRL), Chemical Engineering and Materials Science, Michigan State University, Lansing, MI 48910, USA.

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http://dx.doi.org/10.1073/pnas.1213426110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703979PMC
July 2013

Taste of sugar at the membrane: thermodynamics and kinetics of the interaction of a disaccharide with lipid bilayers.

Biophys J 2013 Feb;104(3):622-32

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

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http://dx.doi.org/10.1016/j.bpj.2012.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566452PMC
February 2013

A coarse-grained model for synergistic action of multiple enzymes on cellulose.

Biotechnol Biofuels 2012 Aug 1;5(1):55. Epub 2012 Aug 1.

Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.

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http://dx.doi.org/10.1186/1754-6834-5-55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475064PMC
August 2012

Identification of minimally interacting modules in an intrinsically disordered protein.

Biophys J 2012 Aug;103(4):748-57

Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.

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http://dx.doi.org/10.1016/j.bpj.2012.06.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3443776PMC
August 2012

Characterization of a disordered protein during micellation: interactions of α-synuclein with sodium dodecyl sulfate.

J Phys Chem B 2012 Apr 6;116(15):4417-24. Epub 2012 Apr 6.

Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.

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http://dx.doi.org/10.1021/jp210339fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3357070PMC
April 2012

Quantifying intramolecular binding in multivalent interactions: a structure-based synergistic study on Grb2-Sos1 complex.

PLoS Comput Biol 2011 Oct 13;7(10):e1002192. Epub 2011 Oct 13.

Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America.

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http://www.lanl.gov/orgs/adtsc/publications/science_highligh
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http://dx.plos.org/10.1371/journal.pcbi.1002192
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http://dx.doi.org/10.1371/journal.pcbi.1002192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192808PMC
October 2011

Exit strategies for charged tRNA from GluRS.

J Mol Biol 2010 Apr 13;397(5):1350-71. Epub 2010 Feb 13.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1016/j.jmb.2010.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232055PMC
April 2010

Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe.

Biophys J 2009 Sep;97(5):1418-27

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.

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http://dx.doi.org/10.1016/j.bpj.2009.06.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749769PMC
September 2009

Dynamical networks in tRNA:protein complexes.

Proc Natl Acad Sci U S A 2009 Apr 7;106(16):6620-5. Epub 2009 Apr 7.

Department of Chemistry,University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.0810961106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672494PMC
April 2009

Molecular signatures of ribosomal evolution.

Proc Natl Acad Sci U S A 2008 Sep 3;105(37):13953-8. Epub 2008 Sep 3.

Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.0804861105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2528867PMC
September 2008

Dynamics of Recognition between tRNA and elongation factor Tu.

J Mol Biol 2008 Apr 4;377(5):1382-405. Epub 2008 Feb 4.

Center for Biophysics and Computational Biology, Urbana, IL, USA.

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http://dx.doi.org/10.1016/j.jmb.2008.01.073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232051PMC
April 2008

A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase.

Biochemistry 2007 Feb 30;46(8):2156-73. Epub 2007 Jan 30.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.

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http://pubs.acs.org/doi/abs/10.1021/bi061708e
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http://dx.doi.org/10.1021/bi061708eDOI Listing
February 2007

The evolutionary history of Cys-tRNACys formation.

Proc Natl Acad Sci U S A 2005 Dec;102(52):19003-8

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.0509617102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1323144PMC
December 2005

Evolutionary profiles from the QR factorization of multiple sequence alignments.

Proc Natl Acad Sci U S A 2005 Mar 1;102(11):4045-50. Epub 2005 Mar 1.

Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1073/pnas.0409715102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC554820PMC
March 2005

Purification and characterization of a short insect toxin from the venom of the scorpion Buthus tamulus.

FEBS Lett 2002 Sep;528(1-3):261-6

Biomembrane Lab, Department of Chemistry and School of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India.

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http://dx.doi.org/10.1016/s0014-5793(02)03326-4DOI Listing
September 2002