Publications by authors named "Rajkumar Sasidharan"

26Publications

Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox.

Planta 2018 Feb 11;247(2):369-379. Epub 2017 Oct 11.

Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA.

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February 2018

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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September 2016

Medial HOXA genes demarcate haematopoietic stem cell fate during human development.

Nat Cell Biol 2016 06 16;18(6):595-606. Epub 2016 May 16.

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, California 90095, USA.

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June 2016

Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence.

EMBO J 2015 Mar 6;34(6):759-77. Epub 2015 Jan 6.

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA Eli and Edythe Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA

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March 2015

GPI-80 defines self-renewal ability in hematopoietic stem cells during human development.

Cell Stem Cell 2015 Jan 13;16(1):80-7. Epub 2014 Nov 13.

Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address:

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January 2015

Expansion on stromal cells preserves the undifferentiated state of human hematopoietic stem cells despite compromised reconstitution ability.

PLoS One 2013 16;8(1):e53912. Epub 2013 Jan 16.

Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America.

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July 2013

Lymphoid priming in human bone marrow begins before expression of CD10 with upregulation of L-selectin.

Nat Immunol 2012 Oct 2;13(10):963-71. Epub 2012 Sep 2.

Department of Pathology & Laboratory Medicine, University of California, Los Angeles, California, USA.

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October 2012

GFam: a platform for automatic annotation of gene families.

Nucleic Acids Res 2012 Oct 11;40(19):e152. Epub 2012 Jul 11.

Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.

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October 2012

Reorganization of the host epigenome by a viral oncogene.

Genome Res 2012 Jul 12;22(7):1212-21. Epub 2012 Apr 12.

Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.

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July 2012

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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December 2010

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.

BMC Genomics 2010 Jun 17;11:383. Epub 2010 Jun 17.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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June 2010

SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale.

BMC Bioinformatics 2010 Mar 9;11:120. Epub 2010 Mar 9.

Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, TW20 0EX, Egham, UK.

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March 2010

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping.

BMC Res Notes 2009 Jul 24;2:150. Epub 2009 Jul 24.

Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.

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July 2009

Transmembrane protein oxygen content and compartmentalization of cells.

PLoS One 2008 Jul 16;3(7):e2726. Epub 2008 Jul 16.

Molecular Biophysics and Biochemistry Department, Yale University, New Haven, Connecticut, United States of America.

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July 2008

The selection of acceptable protein mutations.

Proc Natl Acad Sci U S A 2007 Jun 31;104(24):10080-5. Epub 2007 May 31.

Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom.

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June 2007

Global identification and characterization of transcriptionally active regions in the rice genome.

PLoS One 2007 Mar 14;2(3):e294. Epub 2007 Mar 14.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America.

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March 2007

Domain insertions in protein structures.

J Mol Biol 2004 May;338(4):633-41

The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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May 2004

DomIns: a web resource for domain insertions in known protein structures.

Nucleic Acids Res 2004 Jan;32(Database issue):D193-5

The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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January 2004