Publications by authors named "Peter Ruzanov"

11Publications

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE.

Authors:
Quang M Trinh Fei-Yang Arthur Jen Ziru Zhou Kar Ming Chu Marc D Perry Ellen T Kephart Sergio Contrino Peter Ruzanov Lincoln D Stein

BMC Genomics 2013 Jul 22;14:494. Epub 2013 Jul 22.

Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College Street, Suite 800, Toronto, ON, M5G 0A3, Canada.

View Article and Find Full Text PDF
July 2013

modMine: flexible access to modENCODE data.

Authors:
Sergio Contrino Richard N Smith Daniela Butano Adrian Carr Fengyuan Hu Rachel Lyne Kim Rutherford Alex Kalderimis Julie Sullivan Seth Carbon Ellen T Kephart Paul Lloyd E O Stinson Nicole L Washington Marc D Perry Peter Ruzanov Zheng Zha Suzanna E Lewis Lincoln D Stein Gos Micklem

Nucleic Acids Res 2012 Jan 12;40(Database issue):D1082-8. Epub 2011 Nov 12.

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.

View Article and Find Full Text PDF
January 2012

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.

Authors:
Nicole L Washington E O Stinson Marc D Perry Peter Ruzanov Sergio Contrino Richard Smith Zheng Zha Rachel Lyne Adrian Carr Paul Lloyd Ellen Kephart Sheldon J McKay Gos Micklem Lincoln D Stein Suzanna E Lewis

Database (Oxford) 2011 19;2011:bar023. Epub 2011 Aug 19.

Lawrence Berkeley National Laboratory, Genomics Division, 1 Cyclotron Road MS64-121, Berkeley, CA 94720, USA.

View Article and Find Full Text PDF
November 2011

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.

View Article and Find Full Text PDF
December 2010

Deep SAGE analysis of the Caenorhabditis elegans transcriptome.

Authors:
Peter Ruzanov Donald L Riddle

Nucleic Acids Res 2010 Jun 3;38(10):3252-62. Epub 2010 Feb 3.

Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.

View Article and Find Full Text PDF
June 2010

Translational activation of snail1 and other developmentally regulated transcription factors by YB-1 promotes an epithelial-mesenchymal transition.

Authors:
Valentina Evdokimova Cristina Tognon Tony Ng Peter Ruzanov Natalya Melnyk Dieter Fink Alexey Sorokin Lev P Ovchinnikov Elai Davicioni Timothy J Triche Poul H B Sorensen

Cancer Cell 2009 May;15(5):402-15

Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada.

View Article and Find Full Text PDF
May 2009

ELT-2 is the predominant transcription factor controlling differentiation and function of the C. elegans intestine, from embryo to adult.

Authors:
James D McGhee Tetsunari Fukushige Michael W Krause Stephanie E Minnema Barbara Goszczynski Jeb Gaudet Yuji Kohara Olaf Bossinger Yongjun Zhao Jaswinder Khattra Martin Hirst Steven J M Jones Marco A Marra Peter Ruzanov Adam Warner Richard Zapf Donald G Moerman John M Kalb

Dev Biol 2009 Mar 9;327(2):551-65. Epub 2008 Dec 9.

Department of Biochemistry and Molecular Biology, Department of Medical Genetics, Genes and Development Research Group, University of Calgary, Calgary, Alberta, Canada T2N 4N1.

View Article and Find Full Text PDF
March 2009

Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.

Authors:
Peter Ruzanov Steven J Jones Donald L Riddle

BMC Genomics 2007 Nov 30;8:447. Epub 2007 Nov 30.

Michael Smith Laboratories University of British Columbia, Vancouver BC V6T 1Z4, Canada.

View Article and Find Full Text PDF
November 2007

Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults.

Authors:
Peter Ruzanov Donald L Riddle Marco A Marra Sheldon J McKay Steven M Jones

Exp Gerontol 2007 Aug 21;42(8):825-39. Epub 2007 Apr 21.

Genome Sciences Centre, BC Cancer Research Centre, 570 West 7th Avenue, Vancouver, BC, Canada.

View Article and Find Full Text PDF
August 2007

An interactive tool for visualization of relationships between gene expression profiles.

Authors:
Peter Ruzanov Steven J M Jones

BMC Bioinformatics 2006 Apr 6;7:193. Epub 2006 Apr 6.

Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC V5Z 4S6, Canada.

View Article and Find Full Text PDF
April 2006

Akt-mediated YB-1 phosphorylation activates translation of silent mRNA species.

Authors:
Valentina Evdokimova Peter Ruzanov Michael S Anglesio Alexey V Sorokin Lev P Ovchinnikov Jonathan Buckley Timothy J Triche Nahum Sonenberg Poul H B Sorensen

Mol Cell Biol 2006 Jan;26(1):277-92

Department of Pathology, British Columbia Research Institute for Children's and Women's Health, Vancouver, BC, Canada V5Z 163.

View Article and Find Full Text PDF
January 2006