Publications by authors named "Lucas Lochovsky"

11Publications

NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis.

BMC Bioinformatics 2020 Oct 22;21(1):474. Epub 2020 Oct 22.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CA, 06520, USA.

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http://dx.doi.org/10.1186/s12859-020-03758-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7580035PMC
October 2020

RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.

Genome Biol 2020 07 30;21(1):151. Epub 2020 Jul 30.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

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http://dx.doi.org/10.1186/s13059-020-01979-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391703PMC
July 2020

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

Cell 2020 03 20;180(5):915-927.e16. Epub 2020 Feb 20.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06511, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.01.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210002PMC
March 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054214PMC
February 2020

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.

Nucleic Acids Res 2015 Sep 24;43(17):8123-34. Epub 2015 Aug 24.

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

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787796PMC
September 2015

ACT: aggregation and correlation toolbox for analyses of genome tracks.

Bioinformatics 2011 Apr 23;27(8):1152-4. Epub 2011 Feb 23.

Program in Computational Biology and Bioinformatics, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072554PMC
April 2011

PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya.

Bioinformatics 2011 Mar 19;27(6):877-8. Epub 2011 Jan 19.

Program in Molecular Structure and Function, Hospital for Sick Children, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btr023DOI Listing
March 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.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010