Publications by authors named "Stephen M Mount"

25Publications

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis.

BMC Bioinformatics 2019 Aug 13;20(1):421. Epub 2019 Aug 13.

Department of Computer Science, University of Maryland, College Park, Maryland, USA.

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August 2019

The Splicing Factor Mediates the Cellular Immune Response in .

J Immunol 2018 08 11;201(4):1154-1164. Epub 2018 Jul 11.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742;

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August 2018

Consensus Coexpression Network Analysis Identifies Key Regulators of Flower and Fruit Development in Wild Strawberry.

Plant Physiol 2018 09 10;178(1):202-216. Epub 2018 Jul 10.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742

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September 2018

Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana.

BMC Genomics 2017 Oct 11;18(1):772. Epub 2017 Oct 11.

Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA.

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October 2017

A Genealogical Look at Shared Ancestry on the X Chromosome.

Genetics 2016 09 29;204(1):57-75. Epub 2016 Jun 29.

Center for Population Biology, Department of Evolution and Ecology, University of California, Davis, California 95616.

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September 2016

Recognizing the 35th anniversary of the proposal that snRNPs are involved in splicing.

Mol Biol Cell 2015 Oct;26(20):3557-60

Department of Cell Biology, Yale School of Medicine, New Haven, CT 06536

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October 2015

Erratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm.

BMC Bioinformatics 2015 Aug 28;16:274. Epub 2015 Aug 28.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, 20742, Maryland.

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August 2015

Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm.

BMC Bioinformatics 2015 Jul 10;16:218. Epub 2015 Jul 10.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Baltimore, 20742, Maryland.

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July 2015

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.

Nat Biotechnol 2014 May 20;32(5):462-4. Epub 2014 Apr 20.

Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.

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May 2014

Evolutionary dynamics of U12-type spliceosomal introns.

BMC Evol Biol 2010 Feb 17;10:47. Epub 2010 Feb 17.

Institute of Bioinformatics, University of Muenster, Muenster, Germany.

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February 2010

Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development.

Plant Physiol 2009 Jul 29;150(3):1450-8. Epub 2009 Apr 29.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20740, USA.

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July 2009

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja Annie Lui Pen MacDonald Vasilia Magnisalis Kebede Maru Charles Matthews William McCusker Susan McDonough Teena Mehta James Meldrim Louis Meneus Oana Mihai Atanas Mihalev Tanya Mihova Rachel Mittelman Valentine Mlenga Anna Montmayeur Leonidas Mulrain Adam Navidi Jerome Naylor Tamrat Negash Thu Nguyen Nga Nguyen Robert Nicol Choe Norbu Nyima Norbu Nathaniel Novod Barry O'Neill Sahal Osman Eva Markiewicz Otero L Oyono Christopher Patti Pema Phunkhang Fritz Pierre Margaret Priest Sujaa Raghuraman Filip Rege Rebecca Reyes Cecil Rise Peter Rogov Keenan Ross Elizabeth Ryan Sampath Settipalli Terry Shea Ngawang Sherpa Lu Shi Diana Shih Todd Sparrow Jessica Spaulding John Stalker Nicole Stange-Thomann Sharon Stavropoulos Catherine Stone Christopher Strader Senait Tesfaye Talene Thomson Yama Thoulutsang Dawa Thoulutsang Kerri Topham Ira Topping Tsamla Tsamla Helen Vassiliev Andy Vo Tsering Wangchuk Tsering Wangdi Michael Weiand Jane Wilkinson Adam Wilson Shailendra Yadav Geneva Young Qing Yu Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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November 2007

Features generated for computational splice-site prediction correspond to functional elements.

BMC Bioinformatics 2007 Oct 24;8:410. Epub 2007 Oct 24.

Computer Science Department, University of Maryland, College Park, MD 20742, USA.

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October 2007

SplicePort--an interactive splice-site analysis tool.

Nucleic Acids Res 2007 Jul 18;35(Web Server issue):W285-91. Epub 2007 Jun 18.

Computer Science Department, University of Maryland, College Park, Maryland 20742, USA.

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July 2007

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.

BMC Bioinformatics 2007 May 21;8:159. Epub 2007 May 21.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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May 2007

Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis.

BMC Genomics 2006 Dec 28;7:327. Epub 2006 Dec 28.

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.

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December 2006

Spliceosomal small nuclear RNA genes in 11 insect genomes.

RNA 2007 Jan 9;13(1):5-14. Epub 2006 Nov 9.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815, USA.

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January 2007

The Drosophila U1-70K protein is required for viability, but its arginine-rich domain is dispensable.

Genetics 2004 Dec;168(4):2059-65

Department of Genetics, Case Western Reserve University, Cleveland, Ohio 44106-4955, USA.

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December 2004

Reducing storage requirements for biological sequence comparison.

Bioinformatics 2004 Dec 15;20(18):3363-9. Epub 2004 Jul 15.

Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431, USA.

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December 2004

Evidence for a plastid origin of plant ethylene receptor genes.

Plant Physiol 2002 Sep;130(1):10-4

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742-5815, USA.

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September 2002