Publications by authors named "Leopold Parts"

47Publications

Genomic Epidemiology and Evolution of in Wild Animals in Mexico.

mSphere 2021 Jan 6;6(1). Epub 2021 Jan 6.

Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom

View Article and Find Full Text PDF
January 2021

The ribosomal P-stalk couples amino acid starvation to GCN2 activation in mammalian cells.

Elife 2019 11 21;8. Epub 2019 Nov 21.

Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.

View Article and Find Full Text PDF
November 2019

JACKS: joint analysis of CRISPR/Cas9 knockout screens.

Genome Res 2019 03 23;29(3):464-471. Epub 2019 Jan 23.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom.

View Article and Find Full Text PDF
March 2019

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data.

PLoS Comput Biol 2018 12 14;14(12):e1006258. Epub 2018 Dec 14.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

View Article and Find Full Text PDF
December 2018

SLING: a tool to search for linked genes in bacterial datasets.

Nucleic Acids Res 2018 11;46(21):e128

Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

View Article and Find Full Text PDF
November 2018

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.

G3 (Bethesda) 2017 05 5;7(5):1385-1392. Epub 2017 May 5.

Institute of Computer Science, University of Tartu, 50409, Estonia

View Article and Find Full Text PDF
May 2017

The genetic architecture of low-temperature adaptation in the wine yeast Saccharomyces cerevisiae.

BMC Genomics 2017 02 14;18(1):159. Epub 2017 Feb 14.

Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980-Paterna, Valencia, Spain.

View Article and Find Full Text PDF
February 2017

Powerful decomposition of complex traits in a diploid model.

Nat Commun 2016 11 2;7:13311. Epub 2016 Nov 2.

Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France.

View Article and Find Full Text PDF
November 2016

Deep learning for computational biology.

Mol Syst Biol 2016 07 29;12(7):878. Epub 2016 Jul 29.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK

View Article and Find Full Text PDF
July 2016

Predicting quantitative traits from genome and phenome with near perfect accuracy.

Nat Commun 2016 05 10;7:11512. Epub 2016 May 10.

Institute of Computer Science, University of Tartu, Tartu 50409, Estonia.

View Article and Find Full Text PDF
May 2016

Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design.

Genome Biol 2016 Mar 8;17:45. Epub 2016 Mar 8.

Stanford Genome Technology Center, Department of Biochemistry, Stanford University, 3165 Porter Drive, Palo Alto, CA, 94304, USA.

View Article and Find Full Text PDF
March 2016

Genetic Interaction Scoring Procedure for Bacterial Species.

Adv Exp Med Biol 2015 ;883:169-85

EMBL-EBI (South Building), Wellcome Trust Genome Campus, Saffron Walden, CB10 1SD, UK.

View Article and Find Full Text PDF
April 2016

Heritability and genetic basis of protein level variation in an outbred population.

Genome Res 2014 Aug 13;24(8):1363-70. Epub 2014 May 13.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S3E1, Canada;

View Article and Find Full Text PDF
August 2014

Genome-wide mapping of cellular traits using yeast.

Authors:
Leopold Parts

Yeast 2014 Jun 15;31(6):197-205. Epub 2014 May 15.

Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada.

View Article and Find Full Text PDF
June 2014

gitter: a robust and accurate method for quantification of colony sizes from plate images.

G3 (Bethesda) 2014 Mar 20;4(3):547-52. Epub 2014 Mar 20.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

View Article and Find Full Text PDF
March 2014

SGAtools: one-stop analysis and visualization of array-based genetic interaction screens.

Nucleic Acids Res 2013 Jul 15;41(Web Server issue):W591-6. Epub 2013 May 15.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, Canada.

View Article and Find Full Text PDF
July 2013

Climate change at northern latitudes: rising atmospheric humidity decreases transpiration, N-uptake and growth rate of hybrid aspen.

PLoS One 2012 6;7(8):e42648. Epub 2012 Aug 6.

Department of Silviculture, Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia.

View Article and Find Full Text PDF
January 2013

Quantifying selection acting on a complex trait using allele frequency time series data.

Mol Biol Evol 2012 Apr 23;29(4):1187-97. Epub 2011 Nov 23.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.

View Article and Find Full Text PDF
April 2012

Joint genetic analysis of gene expression data with inferred cellular phenotypes.

PLoS Genet 2011 Jan 20;7(1):e1001276. Epub 2011 Jan 20.

Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.

View Article and Find Full Text PDF
January 2011

Assessing the complex architecture of polygenic traits in diverged yeast populations.

Mol Ecol 2011 Apr 25;20(7):1401-13. Epub 2011 Jan 25.

Centre for Genetics and Genomics, Queen's Medical Centre, University of Nottingham, Nottingham, UK.

View Article and Find Full Text PDF
April 2011

Segregating YKU80 and TLC1 alleles underlying natural variation in telomere properties in wild yeast.

PLoS Genet 2009 Sep 18;5(9):e1000659. Epub 2009 Sep 18.

Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom.

View Article and Find Full Text PDF
September 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.

View Article and Find Full Text PDF
November 2007

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.

Genome Res 2007 Dec 7;17(12):1865-79. Epub 2007 Nov 7.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.

View Article and Find Full Text PDF
December 2007