Publications by authors named "Wilfried Haerty"

54Publications

microRNA profiling in the Weddell seal suggests novel regulatory mechanisms contributing to diving adaptation.

BMC Genomics 2020 Apr 15;21(1):303. Epub 2020 Apr 15.

Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK.

View Article and Find Full Text PDF
April 2020

Identification of functional long non-coding RNAs in C. elegans.

BMC Biol 2019 02 18;17(1):14. Epub 2019 Feb 18.

Earlham Institute, Norwich Research Park, Norwich, UK.

View Article and Find Full Text PDF
February 2019

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status.

Sci Rep 2019 01 24;9(1):485. Epub 2019 Jan 24.

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.

View Article and Find Full Text PDF
January 2019

A quantitative framework for characterizing the evolutionary history of mammalian gene expression.

Genome Res 2019 01 14;29(1):53-63. Epub 2018 Dec 14.

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

View Article and Find Full Text PDF
January 2019

The evolutionary dynamics of microRNAs in domestic mammals.

Sci Rep 2018 11 19;8(1):17050. Epub 2018 Nov 19.

Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, United Kingdom.

View Article and Find Full Text PDF
November 2018

Aequatus: an open-source homology browser.

Gigascience 2018 11 1;7(11). Epub 2018 Nov 1.

Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.

View Article and Find Full Text PDF
November 2018

Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease.

Hum Mol Genet 2017 06;26(11):2164-2176

Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK.

View Article and Find Full Text PDF
June 2017

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq.

Nat Protoc 2016 11 29;11(11):2081-103. Epub 2016 Sep 29.

Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, UK.

View Article and Find Full Text PDF
November 2016

Identification of molecular signatures specific for distinct cranial sensory ganglia in the developing chick.

Neural Dev 2016 Jan 27;11. Epub 2016 Jan 27.

Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.

View Article and Find Full Text PDF
January 2016

Microglia recapitulate a hematopoietic master regulator network in the aging human frontal cortex.

Neurobiol Aging 2015 Aug 25;36(8):2443.e9-2443.e20. Epub 2015 Apr 25.

Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, UK.

View Article and Find Full Text PDF
August 2015

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.

Nat Methods 2015 Jun 27;12(6):519-22. Epub 2015 Apr 27.

1] Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Human Genetics, University of Leuven, Leuven, Belgium.

View Article and Find Full Text PDF
June 2015

Genome-wide discovery of human splicing branchpoints.

Genome Res 2015 Feb 5;25(2):290-303. Epub 2015 Jan 5.

Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia;

View Article and Find Full Text PDF
February 2015

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts.

Genome Res 2015 Jan;25(1):1-13

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom;

View Article and Find Full Text PDF
January 2015

Considerations when investigating lncRNA function in vivo.

Elife 2014 Aug 14;3:e03058. Epub 2014 Aug 14.

Chris P Ponting is in the MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom; Wellcome Trust Sanger Institute, Cambridge, United Kingdom

View Article and Find Full Text PDF
August 2014

No gene in the genome makes sense except in the light of evolution.

Annu Rev Genomics Hum Genet 2014 24;15:71-92. Epub 2014 Apr 24.

MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom; email: ,

View Article and Find Full Text PDF
May 2015

Increased substitution rates surrounding low-complexity regions within primate proteins.

Genome Biol Evol 2014 Mar;6(3):655-65

Department of Biology, McMaster University, Hamilton, Ontario, Canada.

View Article and Find Full Text PDF
March 2014

The African coelacanth genome provides insights into tetrapod evolution.

Nature 2013 Apr;496(7445):311-6

Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA.

View Article and Find Full Text PDF
April 2013

Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles.

Genome Biol Evol 2013 ;5(5):923-33

Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, United Kingdom.

View Article and Find Full Text PDF
December 2013

Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome.

Genome Biol Evol 2012 8;4(4):427-42. Epub 2012 Mar 8.

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom.

View Article and Find Full Text PDF
July 2012

Is speciation accompanied by rapid evolution? Insights from comparing reproductive and nonreproductive transcriptomes in Drosophila.

Int J Evol Biol 2011 22;2011:595121. Epub 2011 Aug 22.

Department of Biology, McMaster University, Hamilton, ON, Canada L8S 4KI.

View Article and Find Full Text PDF
November 2011

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti.

Microbiology (Reading) 2011 Sep 23;157(Pt 9):2522-2533. Epub 2011 Jun 23.

Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton L8S 4K1, Canada.

View Article and Find Full Text PDF
September 2011

Increased polymorphism near low-complexity sequences across the genomes of Plasmodium falciparum isolates.

Genome Biol Evol 2011 21;3:539-50. Epub 2011 May 21.

Department of Biology, McMaster University, Hamilton, Ontario, Canada.

View Article and Find Full Text PDF
October 2011

Low-complexity sequences and single amino acid repeats: not just "junk" peptide sequences.

Genome 2010 Oct;53(10):753-62

Biology Department, McMaster University, Hamilton, ON, Canada.

View Article and Find Full Text PDF
October 2010

Genome-wide evidence for selection acting on single amino acid repeats.

Genome Res 2010 Jun 7;20(6):755-60. Epub 2010 Jan 7.

Biology Department, McMaster University, Hamilton, Ontario L8S4L8, Canada.

View Article and Find Full Text PDF
June 2010

Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila.

BMC Biol 2009 Jul 21;7:42. Epub 2009 Jul 21.

Department of Biology, McMaster University, Hamilton, Ontario, Canada.

View Article and Find Full Text PDF
July 2009

Similar selective factors affect both between-gene and between-exon divergence in Drosophila.

Mol Biol Evol 2009 Apr 15;26(4):859-66. Epub 2009 Jan 15.

Biology Department, McMaster University.

View Article and Find Full Text PDF
April 2009

Association between levels of coding sequence divergence and gene misregulation in Drosophila male hybrids.

J Mol Evol 2007 Dec 20;65(6):697-704. Epub 2007 Nov 20.

Department of Biology, McMaster University, Life Science Building 540, 1280 Main Street West, L8S 4K1 Hamilton, Ontario, Canada.

View Article and Find Full Text PDF
December 2007

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

Gene regulation divergence is a major contributor to the evolution of Dobzhansky-Muller incompatibilities between species of Drosophila.

Mol Biol Evol 2006 Sep 6;23(9):1707-14. Epub 2006 Jun 6.

Department of Biology, McMaster University, Hamilton, Ontario, Canada.

View Article and Find Full Text PDF
September 2006