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Gene duplication and genetic innovation in cereal genomes

JOURNAL ARTICLE published February 2019 in Genome Research

Research funded by Office of Science of the U.S. Department of Energy (DE-AC02-05CH11231)

Authors: Hui Guo | Yuannian Jiao | Xu Tan | Xiyin Wang | Xianzhong Huang | Huizhe Jin | Andrew H. Paterson

https://doi.org/10.1101/gr.237511.118 Actions

Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes

JOURNAL ARTICLE published November 2017 in Genome Research

Research funded by National Institutes of Health (DP3DK085678/DK/NIDDK,AI42288,GM102227/NIGMS)

Authors: Jeremy R.B. Newman | Ana Conesa | Matthew Mika | Felicia N. New | Suna Onengut-Gumuscu | Mark A. Atkinson | Stephen S. Rich | Lauren M. McIntyre | Patrick Concannon

https://doi.org/10.1101/gr.217984.116 Actions

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

JOURNAL ARTICLE published January 2021 in Genome Research

Research funded by NIH/NIDCR (F32-DE026947,K99-DE029228,R00-DE024543)

Authors: Jonathon L. Baker | James T. Morton | Márcia Dinis | Ruth Alvarez | Nini C. Tran | Rob Knight | Anna Edlund

https://doi.org/10.1101/gr.265645.120 Actions

On the origin of prokaryotic species

JOURNAL ARTICLE published May 2009 in Genome Research

Authors: W. Ford Doolittle | Olga Zhaxybayeva

https://doi.org/10.1101/gr.086645.108 Actions

The completion of the Mammalian Gene Collection (MGC)

JOURNAL ARTICLE published December 2009 in Genome Research

Authors: The MGC Project Team | Gary Temple | Daniela S. Gerhard | Rebekah Rasooly | Elise A. Feingold | Peter J. Good | Cristen Robinson | Allison Mandich | Jeffrey G. Derge | Jeanne Lewis | Debonny Shoaf | Francis S. Collins | Wonhee Jang | Lukas Wagner | Carolyn M. Shenmen | Leonie Misquitta | Carl F. Schaefer | Kenneth H. Buetow | Tom I. Bonner | Linda Yankie | Ming Ward | Lon Phan | Alex Astashyn | Garth Brown | Catherine Farrell | Jennifer Hart | Melissa Landrum | Bonnie L. Maidak | Michael Murphy | Terence Murphy | Bhanu Rajput | Lillian Riddick | David Webb | Janet Weber | Wendy Wu | Kim D. Pruitt | Donna Maglott | Adam Siepel | Brona Brejova | Mark Diekhans | Rachel Harte | Robert Baertsch | Jim Kent | David Haussler | Michael Brent | Laura Langton | Charles L.G. Comstock | Michael Stevens | Chaochun Wei | Marijke J. van Baren | Kourosh Salehi-Ashtiani | Ryan R. Murray | Lila Ghamsari | Elizabeth Mello | Chenwei Lin | Christa Pennacchio | Kirsten Schreiber | Nicole Shapiro | Amber Marsh | Elizabeth Pardes | Troy Moore | Anita Lebeau | Mike Muratet | Blake Simmons | David Kloske | Stephanie Sieja | James Hudson | Praveen Sethupathy | Michael Brownstein | Narayan Bhat | Joseph Lazar | Howard Jacob | Chris E. Gruber | Mark R. Smith | John McPherson | Angela M. Garcia | Preethi H. Gunaratne | Jiaqian Wu | Donna Muzny | Richard A. Gibbs | Alice C. Young | Gerard G. Bouffard | Robert W. Blakesley | Jim Mullikin | Eric D. Green | Mark C. Dickson | Alex C. Rodriguez | Jane Grimwood | Jeremy Schmutz | Richard M. Myers | Martin Hirst | Thomas Zeng | Kane Tse | Michelle Moksa | Merinda Deng | Kevin Ma | Diana Mah | Johnson Pang | Greg Taylor | Eric Chuah | Athena Deng | Keith Fichter | Anne Go | Stephanie Lee | Jing Wang | Malachi Griffith | Ryan Morin | Richard A. Moore | Michael Mayo | Sarah Munro | Susan Wagner | Steven J.M. Jones | Robert A. Holt | Marco A. Marra | Sun Lu | Shuwei Yang | James Hartigan | Marcus Graf | Ralf Wagner | Stanley Letovksy | Jacqueline C. Pulido | Keith Robison | Dominic Esposito | James Hartley | Vanessa E. Wall | Ralph F. Hopkins | Osamu Ohara | Stefan Wiemann

https://doi.org/10.1101/gr.095976.109 Actions

Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors

JOURNAL ARTICLE published October 2012 in Genome Research

Authors: Wei Jiang | Chris Johnson | Jyothi Jayaraman | Nikol Simecek | Janelle Noble | Miriam F. Moffatt | William O. Cookson | John Trowsdale | James A. Traherne

https://doi.org/10.1101/gr.137976.112 Actions

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

JOURNAL ARTICLE published November 2012 in Genome Research

Authors: Claudia Fritsch | Alexander Herrmann | Michael Nothnagel | Karol Szafranski | Klaus Huse | Frank Schumann | Stefan Schreiber | Matthias Platzer | Michael Krawczak | Jochen Hampe | Mario Brosch

https://doi.org/10.1101/gr.139568.112 Actions

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

JOURNAL ARTICLE published May 2010 in Genome Research

Authors: Valer Gotea | Axel Visel | John M. Westlund | Marcelo A. Nobrega | Len A. Pennacchio | Ivan Ovcharenko

https://doi.org/10.1101/gr.104471.109 Actions

Features of 5′-splice-site efficiency derived from disease-causing mutations and comparative genomics

JOURNAL ARTICLE published January 2008 in Genome Research

Authors: Xavier Roca | Andrew J. Olson | Atmakuri R. Rao | Espen Enerly | Vessela N. Kristensen | Anne-Lise Børresen-Dale | Brage S. Andresen | Adrian R. Krainer | Ravi Sachidanandam

https://doi.org/10.1101/gr.6859308 Actions

Evolution of the mammalian transcription factor binding repertoire via transposable elements

JOURNAL ARTICLE published November 2008 in Genome Research

Authors: Guillaume Bourque | Bernard Leong | Vinsensius B. Vega | Xi Chen | Yen Ling Lee | Kandhadayar G. Srinivasan | Joon-Lin Chew | Yijun Ruan | Chia-Lin Wei | Huck Hui Ng | Edison T. Liu

https://doi.org/10.1101/gr.080663.108 Actions

Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

JOURNAL ARTICLE published September 2015 in Genome Research

Research funded by Wellcome Trust (098051)

Authors: Simon R. Harris | Carl Robinson | Karen F. Steward | Katy S. Webb | Romain Paillot | Julian Parkhill | Matthew T.G. Holden | Andrew S. Waller

https://doi.org/10.1101/gr.189803.115 Actions

Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences

JOURNAL ARTICLE published December 2017 in Genome Research

Research funded by Defense Advanced Research Projects Agency (W911NF-11-2-0068) | National Science Foundation (CCF 1317653) | National Institutes of Health (P41 GM103533)

Authors: Josh T. Cuperus | Benjamin Groves | Anna Kuchina | Alexander B. Rosenberg | Nebojsa Jojic | Stanley Fields | Georg Seelig

https://doi.org/10.1101/gr.224964.117 Actions

Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

JOURNAL ARTICLE published November 2015 in Genome Research

Research funded by Swiss National Science Foundation (31003A_146137) | European Research Council (260372) | Ministerio de Ciencia e Innovación (BFU2014-55090-P) | National Institutes of Health (HG006696,MH097018,DA033660) | March of Dimes Foundation (6-FY13-92)

Authors: Tugce Bilgin Sonay | Tiago Carvalho | Mark D. Robinson | Maja P. Greminger | Michael Krützen | David Comas | Gareth Highnam | David Mittelman | Andrew Sharp | Tomàs Marques-Bonet | Andreas Wagner

https://doi.org/10.1101/gr.190868.115 Actions

MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum

JOURNAL ARTICLE published January 2016 in Genome Research

Research funded by Wellcome Trust (093161/Z/10/Z)

Authors: Maria Ninova | Matthew Ronshaugen | Sam Griffiths-Jones

https://doi.org/10.1101/gr.193367.115 Actions

Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana

JOURNAL ARTICLE published August 2018 in Genome Research

Research funded by National Institutes of Health (DP2OD008371)

Authors: Maximilian O. Press | Rajiv C. McCoy | Ashley N. Hall | Joshua M. Akey | Christine Queitsch

https://doi.org/10.1101/gr.231753.117 Actions

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

JOURNAL ARTICLE published April 2018 in Genome Research

Research funded by Wellcome Trust (206194) | Wellcome Trust (WT099198MA,104792/Z/14/Z)

Authors: Ulrike Böhme | Thomas D. Otto | James A. Cotton | Sascha Steinbiss | Mandy Sanders | Samuel O. Oyola | Antoine Nicot | Sylvain Gandon | Kailash P. Patra | Colin Herd | Ellen Bushell | Katarzyna K. Modrzynska | Oliver Billker | Joseph M. Vinetz | Ana Rivero | Chris I. Newbold | Matthew Berriman

https://doi.org/10.1101/gr.218123.116 Actions

Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations

JOURNAL ARTICLE published April 2017 in Genome Research

Research funded by Cancer Research UK (C13740/A16629)

Authors: Jonathan S. Brammeld | Mia Petljak | Inigo Martincorena | Steven P. Williams | Luz Garcia Alonso | Alba Dalmases | Beatriz Bellosillo | Carla Daniela Robles-Espinoza | Stacey Price | Syd Barthorpe | Patrick Tarpey | Constantine Alifrangis | Graham Bignell | Joana Vidal | Jamie Young | Lucy Stebbings | Kathryn Beal | Michael R. Stratton | Julio Saez-Rodriguez | Mathew Garnett | Clara Montagut | Francesco Iorio | Ultan McDermott

https://doi.org/10.1101/gr.213546.116 Actions

Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy

JOURNAL ARTICLE published 6 May 2024 in Genome Research

Research funded by DAAD (91730547) | Deutsche Forschungsgemeinschaft (SFB/TR-84 TP C01)

Authors: Dhanur P. Iyer | Lambert Moyon | Lars Wittler | Chieh-Yu Cheng | Francisca R. Ringeling | Stefan Canzar | Annalisa Marsico | Aydan Bulut-Karslioğlu

https://doi.org/10.1101/gr.278662.123 Actions

Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions

JOURNAL ARTICLE published 6 May 2024 in Genome Research

Research funded by Alpe d'HuZes/Dutch Cancer Society (NKI-2014-7140) | “Ministère de l’Économie, de la Science et de l'Innovation du Québec” (PSR-SIIRI-701) | National Institutes of Health (U19 CA148065,X01HG007492) | Cancer Research UK (C1287/A10118,C1287/A16563,C1287/A10710) | The European Union (HEALTH-F2-2009-223175,H2020 633784,634935)

Authors: Stacey E.P. Joosten | Sebastian Gregoricchio | Suzan Stelloo | Elif Yapıcı | Chia-Chi Flora Huang | Kerim Yavuz | Maria Donaldson Collier | Tunç Morova | Umut Berkay Altintaş | Yongsoo Kim | Sander Canisius | Cathy B. Moelans | Paul J. van Diest | Gozde Korkmaz | Nathan A. Lack | Michiel Vermeulen | Sabine C. Linn | Wilbert Zwart

https://doi.org/10.1101/gr.278680.123 Actions

Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes

JOURNAL ARTICLE published July 2022 in Genome Research

Authors: Neel Prabh | Christian Rödelsperger

https://doi.org/10.1101/gr.276431.121 Actions
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