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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...; carefully curated databases compile as many of them as possible, including JASPAR (Rauluseviciute et al. 2024) and ORegAnno (Lesurf et al. 2016), both available via the USCS Genome Browser. MSigDB contains curated gene sets from the literature; the most useful ones for the purpose described here...
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Resource: Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition
- Guillaume Dumas,
- Simon Malesys,
- and Thomas Bourgeron
Genome Res. March 2021 31: 484-496; Published in Advance January 13, 2021, doi:10.1101/gr.262113.120
...GC12 calculationOnce all the alignments had been collected, we extracted the consensus coding sequences (CCDS) of all protein-coding genes referenced in Ensembl BioMart GRCh37, according to the HGNC (date of access May 5, 2015) and NCBI Consensus CDS protein set (date of access August 10, 2015). We...
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Method: Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
- Yi-Fei Huang and
- Adam Siepel
Genome Res. August 2019 29: 1310-1321; Published in Advance June 27, 2019, doi:10.1101/gr.245522.118
...evolving nucleotide sites flanking protein-coding exons. We focused on the 51 high-coverage Yoruba samples from the 1000 Genomes Project, because this population appears to be well described by a pure “expansion” model, without population bottlenecks or introgression events (Williamson et al. 2005; Boyko...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
..., and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape. [Supplemental material is available for this article.] It is often assumed that synonymous sites within protein-coding open reading frames (ORFs) evolve neutrally...
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Resource: GENCODE: The reference human genome annotation for The ENCODE Project
- Jennifer Harrow,
- Adam Frankish,
- Jose M. Gonzalez,
- Electra Tapanari,
- Mark Diekhans,
- Felix Kokocinski,
- Bronwen L. Aken,
- Daniel Barrell,
- Amonida Zadissa,
- Stephen Searle,
- If Barnes,
- Alexandra Bignell,
- Veronika Boychenko,
- Toby Hunt,
- Mike Kay,
- Gaurab Mukherjee,
- Jeena Rajan,
- Gloria Despacio-Reyes,
- Gary Saunders,
- Charles Steward,
- Rachel Harte,
- Michael Lin,
- Cédric Howald,
- Andrea Tanzer,
- Thomas Derrien,
- Jacqueline Chrast,
- Nathalie Walters,
- Suganthi Balasubramanian,
- Baikang Pei,
- Michael Tress,
- Jose Manuel Rodriguez,
- Iakes Ezkurdia,
- Jeltje van Baren,
- Michael Brent,
- David Haussler,
- Manolis Kellis,
- Alfonso Valencia,
- Alexandre Reymond,
- Mark Gerstein,
- Roderic Guigó,
- and Tim J. Hubbard
Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111
...www..org Figure 7. (A) Comparing different publicly available gene sets. The protein-coding content of five major publicly available gene sets— GENCODE, AceView, consensus coding sequence (CCDS), RefSeq, and UCSC—were compared at the level of total gene number, total transcript number, and mean...
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Method: Identification of pathogenic variant enriched regions across genes and gene families
- Eduardo Pérez-Palma,
- Patrick May,
- Sumaiya Iqbal,
- Lisa-Marie Niestroj,
- Juanjiangmeng Du,
- Henrike O. Heyne,
- Jessica A. Castrillon,
- Anne O'Donnell-Luria,
- Peter Nürnberg,
- Aarno Palotie,
- Mark Daly,
- and Dennis Lal
Genome Res. January 2020 30: 62-71; Published in Advance December 23, 2019, doi:10.1101/gr.252601.119
....75 ↵Bodmer W, Bonilla C. 2008. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40: 695–701. doi:10.1038/ng.f.136 ↵Carter H, Douville C, Stenson PD, Cooper DN, Karchin R. 2013. Identifying Mendelian disease genes with the Variant Effect Scoring Tool. BMC Genomics 14: S3...
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Method: Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation
- Joshua Traynelis,
- Michael Silk,
- Quanli Wang,
- Samuel F. Berkovic,
- Liping Liu,
- David B. Ascher,
- David J. Balding,
- and Slavé Petrovski
Genome Res. October 2017 27: 1715-1729; Published in Advance September 1, 2017, doi:10.1101/gr.226589.117
...number of distinct causal variants identified in a growing set of epilepsy-related genes (Epi4K Consortium and Epilepsy Phenome/ Genome Project 2013, 2017; EuroEPINOMICS-RES Consortium et al. 2014). In the current study, we present results of applying a gene-customized framework on 11 genes with epilepsy...
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Resource: The completion of the Mammalian Gene Collection (MGC)
- 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,
- and Stefan Wiemann
Genome Res. December 2009 19: 2324-2333; Published in Advance September 18, 2009, doi:10.1101/gr.095976.109
...the challenge of obtaining a fully comprehensive set of human protein-coding genes, given pervasive genomic transcription, expressed pseudogenes, and true genes that are expressed transiently and at low levels. Although our -wide search for candidate SEGs turned up relatively few instances with, at best...
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Research: A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort
- Danielle M. Greenawalt,
- Radu Dobrin,
- Eugene Chudin,
- Ida J. Hatoum,
- Christine Suver,
- John Beaulaurier,
- Bin Zhang,
- Victor Castro,
- Jun Zhu,
- Solveig K. Sieberts,
- Susanna Wang,
- Cliona Molony,
- Steven B. Heymsfield,
- Daniel M. Kemp,
- Marc L. Reitman,
- Pek Yee Lum,
- Eric E. Schadt,
- and Lee M. Kaplan
Genome Res. July 2011 21: 1008-1016; Published in Advance May 20, 2011, doi:10.1101/gr.112821.110
...distinct genes, were identified, representing >58% of the 17,052 human protein-coding genes (Pruitt et al. 2009). Compared to liver, ;25% more cis and trans eSNPs were identified in the adipose tissues. The increase in eSNPs could be a consequence of greater power in the adipose samples, due to the larger...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...and suggest that similar findings may follow in the future. LOF due to expansions within protein-coding genes: in CCHS, expansions of polyalanine-coding GCN repeats result in impaired function of the protein (Amiel et al. 2003). LOF due to expansions within introns: in Friedreich ataxia (Al-Mahdawi et al...

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