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ARTICLE: Distribution and intensity of constraint in mammalian genomic sequence
- Gregory M. Cooper,
- Eric A. Stone,
- George Asimenos,
- Eric D. Green,
- Serafim Batzoglou,
- and Arend Sidow
Genome Res. July 2005 15: 901-913; Published in Advance June 17, 2005, doi:10.1101/gr.3577405
...substitutions reflect the intensity of past purifying selection and are used to rank and characterize constrained elements. We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer...
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ARTICLE: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- Elliott H. Margulies,
- Gregory M. Cooper,
- George Asimenos,
- Daryl J. Thomas,
- Colin N. Dewey,
- Adam Siepel,
- Ewan Birney,
- Damian Keefe,
- Ariel S. Schwartz,
- Minmei Hou,
- James Taylor,
- Sergey Nikolaev,
- Juan I. Montoya-Burgos,
- Ari Löytynoja,
- Simon Whelan,
- Fabio Pardi,
- Tim Massingham,
- James B. Brown,
- Peter Bickel,
- Ian Holmes,
- James C. Mullikin,
- Abel Ureta-Vidal,
- Benedict Paten,
- Eric A. Stone,
- Kate R. Rosenbloom,
- W. James Kent,
- Gerard G. Bouffard,
- Xiaobin Guan,
- Nancy F. Hansen,
- Jacquelyn R. Idol,
- Valerie V.B. Maduro,
- Baishali Maskeri,
- Jennifer C. McDowell,
- Morgan Park,
- Pamela J. Thomas,
- Alice C. Young,
- Robert W. Blakesley,
- Donna M. Muzny,
- Erica Sodergren,
- David A. Wheeler,
- Kim C. Worley,
- Huaiyang Jiang,
- George M. Weinstock,
- Richard A. Gibbs,
- Tina Graves,
- Robert Fulton,
- Elaine R. Mardis,
- Richard K. Wilson,
- Michele Clamp,
- James Cuff,
- Sante Gnerre,
- David B. Jaffe,
- Jean L. Chang,
- Kerstin Lindblad-Toh,
- Eric S. Lander,
- Angie Hinrichs,
- Heather Trumbower,
- Hiram Clawson,
- Ann Zweig,
- Robert M. Kuhn,
- Galt Barber,
- Rachel Harte,
- Donna Karolchik,
- Matthew A. Field,
- Richard A. Moore,
- Carrie A. Matthewson,
- Jacqueline E. Schein,
- Marco A. Marra,
- Stylianos E. Antonarakis,
- Serafim Batzoglou,
- Nick Goldman,
- Ross Hardison,
- David Haussler,
- Webb Miller,
- Lior Pachter,
- Eric D. Green,
- and Arend Sidow
Genome Res. June 2007 17: 760-774; doi:10.1101/gr.6034307
...Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome Elliott H. Margulies 2 , 8 , 21 , 7 , Gregory M. Cooper 2 , 3 , 9 , George Asimenos 2 , 10 , Daryl J. Thomas 2 , 11 , 12 , Colin N...
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LETTER: Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage
- Belen Hurle,
- Willie Swanson,
- NISC Comparative Sequencing Program,
- and Eric D. Green
Genome Res. March 2007 17: 276-286; Published in Advance January 31, 2007, doi:10.1101/gr.6004607
...Eric D. Green, Eric D W Swanson Hurle Green, E.D Green ED Green B Hurle Eric D Green 10.1101/gr.6004607 1088-9051 genome;gr.6004607 Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage Comparative sequence analyses reveal rapid...
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Methods: Mutation scanning by meltMADGE: Validations using BRCA1 and LDLR, and demonstration of the potential to identify severe, moderate, silent, rare, and paucimorphic mutations in the general population
- Khalid K. Alharbi,
- Mohammed A. Aldahmesh,
- Emmanuel Spanakis,
- Lema Haddad,
- Roslyn A. Whittall,
- Xiao-he Chen,
- Hamid Rassoulian,
- Matt J. Smith,
- Julie Sillibourne,
- Nicola J. Ball,
- Nikki J. Graham,
- Patricia J. Briggs,
- Iain A. Simpson,
- David I.W. Phillips,
- Deborah A. Lawlor,
- Shu Ye,
- Stephen E. Humphries,
- Cyrus Cooper,
- George Davey Smith,
- Shah Ebrahim,
- Diana M. Eccles,
- and Ian N.M. Day
Genome Res. July 2005 15: 967-977; doi:10.1101/gr.3313405
...and melting characteristics, and it should be possible to adopt established DGGE primer pairs and clamps, requiring only checks of suitable thermal ramp start and finish temperatures to achieve a validated assay. Track location within gels and gel location amongst the 10 gels in a tank did not affect...
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Research: Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus
- Julie E. Horvath,
- Christina B. Sheedy,
- Stephanie L. Merrett,
- Abdoulaye Banire Diallo,
- David L. Swofford,
- NISC Comparative Sequencing Program,
- Eric D. Green,
- and Huntington F. Willard
Genome Res. June 2011 21: 850-862; Published in Advance April 25, 2011, doi:10.1101/gr.111849.110
...) (Murphy et al. 2007; Horvath et al. 2008; Perelman et al. 2011), allowing for enough sequence divergence to distinguish functionally conserved regions from regions conserved due to short divergence time. Here, we have focused on genomic analyses of the candidate XIC in two lemur species to elucidate both...
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Methods: A new strategy for genome assembly using short sequence reads and reduced representation libraries
- Andrew L. Young,
- Hatice Ozel Abaan,
- Daniel Zerbino,
- James C. Mullikin,
- Ewan Birney,
- and Elliott H. Margulies
Genome Res. February 2010 20: 249-256; doi:10.1101/gr.097956.109
..., Thomas PJ, McDowell JC, Maskeri B, Young AC, Benjamin B, Brooks SY, Coleman BI, et al. 2004. An intermediate grade of finished genomic sequence suitable for comparative analyses. Genome Res 14: 2235–2244. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...organisms. Accumulating evidence suggests that, from bacteria to human, tsRNAs are not merely intermediates of the tRNA maturation process or residues of the tRNA degradation process as their biogenesis can show elaborate spatiotemporal patterns (Kumar et al. 2016; Sharma et al. 2016; Li et al. 2018; Dou et...
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Method: Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
- Lin Lyu,
- Xue Li,
- Ru Feng,
- Xin Zhou,
- Tuhin K. Guha,
- Xiaofei Yu,
- Guo Qiang Chen,
- Yufeng Yao,
- Bing Su,
- Duowu Zou,
- Michael P. Snyder,
- and Lei Chen
Genome Res. March 2023 33: 401-411; Published in Advance March 27, 2023, doi:10.1101/gr.277178.122
...the Visium kit from 10x Genomics, on both human and murine intestinal samples, in which the presence of microbes is well-known. The human samples included dissected colon samples from two colorectal cancer patients. For each patient, samples from the tumor site and histologically normal site distant from...
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Review: Genome graphs and the evolution of genome inference
- Benedict Paten,
- Adam M. Novak,
- Jordan M. Eizenga,
- and Erik Garrison
Genome Res. May 2017 27: 665-676; Published in Advance March 30, 2017, doi:10.1101/gr.214155.116
...by each tool. Tools are also graded on the presence or absence of several traits. “Genome-scale” tools have been demonstrated on or are marketed as suitable for the analysis of entire human s. “Graph-based” tools make use of an internal graph representation of variation or support adjacency information...
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