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Method: Characterizing polymorphic inversions in human genomes by single-cell sequencing
- Ashley D. Sanders,
- Mark Hills,
- David Porubský,
- Victor Guryev,
- Ester Falconer,
- and Peter M. Lansdorp
Genome Res. November 2016 26: 1575-1587; Published in Advance July 29, 2016, doi:10.1101/gr.201160.115
...October 22, 2015. Accepted June 13, 2016. © 2016 Sanders et al.; Published by Cold Spring Harbor Laboratory Press This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...in the conserved and nonconserved segments. Using the full data set from IRh and CRh animals, 1,075,143 SNVs fall within the 112.1 Mb of conserved sequence regions. This density of 9.6 SNVs/kb contrasts significantly with the density in the remainder of the (17.8 SNVs/kb for combined IRh/CRh data, P < 0.0001).The...
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Research: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome
- Aaron R. Quinlan,
- Royden A. Clark,
- Svetlana Sokolova,
- Mitchell L. Leibowitz,
- Yujun Zhang,
- Matthew E. Hurles,
- Joshua C. Mell,
- and Ira M. Hall
Genome Res. May 2010 20: 623-635; Published in Advance March 22, 2010, doi:10.1101/gr.102970.109
..., and a general approach for the genome-wide assembly and interpretation of breakpoint sequences. We applied these methods to two inbred mouse strains: C57BL/6J and DBA/2J. We demonstrate that HYDRA accurately maps diverse classes of SV, including those involving repetitive elements such as transposons...
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Research: Natural genetic variation caused by small insertions and deletions in the human genome
- Ryan E. Mills,
- W. Stephen Pittard,
- Julienne M. Mullaney,
- Umar Farooq,
- Todd H. Creasy,
- Anup A. Mahurkar,
- David M. Kemeza,
- Daniel S. Strassler,
- Chris P. Ponting,
- Caleb Webber,
- and Scott E. Devine
Genome Res. June 2011 21: 830-839; Published in Advance April 1, 2011, doi:10.1101/gr.115907.110
...in this study have been deposited in the NCBI dbSNP database (http://www.ncbi.nlm.nih.gov/projects/SNP/) (a complete listing of the accession numbers can be found in Supplemental Table 17).] The age of personalized genomics is well under way. Human s are being sequenced at unprecedented rates (Levy et al. 2007...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance Santosh S. Atanur 1 , İnanç Birol 2 , Victor Guryev 3 , Martin Hirst 2 , Oliver Hummel 4 , Catherine Morrissey 1 , Jacques...
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Method: High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
- Adam D. Ewing and
- Haig H. Kazazian, Jr
Genome Res. September 2010 20: 1262-1270; Published in Advance May 20, 2010, doi:10.1101/gr.106419.110
...WY, Kim C. 2009. The first Korean sequence and analysis: Full sequencing for a socio-ethnic group.Genome Res 19: 1622–1629. Badge RM, Alisch RS, Moran JV. 2003. ATLAS: A system to selectively identify human-specific L1 insertions. Am J Hum Genet 72: 823–838. BamshadMJ,Wooding S,WatkinsWS, Ostler CT...
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Resource: Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
- Adam D. Ewing and
- Haig H. Kazazian, Jr.
Genome Res. June 2011 21: 985-990; Published in Advance October 27, 2010, doi:10.1101/gr.114777.110
...population scale sequencing. Nature 467: 1061–1073. Ahn SM, Kim TH, Lee S, KimD, Ghang H, KimDS, Kim BC, Kim SY, KimWY, Kim C. 2009. The first Korean sequence and analysis: full sequencing for a socio-ethnic group. Genome Res 19: 1622– 1629. Akagi K, Li J, Stephens RM, Volfovsky N, Symer DE. 2008. Extensive...
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Method: A reduced representation approach to population genetic analyses and applications to human evolution
- Francesca Luca,
- Richard R. Hudson,
- David B. Witonsky,
- and Anna Di Rienzo
Genome Res. July 2011 21: 1087-1098; Published in Advance May 31, 2011, doi:10.1101/gr.119792.110
.... Accounting for different sources of error in second-generation sequencing data Different sources of errors in second-generation sequencing data have been previously identified (for a review, see Rokas and Abbot 2009; Pool et al. 2010); however, a full understanding of the error structure has not been reached...
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Research: Widespread signatures of recent selection linked to nucleosome positioning in the human lineage
- James G.D. Prendergast and
- Colin A.M. Semple
Genome Res. November 2011 21: 1777-1787; Published in Advance September 8, 2011, doi:10.1101/gr.122275.111
...between genomic sequence composition and nucleosome assembly. By stratifying nucleosomes according to the GC content of their genomic neighborhood, we also show that the strength and direction of selection detected is dictated by local GC content. Intriguingly these signatures of selection...

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