Publications by authors named "Jeffrey M Kidd"

59Publications

Genomic copy number variation study of nine Macaca species provides new insights into their genetic divergence, adaptation and biomedical application.

Genome Biol Evol 2020 Sep 24. Epub 2020 Sep 24.

Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.

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http://dx.doi.org/10.1093/gbe/evaa200DOI Listing
September 2020

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data.

Nucleic Acids Res 2020 04;48(6):e36

Department of Molecular Biology and Genetics, 215 Tower Rd, Cornell University, Ithaca, NY 14853, USA.

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http://dx.doi.org/10.1093/nar/gkaa074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102983PMC
April 2020

Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2.

Genes (Basel) 2020 01 29;11(2). Epub 2020 Jan 29.

Department of Human Genetics and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.3390/genes11020141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073954PMC
January 2020

Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology.

Nucleic Acids Res 2020 02;48(3):1146-1163

Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1093/nar/gkz1173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7026601PMC
February 2020

A Neofunctionalized X-Linked Ampliconic Gene Family Is Essential for Male Fertility and Equal Sex Ratio in Mice.

Curr Biol 2019 11 17;29(21):3699-3706.e5. Epub 2019 Oct 17.

Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2019.08.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7012382PMC
November 2019

Dog10K: the International Consortium of Canine Genome Sequencing.

Natl Sci Rev 2019 Jul 29;6(4):611-613. Epub 2019 May 29.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, China.

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http://dx.doi.org/10.1093/nsr/nwz068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776106PMC
July 2019

Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids.

Retrovirology 2019 03 7;16(1). Epub 2019 Mar 7.

Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.

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http://dx.doi.org/10.1186/s12977-019-0468-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407205PMC
March 2019

Spliced integrated retrotransposed element (SpIRE) formation in the human genome.

PLoS Biol 2018 03 5;16(3):e2003067. Epub 2018 Mar 5.

Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.2003067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860796PMC
March 2018

Modeling Human Population Separation History Using Physically Phased Genomes.

Genetics 2017 01 9;205(1):385-395. Epub 2016 Nov 9.

Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109

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http://dx.doi.org/10.1534/genetics.116.192963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5223516PMC
January 2017

Y-Chromosome Structural Diversity in the Bonobo and Chimpanzee Lineages.

Genome Biol Evol 2016 08 3;8(7):2231-40. Epub 2016 Aug 3.

Department of Human Genetics, University of Michigan Medical School Department of Computational Medicine and Bioinformatics, University of Michigan Medical School

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http://dx.doi.org/10.1093/gbe/evw150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987114PMC
August 2016

Resolving complex structural genomic rearrangements using a randomized approach.

Genome Biol 2016 06 10;17(1):126. Epub 2016 Jun 10.

Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.

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http://dx.doi.org/10.1186/s13059-016-0993-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4901421PMC
June 2016

Discovery of unfixed endogenous retrovirus insertions in diverse human populations.

Proc Natl Acad Sci U S A 2016 Apr 21;113(16):E2326-34. Epub 2016 Mar 21.

Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111;

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http://dx.doi.org/10.1073/pnas.1602336113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843416PMC
April 2016

The Time Scale of Recombination Rate Evolution in Great Apes.

Mol Biol Evol 2016 Apr 15;33(4):928-45. Epub 2015 Dec 15.

Institute for Human Genetics, University of California San Francisco Department of Epidemiology & Biostatistics, University of California San Francisco

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http://dx.doi.org/10.1093/molbev/msv331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870646PMC
April 2016

Discovery and characterization of Alu repeat sequences via precise local read assembly.

Nucleic Acids Res 2015 Dec 25;43(21):10292-307. Epub 2015 Oct 25.

Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA

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http://dx.doi.org/10.1093/nar/gkv1089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666360PMC
December 2015

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

The genomic landscape of polymorphic human nuclear mitochondrial insertions.

Nucleic Acids Res 2014 Nov 27;42(20):12640-9. Epub 2014 Oct 27.

Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA

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http://dx.doi.org/10.1093/nar/gku1038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227756PMC
November 2014

Great ape genetic diversity and population history.

Nature 2013 Jul 3;499(7459):471-5. Epub 2013 Jul 3.

Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.

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http://dx.doi.org/10.1038/nature12228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822165PMC
July 2013

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

LINE-1 retrotransposition activity in human genomes.

Cell 2010 Jun;141(7):1159-70

Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1016/j.cell.2010.05.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013285PMC
June 2010

High-resolution human genome structure by single-molecule analysis.

Proc Natl Acad Sci U S A 2010 Jun 1;107(24):10848-53. Epub 2010 Jun 1.

The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580, USA.

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http://dx.doi.org/10.1073/pnas.0914638107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890719PMC
June 2010

Characterization of six human disease-associated inversion polymorphisms.

Hum Mol Genet 2009 Jul 21;18(14):2555-66. Epub 2009 Apr 21.

Department of Genome Sciences, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/hmg/ddp187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2701327PMC
July 2009

Death and resurrection of the human IRGM gene.

PLoS Genet 2009 Mar 6;5(3):e1000403. Epub 2009 Mar 6.

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644816PMC
March 2009

Haplotype sorting using human fosmid clone end-sequence pairs.

Genome Res 2008 Dec 3;18(12):2016-23. Epub 2008 Oct 3.

Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1101/gr.081786.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593576PMC
December 2008

Systematic assessment of copy number variant detection via genome-wide SNP genotyping.

Nat Genet 2008 Oct 7;40(10):1199-203. Epub 2008 Sep 7.

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.

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http://www.nature.com/articles/ng.236
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http://dx.doi.org/10.1038/ng.236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759751PMC
October 2008

Extensive copy-number variation of the human olfactory receptor gene family.

Am J Hum Genet 2008 Aug;83(2):228-42

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1016/j.ajhg.2008.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2495065PMC
August 2008

Population stratification of a common APOBEC gene deletion polymorphism.

PLoS Genet 2007 Apr;3(4):e63

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

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http://dx.plos.org/10.1371/journal.pgen.0030063
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http://dx.doi.org/10.1371/journal.pgen.0030063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853121PMC
April 2007

A catalog of nonsynonymous polymorphism on mouse chromosome 16.

Mamm Genome 2005 Dec 8;16(12):925-33. Epub 2005 Dec 8.

Department of Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.

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http://dx.doi.org/10.1007/s00335-005-0085-0DOI Listing
December 2005