Todd Richmond

Todd Richmond

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Todd Richmond

Todd Richmond

Publications by authors named "Todd Richmond"

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Long-read sequence capture of the haemoglobin gene clusters across codfish species.

Mol Ecol Resour 2019 Jan 4;19(1):245-259. Epub 2018 Dec 4.

Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.

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http://dx.doi.org/10.1111/1755-0998.12955DOI Listing
January 2019

Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System.

Methods Mol Biol 2018 ;1708:383-405

Roche Sequencing Solutions, 500 S. Rosa Road, Madison, WI, 53719, USA.

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http://dx.doi.org/10.1007/978-1-4939-7481-8_20DOI Listing
July 2018

Targeted LncRNA Sequencing with the SeqCap RNA Enrichment System.

Methods Mol Biol 2016 ;1402:73-100

Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA.

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http://dx.doi.org/10.1007/978-1-4939-3378-5_8DOI Listing
October 2016

Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency.

Cell Stem Cell 2015 Dec;17(6):748-757

Radboud University, Faculty of Science, Department of Molecular Biology, 6525GA Nijmegen, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.11.010DOI Listing
December 2015

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.

Nucleic Acids Res 2015 Jul 26;43(12):e81. Epub 2015 Mar 26.

Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA

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http://dx.doi.org/10.1093/nar/gkv244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499119PMC
July 2015

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants.

Nat Commun 2015 May 29;6:7211. Epub 2015 May 29.

1] Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1 [2] McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1.

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http://dx.doi.org/10.1038/ncomms8211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544751PMC
May 2015

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

Plant J 2014 Sep 11;79(6):993-1008. Epub 2014 Aug 11.

Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.

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http://dx.doi.org/10.1111/tpj.12601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309430PMC
September 2014

Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays.

Mol Cell Proteomics 2014 Jun 4;13(6):1585-97. Epub 2014 Apr 4.

From the ‡Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden; §Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91 Stockholm, Sweden;

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http://dx.doi.org/10.1074/mcp.M113.033308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4047477PMC
June 2014

Detection of clinically relevant copy number variants with whole-exome sequencing.

Hum Mutat 2013 Oct 30;34(10):1439-48. Epub 2013 Aug 30.

Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, 6500 HB, The Netherlands.

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http://dx.doi.org/10.1002/humu.22387DOI Listing
October 2013

Changes in genome content generated via segregation of non-allelic homologs.

Plant J 2012 Nov 30;72(3):390-9. Epub 2012 Aug 30.

Department of Agronomy, 2035 Roy J. Carver Co-Lab, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2012.05087.xDOI Listing
November 2012

Somatic retrotransposition alters the genetic landscape of the human brain.

Nature 2011 Oct 30;479(7374):534-7. Epub 2011 Oct 30.

Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK.

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http://dx.doi.org/10.1038/nature10531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224101PMC
October 2011

An analytical pipeline for genomic representations used for cytosine methylation studies.

Bioinformatics 2008 May 18;24(9):1161-7. Epub 2008 Mar 18.

Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5061929PMC
http://dx.doi.org/10.1093/bioinformatics/btn096DOI Listing
May 2008

wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data.

Nucleic Acids Res 2008 Apr 11;36(7):e41. Epub 2008 Mar 11.

Department of Internal Medicine and Department of Genetics, Division of Oncology, Stem Cell Biology Section, Washington University, St Louis, MO, USA.

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http://dx.doi.org/10.1093/nar/gkn110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367727PMC
April 2008

Methods in high-resolution, array-based comparative genomic hybridization.

Methods Mol Biol 2007 ;381:189-211

NimbleGen Systems Inc., Madison, WI, USA.

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http://link.springer.com/10.1007/978-1-59745-303-5_9
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http://dx.doi.org/10.1007/978-1-59745-303-5_9DOI Listing
December 2007

Direct selection of human genomic loci by microarray hybridization.

Nat Methods 2007 Nov 14;4(11):903-5. Epub 2007 Oct 14.

NimbleGen Systems Inc., 1 Science Court, Madison, Wisconsin 53711, USA.

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http://dx.doi.org/10.1038/nmeth1111DOI Listing
November 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill 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 Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization.

Genome Res 2007 Mar 31;17(3):337-47. Epub 2007 Jan 31.

Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.

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http://dx.doi.org/10.1101/gr.5690307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1800925PMC
March 2007

A high-resolution map of segmental DNA copy number variation in the mouse genome.

PLoS Genet 2007 Jan 22;3(1):e3. Epub 2006 Nov 22.

Department of Medicine, Division of Oncology, Stem Cell Biology Section, Washington University, St. Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0030003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1761046PMC
January 2007

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

Genome Res 2006 Oct 5;16(10):1299-309. Epub 2006 Sep 5.

Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605-0103, USA.

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http://dx.doi.org/10.1101/gr.5571506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581439PMC
October 2006

A self-tuning method for one-chip SNP identification.

Proc IEEE Comput Syst Bioinform Conf 2004 :69-79

University of Wisconsin-Madison, USA.

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July 2006

Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori.

Nat Methods 2005 Dec 18;2(12):951-3. Epub 2005 Nov 18.

NimbleGen Systems Inc., One Science Court, Madison, Wisconsin 53711, USA.

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http://www.nature.com/doifinder/10.1038/nmeth805
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http://dx.doi.org/10.1038/nmeth805DOI Listing
December 2005

Limb chondrogenesis is compromised in the versican deficient hdf mouse.

Biochem Biophys Res Commun 2005 Sep;334(3):960-6

Department of Biology, East Carolina University, Greenville, NC, USA.

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http://dx.doi.org/10.1016/j.bbrc.2005.06.189DOI Listing
September 2005

A high-resolution map of active promoters in the human genome.

Nature 2005 Aug 29;436(7052):876-80. Epub 2005 Jun 29.

Ludwig Institute for Cancer Research, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA.

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http://dx.doi.org/10.1038/nature03877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1895599PMC
August 2005