Publications by authors named "Richa Agarwala"

49Publications

SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees.

Gigascience 2020 04;9(4)

National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/gigascience/giaa023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172022PMC
April 2020

SKESA: strategic k-mer extension for scrupulous assemblies.

Genome Biol 2018 10 4;19(1):153. Epub 2018 Oct 4.

NCBI/NLM/NIH/DHHS, 8600 Rockville Pike, Bethesda, 20894, MD, USA.

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http://dx.doi.org/10.1186/s13059-018-1540-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172800PMC
October 2018

Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Pseudomonas fluorescens PS006.

Genome Announc 2016 May 5;4(3). Epub 2016 May 5.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA

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http://dx.doi.org/10.1128/genomeA.00329-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859179PMC
May 2016

Whole-Genome Sequences of Two Campylobacter coli Isolates from the Antimicrobial Resistance Monitoring Program in Colombia.

Genome Announc 2016 Mar 17;4(2). Epub 2016 Mar 17.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA

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http://dx.doi.org/10.1128/genomeA.00131-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4796127PMC
March 2016

X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species.

BMC Genomics 2016 Jan 7;17:37. Epub 2016 Jan 7.

The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX, 78666, USA.

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http://dx.doi.org/10.1186/s12864-015-2361-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705583PMC
January 2016

Genome Sequence of the Banana Plant Growth-Promoting Rhizobacterium Bacillus amyloliquefaciens BS006.

Genome Announc 2015 Nov 25;3(6). Epub 2015 Nov 25.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia

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http://dx.doi.org/10.1128/genomeA.01391-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661316PMC
November 2015

Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Paratyphi B (dT+) and Heidelberg Strains from the Colombian Poultry Chain.

Genome Announc 2015 Oct 22;3(5). Epub 2015 Oct 22.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA

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http://dx.doi.org/10.1128/genomeA.01265-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616196PMC
October 2015

Domain enhanced lookup time accelerated BLAST.

Biol Direct 2012 Apr 17;7:12. Epub 2012 Apr 17.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://www.biomedcentral.com/content/pdf/1745-6150-7-12.pdf
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http://www.biology-direct.com/content/7/1/12
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http://dx.doi.org/10.1186/1745-6150-7-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438057PMC
April 2012

A novel mitofusin 2 mutation causes canine fetal-onset neuroaxonal dystrophy.

Neurogenetics 2011 Aug 4;12(3):223-32. Epub 2011 Jun 4.

Laboratory of Comparative Medical Genetics, Department of Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA.

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http://link.springer.com/10.1007/s10048-011-0285-6
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http://dx.doi.org/10.1007/s10048-011-0285-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3165057PMC
August 2011

Comparative analysis of genome sequences of the Th2 cytokine region of rabbit (Oryctolagus cuniculus) with those of nine different species.

Immunol Immunogenet Insights 2011 12;3:59-82. Epub 2011 Jun 12.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, DHHS, Bethesda, MD, 20894, USA.

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http://journals.sagepub.com/doi/10.4137/III.S7236
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http://dx.doi.org/10.4137/III.S7236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3519392PMC
June 2011

PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County.

BMC Med Genet 2010 May 2;11:68. Epub 2010 May 2.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://bmcmedgenet.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2350-11-68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880975PMC
May 2010

PSI-BLAST pseudocounts and the minimum description length principle.

Nucleic Acids Res 2009 Feb 16;37(3):815-24. Epub 2008 Dec 16.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/nar/gkn981DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647318PMC
February 2009

A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae.

Genomics 2009 Apr 5;93(4):299-304. Epub 2008 Nov 5.

Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Mail Stop 4458, College Station, TX 77843-4458, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S088875430800230
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http://dx.doi.org/10.1016/j.ygeno.2008.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656592PMC
April 2009

The National Center for Biotechnology Information's Protein Clusters Database.

Nucleic Acids Res 2009 Jan 21;37(Database issue):D216-23. Epub 2008 Oct 21.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/nar/gkn734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686591PMC
January 2009

Database indexing for production MegaBLAST searches.

Bioinformatics 2008 Aug 21;24(16):1757-64. Epub 2008 Jun 21.

Department of Health and Human Services, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn322DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2696921PMC
August 2008

Improved BLAST searches using longer words for protein seeding.

Bioinformatics 2007 Nov 6;23(21):2949-51. Epub 2007 Oct 6.

Department of Health and Human Services, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.

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http://bioinformatics.oxfordjournals.org/content/23/21/2949.
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http://dx.doi.org/10.1093/bioinformatics/btm479DOI Listing
November 2007

COBALT: constraint-based alignment tool for multiple protein sequences.

Bioinformatics 2007 May 1;23(9):1073-9. Epub 2007 Mar 1.

National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm076DOI Listing
May 2007

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control.

Bioinformatics 2007 May 1;23(9):1156-8. Epub 2007 Mar 1.

National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266093PMC
May 2007

Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST.

BMC Biol 2006 Dec 7;4:41. Epub 2006 Dec 7.

National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA.

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http://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-
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http://dx.doi.org/10.1186/1741-7007-4-41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779365PMC
December 2006

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches.

Nucleic Acids Res 2006 26;34(20):5966-73. Epub 2006 Oct 26.

National Center for Biotechnology Information, National Library of Medicine, NIH, DHHS, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/nar/gkl731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635310PMC
December 2006

A 1.5-Mb-resolution radiation hybrid map of the cat genome and comparative analysis with the canine and human genomes.

Genomics 2007 Feb 25;89(2):189-96. Epub 2006 Sep 25.

Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A & M University, Mail Stop 4458, College Station, TX 77843, USA.

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http://dx.doi.org/10.1016/j.ygeno.2006.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760348PMC
February 2007

High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals.

Genomics 2007 Jan 17;89(1):89-112. Epub 2006 Aug 17.

Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.

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http://dx.doi.org/10.1016/j.ygeno.2006.06.012DOI Listing
January 2007

An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival.

Genome Res 2006 Sep 9;16(9):1084-90. Epub 2006 Aug 9.

Laboratory of Comparative Medical Genetics, Department of Microbiology & Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan 48824, USA.

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http://dx.doi.org/10.1101/gr.5268806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557767PMC
September 2006

A fast and symmetric DUST implementation to mask low-complexity DNA sequences.

J Comput Biol 2006 Jun;13(5):1028-40

National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20894 USA.

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http://dx.doi.org/10.1089/cmb.2006.13.1028DOI Listing
June 2006

Novel gene acquisition on carnivore Y chromosomes.

PLoS Genet 2006 Mar 31;2(3):e43. Epub 2006 Mar 31.

Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1420679PMC
March 2006

Does having children extend life span? A genealogical study of parity and longevity in the Amish.

J Gerontol A Biol Sci Med Sci 2006 Feb;61(2):190-5

Department of Epidemiology and Preventive Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1093/gerona/61.2.190DOI Listing
February 2006

WindowMasker: window-based masker for sequenced genomes.

Bioinformatics 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.

National Center for Biotechnology Information, National Institutes of Health, Department of Health and Human Services Building 38A, Room 1003N, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti774DOI Listing
January 2006

Protein database searches using compositionally adjusted substitution matrices.

FEBS J 2005 Oct;272(20):5101-9

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1111/j.1742-4658.2005.04945.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1343503PMC
October 2005

A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals.

Mamm Genome 2005 Aug 14;16(8):631-49. Epub 2005 Sep 14.

Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, USA.

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http://link.springer.com/content/pdf/10.1007%2Fs00335-005-00
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http://link.springer.com/10.1007/s00335-005-0023-1
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http://dx.doi.org/10.1007/s00335-005-0023-1DOI Listing
August 2005

A rhesus macaque radiation hybrid map and comparative analysis with the human genome.

Genomics 2005 Oct;86(4):383-95

Basic Research Laboratory, SAIC-Frederick, Inc., Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702, USA.

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http://dx.doi.org/10.1016/j.ygeno.2005.05.013DOI Listing
October 2005

Reduced incidence of hip fracture in the Old Order Amish.

J Bone Miner Res 2004 Feb 16;19(2):308-13. Epub 2003 Dec 16.

Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.

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http://dx.doi.org/10.1359/JBMR.0301223DOI Listing
February 2004

Anabaptist genealogy database.

Am J Med Genet C Semin Med Genet 2003 Aug;121C(1):32-7

National Center for Biotechnology Information/NIH, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1002/ajmg.c.20004DOI Listing
August 2003

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002

Mutant deoxynucleotide carrier is associated with congenital microcephaly.

Nat Genet 2002 Sep 19;32(1):175-9. Epub 2002 Aug 19.

National Human Genome Research Institute, National Institutes of Health, 49 Convent Drive, Bethesda, Maryland 20892-4472, USA.

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http://dx.doi.org/10.1038/ng948DOI Listing
September 2002