Publications by authors named "Sergey Koren"

79Publications

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.

Genome Biol 2020 09 14;21(1):245. Epub 2020 Sep 14.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1186/s13059-020-02134-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488777PMC
September 2020

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.

Genome Res 2020 Sep 14;30(9):1291-1305. Epub 2020 Aug 14.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1101/gr.263566.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7545148PMC
September 2020

Weighted minimizer sampling improves long read mapping.

Bioinformatics 2020 Jul;36(Supplement_1):i111-i118

National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355284PMC
July 2020

New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes.

BMC Genomics 2019 Dec 19;20(1):1000. Epub 2019 Dec 19.

The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia.

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http://dx.doi.org/10.1186/s12864-019-6364-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923926PMC
December 2019

Mash Screen: high-throughput sequence containment estimation for genome discovery.

Genome Biol 2019 11 5;20(1):232. Epub 2019 Nov 5.

Genome Informatics section, National Human Genome Research Institute, Bethesda, MD, USA.

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http://dx.doi.org/10.1186/s13059-019-1841-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6833257PMC
November 2019

Integrating Hi-C links with assembly graphs for chromosome-scale assembly.

PLoS Comput Biol 2019 08 21;15(8):e1007273. Epub 2019 Aug 21.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719893PMC
August 2019

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps.

Nat Commun 2019 07 11;10(1):3066. Epub 2019 Jul 11.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, 20892, USA.

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http://dx.doi.org/10.1038/s41467-019-10934-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624308PMC
July 2019

A chromosome-scale assembly of the major African malaria vector Anopheles funestus.

Gigascience 2019 06;8(6)

Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, 317 Galvin Life Science Center, Notre Dame, IN 46556, USA.

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http://dx.doi.org/10.1093/gigascience/giz063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6545970PMC
June 2019

HLA*LA-HLA typing from linearly projected graph alignments.

Bioinformatics 2019 11;35(21):4394-4396

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821427PMC
November 2019

Reply to 'Errors in long-read assemblies can critically affect protein prediction'.

Nat Biotechnol 2019 02;37(2):127-128

School of Life Sciences, University of Nottingham, Nottingham, UK.

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http://dx.doi.org/10.1038/s41587-018-0005-yDOI Listing
February 2019

Improved reference genome of Aedes aegypti informs arbovirus vector control.

Nature 2018 11 14;563(7732):501-507. Epub 2018 Nov 14.

Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.

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http://www.nature.com/articles/s41586-018-0692-z
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http://dx.doi.org/10.1038/s41586-018-0692-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6421076PMC
November 2018

A fast adaptive algorithm for computing whole-genome homology maps.

Bioinformatics 2018 09;34(17):i748-i756

School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA.

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https://academic.oup.com/bioinformatics/article/34/17/i748/5
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http://dx.doi.org/10.1093/bioinformatics/bty597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129286PMC
September 2018

De novo assembly of haplotype-resolved genomes with trio binning.

Nat Biotechnol 2018 Oct 22. Epub 2018 Oct 22.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.4277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6476705PMC
October 2018

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

J Comput Biol 2018 07 30;25(7):766-779. Epub 2018 Apr 30.

2 National Human Genome Research Institute, National Institutes of Health , Bethesda, Maryland.

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http://dx.doi.org/10.1089/cmb.2018.0036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6067103PMC
July 2018

Scaffolding of long read assemblies using long range contact information.

BMC Genomics 2017 07 12;18(1):527. Epub 2017 Jul 12.

Pacific Biosciences, 94205 Menlo Park, California, USA.

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http://dx.doi.org/10.1186/s12864-017-3879-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5508778PMC
July 2017

Canu: scalable and accurate long-read assembly via adaptive -mer weighting and repeat separation.

Genome Res 2017 05 15;27(5):722-736. Epub 2017 Mar 15.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.215087.116
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http://dx.doi.org/10.1101/gr.215087.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411767PMC
May 2017

Hybrid assembly of the large and highly repetitive genome of , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

Genome Res 2017 05 27;27(5):787-792. Epub 2017 Jan 27.

Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.213405.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411773PMC
May 2017

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

PLoS One 2016 9;11(9):e0160574. Epub 2016 Sep 9.

Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, 94305, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160574PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5017753PMC
August 2017

Mash: fast genome and metagenome distance estimation using MinHash.

Genome Biol 2016 06 20;17(1):132. Epub 2016 Jun 20.

Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1186/s13059-016-0997-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915045PMC
June 2016

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

Authors:
Monika Gulia-Nuss Andrew B Nuss Jason M Meyer Daniel E Sonenshine R Michael Roe Robert M Waterhouse David B Sattelle José de la Fuente Jose M Ribeiro Karine Megy Jyothi Thimmapuram Jason R Miller Brian P Walenz Sergey Koren Jessica B Hostetler Mathangi Thiagarajan Vinita S Joardar Linda I Hannick Shelby Bidwell Martin P Hammond Sarah Young Qiandong Zeng Jenica L Abrudan Francisca C Almeida Nieves Ayllón Ketaki Bhide Brooke W Bissinger Elena Bonzon-Kulichenko Steven D Buckingham Daniel R Caffrey Melissa J Caimano Vincent Croset Timothy Driscoll Don Gilbert Joseph J Gillespie Gloria I Giraldo-Calderón Jeffrey M Grabowski David Jiang Sayed M S Khalil Donghun Kim Katherine M Kocan Juraj Koči Richard J Kuhn Timothy J Kurtti Kristin Lees Emma G Lang Ryan C Kennedy Hyeogsun Kwon Rushika Perera Yumin Qi Justin D Radolf Joyce M Sakamoto Alejandro Sánchez-Gracia Maiara S Severo Neal Silverman Ladislav Šimo Marta Tojo Cristian Tornador Janice P Van Zee Jesús Vázquez Filipe G Vieira Margarita Villar Adam R Wespiser Yunlong Yang Jiwei Zhu Peter Arensburger Patricia V Pietrantonio Stephen C Barker Renfu Shao Evgeny M Zdobnov Frank Hauser Cornelis J P Grimmelikhuijzen Yoonseong Park Julio Rozas Richard Benton Joao H F Pedra David R Nelson Maria F Unger Jose M C Tubio Zhijian Tu Hugh M Robertson Martin Shumway Granger Sutton Jennifer R Wortman Daniel Lawson Stephen K Wikel Vishvanath M Nene Claire M Fraser Frank H Collins Bruce Birren Karen E Nelson Elisabet Caler Catherine A Hill

Nat Commun 2016 Feb 9;7:10507. Epub 2016 Feb 9.

Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA.

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http://dx.doi.org/10.1038/ncomms10507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748124PMC
February 2016

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.

Nat Biotechnol 2015 Jun 25;33(6):623-30. Epub 2015 May 25.

National Biodefense Analysis and Countermeasures Center, Frederick, Maryland, USA.

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http://dx.doi.org/10.1038/nbt.3238DOI Listing
June 2015

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

Curr Opin Microbiol 2015 Feb 1;23:110-20. Epub 2014 Dec 1.

National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, United States. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S13695274140018
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http://dx.doi.org/10.1016/j.mib.2014.11.014DOI Listing
February 2015

Automated ensemble assembly and validation of microbial genomes.

BMC Bioinformatics 2014 May 3;15:126. Epub 2014 May 3.

National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA.

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http://dx.doi.org/10.1186/1471-2105-15-126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030574PMC
May 2014

De novo likelihood-based measures for comparing genome assemblies.

BMC Res Notes 2013 Aug 22;6:334. Epub 2013 Aug 22.

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

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http://dx.doi.org/10.1186/1756-0500-6-334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765854PMC
August 2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

Bambus 2: scaffolding metagenomes.

Bioinformatics 2011 Nov 16;27(21):2964-71. Epub 2011 Sep 16.

Department of Computer Science, University of Maryland, College Park, MD 20742, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198580PMC
November 2011

Next generation sequence assembly with AMOS.

Curr Protoc Bioinformatics 2011 Mar;Chapter 11:Unit 11.8

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

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http://doi.wiley.com/10.1002/0471250953.bi1108s33
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http://dx.doi.org/10.1002/0471250953.bi1108s33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072823PMC
March 2011

An algorithm for automated closure during assembly.

BMC Bioinformatics 2010 Sep 10;11:457. Epub 2010 Sep 10.

The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA.

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http://dx.doi.org/10.1186/1471-2105-11-457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945939PMC
September 2010

Assembly algorithms for next-generation sequencing data.

Genomics 2010 Jun 6;95(6):315-27. Epub 2010 Mar 6.

J. Craig Venter Institute, Rockville, MD 20850-3343, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S088875431000049
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http://dx.doi.org/10.1016/j.ygeno.2010.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646PMC
June 2010

A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Bioinformatics 2009 May 5;25(9):1118-24. Epub 2009 Mar 5.

International Max Planck Research School for Computational Biology and Scientific Computing, Ihnestr. 63-73, Algorithmische Bioinformatik, Institut für Informatik, Takustr. 9, 14195 Berlin, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732307PMC
May 2009

Aggressive assembly of pyrosequencing reads with mates.

Bioinformatics 2008 Dec 24;24(24):2818-24. Epub 2008 Oct 24.

The J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639302PMC
December 2008