Publications with Sergey Koren, PhD

Staff Scientist

An improved pig reference genome sequence to enable pig genetics and genomics research
Gigascience, June 16, 2020
Warr A … Koren SPhillippy AM … Archibald AL
A robust benchmark for detection of germline large deletions and insertions
Nature Biotechnology, June 15, 2020
Zook JM … Koren S, Phillippy AM … Salit M
Towards complete and error-free genome assemblies of all vertebrate species
bioRxiv, May 23, 2020
Rhie AKoren SGhurye JWalenz BPPhillippy AM, Jarvis ED
Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358
Nature Communications, May 8, 2020
Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam A, Stein J, Llaca V, Manchanda N, Gilbert AM, Wei X, Chin C, Hufnagel DE, Pedersen S, Snodgrass S, Fengler K, Woodhouse M, Walenz BP, Koren S, Phillippy AM, Hannigan B, Kelly DR, Hirsch CN, Hufford MB, Ware D
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Nature Biotechnology, May 4, 2020
Shafin K … Koren SPhillippy AM … Paten B
Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation
Nature Communications, April 29, 2020
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AW, Heaton MP, Phillippy AM, Hiendleder S, Smith TP, Williams JL
Continuous chromosome-scale haplotypes assembled from a single interspecies F1 hybrid of yak and cattle
Gigascience, April 3, 2020
Rice ES, Koren S, Rhie A, Heaton MP, Kalbfleisch TS, Hardy T, Hackett PH, Bickhart DM, Rosen BD, Vander LB, Maurer NW, Green RE, Phillippy AM, Petersen JL, Smith TP
De novo assembly of the cattle reference genome with single-molecule sequencing
Gigascience, March 19, 2020
Rosen BD … Koren SRhie A, Ghurye JPhillippy AM … Medrano JF
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
bioRxiv, March 17, 2020
Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S
Merqury: reference-free quality and phasing assessment for genome assemblies
bioRxiv, March 17, 2020
Rhie A, Walenz BP, Koren S, Phillippy AM
Improved reference genome of the arboviral vector Aedes albopictus
bioRxiv, February 28, 2020
Palatini U … Koren SGhurye J, Rhie APhillippy AM, Bonizzoni M
Weighted minimizer sampling improves long read mapping
bioRxiv, February 11, 2020
Jain C, Rhie A, Zhang H, Chu C, Koren S, Phillippy A
Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Genome medicine, January 8, 2020
Moser KA … Koren S, Phillippy AM … Silva JC
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
BMC biology, January 2, 2020
Waterhouse RM … Koren SPhillippy AM … Sharakhov IV
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
BMC Genomics, December 19, 2019
Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL
Mash Screen: high-throughput sequence containment estimation for genome discovery
Genome biology, November 5, 2019
Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
PLoS Computational Biology, August 21, 2019
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S
Telomere-to-telomere assembly of a complete human X chromosome
bioRxiv, August 16, 2019
Miga KH, Koren S, Rhie AChang AMPhillippy AM
Accurate Circular Consensus Long-Read Sequencing Improves Variant Detection and Assembly of a Human Genome
Nature Biotechnology, August 12, 2019
Wenger AM … Phillippy AMKoren S … Hunkapiller MW
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Genome Biology, August 2, 2019
Bickhart D, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Ghurye J, Pop M, Weimer PJ, Phillippy AM, Smith TPL
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
Nature Communications, July 11, 2019
Dilthey A, Jain C, Koren S, Phillippy AM
The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research
bioRxiv, July 9, 2019
McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan ST, Sone ED, Koren S, Silverstein KAT, Beckman KB, Gohl DM
The whale shark genome reveals patterns of vertebrate gene family evolution
bioRxiv, June 28, 2019
Tan M, Redmond AK, Dooley H, Nozu R, Sato K, Kuraku S, Koren S, Phillippy AM, Dove ADM, and Read TD
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication
Science Advances, June 26, 2019
Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM, NISC, Mullikin JC, Burgess SM
A chromosome-scale assembly of the major African malaria vector Anopheles funestus
Gigascience, June 3, 2019
Ghurye J, Koren S, Small ST, Redmond S, Howell P, Phillippy AM, Besansky NJ
Extended haplotype phasing of de novo genome assemblies with FALCON-Phase
bioRxiv, April 19, 2019
Kronenberg ZN, Rhie A, Koren S, Concepcion G, Peluso P, Munson K, Hiendleder S, Fedrigo O, Jarvis E, Phillippy A, Eichler E, Williams J, Smith TPL, Hall R, Sullivan ST, Kingan SB
HLA*LA - HLA typing from linearly projected graph alignments
Bioinformatics, April 3, 2019
Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM
Reply to 'Errors in long-read assemblies can critically affect protein prediction'
Nature Biotechnology, February 1, 2019
Koren S, Phillippy AM, Simpson JT, Loman NJ, Loose M
Improved reference genome of Aedes aegypti informs arbovirus vector control
Nature, November 14, 2018
Matthews BJ … Koren SPhillippy AM, Vosshall LB
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Genome Biology, October 30, 2018
Nasko DJ, Koren S, Phillippy AM, Treangen TJ
De novo assembly of haplotype-resolved genomes with trio binning
Nature Biotechnology, October 22, 2018
Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM
A fast adaptive algorithm for computing whole-genome homology maps
Bioinformatics, September 1, 2018
Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing
Nucleic Acids Res, July 27, 2018
Kim JH, Dilthey AT, Nagaraja R, Lee HS, Koren S, Dudekula D, Wood III WH, Piao Y, Ogurtsov AY, Utani K, Noskov V, Shabalina SA, Schlessinger D, Phillippy AM, Larionov V
Nanopore sequencing and assembly of a human genome with ultra-long reads
Nature Biotechnology, January 29, 2018
Jain M, Koren SDilthey ATRhie APhillippy AM … & Loose M
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
BMC Biology, January 11, 2018
Eccles D, Chandler J, Camberis M, Henrissat B, Koren S, Gros GL, Ewbank JJ
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation
Gigascience, January 10, 2018
Miller JR, Koren S, Dilley KA, Puri V, Brown DM, Harkins DM, Thibaud-Nissen F, Rosen BD, Chen X, Tu Z, Sharakhov IV, Sharakhova MV, Sebra R, Stockwell TB, Bergman NH, Sutton GG, Phillippy AM, Piermarini PM, Shabman RS
De novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
Plant Cell, October 13, 2017
Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat RT, Maumus F, Aury JM, Koren S, Fernie AR, Zamir D, Bolger A, Usadel B
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Briefings in Bioinformatics, August 7, 2017
Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M
Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station
Genome Announcements, July 12, 2017
Venkateswaran K, Sielaff AC, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy AM, Klubnik J, Treangen TJ, Rosovitz MJ, Bergman NH
Scaffolding of long read assemblies using long range contact information
BMC Genomics, July 12, 2017
Ghurye J, Pop M, Koren S, Bickhart D and Chin CS
Genomic exploration of individual giant ocean viruses
The ISME Journal, May 12, 2017
Wilson WH, Gilg IC, Moniruzzaman M, Field EK, Koren S, LeCleir GR, Martínez JM, Poulton NJ, Swan BK, Stepanauskas R, Wilhelm SW
A fast approximate algorithm for mapping long reads to large reference databases
RECOMB 2017, May 3, 2017
Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Genome Research, May 1, 2017
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
Genome Research, May 1, 2017
Schneider VA … Koren SPhillippy AM … Church DM
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Nature Genetics, March 16, 2017
Bickhart DM … Koren SPhillippy AM … Smith TPL
The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation
Immunogenetics, February 9, 2017
Schwartz JC, Gibson MS, Heimeier D, Koren S, Phillippy AM, Bickhart DM, Smith TPL, Medrano JF, Hammond JA
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
Genome Research, January 27, 2017
Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marcais G, Yorke JA, Dvorak J, Salzberg SL
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers
PLoS one, September 9, 2016
Davison M, Treangen TJ, Koren S, Pop M, Bhaya D
Mash: fast genome and metagenome distance estimation using MinHash
Genome Biol, June 20, 2016
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts
Nat Commun, June 2, 2016
Liu Z … Koren SPhillippy AM … Waldbieser GC
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
Proc Natl Acad Sci U S A, March 29, 2016
Hall AB … Koren SPhillippy AM … Besansky NJ
Genomic insights into the Ixodes scapularis tick vector of Lyme disease
Nature communications, February 9, 2016
Gulia-Nuss M … Walenz BP, Koren S … Hill CA
Single-cell genomics-based analysis of virus–host interactions in marine surface bacterioplankton
ISME, November 1, 2015
Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, Sullivan MB, Woyke T, Wommack KE, Stepanauskas R
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
Nature Biotechnol, May 25, 2015
Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM
Whole-genome sequences of 80 environmental and clinical isolates of Burkholderia pseudomallei
Genome Announcements, January 23, 2015
Johnson SL, Baker AL, Chain PS, Currie BJ, Daligault HE, Davenport KW, Davis CB, Inglis TJJ, Kaestli M, Koren S, Mayo M, Merritt AJ, Price EP, Sarovich DS, Warner J, Rosovitz MJ
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
Curr Opin Microbiol, December 1, 2014
Koren S, Phillippy AM
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Genome Biol, November 19, 2014
Treangen TJ, Ondov BD, Koren S, Phillippy AM
Complete Genome Sequence of the Quality Control Strain Staphylococcus aureus subsp. aureus ATCC 25923
Genome Announc, November 6, 2014
Treangen TJ, Maybank RA, Enke S, Friss MB, Diviak LF, Karaolis DK, Koren S, Ondov B, Phillippy AM, Bergman NH, Rosovitz MJ
High-coverage sequencing and annotated assemblies of the budgerigar genome
Gigascience, July 8, 2014
Ganapathy G, Howard JT, Ward JM, Li J, Li B, Li Y, Xiong Y, Zhang Y, Zhou S, Schwartz DC, Schatz M, Aboukhalil R, Fedrigo O, Bukovnik L, Wang T, Wray G, Rasolonjatovo I, Winer R, Knight JR, Koren S, Warren WC, Zhang G, Phillippy AM, Jarvis ED
Automated ensemble assembly and validation of microbial genomes
BMC Bioinformatics, May 3, 2014
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM
Genomic and metabolic diversity of marine group I thaumarchaeota in the mesopelagic of two subtropical gyres
PLoS one, April 17, 2014
Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland EDP, Harris CC, Sczyrba A, Chain PSG, Koren S, Woyke T, Stepanauskas R
Complete Closed Genome Sequences of Three Bibersteinia trehalosi Nasopharyngeal Isolates from Cattle with Shipping Fever
Genome Announc, February 13, 2014
Harhay GP, McVey DS, Koren S, Phillippy AM, Bono J, Harhay DM, Clawson ML, Heaton MP, Chitko-McKown CG, Korlach J, Smith TP
Complete Closed Genome Sequences of Four Mannheimia varigena Isolates from Cattle with Shipping Fever
Genome Announc, February 13, 2014
Harhay GP, Murray RW, Lubbers B, Griffin D, Koren S, Phillippy AM, Harhay DM, Bono J, Clawson ML, Heaton MP, Chitko-McKown CG, Smith TP
Reducing assembly complexity of microbial genomes with single-molecule sequencing
Genome Biol, September 13, 2013
Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM
De novo likelihood-based measures for comparing genome assemblies
BMC Research Notes, August 22, 2013
Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Gigascience, July 22, 2013
Bradnam KR … Koren SPhillippy AM … Korf IF
Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle
Genome Announc, May 16, 2013
Harhay GP, Koren S, Phillippy AM, McVey DS, Kuszak J, Clawson ML, Harhay DM, Heaton MP, Chitko-McKown CG, Smith TP
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Genome Biol, January 15, 2013
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M
Molecular epidemiologic investigation of an anthrax outbreak among heroin users, Europe
Emerg Infect Dis, August 1, 2012
Price EP, Seymour ML, Sarovich DS, Latham J, Wolken SR, Mason J, Vincent G, Drees KP, Beckstrom-Sternberg SM, Phillippy AM, Koren S, Okinaka RT, Chung WK, Schupp JM, Wagner DM, Vipond R, Foster JT, Bergman NH, Burans J, Pearson T, Brooks T, Keim P
Hybrid error correction and de novo assembly of single-molecule sequencing reads
Nat Biotechnol, July 1, 2012
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM
The bonobo genome compared with the chimpanzee and human genomes
Nature, June 28, 2012
Prüfer K … Walenz BP, Koren S … Pääbo S
A framework for human microbiome research
Nature, June 14, 2012
Methé BA … Koren S … White O
Structure, function and diversity of the healthy human microbiome
Nature, June 14, 2012
Huttenhower C … Koren S … White O
GAGE: A critical evaluation of genome assemblies and assembly algorithms
Genome Res, January 6, 2012
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA
Bambus 2: scaffolding metagenomes
Oxford Bioinformatics, November 1, 2011
Koren S, Treangen TJ, Pop M
Assemblathon 1: a competitive assessment of de novo short read assembly methods
Genome Res, September 16, 2011
Earl D … Phillippy AM, Koren S … Paten B
Next generation sequence assembly with AMOS
Current Protocols in Bioinformatics, March 18, 2011
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M
An algorithm for automated closure during assembly
BMC Bioinformatics, September 10, 2010
Koren S, Miller JR, Walenz BP, Sutton G
Assembly algorithms for next-generation sequencing data
Genomics, June 1, 2010
Miller JR, Koren S, Sutton G
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads
Oxford Bioinformatics, May 1, 2009
Rausch T, Koren S, Denisov G, Weese D, Emde A, Döring A, Reinert K
Aggressive assembly of pyrosequencing reads with mates
Oxford Bioinformatics, December 15, 2008
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G