Publications with Sergey Koren, PhD
Associate Investigator
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
Genome Research, April 16, 2024
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga JM, Juul S, McKenzie S, Simmonds SE, Park J, Asri M, Koren S, Eichler E, Axel R, Martin B, Carnevali P, Miga K, Paten B
The variation and evolution of complete human centromeres
Nature, April 3, 2024
Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Catacchio CR, Porubsky D, Mao Y, Yoo D, Rautiainen M, Koren S, Nurk S, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Ventura M, Alexandrov IA, Eichler EE
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
bioRxiv, March 17, 2024
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautianinen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AHJ, Phillippy AM
Phasing diploid genome assembly graphs with single-cell strand sequencing
bioRxiv, February 16, 2024
Henglin M, Ghareghani M, Harvey W, Porubsky D, Koren S, Eichler EE, Ebert P, Marschall T
The genome of the yellow mealworm, Tenebrio molitor: it's bigger than you think
Genes, December 14, 2023
Oppert B, Dossey AT, Chu FC, Šatović-Vukšić E, Plohl M, Smith TPL, Koren S, Olmstead ML, Leierer D, Ragan G, Johnston JS
The complete sequence and comparative analysis of ape sex chromosomes
bioRxiv, December 1, 2023
Improved sequence mapping using a complete reference genome and lift-over
Nature Methods, November 30, 2023
Chen N-C, Paulin LF, Sedlazeck FJ, Koren S, Phillippy AM, Langmead B
The complete sequence of a human Y chromosome
The reference genome of the paradise fish (Macropodus opercularis)
bioRxiv, August 10, 2023
Fodor E, Okendo J, Szabó K, Czimer D, Tarján-Rácz A, Szeverényi I, Low BW, Liew JH, Koren S, Rhie A, Orbán L, Miklósi Á, Varga M, Burgess SM
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
ArXiv, June 6, 2023
Cheng H, Asri M, Lucas J, Koren S, Li H
A draft human pangenome reference
Recombination between heterologous human acrocentric chromosomes
Nature, May 10, 2023
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C, Human Pangenome Reference Consortium, Gerton JL, Phillippy AM, Colonna V, Garrison E
Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions
BMC Biology, April 3, 2023
Waldbieser GC, Liu S, Yuan Z, Older CE, Gao D, Shi C, Bosworth BG, Li N, Bao L, Kirby MA, Jin Y, Wood ML, Scheffler B, Simpson S, Youngblood RC, Duke MV, Ballard L, Phillippy A, Koren S, Liu Z
Genome and genetic engineering of the house cricket (Acheta domesticus): a resource for sustainable agriculture
Biomolecules, March 24, 2023
Dossey AT, Oppert B, Chu FC, Lorenzen MD, Scheffler B, Simpson S, Koren S, Johnston JS, Kataoka K, Ide K
Telomere-to-telomere assembly of diploid chromosomes with Verkko
Nature Biotechnology, February 16, 2023
Semi-automated assembly of high-quality diploid human reference genomes
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L)
A family of unusual immunoglobulin superfamily genes in an invertebrate histocompatibility complex
Proceedings of the National Academy of Sciences, October 4, 2022
Huene AL, Sanders SM, Ma Z, Nguyen AD, Koren S, Michaca MH, Mullikin JC, Phillippy AM, Schnitzler CE, Baxevanis AD, Nicotra ML
Segmental duplications and their variation in a complete human genome
Science, April 1, 2022
Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AM, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga KH, Phillippy AM, Timp W, Ventura M, Eichler EE
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies
Nature Methods, April 1, 2022
Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JM, Zook JM, Phillippy AM, Rhie A
Long-read mapping to repetitive reference sequences using Winnowmap2
Nature Methods, April 1, 2022
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Nature Methods, April 1, 2022
Formenti G, Rhie A, Walenz BP, Thibaud-Nissen F, Shafin K, Koren S, Myers EW, Jarvis ED, Phillippy AM
Complete genomic and epigenetic maps of human centromeres
Epigenetic Patterns in a Complete Human Genome
Science, April 1, 2022
Gershman A, Sauria ME, Hook PW, Hoyt SJ, Razaghi R, Koren S, Altemose N, Caldas GV, Vollger MR, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O’Neill RJ, Phillippy AM, Miga KH, Timp W
The complete sequence of a human genome
The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success
Genes, February 28, 2022
Oppert B … Koren S … Campbell JF
The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol
G3, December 13, 2021
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
eLife, August 19, 2021
Tan M, Redmond AK, Dooley H, Nozu R, Sato K, Kuraku S, Koren S, Phillippy AM, Dove ADM, and Read TD
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Towards complete and error-free genome assemblies of all vertebrate species
Extended haplotype phasing of long-read de novo genome assemblies using Hi-C
Nature Communications, April 28, 2021
Kronenberg ZN, Rhie A, Koren S, Concepcion G, Peluso P, Munson K, Porubsky D, Kuhn K, Mueller KA, Low WY, Hiendleder S, Fedrigo O, Liachko I, Hall RJ, Phillippy AM, Eichler EE, Williams JL, Smith TPL, Jarvis ED, Sullivan ST, Kingan SB
Evolutionary and biomedical insights from a marmoset diploid genome assembly
The structure, function and evolution of a complete human chromosome 8
A complete reference genome improves analysis of human genetic variation
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Genome Biology, September 14, 2020
Improved reference genome of the arboviral vector Aedes albopictus
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Genome Research, August 14, 2020
Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S
Telomere-to-telomere assembly of a complete human X chromosome
Weighted minimizer sampling improves long read mapping
Bioinformatics, July 13, 2020
An improved pig reference genome sequence to enable pig genetics and genomics research
A robust benchmark for detection of germline large deletions and insertions
Nature Biotechnology, June 15, 2020
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
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle
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
Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies
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
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
PLoS Computational Biology, August 21, 2019
Accurate Circular Consensus Long-Read Sequencing Improves Variant Detection and Assembly of a Human Genome
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
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
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'
Improved reference genome of Aedes aegypti informs arbovirus vector control
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
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
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
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
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
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
The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
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
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Genome Biol, November 19, 2014
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
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 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
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
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
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
Nature Biotechnology, 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
Structure, function and diversity of the healthy human microbiome
Nature, June 14, 2012
Huttenhower C … Koren S … White O
A framework for human microbiome research
Nature, June 14, 2012
Methé BA … 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
Bioinformatics, November 1, 2011
Koren S, Treangen TJ, Pop M
Assemblathon 1: a competitive assessment of de novo short read assembly methods
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
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
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
Bioinformatics, December 15, 2008
Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G