Publications with Sergey Koren, PhD

Staff Scientist

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
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
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
Nanopore sequencing and assembly of a human genome with ultra-long reads
bioRxiv, April 20, 2017
Jain M, Koren SDilthey ATRhie APhillippy AM … Loose M
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 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
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