A high-quality blue whale genome, segmental duplications, and historical demography
Molecular Biology and Evolution, February 20, 2024
Bukhman YV … Rhie APhillippy AM … Stewart R
Parsnp 2.0: Scalable core-genome alignment for massive microbial datasets
bioRxiv, January 31, 2024
Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
Nature Biotechnology, January 26, 2024
Larivière D … Pickett BDRhie APhillippy AM … Formenti G
High-quality metagenome assembly from long accurate reads with metaMDBG
Nature Biotechnology, January 2, 2024
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C
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
Makova KD, Pickett BDNurk SRhie ASolar SJSweeten AKoren SPhillippy AM
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
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Nature Communications, October 19, 2023
Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation
Nature Methods, September 14, 2023
Kolmogorov M … Rhie APhillippy AM … Paten B
The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals
bioRxiv, August 27, 2023
Schnitzler CE … Koren SPhillippy AM … Baxevanis AD
The complete sequence of a human Y chromosome
Nature, August 23, 2023
Rhie A, Nurk SKoren S, Rautiainen MHansen NFMc Cartney AMWalenz BPPhillippy AM
Minmers are a generalization of minimizers that enable unbiased local jaccard estimation
Bioinformatics, August 21, 2023
Kille B, Garrison E, Treangen TJ, Phillippy AM
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
The variation and evolution of complete human centromeres
bioRxiv, May 30, 2023
Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Mao Y, Rautiainen M, Koren S, Nurk S, Porubsky D, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Alexandrov IA, Eichler EE
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
A draft human pangenome reference
Nature, May 10, 2023
Liao W-W … Koren SNurk SRautiainen MRhie AWalenz BPhillippy AM … Paten B
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
Phased nanopore assembly with Shasta and modular graph phasing with GFAse
bioRxiv, February 22, 2023
Lorig-Roach R, Meredith M, Monlong J, Jain M, Olsen H, McNulty B, Porubsky D, Montague T, Lucas J, Condon C, Eizenga J, Juul S, McKenzie S, Simmonds SE, Park J, Asri M, Koren S, Eichler E, Axel R, Martin B, Carnevali P, Miga K, Paten B
Telomere-to-telomere assembly of diploid chromosomes with Verkko
Nature Biotechnology, February 16, 2023
Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S
A chromosome-level reference genome and pangenome for barn swallow population genomics
Cell Reports, January 31, 2023
Secomandi S … Rhie A … Formenti G
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes
BMC Biology, November 8, 2022
Toh H … Rhie A, Phillippy AM … Bukhman YV
Semi-automated assembly of high-quality diploid human reference genomes
Nature, October 19, 2022
Jarvis ED … Rhie AGhurye JKoren SPhillippy AM … Human Pangenome Reference Consortium
A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L)
DNA Research, October 8, 2022
McGrath JM … Koren S, Phillippy A … Dorn K
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
False gene and chromosome losses in genome assemblies caused by GC content variation and repeats
Genome Biology, September 27, 2022
Kim J, Lee C, Ko BJ, Yoo DA, Won S, Phillippy AM, Fedrigo O, Zhang G, Howe K, Wood J, Durbin R, Formenti G, Brown S, Cantin L, Mello CV, Cho S, Rhie A, Kim H, Jarvis ED
The Human Pangenome Project: a global resource to map genomic diversity
Nature, April 20, 2022
Wang T … Phillippy AM … Haussler D; Human Pangenome Reference Consortium
The complete sequence of a human genome
Science, April 1, 2022
Nurk S, Koren S, Rhie A, Rautiainen MHansen NFJain CMc Cartney AMWalenz BPPhillippy AM
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
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
Long-read mapping to repetitive reference sequences using Winnowmap2
Nature Methods, April 1, 2022
Jain C, Rhie A, Hansen N, Koren S, Phillippy AM
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
From telomere to telomere: the transcriptional and epigenetic state of human repeat elements
Science, April 1, 2022
Hoyt SJ … Phillippy AM … O’Neill RJ
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
Science, April 1, 2022
Altemose N … Rhie A, McCartney AMNurk S, Koren SPhillippy AM … Miga KH
The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success
Genes, February 28, 2022
Oppert B … Koren S … Campbell JF
Standards recommendations for the Earth BioGenome Project
Proc Natl Acad Sci USA, January 25, 2022
Lawniczak MKN … Phillippy AMRhie A … Richards S
Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life
Proc Natl Acad Sci USA, January 25, 2022
Mc Cartney AM, Anderson J, Liggins L, Hudson ML, Anderson MZ, TeAika B, Geary J, Cook-Deegan R, Patel HR, Phillippy AM
Ethical, legal, and social issues in the Earth BioGenome Project
Proc Natl Acad Sci USA, January 25, 2022
Sherkow JS, Barker KB, Braverman I, Cook-Deegan R, Durbin R, Easter CL, Goldstein MM, Hudson M, Kress WJ, Lewin HA, Mathews DJH, McCarthy C, McCartney AM, da Silva M, Torrance AW, Greely HT
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps
Bioinformatics, January 10, 2022
Vollger MR, Kerpedjiev P, Phillippy AM, Eichler EE
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
Population genomics of the critically endangered kākāpō
Cell Genomics, October 13, 2021
Dussex N … Rhie A, Phillippy AM … Dalén L
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
STRONG: metagenomics strain resolution on assembly graphs
Genome biology, July 26, 2021
Quince C, Nurk S, Raguideau S, James R, Soyer OS, Summers JK, Limasset A, Eren AM, Chikhi R, Darling AE
Critical Assessment of Metagenome Interpretation - the second round of challenges
bioRxiv, July 12, 2021
Meyer F … Antipov DNurk S … McHardy AC
Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution
Molecular ecology resources, June 27, 2021
Peart CR … Rhie A … Wolf JBW
Reference genome and demographic history of the most endangered marine mammal, the vaquita
Molecular Ecology Resources, May 21, 2021
Morin PA … Phillippy A, Rhie A … Jarvis ED
Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Genome Biology, April 29, 2021
Formenti G, Rhie AKoren SPhillippy AM … The Vertebrate Genomes Project Consortium
Towards complete and error-free genome assemblies of all vertebrate species
Nature, April 28, 2021
Rhie AKoren SGhurye JWalenz BPPhillippy AM, Jarvis ED
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
Nature, April 12, 2021
Yang C … Rhie AKoren SPhillippy AM … Zhang G
The structure, function and evolution of a complete human chromosome 8
Nature, April 7, 2021
Logsdon GA … Koren S, Nurk SRhie AJain CPhillippy AM, Eichler EE
A complete reference genome improves analysis of human genetic variation
Science, April 1, 2021
Aganezov S … Avdeyev PRhie AKoren SHansen NFPhillippy AM … Schatz MC
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
F1000Research, March 26, 2021
Mc Cartney AM … J Sedlazeck F
The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
Scientific reports, February 4, 2021
Kim JH, Noskov VN, Ogurtsov AY, Nagaraja R, Petrov N, Liskovykh M, Walenz BP, Lee HS, Kouprina N, Phillippy AM, Shabalina SA, Schlessinger D, Larionov V
Platypus and echidna genomes reveal mammalian biology and evolution
Nature, January 6, 2021
Zhou Y … Rhie APhillippy AM … Zhang G
Strategic vision for improving human health at The Forefront of Genomics
Nature, October 28, 2020
Green ED … Phillippy AM … Manolio TA
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Genome Biology, September 14, 2020
Rhie A, Walenz BP, Koren S, Phillippy AM
Improved reference genome of the arboviral vector Aedes albopictus
Genome Biology, August 26, 2020
Palatini U … Koren SGhurye J, Rhie APhillippy AM, Bonizzoni M
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
Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs
Communications biology, August 4, 2020
Scott MJ, Benoit JB, Davis RJ, Bailey ST, Varga V, Martinson EO, Hickner PV, Syed Z, Cardoso GA, Torres TT, Weirauch MT, Scholl EH, Phillippy AM, Sagel A, Vasquez M, Quintero G, Skoda SR
Telomere-to-telomere assembly of a complete human X chromosome
Nature, July 14, 2020
Miga KH, Koren S, Rhie AChang AM, Hansen NFPhillippy AM
Weighted minimizer sampling improves long read mapping
Bioinformatics, July 13, 2020
Jain C, Rhie A, Zhang H, Chu C, Koren S, Phillippy A
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, Hansen NFKoren S, Phillippy AM … Salit M
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 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
Rosen BD … Koren SRhie A, Ghurye JPhillippy AM … Medrano JF
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
The Perceptual Proxies of Visual Comparison
IEEE transactions on visualization and computer graphics, August 20, 2019
Jardine N, Ondov BD, Elmqvist N, Franconeri S
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
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
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
High-throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Nature Communications, November 30, 2018
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S
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
Face to Face: Evaluating Visual Comparison
IEEE Trans Vis Comput Graph, August 20, 2018
Ondov BD, Jardine N, Elmqvist N, Franconeri 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
MUMmer4: A fast and versatile genome alignment system
PLoS Comput Biol, January 26, 2018
Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A
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
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
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
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
New advances in sequence assembly
Genome Research, May 1, 2017
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
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod
BMC Genomics, January 18, 2017
Tørresen OK, Star B, Jentoft S, Reinar WB, Grove H, Miller JR, Walenz BP, Knight J, Ekholm JM, Peluso P, Edvardsen RB, Tooming-Klunderud A, Skage M, Lien S, Jakobsen KS, Nederbragt AJ
High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs
PloS Comput Biol, October 28, 2016
Dilthey A, Gourraud PA, Mentzer AJ, Cereb N, Iqbal Z, McVean G
De novo assembly and phasing of a Korean human genome
Nature, October 5, 2016
Seo JS, Rhie A, Kim J, Lee S, Sohn MH, Kim CU, Hastie A, Cao H, Yun J-Y, Kim J, Kuk J, P G H, Kim J, Ryu H, Kim J, Roh M, Baek J, Hunkapiller MW, Korlach J, Shin JY, Kim C
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
The Atlantic salmon genome provides insights into rediploidization
Nature, May 12, 2016
Lien S … Walenz B … Davidson WS
Comprehensive genome-wide evaluation of lapatinib-induced liver injury yields a single genetic signal centered on known risk allele HLA-DRB1*07:01
Pharmacogenomics J., April 16, 2016
Parham LR, Briley LP, Li L, Shen J, Newcombe PJ, King KS, Slater AJ, Dilthey A, Iqbal Z, McVean G, Cox CJ, Nelson MR, Spraggs CF
Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru
PLoS Negl Trop Dis, April 13, 2016
Treangen TJ, Schoeler G, Phillippy AM, Bergman NH, Turell MJ
Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes
Proc Natl Acad Sci USA, 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
Horizontally transferred genes cluster spatially and metabolically
Biology Direct, December 21, 2015
Dilthey A, Lercher MJ
Genomic Copy Number Variations Characterize the Prognosis of Both P16-Positive and P16-Negative Oropharyngeal Squamous Cell Carcinoma After Curative Resection
Medicine, December 1, 2015
Rhie A, Park WS, Choi MK, Kim J-H, Ryu J, Ryu CH, Kim J-I, Jung Y-S
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
Imputation of KIR Types from SNP Variation Data
Am J Hum Genet., October 1, 2015
Vukcevic D, Traherne JA, Næss S, Ellinghaus E, Kamatani Y, Dilthey A, Lathrop M, Karlsen TH, Franke A, Moffatt M, Cookson W, Trowsdale J, McVean G, Sawcer S, Leslie S
Class II HLA interactions modulate genetic risk for multiple sclerosis
Nature Genetics, September 7, 2015
Moutsianas L … Dilthey AT … McVean G; International Multiple Sclerosis Genetics Consortium
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
Improved genome inference in the MHC using a population reference graph
Nature Genetics, April 27, 2015
Dilthey A, Cox C, Iqbal Z, Nelson MR, McVean G
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
Krona: interactive metagenomic visualization in a web browser
Encyclopedia of Metagenomics, January 1, 2015
Ondov BD, Bergman NH, Phillippy AM
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
Curr Opin Microbiol, December 1, 2014
Koren S, Phillippy AM
Long-read, whole-genome shotgun sequence data for five model organisms
Sci Data, November 25, 2014
Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM
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
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
Nature Genetics, September 29, 2013
International Multiple Sclerosis Genetics Consortium (IMSGC) … Dilthey AT … McCauley JL
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
The genome of Anopheles darlingi, the main neotropical malaria vector
Nucleic Acids Res, August 15, 2013
Marinotti O … Walenz BP … de Vasconcelos AT
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
Multi-population classical HLA type imputation
PloS Comput Biol., February 14, 2013
Dilthey A, Leslie S, Moutsianas L, Shen J, Cox C, Nelson MR, McVean G
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
Genome Sequence of the Attenuated Carbosap Vaccine Strain of Bacillus anthracis
Genome Announc, January 15, 2013
Harrington R, Ondov BD, Radune D, Friss MB, Klubnik J, Diviak L, Hnath J, Cendrowski SR, Blank TE, Karaolis D, Friedlander AM, Burans JP, Rosovitz MJ, Treangen T, Phillippy AM, Bergman NH
Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone
Genome Biol, December 27, 2012
Treangen TJ, Phillippy AM
Psoralen Inactivation of Viruses: A Process for the Safe Manipulation of Viral Antigen and Nucleic Acid
Bioinformatics, August 22, 2012
Schneider K, Wronka-Edwards L, Leggett-Embrey M, Walker E, Sun P, Ondov B, Wyman TH, Rosovitz MJ, Bohn SS, Burans J, Kochel T
Strand-Specific RNA-Seq Reveals Ordered Patterns of Sense and Antisense Transcription in Bacillus anthracis
Bioinformatics, August 22, 2012
Passalacqua KD, Varadarajan A, Weist C, Ondov BD, Byrd B, Read TD, Bergman NH
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
The rise of a digital immune system
Gigascience, July 12, 2012
Schatz MC, Phillippy AM
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
Nature, June 28, 2012
Prüfer K … Walenz BP, Koren S … Pääbo S
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
Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles
Nature Genetics, March 25, 2012
Fairfax BP1, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC
Psoriasis patients are enriched for genetic variants that protect against HIV-1 disease
PloS Genet., February 16, 2012
Chen H, Hayashi G, Lai OY, Dilthey A, Kuebler PJ, Wong TV, Martin MP, Fernandez Vina MA, McVean G, Wabl M, Leslie KS, Maurer T, Martin JN, Deeks SG, Carrington M, Bowcock AM, Nixon DF, Liao W
FX: an RNA-Seq analysis tool on the cloud
Bioinformatics, January 17, 2012
Hong D, Rhie A, Park S-S, Lee J, Ju YS, Kim S, Yu S-S, Bleazard T, Park H-S, Rhee H, Chong H, Yang K-S, Lee Y-S, Kim I-H, Lee JS, Kim J-I, Seo J-S
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
A Rickettsia genome overrun by mobile genetic elements provides insight into the acquisition of genes characteristic of an obligate intracellular lifestyle
J Bacteriol, January 1, 2012
Gillespie JJ, Joardar V, Williams KP, Driscoll T, Hostetler JB, Nordberg E, Shukla M, Walenz B, Hill CA, Nene VM, Azad AF, Sobral BW, Caler E
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
Brief Bioinform, December 23, 2011
Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M
Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis
Proc Natl Acad Sci USA, November 28, 2011
Donia MS, Fricke WF, Partensky F, Cox J, Elshahawi SI, White JR, Phillippy AM, Schatz MC, Piel J, Haygood MG, Ravel J, Schmidt EW
Bambus 2: scaffolding metagenomes
Bioinformatics, November 1, 2011
Koren S, Treangen TJ, Pop M
Interactive metagenomic visualization in a Web browser
BMC Bioinformatics, September 30, 2011
Ondov BD, Bergman NH, Phillippy AM
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
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
Nature, August 10, 2011
International Multiple Sclerosis Genetics Consortium; Wellcome Trust Case Control Consortium 2 … Dilthey A … Compston A
Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)
Proc Natl Acad Sci USA, July 26, 2011
Miller W … Walenz B … Schuster SC
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp
J Bacteriol, July 22, 2011
Bogdanove AJ … Phillippy AM … Salzberg SL
Multiple Hodgkin lymphoma-associated loci within the HLA region at chromosome 6p21.3
Blood, July 21, 2011
Moutsianas L, Enciso-Mora V, Ma YP, Leslie S, Dilthey A, Broderick P, Sherborne A, Cooke R, Ashworth A, Swerdlow AJ, McVean G, Houlston RS
Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility
Nature Genetics, July 10, 2011
Evans DM … Dilthey A … Donnelly P; Australo-Anglo-American Spondyloarthritis Consortium (TASC); Wellcome Trust Case Control Consortium 2 (WTCCC2)
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing
Bioinformatics (Oxford, England). 2011; 27(13):1869-70. PubMed [journal], July 1, 2011
Walenz B, Florea L
Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity
BMC Genomics, June 4, 2011
Sahl JW, Johnson JK, Harris AD, Phillippy AM, Hsiao WW, Thom KA, Rasko DA
Next generation sequence assembly with AMOS
Current Protocols in Bioinformatics, March 18, 2011
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation
Proc Natl Acad Sci USA, March 7, 2011
Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, Keim PS, Fraser-Liggett CM, Ravel J
HLA*IMP--an integrated framework for imputing classical HLA alleles from SNP genotypes
Bioinformatics, February 7, 2011
Dilthey AT, Moutsianas L, Leslie S, McVean G
MHC variation and risk of childhood B-cell precursor acute lymphoblastic leukemia
Blood, November 8, 2010
Hosking FJ, Leslie S, Dilthey A, Moutsianas L, Wang Y, Dobbins SE, Papaemmanuil E, Sheridan E, Kinsey SE, Lightfoot T, Roman E, Irving JA, Allan JM, Taylor M, Greaves M, McVean G, Houlston RS
Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences
Science, October 22, 2010
Lawniczak MK … Walenz BP … Besansky NJ
A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1
Nature Genetics, October 17, 2010
Genetic Analysis of Psoriasis Consortium & the Wellcome Trust Case Control Consortium 2 … Dilthey A … Trembath RC
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
BMC Genomics, September 16, 2010
Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W
An algorithm for automated closure during assembly
BMC Bioinformatics, September 10, 2010
Koren S, Miller JR, Walenz BP, Sutton G
An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System
Bioinformatics, August 1, 2010
Ondov BD, Cochran C, Landers M, Meredith GD, Dudas M, Bergman NH
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle
Proc Natl Acad Sci USA, July 6, 2010
Kirkness EF … Walenz B … Pittendrigh BR
Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray
Appl Environ Microbiol, June 25, 2010
Schatz MC, Phillippy AM, Gajer P, DeSantis TZ, Andersen GL, Ravel J
Transcriptomic responses of Salmonella enterica serovars Enteritidis and Typhimurium to chlorine-based oxidative stress
Appl Environ Microbiol, June 18, 2010
Wang S, Phillippy AM, Deng K, Rui X, Li Z, Tortorello ML, Zhang W
Assembly algorithms for next-generation sequencing data
Genomics, June 1, 2010
Miller JR, Koren S, Sutton G
The dynamic genome of Hydra
Nature, March 25, 2010
Chapman JA … Walenz B … Steele RE
Whole-genome sequence analysis for pathogen detection and diagnostics
Thesis, January 1, 2010
Phillippy AM
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
BMC Bioinformatics, September 16, 2009
Phillippy AM, Deng X, Zhang W, Salzberg SL
Insignia: a DNA signature search web server for diagnostic assay development
Nucleic Acids Res, May 5, 2009
Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL
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
Structure and complexity of a bacterial transcriptome
J Bacteriol, May 1, 2009
Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH
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
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
Bioinformatics, December 1, 2008
Ondov BD, Varadarajan A, Passalacqua KD, Bergman NH
Genetic variation in an individual human exome
PLoS Genet, August 15, 2008
Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, Axelrod N, Busam DA, Strausberg RL, Venter JC
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
BMC Genomics, May 1, 2008
Salzberg SL … Phillippy AM … Bogdanove AJ
Consensus generation and variant detection by Celera Assembler
Bioinformatics, April 15, 2008
Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Sutton G
Genome assembly forensics: finding the elusive mis-assembly
Genome Biol, March 14, 2008
Phillippy AM, Schatz MC, Pop M
Evolution of genes and genomes on the Drosophila phylogeny
Nature, November 8, 2007
Drosophila 12 Genomes Consortium … Phillippy AMWalenz B … MacCallum I
The diploid genome sequence of an individual human
PLoS Biol, September 4, 2007
Levy S … Walenz BP … Venter JC
Nanoliter reactors improve multiple displacement amplification of genomes from single cells
PLoS Genet, September 3, 2007
Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR
Knowledge discovery using the sand spatial browser
8th annual international conference on digital government research, May 20, 2007
Samet H, Phillippy A, Sankaranarayanan J
Comprehensive DNA signature discovery and validation
PLoS Comput Biol, April 20, 2007
Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL
Evolutionary and biomedical insights from the rhesus macaque genome
Science, April 13, 2007
Gibbs RA … Walenz BP … Zwieg AS
Hawkeye: an interactive visual analytics tool for genome assemblies
Genome Biol, March 9, 2007
Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL
A space-efficient construction of the Burrows-Wheeler transform for genomic data
J Comput Biol, September 1, 2005
Lippert RA, Mobarry CM, Walenz BP
A tool for analyzing mate pairs in assemblies (TAMPA)
J Comput Biol, June 1, 2005
Dew IM, Walenz B, Sutton G
Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes
Science, January 7, 2005
Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF
Gene and alternative splicing annotation with AIR
Genome Res, January 1, 2005
Florea L, Di Francesco V, Miller J, Turner R, Yao A, Harris M, Walenz B, Mobarry C, Merkulov GV, Charlab R, Dew I, Deng Z, Istrail S, Li P, Sutton G
Comparative genome assembly
Brief Bioinform, September 1, 2004
Pop M, Phillippy A, Delcher AL, Salzberg SL
1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap
J Comput Biol, July 5, 2004
Caprara A, Carr R, Istrail S, Lancia G, Walenz B
Whole-genome shotgun assembly and comparison of human genome assemblies
Proc Natl Acad Sci USA, February 17, 2004
Istrail S … Walenz B … Venter JC
Versatile and open software for comparing large genomes
Genome Biol, January 30, 2004
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL
Using MUMmer to identify similar regions in large sequence sets
Curr Protoc Bioinformatics, February 1, 2003
Delcher AL, Salzberg SL, Phillippy AM
The genome sequence of the malaria mosquito Anopheles gambiae
Science, October 4, 2002
Holt RA … Walenz B … Hoffman SL
Fast algorithms for large-scale genome alignment and comparison
Nucleic Acids Res, June 1, 2002
Delcher AL, Phillippy A, Carlton J, Salzberg SL
The sequence of the human genome
Science, February 16, 2001
Venter JC … Walenz B … Zhu X