Publications

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
Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation
bioRxiv, July 1, 2017
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
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
New advances in sequence assembly
Genome Research, May 1, 2017
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
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 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
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
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 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
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
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
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
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
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
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 U S A, 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
Oxford 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 U S A, 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 U S A, 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 U S A, 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
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
Oxford 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
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
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 U S A, 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