Publications with Brian Walenz

Software Engineer

The complete sequence of a human Y chromosome
Nature, August 23, 2023
Rhie A, Nurk SKoren S, Rautiainen MHansen NFMc Cartney AMWalenz BPPhillippy AM
A draft human pangenome reference
Nature, May 10, 2023
Liao W-W … Koren SNurk SRautiainen MRhie AWalenz BPhillippy AM … 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
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
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
Towards complete and error-free genome assemblies of all vertebrate species
Nature, April 28, 2021
Rhie AKoren SGhurye JWalenz BPPhillippy AM, Jarvis ED
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
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Genome Biology, September 14, 2020
Rhie A, Walenz BP, Koren S, Phillippy AM
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
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
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
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
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
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
The Atlantic salmon genome provides insights into rediploidization
Nature, May 12, 2016
Lien S … Walenz B … Davidson WS
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
The genome of Anopheles darlingi, the main neotropical malaria vector
Nucleic Acids Res, August 15, 2013
Marinotti O … Walenz BP … de Vasconcelos AT
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 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
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
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
Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences
Science, October 22, 2010
Lawniczak MK … Walenz BP … Besansky NJ
An algorithm for automated closure during assembly
BMC Bioinformatics, September 10, 2010
Koren S, Miller JR, Walenz BP, Sutton G
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
The dynamic genome of Hydra
Nature, March 25, 2010
Chapman JA … Walenz B … Steele RE
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
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
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
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
Evolutionary and biomedical insights from the rhesus macaque genome
Science, April 13, 2007
Gibbs RA … Walenz BP … Zwieg AS
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
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
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
The genome sequence of the malaria mosquito Anopheles gambiae
Science, October 4, 2002
Holt RA … Walenz B … Hoffman SL
The sequence of the human genome
Science, February 16, 2001
Venter JC … Walenz B … Zhu X