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42 Article(s) on File
Page 1 of 1
The contribution of de novo coding mutations to autism spectrum disorder
Iossifov I,
ORoak BJ,
Sanders SJ,
Ronemus M,
Krumm N,
Levy D,
Stessman HA,
Witherspoon KT,
Vives L,
Patterson KE,
Smith JD,
Paeper B,
Nickerson DA,
Dea J,
Dong S,
Gonzalez LE,
Mandell JD,
Mane SM,
Murtha MT,
Sullivan CA,
Walker MF,
Waqar Z,
Wei L,
Willsey AJ,
Yamrom B,
Lee YH,
Grabowska E,
Dalkic E,
Wang Z,
Marks S,
Andrews P,
Leotta A,
Kendall J,
Hakker I,
Rosenbaum J,
Ma B,
Rodgers L,
Troge J,
Narzisi G,
Yoon S,
Schatz MC,
Ye K,
McCombie WR,
Shendure J,
Eichler EE,
State MW,
Wigler M

Nature
  515 (7526): 2160-U136; Nov 13 2014   NLM
[Abstract]
[DOI] [Full Text]

SplitMEM: A graphical algorithm for pan-genome analysis with suffix skips
Marcus S,
Lee H,
Schatz MC

Bioinformatics
  (0): Nov 13 2014   Nlm
[Abstract]
[DOI] [Full Text]

Accurate de novo and transmitted indel detection in exome-capture data using microassembly
Narzisi G,
ORawe JA,
Iossifov I,
Fang H,
Lee Yh,
Wang Z,
Wu Y,
Lyon GJ,
Wigler M,
Schatz MC

Nature Methods
  11 (10): 1033-1036; Oct 2014   NLM
[Abstract]
[DOI] [Full Text]

Large-scale sequencing and assembly of cereal genomes using blacklight
Blood PD,
Marcus S,
Schatz MC

ACM International Conference Proceeding Series
  Article number 20; Jul 13 2014   Elsevier
[Abstract]
[DOI] [Full Text]

High-coverage sequencing and annotated assemblies of the budgerigar genome
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

Gigascience
  3 (0): 11; Jul 8 2014   Nlm
[Abstract]
[DOI] [Full Text]

On algorithmic complexity of biomolecular sequence assembly problem
Narzisi G,
Mishra B,
Schatz MC
In:
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
(ed. ) : ; 2014. 8542 : 183-195   Elsevier
[Abstract]
[DOI] [Full Text]

Answering the demands of digital genomics
Titmus MA,
Gurtowski J,
Schatz MC

Concurrency Computation Practice and Experience
  26 (4): 917-928; Mar 24 2014   Web of Science
[Abstract]
[DOI] [Full Text]

Reducing INDEL calling errors in whole genome and exome sequencing data
Fang H,
Wu Y,
Narzisi G,
ORawe JA,
Barron LT,
Rosenbaum J,
Ronemus M,
Iossifov I,
Schatz MC,
Lyon GJ

Genome Med
  6 (10): 89; 2014   Nlm
[Abstract]
[DOI] [Full Text]

Cultivation and Complete Genome Sequencing of Gloeobacter kilaueensis sp. nov., from a Lava Cave in Kīlauea Caldera, Hawaii
Saw JH,
Schatz M,
Brown MV,
Kunkel DD,
Foster JS,
Shick H,
Christensen S,
Hou S,
Wan X,
Donachie SP

PLoS ONE
  8 (10): Oct 2013   NLM
[Abstract]
[DOI] [Full Text]

The DNA Data Deluge
Schatz MC,
Langmead B

IEEE Spectrum
  50 (7): 28-33; Jul 2013  
[DOI] [Full Text]

The DNA60IFX contest
Schatz MC,
Taylor J,
Schelhorn SE

Genome Biol
  14 (6): 124; Jun 28 2013   NLM
[DOI] [Full Text]

Sixty years of genome biology
Doolittle WF,
Fraser P,
Gerstein MB,
Graveley BR,
Henikoff S,
Huttenhower C,
Oshlack A,
Ponting CP,
Rinn JL,
Schatz MC,
Ule J,
Weigel D,
Weinstock GM

Genome Biol
  14 (4): Apr 25 2013   NLM
[Abstract]
[DOI] [Full Text]

Aluminum tolerance in maize is associated with higher MATE1 gene copy number
Maron LG,
Guimarães CT,
Kirst M,
Albert PS,
Birchler JA,
Bradbury PJ,
Buckler ES,
Coluccio AE,
Danilova TV,
Kudrna D,
Magalhaes JV,
Piñeros MA,
Schatz MC,
Wing RA,
Kochian LV

Proceedings of the National Academy of Sciences of the United States of America
  110 (13): 5241-5246; Mar 26 2013  
[Abstract]
[DOI] [Full Text]

Hawkeye and AMOS: Visualizing and assessing the quality of genome assemblies
Schatz MC,
Phillippy AM,
Sommer DD,
Delcher AL,
Puiu D,
Narzisi G,
Salzberg SL,
Pop M

Briefings in Bioinformatics
  14 (2): 213-224; Mar 2013  
[DOI] [Full Text]

The advantages of SMRT sequencing
Roberts RJ,
Carneiro MO,
Schatz MC

Genome Biology
  14 (7): 4; 2013  
[Abstract]
[DOI] [Full Text]

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
Ming R,
VanBuren R,
Liu YL,
Yang M,
Han YP,
Li LT,
Zhang Q,
Kim MJ,
Schatz MC,
Campbell M,
Li JP,
Bowers JE,
Tang HB,
Lyons E,
Ferguson AA,
Narzisi G,
Nelson DR,
Blaby-Haas CE,
Gschwend AR,
Jiao YN,
Der JP,
Zeng FC,
Han J,
Min XJ,
Hudson KA,
Singh R,
Grennan AK,
Karpowicz SJ,
Watling JR,
Ito K,
Robinson SA,
Hudson ME,
Yu QY,
Mockler TC,
Carroll A,
Zheng Y,
Sunkar R,
Jia RZ,
Chen N,
Arro J,
Wai CM,
Wafula E,
Spence A,
Han YN,
Xu LM,
Zhang JS,
Peery R,
Haus MJ,
Xiong WW,
Walsh JA,
Wu J,
Wang ML,
Zhu YJ,
Paull RE,
Britt AB,
Du CG,
Downie SR,
Schuler MA,
Michael TP,
Long SP,
Ort DR,
Schopf JW,
Gang DR,
Jiang N,
Yandell M,
dePamphilis CW,
Merchant SS,
Paterson AH,
Buchanan BB,
Li SH,
Shen-Miller J

Genome Biology
  14 (5): 2013  
[Abstract]
[DOI] [Full Text]

Computational thinking in the era of big data biology
Schatz MC

Genome Biology
  13 (11): Article no. 177; Nov 29 2012  
[DOI] [Full Text]

Answering the demands of digital genomics
Titmus MA,
Gurtowski J,
Schatz MC

Concurrency Computation Practice and Experience
  (0): Oct 4 2012  
[Abstract]
[DOI] [Full Text]

Genotyping in the cloud with crossbow
Gurtowski J,
Schatz MC,
Langmead B

Curr Protoc Bioinformatics
  Chapt (0): Unit15.3; Sep 2012   NLM
[Abstract]
[DOI] [Full Text]

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score
Lee H,
Schatz MC

Bioinformatics
  28 (16): 2097-2105; Aug 15 2012  
[Abstract]
[DOI] [Full Text]

Hybrid error correction and de novo assembly of single-molecule sequencing reads
Koren S,
Schatz MC,
Walenz BP,
Martin J,
Howard JT,
Ganapathy G,
Wang Z,
Rasko DA,
McCombie WR,
Jarvis ED,
Phillippy AM

Nat Biotechnol
  30 (7): 693-700; Jul 1 2012   Nlm
[Abstract]
[DOI] [Full Text]

Current challenges in de novo plant genome sequencing and assembly
Schatz MC,
Witkowski J,
McCombie WR

Genome Biology
  13 (4): 243; Apr 27 2012   Nlm
[Abstract]
[DOI] [Full Text]

De novo gene disruptions in children on the autistic spectrum
Iossifov I,
Ronemus M,
Levy D,
Wang Z,
Hakker I,
Rosenbaum J,
Yamrom B,
Lee YH,
Narzisi G,
Leotta A,
Kendall J,
Grabowska E,
Ma B,
Marks S,
Rodgers L,
Stepansky A,
Troge J,
Andrews P,
Bekritsky M,
Pradhan K,
Ghiban E,
Kramer M,
Parla J,
Demeter R,
Fulton LL,
Fulton RS,
Magrini VJ,
Ye K,
Darnell JC,
Darnell RB,
Mardis ER,
Wilson RK,
Schatz MC,
McCombie WR,
Wigler M

Neuron
  74 (2): 285-99; Apr 26 2012   Nlm
[Abstract]
[DOI] [Full Text]

GAGE: A critical evaluation of genome assemblies and assembly algorithms
Salzberg SL,
Phillippy AM,
Zimin A,
Puiu D,
Magoc T,
Koren S,
Treangen TJ,
Schatz MC,
Delcher AL,
Roberts M,
Marcais G,
Pop M,
Yorke JA

Genome Res
  22 (3): 557-67; Mar 2012   NLM
[Abstract]
[DOI] [Full Text]

Rate of meristem maturation determines inflorescence architecture in tomato
Park SJ,
Jiang K,
Schatz MC,
Lippman ZB

Proc Natl Acad Sci U S A
  109 (2): 639-44; Jan 10 2012   NLM
[Abstract]
[DOI] [Full Text]

The rise of a digital immune system
Schatz MC,
Phillippy AM

Gigascience
  1 (1): 4; 2012   Nlm
[Abstract]
[DOI] [Full Text]

Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp
Bogdanove AJ,
Koebnik R,
Lu H,
Furutani A,
Angiuoli SV,
Patil PB,
Van Sluys MA,
Ryan RP,
Meyer DF,
Han SW,
Aparna G,
Rajaram M,
Delcher AL,
Phillippy AM,
Puiu D,
Schatz MC,
Shumway M,
Sommer DD,
Trapnell C,
Benahmed F,
Dimitrov G,
Madupu R,
Radune D,
Sullivan S,
Jha G,
Ishihara H,
Lee SW,
Pandey A,
Sharma V,
Sriariyanun M,
Szurek B,
Vera-Cruz CM,
Dorman KS,
Ronald PC,
Verdier V,
Dow JM,
Sonti RV,
Tsuge S,
Brendel VP,
Rabinowicz PD,
Leach JE,
White FF,
Salzberg SL

Journal of Bacteriology
  193 (19): 5450-5464; Oct 2011   PMC3187462
[Abstract]
[DOI]

Rapid parallel genome indexing with MapReduce
Menon RK,
Bhat GP,
Schatz MC

2nd International Workshop on MapReduce and Its Applications, MapReduce11
  51-58; 2011  
[Abstract]
[DOI] [Full Text]

Assemblathon 1: A competitive assessment of de novo short read assembly methods
Earl D,
Bradnam K,
St. John J,
Darling A,
Lin D,
Fass J,
Yu HO,
Buffalo V,
Zerbino DR,
Diekhans M,
Nguyen N,
Ariyaratne PN,
Sung WK,
Ning Z,
Haimel M,
Simpson JT,
Fonseca NA,
Birol I,
Docking TR,
Ho IY,
Rokhsar DS,
Chikhi R,
Lavenier D,
Chapuis G,
Naquin D,
Maillet N,
Schatz MC,
Kelley DR,
Phillippy AM,
Koren S,
Yang SP,
Wu W,
Chou WC,
Srivastava A,
Shaw TI,
Ruby JG,
Skewes-Cox P,
Betegon M,
Dimon MT,
Solovyev V,
Seledtsov I,
Kosarev P,
Vorobyev D,
Ramirez-Gonzalez R,
Leggett R,
MacLean D,
Xia F,
Luo R,
Li Z,
Xie Y,
Liu B,
Gnerre S,
MacCallum I,
Przybylski D,
Ribeiro FJ,
Sharpe T,
Hall G,
Kersey PJ,
Durbin R,
Jackman SD,
Chapman JA,
Huang X,
DeRisi JL,
Caccamo M,
Li Y,
Jaffe DB,
Green RE,
Haussler D,
Korf I,
Paten B

Genome Research
  21 (12): 2224-2241; 2011  
[Abstract]
[DOI] [Full Text]

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis
Donia MS,
Fricke WF,
Partensky F,
Cox J,
Elshahawi SI,
White JR,
Phillippy AM,
Schatz MC,
Piel J,
Haygood MG,
Ravel J,
Schmidt EW

Proceedings of the National Academy of Sciences of the United States of America
  108 (51): E1423-E1432; 2011  
[Abstract]
[DOI] [Full Text]

Quake: Quality-aware detection and correction of sequencing errors
Kelley DR,
Schatz MC,
Salzberg SL

Genome Biology
  11 (11): Nov 29 2010   PMC3156955
[Abstract]
[DOI] [Full Text]

Cloud computing and the DNA data race
Schatz MC,
Langmead B,
Salzberg SL

Nature Biotechnology
  28 (7): 691-693; Jul 2010   PMCID: PMC2904649
[Abstract]
[DOI] [Full Text] [PDF]

Assembly complexity of prokaryotic genomes using short reads
Kingsford C,
Schatz MC,
Pop M

BMC Bioinformatics
  11 (0): 2010  
[Abstract]
[DOI] [Full Text]

Assembly of large genomes using second-generation sequencing
Schatz MC,
Delcher AL,
Salzberg SL

Genome Research
  20 (9): 1165-1173; 2010  
[Abstract]
[DOI] [Full Text]

Design patterns for efficient graph algorithms in MapReduce
Lin J,
Schatz M

  78-85; 2010  
[Abstract]
[Full Text]

Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera
Cornman SR,
Schatz MC,
Johnston SJ,
Chen Y,
Pettis J,
Hunt G,
Bourgeois L,
Elsik C,
Anderson D,
Grozinger CM,
Evans JD

BMC Genomics
  11 (1): 2010  
[Abstract]
[DOI] [Full Text]

Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray
Schatz MC,
Phillippy AM,
Gajer P,
DeSantis TZ,
Andersen GL,
Ravel J

Applied and Environmental Microbiology
  76 (16): 5636-5638; 2010  
[Abstract]
[DOI] [Full Text]

The missing graphical user interface for genomics
Schatz MC

Genome Biology
  11 (8): 128; 2010   Elsevier PMC294577
[Abstract]


Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): Genome assembly and analysis
Dalloul RA,
Long JA,
Zimin AV,
Aslam L,
Beal K,
Blomberg LA,
Bouffard P,
Burt DW,
Crasta O,
Crooijmans RP,
Cooper K,
Coulombe RA,
De S,
Delany ME,
Dodgson JB,
Dong JJ,
Evans C,
Frederickson KM,
Flicek P,
Florea L,
Folkerts O,
Groenen MA,
Harkins TT,
Herrero J,
Hoffmann S,
Megens HJ,
Jiang A,
de Jong P,
Kaiser P,
Kim H,
Kim KW,
Kim S,
Langenberger D,
Lee MK,
Lee T,
Mane S,
Marcais G,
Marz M,
McElroy AP,
Modise T,
Nefedov M,
Notredame C,
Paton IR,
Payne WS,
Pertea G,
Prickett D,
Puiu D,
Qioa D,
Raineri E,
Ruffier M,
Salzberg SL,
Schatz MC,
Scheuring C,
Schmidt CJ,
Schroeder S,
Searle SM,
Smith EJ,
Smith J,
Sonstegard TS,
Stadler PF,
Tafer H,
Tu Z,
van Tassell CP,
Vilella AJ,
Williams KP,
Yorke JA,
Zhang L,
Zhang HB,
Zhang X,
Zhang Y,
Reed KM

Plos Biology
  8 (9): 2010  
[Abstract]
[DOI] [Full Text]

Genomic analyses of the microsporidian Nosema ceranae, an emergent pathogen of honey bees
Cornman RS,
Chen YP,
Schatz MC,
Street C,
Zhao Y,
Desany B,
Egholm M,
Hutchison S,
Pettis JS,
Lipkin WI,
Evans JD

Plos Pathogens
  5 (6): 2009  
[Abstract]
[DOI] [Full Text]

Optimizing data intensive GPGPU computations for DNA sequence alignment
Trapnell C,
Schatz MC

Parallel Computing
  35 (8): 429-440; 2009  
[Abstract]
[DOI] [Full Text]

Searching for SNPs with cloud computing
Langmead B,
Schatz MC,
Lin J,
Pop M,
Salzberg SL

Genome Biology
  10 (11): 2009  
[Abstract]
[DOI] [Full Text]


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