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98 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]

Validation and assessment of variant calling pipelines for next-generation sequencing
Pirooznia M,
Kramer M,
Parla J,
Goes FS,
Potash JB,
McCombie WR,
Zandi PP

Human Genomics
  8 (0): Jul 30 2014   NLM
[Abstract]
[DOI] [Full Text]

Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis
Para A,
Li Y,
Marshall-Colon A,
Varala K,
Francoeur NJ,
Moran TM,
Edwards MB,
Hackley C,
Bargmann BO,
Birnbaum KD,
McCombie WR,
Krouk G,
Coruzzi GM

Proceedings of the National Academy of Sciences of the United States of America
  111 (28): 10371-10376; Jul 15 2014   Nlm
[Abstract]
[DOI] [Full Text]

Two waves of de novo methylation during mouse germ cell development
Molaro A,
Falciatori I,
Hodges E,
Aravin AA,
Marran K,
Rafii S,
McCombie WR,
Smith AD,
Hannon GJ

Genes Dev
  28 (14): 1544-9; Jul 15 2014   Nlm
[Abstract]
[DOI] [Full Text]

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum
Grativol C,
Regulski M,
Bertalan M,
McCombie WR,
da Silva FR,
Zerlotini Neto A,
Vicentini R,
Farinelli L,
Hemerly AS,
Martienssen RA,
Ferreira PC

Plant Journal
  79 (1): 162-172; Jul 2014   NLM
[DOI] [Full Text]

De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability
McCarthy SE,
Gillis J,
Kramer M,
Lihm J,
Yoon S,
Berstein Y,
Mistry M,
Pavlidis P,
Solomon R,
Ghiban E,
Antoniou E,
Kelleher E,
OBrien C,
Donohoe G,
Gill M,
Morris DW,
McCombie WR,
Corvin A

Molecular Psychiatry
  19 (6): 652-658; Jun 2014   NLM
[Abstract]
[DOI] [Full Text]

708 Common and 2010 rare DISC1 locus variants identified in 1542 subjects: Analysis for association with psychiatric disorder and cognitive traits
Thomson PA,
Parla JS,
McRae AF,
Kramer M,
Ramakrishnan K,
Yao J,
Soares DC,
McCarthy S,
Morris SW,
Cardone L,
Cass S,
Ghiban E,
Hennah W,
Evans KL,
Rebolini D,
Millar JK,
Harris SE,
Starr JM,
MacIntyre DJ,
McIntosh AM,
Watson JD,
Deary IJ,
Visscher PM,
Blackwood DH,
McCombie WR,
Porteous DJ

Molecular Psychiatry
  19 (6): 668-675; Jun 2014   NLM
[Abstract]
[DOI] [Full Text]

Unlocking the Treasure Trove: From Genes to Schizophrenia Biology
McCarthy SE,
McCombie WR,
Corvin A

Schizophrenia Bulletin
  (0): Mar 27 2014   NLM
[Abstract]
[DOI] [Full Text]

DISC1 as a genetic risk factor for schizophrenia and related major mental illness: response to Sullivan
Porteous DJ,
Thomson PA,
Millar JK,
Evans KL,
Hennah W,
Soares DC,
McCarthy S,
McCombie WR,
Clapcote SJ,
Korth C,
Brandon NJ,
Sawa A,
Kamiya A,
Roder JC,
Lawrie SM,
McIntosh AM,
St Clair D,
Blackwood DH

Molecular Psychiatry
  19 (2): 141-3; Feb 2014   Nlm
[Abstract]
[DOI] [Full Text]

Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barretts esophagus
Streppel MM,
Lata S,
Delabastide M,
Montgomery EA,
Wang JS,
Canto MI,
Macgregor-Das AM,
Pai S,
Morsink FH,
Offerhaus GJ,
Antoniou E,
Maitra A,
McCombie WR

Oncogene
  33 (3): 347-57; Jan 16 2014   Nlm
[Abstract]
[DOI] [Full Text]

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies
Yao J,
Zhang KX,
Kramer M,
Pellegrini M,
McCombie WR

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

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots
Vidal EA,
Moyano TC,
Krouk G,
Katari MS,
Tanurdzic M,
McCombie WR,
Coruzzi GM,
Gutierrez RA

BMC Genomics
  14 (0): 701; Oct 2013  
[Abstract]
[DOI] [Full Text]

The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development
May P,
Liao W,
Wu Y,
Shuai B,
McCombie WR,
Zhang MQ,
Liu QA

Nature Communications
  4 (0): Jul 31 2013   NLM
[DOI] [Full Text]

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
Xu X,
Zhang Y,
Williams J,
Antoniou E,
McCombie WR,
Wu S,
Zhu W,
Davidson NO,
Denoya P,
Li E

BMC Bioinformatics
  14 Su (0): S1; Jun 28 2013   NLM
[Abstract]
[DOI] [Full Text]

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
Regulski M,
Lu Z,
Kendall J,
Donoghue MT,
Reinders J,
Llaca V,
Deschamps S,
Smith A,
Levy D,
McCombie WR,
Tingey S,
Rafalski A,
Hicks J,
Ware D,
Martienssen R

Genome Res
  (0): Jun 5 2013   NLM
[Abstract]
[DOI] [Full Text]

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor
Luo MC,
Gu YQ,
You FM,
Deal KR,
Ma Y,
Hu Y,
Huo N,
Wang Y,
Wang J,
Chen S,
Jorgensen CM,
Zhang Y,
McGuire PE,
Pasternak S,
Stein JC,
Ware D,
Kramer M,
McCombie WR,
Kianian SF,
Martis MM,
Mayer KF,
Sehgal SK,
Li W,
Gill BS,
Bevan MW,
Šimková H,
Doležel J,
Weining S,
Lazo GR,
Anderson OD,
Dvorak J

Proceedings of the National Academy of Sciences of the United States of America
  110 (19): 7940-7945; May 7 2013  
[DOI] [Full Text]

Improvement of the oryza sativa nipponbare reference genome using next generation sequence and optical map data
Kawahara Y,
de la Bastide M,
Cabal R,
Hamilton JP,
Kanamori H,
McCombie WR,
Ouyang S,
Schwartz DC,
Tanaka T,
Wu J,
Zhou S,
Childs KL,
Davidson RM,
Lin H,
Quesada-Ocampo L,
Vaillancourt B,
Sakai H,
Lee SS,
Kim J,
Numa H,
Itoh T,
Buell CR,
Matsumoto T

Rice
  6 (1): 1-10; Feb 6 2013   Springer
[Abstract]
[DOI] [Full Text]

Chd5 Requires PHD-Mediated Histone 3 Binding for Tumor Suppression
Paul S,
Kuo A,
Schalch T,
Vogel H,
Joshua-Tor L,
McCombie WR,
Gozani O,
Hammell M,
Mills AA

Cell Rep
  3 (1): 92-102; Jan 10 2013   NLM
[Abstract]
[DOI] [Full Text]

A Hybrid Likelihood Model for Sequence-Based Disease Association Studies
Chen YC,
Carter H,
Parla J,
Kramer M,
Goes FS,
Pirooznia M,
Zandi PP,
McCombie WR,
Potash JB,
Karchin R

PLoS Genetics
  9 (1): Jan 2013  
[Abstract]
[DOI] [Full Text]

Analysis of the bread wheat genome using whole-genome shotgun sequencing
Brenchley R,
Spannagl M,
Pfeifer M,
Barker GL,
DAmore R,
Allen AM,
McKenzie N,
Kramer M,
Kerhornou A,
Bolser D,
Kay S,
Waite D,
Trick M,
Bancroft I,
Gu Y,
Huo N,
Luo MC,
Sehgal S,
Gill B,
Kianian S,
Anderson O,
Kersey P,
Dvorak J,
McCombie WR,
Hall A,
Mayer KF,
Edwards KJ,
Bevan MW,
Hall N

Nature
  491 (7426): 705-710; Nov 26 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]

The tomato genome sequence provides insights into fleshy fruit evolution
Sato S,
Tabata S,
Hirakawa H,
Asamizu E,
Shirasawa K,
Isobe S,
Kaneko T,
Nakamura Y,
Shibata D,
Aoki K,
Egholm M,
Knight J,
Bogden R,
Li CB,
Shuang Y,
Xu X,
Pan SK,
Cheng SF,
Liu X,
Ren YY,
Wang J,
Albiero A,
Dal Pero F,
Todesco S,
Van Eck J,
Buels RM,
Bombarely A,
Gosselin JR,
Huang MY,
Leto JA,
Menda N,
Strickler S,
Mao LY,
Gao S,
Tecle IY,
York T,
Zheng Y,
Vrebalov JT,
Lee J,
Zhong SL,
Mueller LA,
Stiekema WJ,
Ribeca P,
Alioto T,
Yang WC,
Huang SW,
Du YC,
Zhang ZH,
Gao JC,
Guo YM,
Wang XX,
Li Y,
He J,
Li CY,
Cheng ZK,
Zuo JR,
Ren JF,
Zhao JH,
Yan LH,
Jiang HL,
Wang B,
Li HS,
Li ZJ,
Fu FY,
Chen BT,
Han B,
Feng Q,
Fan DL,
Wang Y,
Ling HQ,
Xue YB,
Ware D,
McCombie WR,
Lippman ZB,
Chia JM,
Jiang K,
Pasternak S,
Gelley L,
Kramer M,
Anderson LK,
Chang SB,
Royer SM,
Shearer LA,
Stack SM,
Rose JK,
Xu YM,
Eannetta N,
Matas AJ,
McQuinn R,
Tanksley SD,
Camara F,
Guigo R,
Rombauts S,
Fawcett J,
Van de Peer Y,
Zamir D,
Liang CB,
Spannagl M,
Gundlach H,
Bruggmann R,
Mayer K,
Jia ZQ,
Zhang JH,
Ye ZB,
Bishop GJ,
Butcher S,
Lopez-Cobollo R,
Buchan D,
Filippis I,
Abbott J,
Dixit R,
Singh M,
Singh A,
Pal JK,
Pandit A,
Singh PK,
Mahato AK,
Dogra V,
Gaikwad K,
Sharma TR,
Mohapatra T,
Singh NK,
Causse M,
Rothan C,
Schiex T,
Noirot C,
Bellec A,
Klopp C,
Delalande C,
Berges H,
Mariette J,
Frasse P,
Vautrin S,
Zouine M,
Latche A,
Rousseau C,
Regad F,
Pech JC,
Philippot M,
Bouzayen M,
Pericard P,
Osorio S,
del Carmen AF,
Monforte A,
Granell A,
Fernandez-Munoz R,
Conte M,
Lichtenstein G,
Carrari F,
De Bellis G,
Fuligni F,
Peano C,
Grandillo S,
Termolino P,
Pietrella M,
Fantini E,
Falcone G,
Fiore A,
Giuliano G,
Lopez L,
Facella P,
Perrotta G,
Daddiego L,
Bryan G,
Orozco M,
Pastor X,
Torrents D,
van Schriek K,
Feron RM,
van Oeveren J,
de Heer P,
daPonte L,
Jacobs-Oomen S,
Cariaso M,
Prins M,
van Eijk MJ,
Janssen A,
van Haaren MJ,
Jo SH,
Kim J,
Kwon SY,
Kim S,
Koo DH,
Lee S,
Hur CG,
Clouser C,
Rico A,
Hallab A,
Gebhardt C,
Klee K,
Jocker A,
Warfsmann J,
Gobel U,
Kawamura S,
Yano K,
Sherman JD,
Fukuoka H,
Negoro S,
Bhutty S,
Chowdhury P,
Chattopadhyay D,
Datema E,
Smit S,
Schijlen EW,
van de Belt J,
van Haarst JC,
Peters SA,
van Staveren MJ,
Henkens MH,
Mooyman PJ,
Hesselink T,
van Ham R,
Jiang GY,
Droege M,
Choi D,
Kang BC,
Kim BD,
Park M,
Yeom SI,
Lee YH,
Choi YD,
Li GC,
Gao JW,
Liu YS,
Huang SX,
Fernandez-Pedrosa V,
Collado C,
Zuniga S,
Wang GP,
Cade R,
Dietrich RA,
Rogers J,
Knapp S,
Fei ZJ,
White RA,
Thannhauser TW,
Giovannoni JJ,
Botella MA,
Gilbert L,
Gonzalez R,
Goicoechea JL,
Yu Y,
Kudrna D,
Collura K,
Wissotski M,
Wing R,
Schoof H,
Meyers BC,
Gurazada AB,
Green PJ,
Mathur S,
Vyas S,
Solanke AU,
Kumar R,
Gupta V,
Sharma AK,
Khurana P,
Khurana JP,
Tyagi AK,
Dalmay T,
Mohorianu I,
Walts B,
Chamala S,
Barbazuk WB,
Li JP,
Guo H,
Lee TH,
Wang YP,
Zhang D,
Paterson AH,
Wang XY,
Tang HB,
Barone A,
Chiusano ML,
Ercolano MR,
DAgostino N,
Di Filippo M,
Traini A,
Sanseverino W,
Frusciante L,
Seymour GB,
Elharam M,
Fu Y,
Hua A,
Kenton S,
Lewis J,
Lin SP,
Najar F,
Lai HS,
Qin BF,
Qu CM,
Shi RH,
White D,
White J,
Xing YB,
Yang KQ,
Yi J,
Yao ZY,
Zhou LP,
Roe BA,
Vezzi A,
DAngelo M,
Zimbello R,
Schiavon R,
Caniato E,
Rigobello C,
Campagna D,
Vitulo N,
Valle G,
Nelson DR,
De Paoli E,
Szinay D,
de Jong HH,
Bai YL,
Visser RG,
Lankhorst RM,
Beasley H,
McLaren K,
Nicholson C,
Riddle C,
Gianese G

Nature
  485 (7400): 635-641; May 2012  
[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]

Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)
McKain MR,
Wickett N,
Zhang Y,
Ayyampalayam S,
McCombie WR,
Chase MW,
Pires JC,
dePamphilis CW,
Leebens-Mack J

American Journal of Botany
  99 (2): 397-406; Feb 2012  
[Abstract]
[DOI] [Full Text]

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers
Varshney RK,
Chen WB,
Li YP,
Bharti AK,
Saxena RK,
Schlueter JA,
Donoghue MT,
Azam S,
Fan GY,
Whaley AM,
Farmer AD,
Sheridan J,
Iwata A,
Tuteja R,
Penmetsa RV,
Wu W,
Upadhyaya HD,
Yang SP,
Shah T,
Saxena KB,
Michael T,
McCombie WR,
Yang BC,
Zhang GY,
Yang HM,
Wang J,
Spillane C,
Cook DR,
May GD,
Xu X,
Jackson SA

Nature Biotechnology
  30 (1): 83-U128; Jan 2012  
[Abstract]
[DOI] [Full Text]

A functional phylogenomic view of the seed plants
Lee EK,
Cibrian-Jaramillo A,
Kolokotronis SO,
Katari MS,
Stamatakis A,
Ott M,
Chiu JC,
Little DP,
Stevenson DW,
McCombie WR,
Martienssen RA,
Coruzzi G,
Desalle R

PLoS genetics
  7 (12): e1002411; Dec 2011  
[Abstract]
[DOI] [Full Text]

Distinct p53 genomic binding patterns in normal and cancer-derived human cells
Botcheva K,
McCorkle SR,
McCombie WR,
Dunn JJ,
Anderson CW

Cell Cycle
  10 (24): 4237-4249; Dec 2011  
[Abstract]
[DOI]

SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Wu J,
Akerman M,
Sun S,
McCombie WR,
Krainer AR,
Zhang MQ

Bioinformatics
  27 (21): 3010-3016 ; Nov 2011   PMC3198574
[Abstract]
[DOI]

Establishing the baseline level of repetitive element expression in the human cortex
Tyekucheva S,
Yolken RH,
McCombie WR,
Parla J,
Kramer M,
Wheelan SJ,
Sabunciyan S

BMC Genomics
  12 (0): article number 495; Oct 10 2011   PMC3207997
[Abstract]
[DOI] [Full Text]

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment
Hodges E,
Molaro A,
Dos Santos CO,
Thekkat P,
Song Q,
Uren PJ,
Park JH,
Butler J,
Rafii S,
McCombie WR,
Smith A,
Hannon GJ

Molecular Cell
  44 (1): 17-28; Oct. 7 2011  
[Abstract]
[DOI]

A comparative analysis of exome capture
Parla JS,
Iossifov I,
Grabill I,
Spector MS,
Kramer M,
McCombie WR

Genome Biol
  12 (9): R97; Sep 29 2011   NLM
[Abstract]
[DOI] [Full Text]

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates
Molaro A,
Hodges E,
Fang F,
Song Q,
McCombie WR,
Hannon GJ,
Smith A

Cell
  146 (6): 1029-1041; Sep 16 2011   PMC3205962
[Abstract]
[DOI]

Discovery of novel human breast cancer micrornas from deep sequencing data by analysis of pri-microrna secondary structures
Ryu S,
Joshi N,
McDonnell K,
Woo J,
Choi H,
Gao D,
McCombie WR,
Mittal V

PLoS ONE
  6 (2): Feb 8 2011   PMC3035615
[Abstract]
[DOI] [Full Text] [PDF]

Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data
Sabot F,
Picault N,
Elbaidouri M,
Llauro C,
Chaparro C,
Piegu B,
Roulin A,
Guiderdoni E,
Delabastide M,
McCombie WR,
Panaud O

Plant J
  66 (2): 241-246; Jan 10 2011  
[Abstract]
[DOI]

Whole transcriptome analysis of the fasting and fed Burmese python heart: insights into extreme physiological cardiac adaptation
Wall CE,
Cozza S,
Riquelme CA,
McCombie WR,
Heimiller JK,
Marr TG,
Leinwand LA

Physiological Genomics
  43 (2): 69-76; Jan 2011   PMC3026562
[Abstract]
[DOI]

High-Throughput Sequencing
Parla J,
Kramer MR,
McCombie WR
In:
Microbial Forensics (Second Edition)
(ed. ) San Diego: Academic Press; 2011. : 461-478  
[Abstract]
[DOI] [Full Text] [PDF]

Tumour evolution inferred by single-cell sequencing
Navin NE,
Kendall JT,
Troge JE,
Andrews P,
Rodgers ,
McIndoo J,
Cook K,
Stepansky ,
Levy D,
Esposito D,
Muthuswamy L,
Krasnitz A,
McCombie WR,
Hicks JB,
Wigler MH

Nature
  (0): 2011   Elsevier
[Abstract]
[DOI] [Full Text]

The genome of Theobroma cacao
Argout X,
Salse J,
Aury JM,
Guiltinan MJ,
Droc G,
Gouzy J,
Allegre M,
Chaparro C,
Legavre T,
Maximova SN,
Abrouk M,
Murat F,
Fouet O,
Poulain J,
Ruiz M,
Roguet Y,
Rodier-Goud M,
Barbosa-Neto JF,
Sabot F,
Kudrna D,
Ammiraju JS,
Schuster SC,
Carlson JE,
Sallet E,
Schiex T,
Dievart A,
Kramer MR,
Gelley L,
Shi Z,
Bérard A,
Viot C,
Boccara M,
Risterucci AM,
Guignon V,
Sabau X,
Axtell MJ,
Ma Z,
Zhang Y,
Brown S,
Bourge M,
Golser W,
Song X,
Clement D,
Rivallan R,
Tahi M,
Akaza JM,
Pitollat B,
Gramacho K,
DHont A,
Brunel D,
Infante D,
Kebe I,
Costet P,
Wing R,
McCombie WR,
Guiderdoni E,
Quetier F,
Panaud O,
Wincker P,
Bocs S,
Lanaud C

Nature Genetics
  43 (2): 101-108; 2011   Elsevier Scopus
[Abstract]
[DOI]

Small RNA-based silencing strategies for transposons in the process of invading Drosophila species
Rozhkov NV,
Aravin AA,
Zelentsova ES,
Schostak NG,
Sachidanandam R,
McCombie WR,
Hannon GJ,
Evgenev MB

RNA
  16 (8): 1634-1645; Aug 2010   PMCID: PMC2905761
[Abstract]
[DOI] [Full Text] [PDF]

Pigeonpea genomics initiative (PGI): An international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)
Varshney RK,
Penmetsa RV,
Dutta S,
Kulwal PL,
Saxena RK,
Datta S,
Sharma TR,
Rosen B,
Carrasquilla-Garcia N,
Farmer AD,
Dubey A,
Saxena KB,
Gao J,
Fakrudin B,
Singh MN,
Singh BP,
Wanjari KB,
Yuan M,
Srivastava RK,
Kilian A,
Upadhyaya HD,
Mallikarjuna N,
Town CD,
Bruening GE,
He G,
May GD,
McCombie WR,
Jackson SA,
Singh NK,
Cook DR

Molecular Breeding
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[Abstract]
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The B73 Maize Genome: Complexity, Diversity, and Dynamics
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Ware DH,
Fulton RS,
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Wei FS,
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Zhang JW,
Fulton L,
Graves TA,
Minx P,
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Tomlinson C,
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Delehaunty K,
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Du FY,
Kim K,
Abbott RM,
Cotton M,
Levy A,
Marchetto P,
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Jackson SM,
Gillam B,
Chen WZ,
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Cardenas M,
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Applebaum E,
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Kanchi K,
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Scimone A,
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Wang T,
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Hodges J,
Ingenthron E,
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Delgado B,
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Chinwalla A,
Leonard S,
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Kudrna D,
Currie J,
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Angelova A,
Rajasekar S,
Mueller T,
Lomeli R,
Scara G,
Ko A,
Delaney K,
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Lopez G,
Campos D,
Braidotti M,
Ashley E,
Golser W,
Kim H,
Lee S,
Lin JK,
Dujmic Z,
Kim W,
Talag J,
Zuccolo A,
Fan C,
Sebastian A,
Kramer MR,
Spiegel L,
Nascimento L,
Zutavern T,
Miller B,
Ambroise C,
Muller S,
Spooner W,
Narechania A,
Ren LY,
Wei S,
Kumari S,
Faga BP,
Levy MJ,
McMahan L,
Van Buren P,
Vaughn MW,
Ying K,
Yeh CT,
Emrich SJ,
Jia Y,
Kalyanaraman A,
Hsia AP,
Barbazuk WB,
Baucom RS,
Brutnell TP,
Carpita NC,
Chaparro C,
Chia JM,
Deragon JM,
Estill JC,
Fu Y,
Jeddeloh JA,
Han YJ,
Lee H,
Li PH,
Lisch DR,
Liu SZ,
Liu ZJ,
Nagel DH,
McCann MC,
SanMiguel P,
Myers AM,
Nettleton D,
Nguyen J,
Penning BW,
Ponnala L,
Schneider KL,
Schwartz DC,
Sharma A,
Soderlund C,
Springer NM,
Sun Q,
Wang H,
Waterman M,
Westerman R,
Wolfgruber TK,
Yang LX,
Yu Y,
Zhang LF,
Zhou SG,
Zhu Q,
Bennetzen JL,
Dawe RK,
Jiang JM,
Jiang N,
Presting GG,
Wessler SR,
Aluru S,
Martienssen RA,
Clifton SW,
McCombie WR,
Wing RA,
Wilson RK

Science
  326 (5956): 1112-1115; Nov 20 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Detailed analysis of a contiguous 22-Mb region of the maize genome
Wei F,
Stein JC,
Liang C,
Zhang J,
Fulton RS,
Baucom RS,
De Paoli E,
Zhou S,
Yang L,
Han Y,
Pasternak S,
Narechania A,
Zhang L,
Yeh CT,
Ying K,
Nagel DH,
Collura K,
Kudrna D,
Currie J,
Lin J,
Kim H,
Angelova A,
Scara G,
Wissotski M,
Golser W,
Courtney L,
Kruchowski S,
Graves TA,
Rock SM,
Adams S,
Fulton LA,
Fronick C,
Courtney W,
Kramer M,
Spiegel L,
Nascimento L,
Kalyanaraman A,
Chaparro C,
Deragon JM,
Miguel PS,
Jiang N,
Wessler SR,
Green PJ,
Yu Y,
Schwartz DC,
Meyers BC,
Bennetzen JL,
Martienssen RA,
McCombie WR,
Aluru S,
Clifton SW,
Schnable PS,
Ware D,
Wilson RK,
Wing RA

PLoS genetics
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[Abstract]
[DOI] [Full Text]

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing Dup removed 04/2012
Hodges E,
Smith AD,
Kendall JT,
Xuan Z,
Ravi K,
Rooks M,
Zhang MQ,
Ye K,
Bhattacharjee A,
Brizuela L,
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Wigler MH,
Hannon GJ,
Hicks JB

Genome Res
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[Abstract]
[DOI] [Full Text] [PDF]

Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing
Irvine DV,
Goto DB,
Vaughn MW,
Nakaseko Y,
McCombie WR,
Yanagida M,
Martienssen RA

Genome Res
  19 (6): 1077-1083; Jul 2009   PMCID: PMC2694473
[Abstract]
[DOI] [Full Text] [PDF]

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing
Hodges E,
Rooks M,
Xuan Z,
Bhattacharjee A,
Gordon D,
Brizuela L,
McCombie WR,
Hannon GJ

Nat. Protocols
  4 (6): 960-974; May 28 2009  
[Abstract]
[DOI] [Full Text] [PDF]

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary
Malone CD,
Brennecke J,
Dus M,
Stark A,
McCombie WR,
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Hannon GJ

Cell
  137 (3): 522-535 ; May 1 2009  
[Abstract]
[DOI] [Full Text] [PDF]

An Oncogenomics-Based In Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer
Zender L,
Xue W,
Zuber J,
Semighini CP,
Krasnitz A,
Ma B,
Zender P,
Kubicka S,
Luk JM,
Schirmacher P,
McCombie WR,
Wigler MH,
Hicks JB,
Hannon GJ,
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Cell
  135 (5): 852-864; Nov 28 2008   PMC2990916
[Abstract]
[DOI] [Full Text] [PDF]

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing
Erlich Y,
Mitra PP,
Delabastide M,
McCombie WR,
Hannon GJ

Nat Methods
  5 (8): 679 - 682; Aug 2008  
[Abstract]
[DOI] [Full Text] [PDF]

Topoisomerase levels determine chemotherapy response in vitro and in vivo
Burgess DJ,
Doles J,
Zender L,
Xue W,
Ma B,
McCombie WR,
Hannon GJ,
Lowe SW,
Hemann MT

Proc Natl Acad Sci U S A
  105 (25): 9053-9058; Jul 1 2008   PMCID: PMC2435590
[Abstract]
[DOI] [Full Text] [PDF]

Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA
Korshunova Y,
Maloney RK,
Lakey N,
Citek RW,
Bacher B,
Budiman A,
Ordway JM,
McCombie WR,
Leon J,
Jeddeloh JA,
McPherson JD

Genome Res
  18 (1): 19-29; Jan 2008   PMCID: PMC2134785
[Abstract]
[DOI] [Full Text] [PDF]

Genome-wide in situ exon capture for selective resequencing
Hodges E,
Xuan ZY,
Balija V,
Kramer MR,
Molla MN,
Smith SW,
Middle CM,
Rodesch MJ,
Albert TJ,
Hannon GJ,
McCombie WR

Nat Genet
  39 (12): 1522-7; Nov 4 2007  
[Abstract]
[DOI] [Full Text] [PDF]

Epigenetic natural variation in Arabidopsis thaliana
Vaughn MW,
Tanurdzic M,
Lippman Z,
Jiang H,
Carrasquillo R,
Rabinowicz PD,
Dedhia N,
McCombie WR,
Agier N,
Bulski A,
Colot V,