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17 Article(s) on File
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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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

The B73 Maize Genome: Complexity, Diversity, and Dynamics
Schnable PS,
Ware DH,
Fulton RS,
Stein JC,
Wei FS,
Pasternak S,
Liang CZ,
Zhang JW,
Fulton L,
Graves TA,
Minx P,
Reily AD,
Courtney L,
Kruchowski SS,
Tomlinson C,
Strong C,
Delehaunty K,
Fronick C,
Courtney B,
Rock SM,
Belter E,
Du FY,
Kim K,
Abbott RM,
Cotton M,
Levy A,
Marchetto P,
Ochoa K,
Jackson SM,
Gillam B,
Chen WZ,
Yan L,
Higginbotham J,
Cardenas M,
Waligorski J,
Applebaum E,
Phelps L,
Falcone J,
Kanchi K,
Thane T,
Scimone A,
Thane N,
Henke J,
Wang T,
Ruppert J,
Shah N,
Rotter K,
Hodges J,
Ingenthron E,
Cordes M,
Kohlberg S,
Sgro J,
Delgado B,
Mead K,
Chinwalla A,
Leonard S,
Crouse K,
Collura K,
Kudrna D,
Currie J,
He RF,
Angelova A,
Rajasekar S,
Mueller T,
Lomeli R,
Scara G,
Ko A,
Delaney K,
Wissotski M,
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
  5 (11): e1000728; Nov 2009  
[Abstract]
[DOI] [Full Text]

The rice annotation project database (RAP-DB): 2008 update
Tanaka T,
Antonio BA,
Kikuchi S,
Matsumoto T,
Nagamura Y,
Numa H,
Sakai H,
Wu J,
Itoh T,
Sasaki T,
Aono R,
Fujii Y,
Habara T,
Harada E,
Kanno M,
Kawahara Y,
Kawashima H,
Kubooka H,
Matsuya A,
Nakaoka H,
Saichi N,
Sanbonmatsu R,
Sato Y,
Shinso Y,
Suzuki M,
Takeda JI,
Tanino M,
Todokoro F,
Yamaguchi K,
Yamamoto N,
Yamasaki C,
Imanishi T,
Okido T,
Tada M,
Ikeo K,
Tateno Y,
Gojobori T,
Lin YC,
Wei FJ,
Hsing YI,
Zhao Q,
Han B,
Kramer MR,
McCombie RW,
Lonsdale D,
ODonovan CC,
Whitfield EJ,
Apweiler R,
Koyanagi KO,
Khurana JP,
Raghuvanshi S,
Singh NK,
Tyagi AK,
Haberer G,
Fujisawa M,
Hosokawa S,
Ito Y,
Ikawa H,
Shibata M,
Yamamoto M,
Bruskiewich RM,
Hoen DR,
Bureau TE,
Namiki N,
Ohyanagi H,
Sakai Y,
Nobushima S,
Sakata K,
Barrero RA,
Souvorov A,
Smith-White B,
Tatusova T,
An S,
An G,
Oota S,
Fuks G,
Messing J,
Christie KR,
Lieberherr D,
Kim H,
Zuccolo A,
Wing RA,
Nobuta K,
Green PJ,
Lu C,
Meyers BC,
Chaparro C,
Piegu B,
Panaud O

Nucleic Acids Research
  36 (0): D1028-D1033; Jan 2008   PMCID: PMC2238920
[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]


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