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12 Article(s) on File
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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]

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]

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]

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

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

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]

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]

The transcriptional landscape of the mammalian genome
Carninci P,
Kasukawa T,
Katayama S,
Gough J,
Frith MC,
Maeda N,
Oyama R,
Ravasi T,
Lenhard B,
Wells C,
Kodzius R,
Shimokawa K,
Bajic VB,
Brenner SE,
Batalov S,
Forrest AR,
Zavolan M,
Davis MJ,
Wilming LG,
Aidinis V,
Allen JE,
Ambesi-Impiombato A,
Apweiler R,
Aturaliya RN,
Bailey TL,
Bansal M,
Baxter L,
Beisel KW,
Bersano T,
Bono H,
Chalk AM,
Chiu KP,
Choudhary V,
Christoffels A,
Clutterbuck DR,
Crowe ML,
Dalla E,
Dalrymple BP,
de Bono B,
della Gatta G,
di Bernardo D,
Down T,
Engstrom P,
Fagiolini M,
Faulkner G,
Fletcher CF,
Fukushima T,
Furuno M,
Futaki S,
Gariboldi M,
Georgii-Hemming P,
Gingeras TR,
Gojobori T,
Green RE,
Gustincich S,
Harbers M,
Hayashi Y,
Hensch TK,
Hirokawa N,
Hill D,
Huminiecki L,
Iacono M,
Ikeo K,
Iwama A,
Ishikawa T,
Jakt M,
Kanapin A,
Katoh M,
Kawasawa Y,
Kelso J,
Kitamura H,
Kitano H,
Kollias G,
Krishnan SP,
Kruger AF,
Kummerfeld SK,
Kurochkin IV,
Lareau LF,
Lazarevic D,
Lipovich L,
Liu J,
Liuni S,
McWilliam S,
Madan Babu M,
Madera M,
Marchionni L,
Matsuda H,
Matsuzawa S,
Miki H,
Mignone F,
Miyake S,
Morris K,
Mottagui-Tabar S,
Mulder N,
Nakano N,
Nakauchi H,
Ng P,
Nilsson R,
Nishiguchi S,
Nishikawa S,
Nori F,
Ohara O,
Okazaki Y,
Orlando V,
Pang KC,
Pavan WJ,
Pavesi G,
Pesole G,
Petrovsky N,
Piazza S,
Reed J,
Reid JF,
Ring BZ,
Ringwald M,
Rost B,
Ruan Y,
Salzberg SL,
Sandelin A,
Schneider C,
Schönbach C,
Sekiguchi K,
Semple CA,
Seno S,
Sessa L,
Sheng Y,
Shibata Y,
Shimada H,
Shimada K,
Silva D,
Sinclair B,
Sperling S,
Stupka E,
Sugiura K,
Sultana R,
Takenaka Y,
Taki K,
Tammoja K,
Tan SL,
Tang S,
Taylor MS,
Tegner J,
Teichmann SA,
Ueda HR,
van Nimwegene E,
Verardo R,
Wei CL,
Yagi K,
Yamanishi H,
Zabarovsky E,
Zhu S,
Zimmer A,
Hide W,
Bult C,
Grimmond SM,
Teasdale RD,
Liu ET,
Brusic V,
Quackenbush J,
Wahlestedt C,
Mattick JS,
Hume DA,
Kai C,
Sasaki D,
Tomaru Y,
Fukuda S,
Kanamori-Katayama M,
Suzuki M,
Aoki J,
Arakawa T,
Iida J,
Imamura K,
Itoh M,
Kato T,
Kawaji H,
Kawagashira N,
Kawashima T,
Kojima M,
Kondo S,
Konno H,
Nakano K,
Ninomiya N,
Nishio T,
Okada M,
Plessy C,
Shibata K,
Shiraki T,
Suzuki S,
Tagami M,
Waki K,
Watahiki A,
Okamura-Oho Y,
Suzuki H,
Kawai J,
Hayashizaki Y

Science
  309 (5740): 1559-1563; 2005  
[Abstract]
[Full Text]

The ENCODE (ENCyclopedia of DNA Elements) Project
Feingold EA,
Good PJ,
Guyer MS,
Kamholz S,
Liefer L,
Wetterstrand K,
Collins FS,
Gingeras TR,
Kampa D,
Sekinger EA,
Cheng J,
Hirsch H,
Ghosh S,
Zhu Z,
Patel S,
Piccolboni A,
Yang A,
Tammana H,
Bekiranov S,
Kapranov P,
Harrison R,
Church G,
Struhl K,
Ren B,
Kim TH,
Barrera LO,
Qu C,
van Calcar S,
Luna R,
Glass CK,
Rosenfeld MG,
Guigo R,
Antonarakis SE,
Birney E,
Brent M,
Pachter L,
Reymond A,
Dermitzakis ET,
Dewey C,
Keefe D,
Denoeud F,
Lagarde J,
Ashurst J,
Hubbard T,
Wesselink JJ,
Castelo R,
Eyras E,
Myers RM,
Sidow A,
Batzoglou S,
Trinklein ND,
Hartman SJ,
Aldred SF,
Anton E,
Schroeder DI,
Marticke SS,
Nguyen L,
Schmutz J,
Grimwood J,
Dickson M,
Cooper GM,
Stone EA,
Asimenos G,
Brudno M,
Dutta A,
Karnani N,
Taylor CM,
Kim HK,
Robins G,
Stamatoyannopoulos G,
Stamatoyannopoulos JA,
Dorschner M,
Sabo P,
Hawrylycz M,
Humbert R,
Wallace J,
Yu M,
Navas PA,
McArthur M,
Noble WS,
Dunham I,
Koch CM,
Andrews RM,
Clelland GK,
Wilcox S,
Fowler JC,
James KD,
Groth P,
Dovey OM,
Ellis PD,
Wraight VL,
Mungall AJ,
Dhami P,
Fiegler H,
Langford CF,
Carter NP,
Vetrie D,
Snyder M,
Euskirchen G,
Urban AE,
Nagalakshmi U,
Rinn J,
Popescu G,
Bertone P,
Hartman S,
Rozowsky J,
Emanuelsson O,
Royce T,
Chung S,
Gerstein M,
Lian Z,
Lian J,
Nakayama Y,
Weissman S,
Stolc V,
Tongprasit W,
Sethi H,
Jones S,
Marra M,
Shin H,
Schein J,
Clamp M,
Lindblad-Toh K,
Chang J,
Jaffe DB,
Kamal M,
Lander ES,
Mikkelsen TS,
Vinson J,
Zody MC,
de Jong PJ,
Osoegawa K,
Nefedov M,
Zhu B,
Baxevanis AD,
Wolfsberg TG,
Crawford GE,
Whittle J,
Holt IE,
Vasicek TJ,
Zhou D,
Luo S,
Green ED,
Bouffard GG,
Margulies EH,
Portnoy ME,
Hansen NF,
Thomas PJ,
McDowell JC,
Maskeri B,
Young AC,
Idol JR,
Blakesley RW,
Schuler G,
Miller W,
Hardison R,
Elnitski L,
Shah P,
Salzberg SL,
Pertea M,
Majoros WH,
Haussler D,
Thomas D,
Rosenbloom KR,
Clawson H,
Siepel A,
Kent WJ,
Weng Z,
Jin S,
Halees A,
Burden H,
Karaoz U,
Fu Y,
Yu Y,
Ding C,
Cantor CR,
Kingston RE,
Dennis J,
Green RD,
Singer MA,
Richmond TA,
Norton JE,
Farnham PJ,
Oberley MJ,
Inman DR,
McCormick MR,
Kim H,
Middle CL,
Pirrung MC,
Fu XD,
Kwon YS,
Ye Z,
Dekker J,
Tabuchi TM,
Gheldof N,
Dostie J,
Harvey SC

Science
  306 (5696): 636-640; 2004  
[Abstract]
[DOI] [Full Text]

In-depth view of structure, activity, and evolution of rice chromosome 10
Yu YS,
Rambo T,
Currie J,
Saski C,
Kim HR,
Collura K,
Thompson S,
Simmons J,
Yang TJ,
Nah G,
Patel AJ,
Thurmond S,
Henry D,
Oates R,
Palmer M,
Pries G,
Gibson J,
Anderson H,
Paradkar M,
Crane L,
Dale J,
Carver MB,
Wood T,
Frisch D,
Engler F,
Soderlund C,
Palmer LE,
Tetylman L,
Nascimento L,
de la Bastide M,
Spiegel L,
Ware D,
OShaughnessy A,
Dike S,
Dedhia N,
Preston R,
Huang E,
Ferraro K,
Kuit K,
Miller B,
Zutavern T,
Katzenberger F,
Muller S,
Balija V,
Martienssen RA,
Stein L,
Minx P,
Johnson D,
Cordum H,
Mardis E,
Cheng ZK,
Jiang JM,
Wilson R,
McCombie WR,
Wing RA,
Yuan QP,
Shu OY,
Liu J,
Jones KM,
Gansberger K,
Moffat K,
Hill J,
Tsitrin T,
Overton L,
Bera J,
Kim M,
Jin SH,
Tallon L,
Ciecko A,
Pai G,
Van Aken S,
Utterback T,
Reidmuller S,
Bormann J,
Feldblyum T,
Hsiao J,
Zismann V,
Blunt S,
de Vazeilles A,
Shaffer T,
Koo H,
Suh B,
Yang Q,
Haas B,
Peterson J,
Pertea M,
Volfovsky N,
Wortman J,
White O,
Salzberg SL,
Fraser CM,
Buell CR,
Messing J,
Song RT,
Fuks G,
Llaca V,
Kovchak S,
Young S,
Bowers JE,
Paterson AH,
Johns MA,
Mao L,
Pan HQ,
Dean RA,
Rice Chromosome 10 S

Science
  300 (5625): 1566-1569; Jun 6 2003  
[Abstract]
[Full Text]

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Kaul S,
Koo HL,
Jenkins J,
Rizzo M,
Rooney T,
Tallon LJ,
Feldblyum T,
Nierman W,
Benito MI,
Lin XY,
Town CD,
Venter JC,
Fraser CM,
Tabata S,
Nakamura Y,
Kaneko T,
Sato S,
Asamizu E,
Kato T,
Kotani H,
Sasamoto S,
Ecker JR,
Theologis A,
Federspiel NA,
Palm CJ,
Osborne BI,
Shinn P,
Conway AB,
Vysotskaia VS,
Dewar K,
Conn L,
Lenz CA,
Kim CJ,
Hansen NF,
Liu SX,
Buehler E,
Altafi H,
Sakano H,
Dunn P,
Lam B,
Pham PK,
Chao Q,
Nguyen M,
Yu GX,
Chen HM,
Southwick A,
Lee JM,
Miranda M,
Toriumi MJ,
Davis RW,
Wambutt R,
Murphy G,
Dusterhoft A,
Stiekema W,
Pohl T,
Entian KD,
Terryn N,
Volckaert G,
Salanoubat M,
Choisne N,
Rieger M,
Ansorge W,
Unseld M,
Fartmann B,
Valle G,
Artiguenave F,
Weissenbach J,
Quetier F,
Wilson RK,
de la Bastide M,
Sekhon M,
Huang E,
Spiegel L,
Gnoj L,
Pepin K,
Murray J,
Johnson D,
Habermann K,
Dedhia N,
Parnell L,
Preston R,
Hillier L,
Chen E,
Marra M,
Martienssen R,
McCombie WR,
Mayer K,
White O,
Bevan M,
Lemcke K,
Creasy TH,
Bielke C,
Haas B,
Haase D,
Maiti R,
Rudd S,
Peterson J,
Schoof H,
Frishman D,
Morgenstern B,
Zaccaria P,
Ermolaeva M,
Pertea M,
Quackenbush J,
Volfovsky N,
Wu DY,
Lowe TM,
Salzberg SL,
Mewes HW,
Rounsley S,
Bush D,
Subramaniam S,
Levin I,
Norris S,
Schmidt R,
Acarkan A,
Bancroft I,
Brennicke A,
Eisen JA,
Bureau T,
Legault BA,
Le QH,
Agrawal N,
Yu Z,
Copenhaver GP,
Luo S,
Pikaard CS,
Preuss D,
Paulsen IT,
Sussman M,
Britt AB,
Selinger DA,
Pandey R,
Mount DW,
Chandler VL,
Jorgensen RA,
Pikaard C,
Juergens G,
Meyerowitz EM,
Dangl J,
Jones JD,
Chen M

Nature
  408 (6814): 796-815; Dec 14 2000  
[Abstract]
[Full Text]


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