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16 Article(s) on File
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Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
Berezikov E,
Robine N,
Samsonova A,
Westholm JO,
Naqvi A,
Hung JH,
Okamura K,
Dai Q,
Bortolamiol-Becet D,
Martin R,
Zhao YJ,
Zamore PD,
Hannon GJ,
Marra MA,
Weng ZP,
Perrimon N,
Lai EC

Genome Research
  21 (2): 203-215; Feb 2011   PMC3032924
[Abstract]
[DOI]

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
Harris RA,
Wang T,
Coarfa C,
Nagarajan RP,
Hong C,
Downey SL,
Johnson BE,
Fouse SD,
Delaney A,
Zhao Y,
Olshen A,
Ballinger T,
Zhou X,
Forsberg KJ,
Gu J,
Echipare L,
OGeen H,
Lister R,
Pelizzola M,
Xi Y,
Epstein CB,
Bernstein BE,
Hawkins RD,
Ren B,
Chung WY,
Gu H,
Bock C,
Gnirke A,
Zhang MQ,
Haussler D,
Ecker JR,
Li W,
Farnham PJ,
Waterland RA,
Meissner A,
Marra MA,
Hirst M,
Milosavljevic A,
Costello JF

Nature Biotechnology
  28 (10): 1097-1105; 2010   PMCID: PMC2955169
[Abstract]
[DOI] [Full Text] [PDF]

An integrated strategy to study muscle development and myofilament structure in Caenorhabditis elegans
Meissner B,
Warner A,
Wong K,
Dube N,
Lorch A,
McKay SJ,
Khattra J,
Rogalski T,
Somasiri A,
Chaudhry I,
Fox RM,
Miller Iii DM,
Baillie DL,
Holt RA,
Jones SJ,
Marra MA,
Moerman DG

PLoS Genet
  5 (6): e1000537; Jun 2009   PMCID: PMC2694363
[Abstract]
[DOI] [Full Text] [PDF]

Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics
Chen N,
Mah A,
Blacque OE,
Chu J,
Phgora K,
Bakhoum MW,
Newbury CR,
Khattra J,
Chan SW,
Go A,
Efimenko E,
Johnsen RC,
Phirke P,
Swoboda P,
Marra M,
Moerman DG,
Leroux MR,
Baillie DL,
Stein LD

Genome Biology
  7 (12): R126; Dec 22 2006  
[Abstract]
[DOI] [Full Text] [PDF]

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]

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics
Stein LD,
Bao Z,
Blasiar D,
Blumenthal T,
Brent MR,
Chen N,
Chinwalla A,
Clarke L,
Clee C,
Coghlan A,
Coulson A,
DEustachio P,
Fitch DH,
Fulton LA,
Fulton RE,
Griffiths-Jones S,
Harris TW,
Hillier LW,
Kamath R,
Kuwabara PE,
Mardis ER,
Marra MA,
Miner TL,
Minx P,
Mullikin JC,
Plumb RW,
Rogers J,
Schein JE,
Sohrmann M,
Spieth J,
Stajich JE,
Wei C,
Willey D,
Wilson RK,
Durbin R,
Waterston RH

PLoS Biol
  1 (2): E45; Nov 2003  
[Abstract]
[DOI] [Full Text]

Initial sequencing and analysis of the human genome
Lander ES,
Linton LM,
Birren B,
Nusbaum C,
Zody MC,
Baldwin J,
Devon K,
Dewar K,
Doyle M,
FitzHugh W,
Funke R,
Gage D,
Harris K,
Heaford A,
Howland J,
Kann L,
Lehoczky J,
LeVine R,
McEwan P,
McKernan K,
Meldrim J,
Mesirov JP,
Miranda C,
Morris W,
Naylor J,
Raymond C,
Rosetti M,
Santos R,
Sheridan A,
Sougnez C,
Stange-Thomann N,
Stojanovic N,
Subramanian A,
Wyman D,
Rogers J,
Sulston J,
Ainscough R,
Beck S,
Bentley D,
Burton J,
Clee C,
Carter N,
Coulson A,
Deadman R,
Deloukas P,
Dunham A,
Dunham I,
Durbin R,
French L,
Grafham D,
Gregory S,
Hubbard T,
Humphray S,
Hunt A,
Jones M,
Lloyd C,
McMurray A,
Matthews L,
Mercer S,
Milne S,
Mullikin JC,
Mungall A,
Plumb R,
Ross M,
Shownkeen R,
Sims S,
Waterston RH,
Wilson RK,
Hillier LW,
McPherson JD,
Marra MA,
Mardis ER,
Fulton LA,
Chinwalla AT,
Pepin KH,
Gish WR,
Chissoe SL,
Wendl MC,
Delehaunty KD,
Miner TL,
Delehaunty A,
Kramer JB,
Cook LL,
Fulton RS,
Johnson DL,
Minx PJ,
Clifton SW,
Hawkins T,
Branscomb E,
Predki P,
Richardson P,
Wenning S,
Slezak T,
Doggett N,
Cheng JF,
Olsen A,
Lucas S,
Elkin C,
Uberbacher E,
Frazier M,
Gibbs RA,
Muzny DM,
Scherer SE,
Bouck JB,
Sodergren EJ,
Worley KC,
Rives CM,
Gorrell JH,
Metzker ML,
Naylor SL,
Kucherlapati RS,
Nelson DL,
Weinstock GM,
Sakaki Y,
Fujiyama A,
Hattori M,
Yada T,
Toyoda A,
Itoh T,
Kawagoe C,
Watanabe H,
Totoki Y,
Taylor T,
Weissenbach J,
Heilig R,
Saurin W,
Artiguenave F,
Brottier P,
Bruls T,
Pelletier E,
Robert C,
Wincker P,
Rosenthal A,
Platzer M,
Nyakatura G,
Taudien S,
Rump A,
Yang HM,
Yu J,
Wang J,
Huang GY,
Gu J,
Hood L,
Rowen L,
Madan A,
Qin SZ,
Davis RW,
Federspiel NA,
Abola AP,
Proctor MJ,
Myers RM,
Schmutz J,
Dickson M,
Grimwood J,
Cox DR,
Olson MV,
Kaul R,
Shimizu N,
Kawasaki K,
Minoshima S,
Evans GA,
Athanasiou M,
Schultz R,
Roe BA,
Chen F,
Pan HQ,
Ramser J,
Lehrach H,
Reinhardt R,
McCombie WR,
de la Bastide M,
Dedhia N,
Blocker H,
Hornischer K,
Nordsiek G,
Agarwala R,
Aravind L,
Bailey JA,
Bateman A,
Batzoglou S,
Birney E,
Bork P,
Brown DG,
Burge CB,
Cerutti L,
Chen HC,
Church D,
Clamp M,
Copley RR,
Doerks T,
Eddy SR,
Eichler EE,
Furey TS,
Galagan J,
Gilbert JG,
Harmon C,
Hayashizaki Y,
Haussler D,
Hermjakob H,
Hokamp K,
Jang WH,
Johnson LS,
Jones TA,
Kasif S,
Kaspryzk A,
Kennedy S,
Kent WJ,
Kitts P,
Koonin EV,
Korf I,
Kulp D,
Lancet D,
Lowe TM,
McLysaght A,
Mikkelsen T,
Moran JV,
Mulder N,
Pollara VJ,
Ponting CP,
Schuler G,
Schultz JR,
Slater G,
Smit AF,
Stupka E,
Szustakowki J,
Thierry-Mieg D,
Thierry-Mieg J,
Wagner L,
Wallis J,
Wheeler R,
Williams A,
Wolf YI,
Wolfe KH,
Yang SP,
Yeh RF,
Collins F,
Guyer MS,
Peterson J,
Felsenfeld A,
Wetterstrand KA,
Patrinos A

Nature
  409 (6822): 860-921; Feb 2001  
[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]

Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana
Tabata S,
Kaneko T,
Nakamura Y,
Kotani H,
Kato T,
Asamizu E,
Miyajima N,
Sasamoto S,
Kimura T,
Hosouchi T,
Kawashima K,
Kohara M,
Matsumoto M,
Matsuno A,
Muraki A,
Nakayama S,
Nakazaki N,
Naruo K,
Okumura S,
Shinpo S,
Takeuchi C,
Wada T,
Watanabe A,
Yamada M,
Yasuda M,
Sato S,
de la Bastide M,
Huang E,
Spiegel L,
Gnoj L,
OShaughnessy A,
Preston R,
Habermann K,
Murray J,
Johnson D,
Rohlfing T,
Nelson J,
Stoneking T,
Pepin K,
Spieth J,
Sekhon M,
Armstrong J,
Becker M,
Belter E,
Cordum H,
Cordes M,
Courtney L,
Courtney W,
Dante M,
Du H,
Edwards J,
Fryman J,
Haakensen B,
Lamar E,
Latreille P,
Leonard S,
Meyer R,
Mulvaney E,
Ozersky P,
Riley A,
Strowmatt C,
Wagner-McPherson C,
Wollam A,
Yoakum M,
Bell M,
Dedhia N,
Parnell L,
Shah R,
Rodriguez M,
See LH,
Vil D,
Baker J,
Kirchoff K,
Toth K,
King L,
Bahret A,
Miller B,
Marra M,
Martienssen R,
McCombie WR,
Wilson RK,
Murphy G,
Bancroft I,
Volckaert G,
Wambutt R,
Dusterhoft A,
Stiekema W,
Pohl T,
Entian KD,
Terryn N,
Hartley N,
Bent E,
Johnson S,
Langham SA,
McCullagh B,
Robben J,
Grymonprez B,
Zimmermann W,
Ramsperger U,
Wedler H,
Balke K,
Wedler E,
Peters S,
van Staveren M,
Dirkse W,
Mooijman P,
Lankhorst RK,
Weitzenegger T,
Bothe G,
Rose M,
Hauf J,
Berneiser S,
Hempel S,
Feldpausch M,
Lamberth S,
Villarroel R,
Gielen J,
Ardiles W,
Bents O,
Lemcke K,
Kolesov G,
Mayer K,
Rudd S,
Schoof H,
Schueller C,
Zaccaria P,
Mewes HW,
Bevan M,
Fransz P

Nature
  408 (6814): 823-6; Dec 14 2000  
[Abstract]
[DOI] [Full Text]

The complete sequence of a heterochromatic island from a higher eukaryote
McCombie WR,
de la Bastide M,
Habermann K,
Parnell L,
Dedhia N,
Gnoj L,
Schutz K,
Huang E,
Spiegel L,
Yordan C,
Sehkon M,
Murray J,
Sheet P,
Cordes M,
Threideh J,
Stoneking T,
Kalicki J,
Graves T,
Harmon G,
Edwards J,
Latreille P,
Courtney L,
Cloud J,
Abbott A,
Scott K,
Johnson D,
Minx P,
Bentley D,
Fulton B,
Miller N,
Greco T,
Kemp K,
Kramer J,
Fulton L,
Mardis E,
Dante M,
Pepin K,
Hillier L,
Nelson J,
Spieth J,
Simorowski J,
May B,
Ma P,
Preston R,
Vil D,
See LH,
Shekher M,
Matero A,
Shah R,
Swaby I,
OShaughnessy A,
Rodriguez M,
Hoffman J,
Till S,
Granat S,
Shohdy N,
Hasegawa A,
Hameed A,
Lodhi M,
Johnson A,
Chen E,
Marra M,
Wilson RK,
Martienssen R,
Washington Univ Geno ,
PE Biosyst Arabidops

Cell
  100 (3): 377-386; Feb 4 2000  
[Abstract]
[Full Text]

Genetic definition and sequence analysis of Arabidopsis centromeres
Copenhaver GP,
Nickel K,
Kuromori T,
Benito MI,
Kaul S,
Lin XY,
Bevan M,
Murphy G,
Harris B,
Parnell LD,
McCombie WR,
Martienssen RA,
Marra M,
Preuss D

Science
  286 (5449): 2468-2474; Dec 24 1999  
[Abstract]
[DOI] [Full Text]

Genetic definition and sequence analysis of Arabidopsis centromeres
Copenhaver GP,
Nickel K,
Kuromori T,
Benito MI,
Kaul S,
Lin X,
Bevan M,
Murphy G,
Harris B,
Parnell LD,
McCombie WR,
Martienssen RA,
Marra M,
Preuss D

Science
  286 (5449): 2468-74; Dec 24 1999  
[Abstract]
[DOI] [Full Text]

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
Mayer K,
Schuller C,
Wambutt R,
Murphy G,
Volckaert G,
Pohl T,
Dusterhoft A,
Stiekema W,
Entian KD,
Terryn N,
Harris B,
Ansorge W,
Brandt P,
Grivell L,
Rieger M,
Weichselgartner M,
de Simone V,
Obermaier B,
Mache R,
Muller M,
Kreis M,
Delseny M,
Puigdomenech P,
Watson M,
Schmidtheini T,
Reichert B,
Portatelle D,
Perez-Alonso M,
Boutry M,
Bancroft I,
Vos P,
Hoheisel J,
Zimmermann W,
Wedler H,
Ridley P,
Langham SA,
McCullagh B,
Bilham L,
Robben J,
Van der Schueren J,
Grymonprez B,
Chuang YJ,
Vandenbussche F,
Braeken M,
Weltjens I,
Voet M,
Bastiaens I,
Aert R,
Defoor E,
Weitzenegger T,
Bothe G,
Ramsperger U,
Hilbert H,
Braun M,
Holzer E,
Brandt A,
Peters S,
van Staveren M,
Dirske W,
Mooijman P,
Klein Lankhorst R,
Rose M,
Hauf J,
Kotter P,
Berneiser S,
Hempel S,
Feldpausch M,
Lamberth S,
Van den Daele H,
De Keyser A,
Buysshaert C,
Gielen J,
Villarroel R,
De Clercq R,
Van Montagu M,
Rogers J,
Cronin A,
Quail M,
Bray-Allen S,
Clark L,
Doggett J,
Hall S,
Kay M,
Lennard N,
McLay K,
Mayes R,
Pettett A,
Rajandream MA,
Lyne M,
Benes V,
Rechmann S,
Borkova D,
Blocker H,
Scharfe M,
Grimm M,
Lohnert TH,
Dose S,
de Haan M,
Maarse A,
Schafer M,
Muller-Auer S,
Gabel C,
Fuchs M,
Fartmann B,
Granderath K,
Dauner D,
Herzl A,
Neumann S,
Argiriou A,
Vitale D,
Liguori R,
Piravandi E,
Massenet O,
Quigley F,
Clabauld G,
Mundlein A,
Felber R,
Schnabl S,
Hiller R,
Schmidt W,
Lecharny A,
Aubourg S,
Chefdor F,
Cooke R,
Berger C,
Montfort A,
Casacuberta E,
Gibbons T,
Weber N,
Vandenbol M,
Bargues M,
Terol J,
Torres A,
Perez-Perez A,
Purnelle B,
Bent E,
Johnson S,
Tacon D,
Jesse T,
Heijnen L,
Schwarz S,
Scholler P,
Heber S,
Francs P,
Bielke C,
Frishman D,
Haase D,
Lemcke K,
Mewes HW,
Stocker S,
Zaccaria P,
Bevan M,
Wilson RK,
de la Bastide M,
Habermann K,
Parnell L,
Dedhia N,
Gnoj L,
Schutz K,
Huang E,
Spiegel L,
Sehkon M,
Murray J,
Sheet P,
Cordes M,
Abu-Threideh J,
Stoneking T,
Kalicki J,
Graves T,
Harmon G,
Edwards J,
Latreille P,
Courtney L,
Cloud J,
Abbott A,
Scott K,
Johnson D,
Minx P,
Bentley D,
Fulton B,
Miller N,
Greco T,
Kemp K,
Kramer J,
Fulton L,
Mardis E,
Dante M,
Pepin K,
Hillier L,
Nelson J,
Spieth J,
Ryan E,
Andrews S,
Geisel C,
Layman D,
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Nature
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