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257 Article(s) on File
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Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
Pervouchine DD,
Djebali S,
Breschi A,
Davis CA,
Barja PP,
Dobin A,
Tanzer A,
Lagarde J,
Zaleski C,
See LH,
Fastuca M,
Drenkow J,
Wang H,
Bussotti G,
Pei B,
Balasubramanian S,
Monlong J,
Harmanci A,
Gerstein M,
Beer MA,
Notredame C,
Guigo R,
Gingeras TR

Nat Commun
  6 (0): 5903; Jan 13 2015   Nlm
[Abstract]
[DOI] [Full Text]

SeqHBase: a big data toolset for family based sequencing data analysis
He M,
Person TN,
Hebbring SJ,
Heinzen E,
Ye Z,
Schrodi SJ,
McPherson EW,
Lin SM,
Peissig PL,
Brilliant MH,
ORawe J,
Robison RJ,
Lyon GJ,
Wang K

J Med Genet
  (0): Jan 13 2015   Nlm
[Abstract]
[DOI] [Full Text]

An Arabidopsis gene regulatory network for secondary cell wall synthesis
Taylor-Teeples M,
Lin L,
de Lucas M,
Turco G,
Toal TW,
Gaudinier A,
Young NF,
Trabucco GM,
Veling MT,
Lamothe R,
Handakumbura PP,
Xiong G,
Wang C,
Corwin J,
Tsoukalas A,
Zhang L,
Ware D,
Pauly M,
Kliebenstein DJ,
Dehesh K,
Tagkopoulos I,
Breton G,
Pruneda-Paz JL,
Ahnert SE,
Kay SA,
Hazen SP,
Brady SM

Nature
  (0): Dec 24 2014   Nlm
[Abstract]
[DOI] [Full Text]

ErbB4 regulation of a thalamic reticular nucleus circuit for sensory selection
Ahrens S,
Jaramillo S,
Yu K,
Ghosh S,
Hwang G,
Paik R,
Lai C,
He M,
Huang ZJ,
Li B

Nature Neuroscience
  (0): Dec 15 2014   Nlm
[Abstract]
[DOI] [Full Text]

Organoid Models of Human and Mouse Ductal Pancreatic Cancer
Boj S,
Hwang C,
Baker L,
Chio I,
Engle D,
Corbo V,
Jager M,
Ponz-Sarvise M,
Tiriac H,
Spector M,
Gracanin A,
Oni T,
Yu K,
van Boxtel R,
Huch M,
Rivera K,
Wilson J,
Feigin M,
Öhlund D,
Handly-Santana A,
Ardito-Abraham C,
Ludwig M,
Elyada E,
Alagesan B,
Biffi G,
Yordanov G,
Delcuze B,
Creighton B,
Wright K,
Park Y,
Morsink FM,
Molenaar I,
Borel Rinkes I,
Cuppen E,
Hao Y,
Jin Y,
Nijman I,
Iacobuzio-Donahue C,
Leach S,
Pappin D,
Hammell M,
Klimstra D,
Basturk O,
Hruban R,
Offerhaus G,
Vries RJ,
Clevers H,
Tuveson D

Cell
  (0): Dec 2014 2014   NLM
[Abstract]
[DOI] [Full Text]

A comparative encyclopedia of DNA elements in the mouse genome
Yue F,
Cheng Y,
Breschi A,
Vierstra J,
Wu W,
Ryba T,
Sandstrom R,
Ma Z,
Davis C,
Pope BD,
Shen Y,
Pervouchine DD,
Djebali S,
Thurman RE,
Kaul R,
Rynes E,
Kirilusha A,
Marinov GK,
Williams BA,
Trout D,
Amrhein H,
Fisher-Aylor K,
Antoshechkin I,
DeSalvo G,
See LH,
Fastuca M,
Drenkow J,
Zaleski C,
Dobin A,
Prieto P,
Lagarde J,
Bussotti G,
Tanzer A,
Denas O,
Li K,
Bender MA,
Zhang M,
Byron R,
Groudine MT,
McCleary D,
Pham L,
Ye Z,
Kuan S,
Edsall L,
Wu YC,
Rasmussen MD,
Bansal MS,
Kellis M,
Keller CA,
Morrissey CS,
Mishra T,
Jain D,
Dogan N,
Harris RS,
Cayting P,
Kawli T,
Boyle AP,
Euskirchen G,
Kundaje A,
Lin S,
Lin Y,
Jansen C,
Malladi VS,
Cline MS,
Erickson DT,
Kirkup VM,
Learned K,
Sloan CA,
Rosenbloom KR,
Lacerda de Sousa B,
Beal K,
Pignatelli M,
Flicek P,
Lian J,
Kahveci T,
Lee D,
Kent WJ,
Ramalho Santos M,
Herrero J,
Notredame C,
Johnson A,
Vong S,
Lee K,
Bates D,
Neri F,
Diegel M,
Canfield T,
Sabo PJ,
Wilken MS,
Reh TA,
Giste E,
Shafer A,
Kutyavin T,
Haugen E,
Dunn D,
Reynolds AP,
Neph S,
Humbert R,
Hansen RS,
De Bruijn M,
Selleri L,
Rudensky A,
Josefowicz S,
Samstein R,
Eichler EE,
Orkin SH,
Levasseur D,
Papayannopoulou T,
Chang KH,
Skoultchi A,
Gosh S,
Disteche C,
Treuting P,
Wang Y,
Weiss MJ,
Blobel GA,
Cao X,
Zhong S,
Wang T,
Good PJ,
Lowdon RF,
Adams LB,
Zhou XQ,
Pazin MJ,
Feingold EA,
Wold B,
Taylor J,
Mortazavi A,
Weissman SM,
Stamatoyannopoulos JA,
Snyder MP,
Guigo R,
Gingeras TR,
Gilbert DM,
Hardison RC,
Beer MA,
Ren B

Nature
  515 (7527): 355-64; Nov 20 2014   Nlm
[Abstract]
[DOI] [Full Text]

microRNA100 inhibits self-renewal of breast cancer stem-like cells and breast tumor development
Deng L,
Shang L,
Bai S,
Chen J,
He X,
Trevino RM,
Chen S,
Li X,
Meng X,
Yu B,
Wang X,
Liu Y,
McDermott SP,
Ariazi AE,
Ginestier C,
Ibarra I,
Ke J,
Luther TK,
Clouthier SG,
Xu L,
Shan G,
Song E,
Yao H,
Hannon GJ,
Weiss SJ,
Wicha MS,
Liu S

Cancer Research
  74 (22): 6648-6660; Nov 15 2014   Nlm
[Abstract]
[DOI] [Full Text]

Global Ablation of Mouse Rab11a Impairs Early Embryogenesis and Matrix Metalloproteinase Secretion
Yu S,
Yehia G,
Wang J,
Stypulkowski E,
Sakamori R,
Jiang P,
Hernandez-Enriquez EB,
Tran TS,
Bonder EM,
Guo W,
Gao N

Journal of Biological Chemistry
  289 (6): 32030-32043; Nov 14 2014  
[Abstract]
[DOI] [Full Text]

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]

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil
Malaspinas A,
Lao O,
Schroeder H,
Rasmussen M,
Raghavan M,
Moltke I,
Campos PF,
Sagredo FS,
Rasmussen S,
Gonçalves VF,
Albrechtsen A,
Allentoft ME,
Johnson PL,
Li M,
Reis S,
Bernardo DV,
DeGiorgio M,
Duggan AT,
Bastos M,
Wang Y,
Stenderup J,
Moreno-Mayar JV,
Brunak S,
Sicheritz-Ponten T,
Hodges E,
Hannon GJ,
Orlando L,
Price TD,
Jensen JD,
Nielsen R,
Heinemeier J,
Olsen J,
Rodrigues-Carvalho C,
Lahr MM,
Neves WA,
Kayser M,
Higham T,
Stoneking M,
Pena SD,
Willerslev E

Current Biology
  24 (21): R1035-R1037; Nov 3 2014  
[Abstract]
[DOI] [Full Text]

Brain stem cell division and maintenance studied using multi-isotope imaging mass spectrometry (MIMS)
Enikolopov G,
Guillermier C,
Wang M,
Trakimas L,
Steinhauser ML,
Lechene C

Surface and Interface Analysis
  46 (0): 140-143; Nov 1 2014   Elsevier
[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]

Comparative analysis of the transcriptome across distant species
Gerstein MB,
Rozowsky J,
Yan KK,
Wang D,
Cheng C,
Brown JB,
Davis CA,
Hillier L,
Sisu C,
Li JJ,
Pei B,
Harmanci AO,
Duff MO,
Djebali S,
Alexander RP,
Alver BH,
Auerbach R,
Bell K,
Bickel PJ,
Boeck ME,
Boley NP,
Booth BW,
Cherbas L,
Cherbas P,
Di C,
Dobin A,
Drenkow J,
Ewing B,
Fang G,
Fastuca M,
Feingold EA,
Frankish A,
Gao G,
Good PJ,
Guigo R,
Hammonds A,
Harrow J,
Hoskins RA,
Howald C,
Hu L,
Huang H,
Hubbard TJ,
Huynh C,
Jha S,
Kasper D,
Kato M,
Kaufman TC,
Kitchen RR,
Ladewig E,
Lagarde J,
Lai E,
Leng J,
Lu Z,
MacCoss M,
May G,
McWhirter R,
Merrihew G,
Miller DM,
Mortazavi A,
Murad R,
Oliver B,
Olson S,
Park PJ,
Pazin MJ,
Perrimon N,
Pervouchine D,
Reinke V,
Reymond A,
Robinson G,
Samsonova A,
Saunders GI,
Schlesinger F,
Sethi A,
Slack FJ,
Spencer WC,
Stoiber MH,
Strasbourger P,
Tanzer A,
Thompson OA,
Wan KH,
Wang G,
Wang H,
Watkins KL,
Wen J,
Wen K,
Xue C,
Yang L,
Yip K,
Zaleski C,
Zhang Y,
Zheng H,
Brenner SE,
Graveley BR,
Celniker SE,
Gingeras TR,
Waterston R

Nature
  512 (7515): 445-8; Aug 28 2014   Nlm
[Abstract]
[DOI] [Full Text]

Copy number variation in obsessive-compulsive disorder and tourette syndrome: a cross-disorder study
McGrath LM,
Yu D,
Marshall C,
Davis LK,
Thiruvahindrapuram B,
Li B,
Cappi C,
Gerber G,
Wolf A,
Schroeder FA,
Osiecki L,
ODushlaine C,
Kirby A,
Illmann C,
Haddad S,
Gallagher P,
Fagerness JA,
Barr CL,
Bellodi L,
Benarroch F,
Bienvenu OJ,
Black DW,
Bloch MH,
Bruun RD,
Budman CL,
Camarena B,
Cath DC,
Cavallini MC,
Chouinard S,
Coric V,
Cullen B,
Delorme R,
Denys D,
Derks EM,
Dion Y,
Rosario MC,
Eapen V,
Evans P,
Falkai P,
Fernandez TV,
Garrido H,
Geller D,
Grabe HJ,
Grados MA,
Greenberg BD,
Gross-Tsur V,
Grunblatt E,
Heiman GA,
Hemmings SM,
Herrera LD,
Hounie AG,
Jankovic J,
Kennedy JL,
King RA,
Kurlan R,
Lanzagorta N,
Leboyer M,
Leckman JF,
Lennertz L,
Lochner C,
Lowe TL,
Lyon GJ,
Macciardi F,
Maier W,
McCracken JT,
McMahon W,
Murphy DL,
Naarden AL,
Neale BM,
Nurmi E,
Pakstis AJ,
Pato MT,
Pato CN,
Piacentini J,
Pittenger C,
Pollak Y,
Reus VI,
Richter MA,
Riddle M,
Robertson MM,
Rosenberg D,
Rouleau GA,
Ruhrmann S,
Sampaio AS,
Samuels J,
Sandor P,
Sheppard B,
Singer HS,
Smit JH,
Stein DJ,
Tischfield JA,
Vallada H,
Veenstra-VanderWeele J,
Walitza S,
Wang Y,
Wendland JR,
Shugart YY,
Miguel EC,
Nicolini H,
Oostra BA,
Moessner R,
Wagner M,
Ruiz-Linares A,
Heutink P,
Nestadt G,
Freimer N,
Petryshen T,
Posthuma D,
Jenike MA,
Cox NJ,
Hanna GL,
Brentani H,
Scherer SW,
Arnold PD,
Stewart SE,
Mathews CA,
Knowles JA,
Cook EH,
Pauls DL,
Wang K,
Scharf JM

Journal of the American Academy of Child and Adolescent Psychiatry
  53 (8): 910-9; Aug 2014   Nlm
[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]

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
Delaneau O,
Marchini J,
McVeanh GA,
Donnelly P,
Lunter G,
Marchini JL,
Myers S,
Gupta-Hinch A,
Iqbal Z,
Mathieson I,
Rimmer A,
Xifara DK,
Kerasidou A,
Churchhouse C,
Altshuler DM,
Gabriel SB,
Lander ES,
Gupta N,
Daly MJ,
DePristo MA,
Banks E,
Bhatia G,
Carneiro MO,
Del Angel G,
Genovese G,
Handsaker RE,
Hartl C,
McCarroll SA,
Nemesh JC,
Poplin RE,
Schaffner SF,
Shakir K,
Sabeti PC,
Grossman SR,
Tabrizi S,
Tariyal R,
Li H,
Reich D,
Durbin RM,
Hurles ME,
Balasubramaniam S,
Burton J,
Danecek P,
Keane TM,
Kolb-Kokocinski A,
McCarthy S,
Stalker J,
Quail M,
Ayub Q,
Chen Y,
Coffey AJ,
Colonna V,
Huang N,
Jostins L,
Scally A,
Walter K,
Xue Y,
Zhang Y,
Blackburne B,
Lindsay SJ,
Ning Z,
Frankish A,
Harrow J,
Chris TS,
Abecasis GR,
Kang HM,
Anderson P,
Blackwell T,
Busonero F,
Fuchsberger C,
Jun G,
Maschio A,
Porcu E,
Sidore C,
Tan A,
Trost MK,
Bentley DR,
Grocock R,
Humphray S,
James T,
Kingsbury Z,
Bauer M,
Cheetham RK,
Cox T,
Eberle M,
Murray L,
Shaw R,
Chakravarti A,
Clark AG,
Keinan A,
Rodriguez-Flores JL,
De LaVega FM,
Degenhardt J,
Eichler EE,
Flicek P,
Clarke L,
Leinonen R,
Smith RE,
Zheng-Bradley X,
Beal K,
Cunningham F,
Herrero J,
McLaren WM,
Ritchie GR,
Barker J,
Kelman G,
Kulesha E,
Radhakrishnan R,
Roa A,
Smirnov D,
Streeter I,
Toneva I,
Gibbs RA,
Dinh H,
Kovar C,
Lee S,
Lewis L,
Muzny D,
Reid J,
Wang M,
Yu F,
Bainbridge M,
Challis D,
Evani US,
Lu J,
Nagaswamy U,
Sabo A,
Wang Y,
Yu J,
Fowler G,
Hale W,
Kalra D,
Green ED,
Knoppers BM,
Korbel JO,
Rausch T,
Sttz AM,
Lee C,
Griffin L,
Hsieh CH,
Mills RE,
Von Grotthuss M,
Zhang C,
Shi X,
Lehrach H,
Sudbrak R,
Amstislavskiy VS,
Lienhard M,
Mertes F,
Sultan M,
Timmermann B,
Yaspo ML,
Herwig SR,
Mardis ER,
Wilson RK,
Fulton L,
Fulton R,
Weinstock GM,
Chinwalla A,
Ding L,
Dooling D,
Koboldt DC,
McLellan MD,
Wallis JW,
Wendl MC,
Zhang Q,
Marth GT,
Garrison EP,
Kural D,
Lee WP,
Leong WF,
Ward AN,
Wu J,
Zhang M,
Nickerson DA,
Alkan C,
Hormozdiari F,
Ko A,
Sudmant PH,
Schmidt JP,
Davies CJ,
Gollub J,
Webster T,
Wong B,
Zhan Y,
Sherry ST,
Xiao C,
Church D,
Ananiev V,
Belaia Z,
Beloslyudtsev D,
Bouk N,
Chen C,
Cohen R,
Cook C,
Garner J,
Hefferon T,
Kimelman M,
Liu C,
Lopez J,
Meric P,
Ostapchuk Y,
Phan L,
Ponomarov S,
Schneider V,
Shekhtman E,
Sirotkin K,
Slotta D,
Zhang H,
Wang J,
Fang X,
Guo X,
Jian M,
Jiang H,
Jin X,
Li G,
Li J,
Li Y,
Liu X,
Lu Y,
Ma X,
Tai S,
Tang M,
Wang B,
Wang G,
Wu H,
Wu R,
Yin Y,
Zhang W,
Zhao J,
Zhao M,
Zheng X,
Lachlan H,
Fang L,
Li Q,
Li Z,
Lin H,
Liu B,
Luo R,
Shao H,
Xie Y,
Ye C,
Yu C,
Zheng H,
Zhu H,
Cai H,
Cao H,
Su Y,
Tian Z,
Yang H,
Yang L,
Zhu J,
Cai Z,
Albrecht MW,
Borodina TA,
Auton A,
Yoon SC,
Lihm J,
Makarov V,
Jin H,
Kim W,
Kim KC,
Gottipati S,
Jones D,
Cooper DN,
Ball EV,
Stenson PD,
Barnes B,
Kahn S,
Ye K,
Batzer MA,
Konkel MK,
Walker JA,
MacArthur DG,
Lek M,
Shriver MD,
Bustamante CD,
Gravel S,
Kenny EE,
Kidd JM,
Lacroute P,
Maples BK,
Moreno-Estrada A,
Zakharia F,
Henn B,
Sandoval K,
Byrnes JK,
Halperin E,
Baran Y,
Craig DW,
Christoforides A,
Izatt T,
Kurdoglu AA,
Sinari SA,
Homer N,
Squire K,
Sebat J,
Bafna V,
Burchard EG,
Hernandez RD,
Gignoux CR,
Haussler D,
Katzman SJ,
Kent WJ,
Howie B,
Ruiz-Linares A,
Dermitzakis ET,
Lappalainen T,
Devine SE,
Maroo A,
Tallon LJ,
Rosenfeld JA,
Michelson LP,
Angius A,
Cucca F,
Sanna S,
Bigham A,
Jones C,
Reinier F,
Lyons R,
Schlessinger D,
Awadalla P,
Hodgkinson A,
Oleksyk TK,
Martinez-Cruzado JC,
Fu Y,
Xiong M,
Jorde L,
Witherspoon D,
Xing J,
Browning BL,
Hajirasouliha I,
Chen K,
Albers CA,
Gerstein MB,
Abyzov A,
Chen J,
Habegger L,
Harmanci AO,
Mu XJ,
Sisu C,
Balasubramanian S,
Jin M,
Khurana E,
Clarke D,
Michaelson JJ,
Osullivan C,
Barnes KC,
Gharani N,
Toji LH,
Gerry N,
Kaye JS,
Kent A,
Mathias R,
Ossorio PN,
Parker M,
Rotimi CN,
Royal CD,
Tishkoff S,
Via M,
Bodmer W,
Bedoya G,
Yang G,
You CJ,
Garcia-Montero A,
Orfao A,
Dutil J,
Brooks LD,
Felsenfeld AL

Nature Communications
  5 (0): Jun 13 2014   Elsevier
[Abstract]
[DOI] [Full Text]

The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB
Singh R,
Low ET,
Ooi LC,
Ong-Abdullah M,
Nookiah R,
Ting NC,
Marjuni M,
Chan PL,
Ithnin M,
Manaf MA,
Nagappan J,
Chan KL,
Rosli R,
Halim MA,
Azizi N,
Budiman MA,
Lakey N,
Bacher B,
Van Brunt A,
Wang C,
Hogan M,
He D,
MacDonald JD,
Smith SW,
Ordway JM,
Martienssen RA,
Sambanthamurthi R

Nat Commun
  5 (0): 4106; Jun30 2014   Nlm
[Abstract]
[DOI] [Full Text]

Synaptic modifications in the medial prefrontal cortex in susceptibility and resilience to stress
Wang M,
Perova Z,
Arenkiel BR,
Li B

J Neurosci
  34 (22): 7485-92; May 28 2014   NLM
[Abstract]
[DOI] [Full Text]

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
Brownstein CA,
Beggs AH,
Homer N,
Merriman B,
Yu TW,
Flannery KC,
Dechene ET,
Towne MC,
Savage SK,
Price EN,
Holm IA,
Luquette LJ,
Lyon E,
Majzoub J,
Neupert P,
McCallie D,
Szolovits P,
Willard HF,
Mendelsohn NJ,
Temme R,
Finkel RS,
Yum SW,
Medne L,
Sunyaev SR,
Adzhubey I,
Cassa CA,
de Bakker PI,
Duzkale H,
Dworzy Ski P,
Fairbrother W,
Francioli L,
Funke BH,
Giovanni MA,
Handsaker RE,
Lage K,
Lebo MS,
Lek M,
Leshchiner I,
Macarthur DG,
McLaughlin HM,
Murray MF,
Pers TH,
Polak PP,
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2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
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Genome Medicine
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