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Results: 1 to 20 of 50

1.

Cryptococcus neoformans dual GDP-mannose transporters and their role in biology and virulence.

Wang ZA, Griffith CL, Skowyra ML, Salinas N, Williams M, Maier EJ, Gish SR, Liu H, Brent MR, Doering TL.

Eukaryot Cell. 2014 Jun;13(6):832-42. doi: 10.1128/EC.00054-14. Epub 2014 Apr 18.

PMID:
24747214
[PubMed - in process]
2.

Mapping functional transcription factor networks from gene expression data.

Haynes BC, Maier EJ, Kramer MH, Wang PI, Brown H, Brent MR.

Genome Res. 2013 Aug;23(8):1319-28. doi: 10.1101/gr.150904.112. Epub 2013 May 1.

PMID:
23636944
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Role of fat body lipogenesis in protection against the effects of caloric overload in Drosophila.

Musselman LP, Fink JL, Ramachandran PV, Patterson BW, Okunade AL, Maier E, Brent MR, Turk J, Baranski TJ.

J Biol Chem. 2013 Mar 22;288(12):8028-42. doi: 10.1074/jbc.M112.371047. Epub 2013 Jan 25.

PMID:
23355467
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Reduced DICER1 elicits an interferon response in endometrial cancer cells.

Chiappinelli KB, Haynes BC, Brent MR, Goodfellow PJ.

Mol Cancer Res. 2012 Mar;10(3):316-25. doi: 10.1158/1541-7786.MCR-11-0520. Epub 2012 Jan 17.

PMID:
22252463
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Toward an integrated model of capsule regulation in Cryptococcus neoformans.

Haynes BC, Skowyra ML, Spencer SJ, Gish SR, Williams M, Held EP, Brent MR, Doering TL.

PLoS Pathog. 2011 Dec;7(12):e1002411. doi: 10.1371/journal.ppat.1002411. Epub 2011 Dec 8.

PMID:
22174677
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The developmental transcriptome of Drosophila melanogaster.

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, Celniker SE.

Nature. 2011 Mar 24;471(7339):473-9. doi: 10.1038/nature09715. Epub 2010 Dec 22.

PMID:
21179090
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.

Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.

PMID:
21177974
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The transcriptional diversity of 25 Drosophila cell lines.

Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J, Samsonova A, Choi JH, Roberts J, Davis CA, Tang H, van Baren MJ, Ghosh S, Dobin A, Bell K, Lin W, Langton L, Duff MO, Tenney AE, Zaleski C, Brent MR, Hoskins RA, Kaufman TC, Andrews J, Graveley BR, Perrimon N, Celniker SE, Gingeras TR, Cherbas P.

Genome Res. 2011 Feb;21(2):301-14. doi: 10.1101/gr.112961.110. Epub 2010 Dec 22.

PMID:
21177962
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription.

Kuttykrishnan S, Sabina J, Langton LL, Johnston M, Brent MR.

Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16743-8. doi: 10.1073/pnas.0912483107. Epub 2010 Sep 1.

PMID:
20810924
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

Lu DV, Brown RH, Arumugam M, Brent MR.

Bioinformatics. 2009 Jul 1;25(13):1587-93. doi: 10.1093/bioinformatics/btp273. Epub 2009 May 4.

PMID:
19414532
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Benchmarking regulatory network reconstruction with GRENDEL.

Haynes BC, Brent MR.

Bioinformatics. 2009 Mar 15;25(6):801-7. doi: 10.1093/bioinformatics/btp068. Epub 2009 Feb 2.

PMID:
19188190
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.

van Baren MJ, Koebbe BC, Brent MR.

Curr Protoc Bioinformatics. 2007 Dec;Chapter 4:Unit 4.8. doi: 10.1002/0471250953.bi0408s20.

PMID:
18428682
[PubMed - indexed for MEDLINE]
13.

Steady progress and recent breakthroughs in the accuracy of automated genome annotation.

Brent MR.

Nat Rev Genet. 2008 Jan;9(1):62-73. Review.

PMID:
18087260
[PubMed - indexed for MEDLINE]
14.

Evolution of genes and genomes on the Drosophila phylogeny.

Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I.

Nature. 2007 Nov 8;450(7167):203-18.

PMID:
17994087
[PubMed - indexed for MEDLINE]
15.

Targeted discovery of novel human exons by comparative genomics.

Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C, Yu HC, Li J, Roe BA, Green P, Gerhard DS, Temple G, Haussler D, Brent MR.

Genome Res. 2007 Dec;17(12):1763-73. Epub 2007 Nov 7.

PMID:
17989246
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

How does eukaryotic gene prediction work?

Brent MR.

Nat Biotechnol. 2007 Aug;25(8):883-5. Review. No abstract available.

PMID:
17687368
[PubMed - indexed for MEDLINE]
17.

Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping.

Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJ.

Nat Methods. 2007 Aug;4(8):659-64. Epub 2007 Jun 24.

PMID:
17589517
[PubMed - indexed for MEDLINE]
18.

The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs.

Keibler E, Arumugam M, Brent MR.

Bioinformatics. 2007 Mar 1;23(5):545-54. Epub 2007 Jan 18.

PMID:
17237054
[PubMed - indexed for MEDLINE]
Free Article
19.

A tale of two templates: automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices.

Tenney AE, Wu JQ, Langton L, Klueh P, Quatrano R, Brent MR.

Genome Res. 2007 Feb;17(2):212-8. Epub 2007 Jan 8.

PMID:
17210930
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

Flicek P, Brent MR.

Genome Biol. 2006;7 Suppl 1:S8.1-9. Epub 2006 Aug 7.

PMID:
16925842
[PubMed - indexed for MEDLINE]
Free PMC Article

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