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Results: 1 to 20 of 46

1.

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.

Patro R, Mount SM, Kingsford C.

Nat Biotechnol. 2014 May;32(5):462-4. doi: 10.1038/nbt.2862. Epub 2014 Apr 20.

PMID:
24752080
[PubMed - in process]
2.

Evolutionary dynamics of U12-type spliceosomal introns.

Lin CF, Mount SM, Jarmołowski A, Makałowski W.

BMC Evol Biol. 2010 Feb 17;10:47. doi: 10.1186/1471-2148-10-47.

PMID:
20163699
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development.

Zhang XN, Mount SM.

Plant Physiol. 2009 Jul;150(3):1450-8. doi: 10.1104/pp.109.138180. Epub 2009 Apr 29.

PMID:
19403727
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M.

Nature. 2008 Apr 24;452(7190):991-6. doi: 10.1038/nature06856.

PMID:
18432245
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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]
6.

Features generated for computational splice-site prediction correspond to functional elements.

Dogan RI, Getoor L, Wilbur WJ, Mount SM.

BMC Bioinformatics. 2007 Oct 24;8:410.

PMID:
17958908
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

SplicePort--an interactive splice-site analysis tool.

Dogan RI, Getoor L, Wilbur WJ, Mount SM.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W285-91. Epub 2007 Jun 18.

PMID:
17576680
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.

Pertea M, Mount SM, Salzberg SL.

BMC Bioinformatics. 2007 May 21;8:159.

PMID:
17517127
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis.

Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR.

BMC Genomics. 2006 Dec 28;7:327.

PMID:
17194304
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Spliceosomal small nuclear RNA genes in 11 insect genomes.

Mount SM, Gotea V, Lin CF, Hernandez K, Makalowski W.

RNA. 2007 Jan;13(1):5-14. Epub 2006 Nov 9.

PMID:
17095541
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The Drosophila U1-70K protein is required for viability, but its arginine-rich domain is dispensable.

Salz HK, Mancebo RS, Nagengast AA, Speck O, Psotka M, Mount SM.

Genetics. 2004 Dec;168(4):2059-65.

PMID:
15611175
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Reducing storage requirements for biological sequence comparison.

Roberts M, Hayes W, Hunt BR, Mount SM, Yorke JA.

Bioinformatics. 2004 Dec 12;20(18):3363-9. Epub 2004 Jul 15.

PMID:
15256412
[PubMed - indexed for MEDLINE]
Free Article
13.

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O.

Nucleic Acids Res. 2003 Oct 1;31(19):5654-66.

PMID:
14500829
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Sex-lethal splicing autoregulation in vivo: interactions between SEX-LETHAL, the U1 snRNP and U2AF underlie male exon skipping.

Nagengast AA, Stitzinger SM, Tseng CH, Mount SM, Salz HK.

Development. 2003 Feb;130(3):463-71.

PMID:
12490553
[PubMed - indexed for MEDLINE]
Free Article
15.

Evidence for a plastid origin of plant ethylene receptor genes.

Mount SM, Chang C.

Plant Physiol. 2002 Sep;130(1):10-4. No abstract available.

PMID:
12226482
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Genomic sequence, splicing, and gene annotation.

Mount SM.

Am J Hum Genet. 2000 Oct;67(4):788-92. Epub 2000 Sep 8. Review. No abstract available.

PMID:
10986039
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Pre-messenger RNA processing factors in the Drosophila genome.

Mount SM, Salz HK.

J Cell Biol. 2000 Jul 24;150(2):F37-44. Review. No abstract available.

PMID:
10908584
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

The genome sequence of Drosophila melanogaster.

Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, WoodageT, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC.

Science. 2000 Mar 24;287(5461):2185-95.

PMID:
10731132
[PubMed - indexed for MEDLINE]
19.

Expanding the definition of informational suppression.

Mount SM, Anderson P.

Trends Genet. 2000 Apr;16(4):157. No abstract available.

PMID:
10729829
[PubMed - indexed for MEDLINE]
20.

Genetic depletion reveals an essential role for an SR protein splicing factor in vertebrate cells.

Mount SM.

Bioessays. 1997 Mar;19(3):189-92. Review.

PMID:
9080768
[PubMed - indexed for MEDLINE]

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