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Results: 1 to 20 of 89

1.

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.

Reid I, O'Toole N, Zabaneh O, Nourzadeh R, Dahdouli M, Abdellateef M, Gordon PM, Soh J, Butler G, Sensen CW, Tsang A.

BMC Bioinformatics. 2014 Jul 1;15:229. doi: 10.1186/1471-2105-15-229.

PMID:
24980894
[PubMed - in process]
Free PMC Article
2.

Size polymorphism in alleles of the myoglobin gene from biomphalaria mollusks.

Teixeira KN, Souza KN, Vidigal TH, Brito CA, Santos AM, Santoro MM.

Genes (Basel). 2010 Oct 20;1(3):357-70. doi: 10.3390/genes1030357.

PMID:
24710092
[PubMed]
Free PMC Article
3.

FixPred: a resource for correction of erroneous protein sequences.

Nagy A, Patthy L.

Database (Oxford). 2014 Apr 4;2014:bau032. doi: 10.1093/database/bau032. Print 2014.

PMID:
24705206
[PubMed - in process]
Free PMC Article
4.

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 Jr, 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, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, Deluca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovre I L, Palanda I A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM.

Genome Biol. 2014 Mar 25;15(3):R53. [Epub ahead of print]

PMID:
24667040
[PubMed - as supplied by publisher]
Free PMC Article
5.

ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.

Alioto T, Picardi E, Guigó R, Pesole G.

Biomed Res Int. 2013;2013:502827. doi: 10.1155/2013/502827. Epub 2013 Nov 7.

PMID:
24308000
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.

Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2014 Feb;164(2):513-24. doi: 10.1104/pp.113.230144. Epub 2013 Dec 4.

PMID:
24306534
[PubMed - in process]
Free PMC Article
7.

Assessment of transcript reconstruction methods for RNA-seq.

Steijger T, Abril JF, Engström PG, Kokocinski F; RGASP Consortium, Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P.

Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3.

PMID:
24185837
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A; RGASP Consortium, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P.

Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.

PMID:
24185836
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Combining different mRNA capture methods to analyze the transcriptome: analysis of the Xenopus laevis transcriptome.

Blower MD, Jambhekar A, Schwarz DS, Toombs JA.

PLoS One. 2013 Oct 15;8(10):e77700. doi: 10.1371/journal.pone.0077700. eCollection 2013.

PMID:
24143257
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.

Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA.

Genome Biol. 2013 Aug 28;14(8):R88. doi: 10.1186/gb-2013-14-8-r88.

PMID:
23985316
[PubMed - in process]
Free PMC Article
11.

MisPred: a resource for identification of erroneous protein sequences in public databases.

Nagy A, Patthy L.

Database (Oxford). 2013 Jul 17;2013:bat053. doi: 10.1093/database/bat053. Print 2013.

PMID:
23864220
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes.

Hoff KJ, Stanke M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W123-8. doi: 10.1093/nar/gkt418. Epub 2013 May 21.

PMID:
23700307
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Sequencing and comparative analysis of the gorilla MHC genomic sequence.

Wilming LG, Hart EA, Coggill PC, Horton R, Gilbert JG, Clee C, Jones M, Lloyd C, Palmer S, Sims S, Whitehead S, Wiley D, Beck S, Harrow JL.

Database (Oxford). 2013 Apr 15;2013:bat011. doi: 10.1093/database/bat011. Print 2013.

PMID:
23589541
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics.

Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJ.

J Pathol Inform. 2012;3:40. doi: 10.4103/2153-3539.103013. Epub 2012 Oct 31.

PMID:
23248761
[PubMed]
Free PMC Article
15.

Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques.

Goodswen SJ, Kennedy PJ, Ellis JT.

PLoS One. 2012;7(11):e50609. doi: 10.1371/journal.pone.0050609. Epub 2012 Nov 30.

PMID:
23226328
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A.

Nucleic Acids Res. 2013 Jan;41(Database issue):D142-51. doi: 10.1093/nar/gks1041. Epub 2012 Nov 9.

PMID:
23143107
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A.

Genome Res. 2012 Jul;22(7):1231-42. doi: 10.1101/gr.130062.111. Epub 2012 May 15.

PMID:
22588898
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.

Pirola Y, Rizzi R, Picardi E, Pesole G, Della Vedova G, Bonizzoni P.

BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S2. doi: 10.1186/1471-2105-13-S5-S2.

PMID:
22537006
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.

Mol Biol Evol. 2012 Sep;29(9):2265-83. doi: 10.1093/molbev/mss100. Epub 2012 Mar 22.

PMID:
22446687
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The importance of identifying alternative splicing in vertebrate genome annotation.

Frankish A, Mudge JM, Thomas M, Harrow J.

Database (Oxford). 2012 Mar 20;2012:bas014. doi: 10.1093/database/bas014. Print 2012.

PMID:
22434846
[PubMed - indexed for MEDLINE]
Free PMC Article

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