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Results: 1 to 20 of 22

1.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL.

Genome Biol. 2013 Apr 25;14(4):R36. [Epub ahead of print]

PMID:
23618408
[PubMed - as supplied by publisher]
Free PMC Article
2.

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L.

Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016.

PMID:
22383036
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Detection of lineage-specific evolutionary changes among primate species.

Pertea M, Pertea GM, Salzberg SL.

BMC Bioinformatics. 2011 Jul 4;12:274. doi: 10.1186/1471-2105-12-274.

PMID:
21726447
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.

PLoS Biol. 2010 Sep 7;8(9). pii: e1000475. doi: 10.1371/journal.pbio.1000475.

PMID:
20838655
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.

Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2.

PMID:
20436464
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

A whole-genome assembly of the domestic cow, Bos taurus.

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL.

Genome Biol. 2009;10(4):R42. doi: 10.1186/gb-2009-10-4-r42. Epub 2009 Apr 24.

PMID:
19393038
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Elevated expression of protein biosynthesis genes in liver and muscle of hibernating black bears (Ursus americanus).

Fedorov VB, Goropashnaya AV, Tøien O, Stewart NC, Gracey AY, Chang C, Qin S, Pertea G, Quackenbush J, Showe LC, Showe MK, Boyer BB, Barnes BM.

Physiol Genomics. 2009 Apr 10;37(2):108-18. doi: 10.1152/physiolgenomics.90398.2008. Epub 2009 Feb 24.

PMID:
19240299
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus.

Wang M, Guerrero FD, Pertea G, Nene VM.

BMC Genomics. 2007 Oct 12;8:368.

PMID:
17935616
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The TIGR Maize Database.

Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D771-6.

PMID:
16381977
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

RESOURCERER: a database for annotating and linking microarray resources within and across species.

Tsai J, Sultana R, Lee Y, Pertea G, Karamycheva S, Antonescu V, Cho J, Parvizi B, Cheung F, Quackenbush J.

Genome Biol. 2001;2(11):SOFTWARE0002.

PMID:
16173164
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D71-4.

PMID:
15608288
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Enrichment of gene-coding sequences in maize by genome filtration.

Whitelaw CA, Barbazuk WB, Pertea G, Chan AP, Cheung F, Lee Y, Zheng L, van Heeringen S, Karamycheva S, Bennetzen JL, SanMiguel P, Lakey N, Bedell J, Yuan Y, Budiman MA, Resnick A, Van Aken S, Utterback T, Riedmuller S, Williams M, Feldblyum T, Schubert K, Beachy R, Fraser CM, Quackenbush J.

Science. 2003 Dec 19;302(5653):2118-20.

PMID:
14684821
[PubMed - indexed for MEDLINE]
Free Article
13.

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J.

Bioinformatics. 2003 Mar 22;19(5):651-2.

PMID:
12651724
[PubMed - indexed for MEDLINE]
Free Article
14.

Comparative analyses of potato expressed sequence tag libraries.

Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Griffiths HM, Restrepo S, Smart CD, Fry WE, Van Der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto ML, Baker BJ, Buell CR.

Plant Physiol. 2003 Feb;131(2):419-29.

PMID:
12586867
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team.

Nature. 2002 Dec 5;420(6915):563-73.

PMID:
12466851
[PubMed - indexed for MEDLINE]
16.

Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly.

Fahrenkrug SC, Smith TP, Freking BA, Cho J, White J, Vallet J, Wise T, Rohrer G, Pertea G, Sultana R, Quackenbush J, Keele JW.

Mamm Genome. 2002 Aug;13(8):475-8.

PMID:
12226715
[PubMed - indexed for MEDLINE]
17.

Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).

Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J.

Genome Res. 2002 Mar;12(3):493-502.

PMID:
11875039
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle.

Smith TP, Grosse WM, Freking BA, Roberts AJ, Stone RT, Casas E, Wray JE, White J, Cho J, Fahrenkrug SC, Bennett GL, Heaton MP, Laegreid WW, Rohrer GA, Chitko-McKown CG, Pertea G, Holt I, Karamycheva S, Liang F, Quackenbush J, Keele JW.

Genome Res. 2001 Apr;11(4):626-30.

PMID:
11282978
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An optimized protocol for analysis of EST sequences.

Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J.

Nucleic Acids Res. 2000 Sep 15;28(18):3657-65.

PMID:
10982889
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Gene index analysis of the human genome estimates approximately 120,000 genes.

Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J.

Nat Genet. 2000 Jun;25(2):239-40. Erratum in: Nat Genet 2000 Dec;26(4):501.

PMID:
10835646
[PubMed - indexed for MEDLINE]

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