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Items: 1 to 20 of 180

1.

Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LD, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TS, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A.

Mol Cell Proteomics. 2014 Nov;13(11):3184-98. doi: 10.1074/mcp.M114.038299. Epub 2014 Jul 24.

2.

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes.

Prasad TS, Mohanty AK, Kumar M, Sreenivasamurthy SK, Dey G, Nirujogi RS, Pinto SM, Madugundu AK, Patil AH, Advani J, Manda SS, Gupta MK, Dwivedi SB, Kelkar DS, Hall B, Jiang X, Peery A, Rajagopalan P, Yelamanchi SD, Solanki HS, Raja R, Sathe GJ, Chavan S, Verma R, Patel KM, Jain AP, Syed N, Datta KK, Khan AA, Dammalli M, Jayaram S, Radhakrishnan A, Mitchell CJ, Na CH, Kumar N, Sinnis P, Sharakhov IV, Wang C, Gowda H, Tu Z, Kumar A, Pandey A.

Genome Res. 2017 Jan;27(1):133-144. doi: 10.1101/gr.201368.115. Epub 2016 Nov 15.

3.

Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation.

Kumar D, Yadav AK, Jia X, Mulvenna J, Dash D.

Mol Cell Proteomics. 2016 Jan;15(1):329-39. doi: 10.1074/mcp.M114.047126. Epub 2015 Nov 11.

5.

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes.

Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME, Mattick JS.

Bioinformatics. 2012 Dec 1;28(23):3042-50. doi: 10.1093/bioinformatics/bts582. Epub 2012 Oct 7.

PMID:
23044541
6.

The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation.

Salisbury JP, Sîrbulescu RF, Moran BM, Auclair JR, Zupanc GK, Agar JN.

BMC Genomics. 2015 Mar 11;16:166. doi: 10.1186/s12864-015-1354-2.

7.
8.

Improvement of genome assembly completeness and identification of novel full-length protein-coding genes by RNA-seq in the giant panda genome.

Chen M, Hu Y, Liu J, Wu Q, Zhang C, Yu J, Xiao J, Wei F, Wu J.

Sci Rep. 2015 Dec 11;5:18019. doi: 10.1038/srep18019.

9.

Parallel deep transcriptome and proteome analysis of zebrafish larvae.

Palmblad M, Henkel CV, Dirks RP, Meijer AH, Deelder AM, Spaink HP.

BMC Res Notes. 2013 Oct 24;6:428. doi: 10.1186/1756-0500-6-428.

10.

Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.

Schellenberg JJ, Verbeke TJ, McQueen P, Krokhin OV, Zhang X, Alvare G, Fristensky B, Thallinger GG, Henrissat B, Wilkins JA, Levin DB, Sparling R.

BMC Genomics. 2014 Jul 7;15:567. doi: 10.1186/1471-2164-15-567.

11.
12.

A full-body transcriptome and proteome resource for the European common carp.

Kolder IC, van der Plas-Duivesteijn SJ, Tan G, Wiegertjes GF, Forlenza M, Guler AT, Travin DY, Nakao M, Moritomo T, Irnazarow I, den Dunnen JT, Anvar SY, Jansen HJ, Dirks RP, Palmblad M, Lenhard B, Henkel CV, Spaink HP.

BMC Genomics. 2016 Sep 2;17:701. doi: 10.1186/s12864-016-3038-y.

13.

Discovery of novel genes and gene isoforms by integrating transcriptomic and proteomic profiling from mouse liver.

Wu P, Zhang H, Lin W, Hao Y, Ren L, Zhang C, Li N, Wei H, Jiang Y, He F.

J Proteome Res. 2014 May 2;13(5):2409-19. doi: 10.1021/pr4012206. Epub 2014 Apr 18.

PMID:
24717071
14.

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish.

Aanes H, Østrup O, Andersen IS, Moen LF, Mathavan S, Collas P, Alestrom P.

BMC Genomics. 2013 May 15;14:331. doi: 10.1186/1471-2164-14-331.

15.

In depth annotation of the Anopheles gambiae mosquito midgut transcriptome.

Padrón A, Molina-Cruz A, Quinones M, Ribeiro JM, Ramphul U, Rodrigues J, Shen K, Haile A, Ramirez JL, Barillas-Mury C.

BMC Genomics. 2014 Jul 29;15:636. doi: 10.1186/1471-2164-15-636.

16.

zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs.

Dhiman H, Kapoor S, Sivadas A, Sivasubbu S, Scaria V.

PLoS One. 2015 Jun 11;10(6):e0129997. doi: 10.1371/journal.pone.0129997. eCollection 2015.

17.

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration.

Looso M, Preussner J, Sousounis K, Bruckskotten M, Michel CS, Lignelli E, Reinhardt R, Höffner S, Krüger M, Tsonis PA, Borchardt T, Braun T.

Genome Biol. 2013 Feb 20;14(2):R16. doi: 10.1186/gb-2013-14-2-r16.

18.

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica.

Fernandez-Valverde SL, Calcino AD, Degnan BM.

BMC Genomics. 2015 May 15;16:387. doi: 10.1186/s12864-015-1588-z.

19.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.

Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, Walker H, Kobold MA, Webb SR, Payne SH, Ansong C, Adkins JN, Cannon WR, Webb-Robertson BJ.

BMC Genomics. 2012 Apr 5;13:131. doi: 10.1186/1471-2164-13-131.

20.

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S.

J Proteomics. 2013 Jun 28;86:27-42. doi: 10.1016/j.jprot.2013.04.036. Epub 2013 May 9.

PMID:
23665149

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