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Items: 11

1.

Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing.

Anvar SY, Allard G, Tseng E, Sheynkman GM, de Klerk E, Vermaat M, Yin RH, Johansson HE, Ariyurek Y, den Dunnen JT, Turner SW, 't Hoen PAC.

Genome Biol. 2018 Mar 29;19(1):46. doi: 10.1186/s13059-018-1418-0.

2.

Proteome-Scale Human Interactomics.

Luck K, Sheynkman GM, Zhang I, Vidal M.

Trends Biochem Sci. 2017 May;42(5):342-354. doi: 10.1016/j.tibs.2017.02.006. Epub 2017 Mar 8. Review.

3.

The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets.

Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell BS, Kendziorski C, Attie AD.

PLoS Genet. 2016 Dec 9;12(12):e1006466. doi: 10.1371/journal.pgen.1006466. eCollection 2016 Dec.

4.

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.

Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM.

Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):521-45. doi: 10.1146/annurev-anchem-071015-041722. Epub 2016 Mar 30. Review.

5.

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M.

Cell. 2016 Feb 11;164(4):805-17. doi: 10.1016/j.cell.2016.01.029.

6.

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy.

Cesnik AJ, Shortreed MR, Sheynkman GM, Frey BL, Smith LM.

J Proteome Res. 2016 Mar 4;15(3):800-8. doi: 10.1021/acs.jproteome.5b00817. Epub 2016 Jan 12.

7.

Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search.

Shortreed MR, Wenger CD, Frey BL, Sheynkman GM, Scalf M, Keller MP, Attie AD, Smith LM.

J Proteome Res. 2015 Nov 6;14(11):4714-20. doi: 10.1021/acs.jproteome.5b00599. Epub 2015 Sep 29.

8.

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM.

BMC Genomics. 2014 Aug 22;15:703. doi: 10.1186/1471-2164-15-703.

9.

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.

Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.

Bioinformatics. 2014 Nov 1;30(21):3136-8. doi: 10.1093/bioinformatics/btu397. Epub 2014 Jul 22.

10.

Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences.

Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM.

J Proteome Res. 2014 Jan 3;13(1):228-40. doi: 10.1021/pr4009207. Epub 2013 Nov 11.

11.

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq.

Sheynkman GM, Shortreed MR, Frey BL, Smith LM.

Mol Cell Proteomics. 2013 Aug;12(8):2341-53. doi: 10.1074/mcp.O113.028142. Epub 2013 Apr 29.

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