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Results: 1 to 20 of 479

1.

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies.

Subramanian SL, Kitchen RR, Alexander R, Carter BS, Cheung KH, Laurent LC, Pico A, Roberts LR, Roth ME, Rozowsky JS, Su AI, Gerstein MB, Milosavljevic A.

J Extracell Vesicles. 2015 Aug 28;4:27497. doi: 10.3402/jev.v4.27497. eCollection 2015.

2.

LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations.

Lochovsky L, Zhang J, Fu Y, Khurana E, Gerstein M.

Nucleic Acids Res. 2015 Aug 24. pii: gkv803. [Epub ahead of print]

3.

High-order neural networks and kernel methods for peptide-MHC binding prediction.

Kuksa PP, Min MR, Dugar R, Gerstein M.

Bioinformatics. 2015 Jul 23. pii: btv371. [Epub ahead of print]

PMID:
26206306
4.

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.

Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM.

Cell. 2015 Jul 16;162(2):375-90. doi: 10.1016/j.cell.2015.06.034.

PMID:
26186191
5.

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms.

Abyzov A, Li S, Kim DR, Mohiyuddin M, Stütz AM, Parrish NF, Mu XJ, Clark W, Chen K, Hurles M, Korbel JO, Lam HY, Lee C, Gerstein MB.

Nat Commun. 2015 Jun 1;6:7256. doi: 10.1038/ncomms8256.

PMID:
26028266
6.

Loregic: a method to characterize the cooperative logic of regulatory factors.

Wang D, Yan KK, Sisu C, Cheng C, Rozowsky J, Meyerson W, Gerstein MB.

PLoS Comput Biol. 2015 Apr 17;11(4):e1004132. doi: 10.1371/journal.pcbi.1004132. eCollection 2015 Apr.

7.

An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.

Cheng C, Andrews E, Yan KK, Ung M, Wang D, Gerstein M.

Genome Biol. 2015 Mar 31;16:63. doi: 10.1186/s13059-015-0624-2.

8.

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.

Mohiyuddin M, Mu JC, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 Aug 15;31(16):2741-4. doi: 10.1093/bioinformatics/btv204. Epub 2015 Apr 10.

9.

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See LH, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR.

Nat Commun. 2015 Jan 13;6:5903. doi: 10.1038/ncomms6903.

10.

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 May 1;31(9):1469-71. doi: 10.1093/bioinformatics/btu828. Epub 2014 Dec 17.

11.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy.

Kitchen RR, Rozowsky JS, Gerstein MB, Nairn AC.

Nat Neurosci. 2014 Nov;17(11):1491-9. doi: 10.1038/nn.3829. Epub 2014 Oct 28. Review.

PMID:
25349915
13.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.

14.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.

Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M.

Genome Biol. 2014;15(10):480.

15.

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

Di C, Yuan J, Wu Y, Li J, Lin H, Hu L, Zhang T, Qi Y, Gerstein MB, Guo Y, Lu ZJ.

Plant J. 2014 Dec;80(5):848-61. doi: 10.1111/tpj.12679. Epub 2014 Oct 21.

PMID:
25256571
16.

OrthoClust: an orthology-based network framework for clustering data across multiple species.

Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M.

Genome Biol. 2014 Aug 28;15(8):R100. doi: 10.1186/gb-2014-15-8-r100.

17.

Comparative analysis of regulatory information and circuits across distant species.

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

Nature. 2014 Aug 28;512(7515):453-6. doi: 10.1038/nature13668.

18.

Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

19.

Comparative analysis of pseudogenes across three phyla.

Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB.

Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13361-6. doi: 10.1073/pnas.1407293111. Epub 2014 Aug 25.

20.

Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.

Talbert-Slagle K, Atkins KE, Yan KK, Khurana E, Gerstein M, Bradley EH, Berg D, Galvani AP, Townsend JP.

PLoS Pathog. 2014 May 8;10(5):e1004092. doi: 10.1371/journal.ppat.1004092. eCollection 2014 May. No abstract available.

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