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Items: 1 to 20 of 63

1.

Corrigendum: Diverse human extracellular RNAs are widely detected in human plasma.

Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova M, Mikhalev E, Tanriverdi K.

Nat Commun. 2016 Jun 3;7:11902. doi: 10.1038/ncomms11902. No abstract available.

2.

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Apr 28;17:78. doi: 10.1186/s13059-016-0961-9. No abstract available.

3.

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources.

Shah R, Tanriverdi K, Levy D, Larson M, Gerstein M, Mick E, Rozowsky J, Kitchen R, Murthy V, Mikalev E, Freedman JE.

PLoS One. 2016 Apr 28;11(4):e0153691. doi: 10.1371/journal.pone.0153691.

4.

Diverse human extracellular RNAs are widely detected in human plasma.

Freedman JE, Gerstein M, Mick E, Rozowsky J, Levy D, Kitchen R, Das S, Shah R, Danielson K, Beaulieu L, Navarro FC, Wang Y, Galeev TR, Holman A, Kwong RY, Murthy V, Tanriverdi SE, Koupenova-Zamor M, Mikhalev E, Tanriverdi K.

Nat Commun. 2016 Apr 26;7:11106. doi: 10.1038/ncomms11106.

5.

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Chen J, Rozowsky J, Galeev TR, Harmanci A, Kitchen R, Bedford J, Abyzov A, Kong Y, Regan L, Gerstein M.

Nat Commun. 2016 Apr 18;7:11101. doi: 10.1038/ncomms11101.

6.

Extending gene ontology in the context of extracellular RNA and vesicle communication.

Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC.

J Biomed Semantics. 2016 Apr 12;7:19. doi: 10.1186/s13326-016-0061-5.

7.

The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Mar 23;17:53. doi: 10.1186/s13059-016-0917-0. Erratum in: Genome Biol. 2016;17:78.

8.

Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.

Wang D, Yan KK, Rozowsky J, Pan E, Gerstein M.

Trends Genet. 2016 May;32(5):251-3. doi: 10.1016/j.tig.2016.02.006.

PMID:
27005445
9.

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.

10.

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.

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. Review.

13.

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.

14.

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.

15.

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.

16.

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.

17.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

18.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M.

Genome Res. 2012 Sep;22(9):1658-67. doi: 10.1101/gr.136838.111.

19.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

20.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

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