Format
Items per page
Sort by

Send to:

Choose Destination

Results: 14

1.

Principles of regulatory information conservation between mouse and human.

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; Mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP.

Nature. 2014 Nov 20;515(7527):371-5. doi: 10.1038/nature13985.

PMID:
25409826
[PubMed - in process]
2.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

PMID:
25409824
[PubMed - in process]
3.

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.

PMID:
25164757
[PubMed - indexed for MEDLINE]
4.

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.

PMID:
22955991
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22955619
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB.

Genome Biol. 2012 Aug 13;13(8):418. doi: 10.1186/gb-2012-13-8-418.

PMID:
22889292
[PubMed - in process]
Free PMC Article
7.

Segmental duplications in the human genome reveal details of pseudogene formation.

Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB.

Nucleic Acids Res. 2010 Nov;38(20):6997-7007. doi: 10.1093/nar/gkq587. Epub 2010 Jul 8.

PMID:
20615899
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Lam HY, Mu XJ, St├╝tz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB.

Nat Biotechnol. 2010 Jan;28(1):47-55. doi: 10.1038/nbt.1600. Epub 2009 Dec 27.

PMID:
20037582
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data.

Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB.

Genome Biol. 2009 Feb 23;10(2):R23. doi: 10.1186/gb-2009-10-2-r23.

PMID:
19236709
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.

Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M.

Genome Biol. 2009;10(1):R2. doi: 10.1186/gb-2009-10-1-r2. Epub 2009 Jan 5.

PMID:
19123937
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Pseudofam: the pseudogene families database.

Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB.

Nucleic Acids Res. 2009 Jan;37(Database issue):D738-43. doi: 10.1093/nar/gkn758. Epub 2008 Oct 28.

PMID:
18957444
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Uncovering trends in gene naming.

Seringhaus MR, Cayting PD, Gerstein MB.

Genome Biol. 2008 Jan 31;9(1):401. doi: 10.1186/gb-2008-9-1-401.

PMID:
18254929
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.

Zhang ZD, Cayting P, Weinstock G, Gerstein M.

Mol Biol Evol. 2008 Jan;25(1):131-43. Epub 2007 Dec 7.

PMID:
18065488
[PubMed - indexed for MEDLINE]
Free Article
14.

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.

Karro JE, Yan Y, Zheng D, Zhang Z, Carriero N, Cayting P, Harrrison P, Gerstein M.

Nucleic Acids Res. 2007 Jan;35(Database issue):D55-60. Epub 2006 Nov 11.

PMID:
17099229
[PubMed - indexed for MEDLINE]
Free PMC Article
Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk