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Results: 12

1.

A cell-based method for screening RNA-protein interactions: identification of constitutive transport element-interacting proteins.

Nakamura RL, Landt SG, Mai E, Nejim J, Chen L, Frankel AD.

PLoS One. 2012;7(10):e48194. doi: 10.1371/journal.pone.0048194. Epub 2012 Oct 25.

PMID:
23133567
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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
3.

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]
4.

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, Lajoie1 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.

PMID:
22889292
[PubMed - as supplied by publisher]
Free PMC Article
5.

A strategy for identifying noncoding RNAs using whole-genome tiling arrays.

Landt SG, Abeliuk E.

Methods Mol Biol. 2012;905:29-39. doi: 10.1007/978-1-61779-949-5_3.

PMID:
22735996
[PubMed - indexed for MEDLINE]
6.

Characterization of enhancer function from genome-wide analyses.

Maston GA, Landt SG, Snyder M, Green MR.

Annu Rev Genomics Hum Genet. 2012;13:29-57. doi: 10.1146/annurev-genom-090711-163723. Epub 2012 Jun 11. Review.

PMID:
22703170
[PubMed - indexed for MEDLINE]
7.

Cooperative transcription factor associations discovered using regulatory variation.

Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13353-8. doi: 10.1073/pnas.1103105108. Epub 2011 Jul 26.

PMID:
21828005
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

CrfA, a small noncoding RNA regulator of adaptation to carbon starvation in Caulobacter crescentus.

Landt SG, Lesley JA, Britos L, Shapiro L.

J Bacteriol. 2010 Sep;192(18):4763-75. doi: 10.1128/JB.00343-10. Epub 2010 Jul 2.

PMID:
20601471
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Small non-coding RNAs in Caulobacter crescentus.

Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L.

Mol Microbiol. 2008 May;68(3):600-14. doi: 10.1111/j.1365-2958.2008.06172.x. Epub 2008 Mar 25.

PMID:
18373523
[PubMed - indexed for MEDLINE]
10.

A simple motif for protein recognition in DNA secondary structures.

Landt SG, Ramirez A, Daugherty MD, Frankel AD.

J Mol Biol. 2005 Sep 2;351(5):982-94.

PMID:
16055152
[PubMed - indexed for MEDLINE]
11.

Localized influence of 2'-hydroxyl groups and helix geometry on protein recognition in the RNA major groove.

Landt SG, Tipton AR, Frankel AD.

Biochemistry. 2005 May 3;44(17):6547-58.

PMID:
15850388
[PubMed - indexed for MEDLINE]
12.

Screening RNA-binding libraries using Tat-fusion system in mammalian cells.

Landt SG, Tan R, Frankel AD.

Methods Enzymol. 2000;318:350-63. No abstract available.

PMID:
10889998
[PubMed - indexed for MEDLINE]

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