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Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context.

Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS; Cancer Genome Atlas Research Network, Sood AK, Gunaratne PH, Sumazin P.

Cell Rep. 2018 Apr 3;23(1):297-312.e12. doi: 10.1016/j.celrep.2018.03.064.


Computational exploration of cis-regulatory modules in rhythmic expression data using the "Exploration of Distinctive CREs and CRMs" (EDCC) and "CRM Network Generator" (CNG) programs.

Bekiaris PS, Tekath T, Staiger D, Danisman S.

PLoS One. 2018 Jan 3;13(1):e0190421. doi: 10.1371/journal.pone.0190421. eCollection 2018.


Control of species-dependent cortico-motoneuronal connections underlying manual dexterity.

Gu Z, Kalambogias J, Yoshioka S, Han W, Li Z, Kawasawa YI, Pochareddy S, Li Z, Liu F, Xu X, Wijeratne HRS, Ueno M, Blatz E, Salomone J, Kumanogoh A, Rasin MR, Gebelein B, Weirauch MT, Sestan N, Martin JH, Yoshida Y.

Science. 2017 Jul 28;357(6349):400-404. doi: 10.1126/science.aan3721.


Two Types of Etiological Mutation in the Limb-Specific Enhancer of Shh.

Amano T, Sagai T, Seki R, Shiroishi T.

G3 (Bethesda). 2017 Sep 7;7(9):2991-2998. doi: 10.1534/g3.117.044669.


Enhancers and chromatin structures: regulatory hubs in gene expression and diseases.

Hu Z, Tee WW.

Biosci Rep. 2017 Apr 28;37(2). pii: BSR20160183. doi: 10.1042/BSR20160183. Print 2017 Apr 30. Review.


Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.

Chen X, Yu B, Carriero N, Silva C, Bonneau R.

Nucleic Acids Res. 2017 May 5;45(8):4315-4329. doi: 10.1093/nar/gkx174.


Crystal structures reveal a new and novel FoxO1 binding site within the human glucose-6-phosphatase catalytic subunit 1 gene promoter.

Singh P, Han EH, Endrizzi JA, O'Brien RM, Chi YI.

J Struct Biol. 2017 Apr;198(1):54-64. doi: 10.1016/j.jsb.2017.02.006. Epub 2017 Feb 20.


Systematic dissection of genomic features determining transcription factor binding and enhancer function.

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1291-E1300. doi: 10.1073/pnas.1621150114. Epub 2017 Jan 30.


Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.

Acevedo-Luna N, Mariño-Ramírez L, Halbert A, Hansen U, Landsman D, Spouge JL.

BMC Bioinformatics. 2016 Nov 21;17(1):479.


Genetic dissection of host immune response in pneumonia development and progression.

Smelaya TV, Belopolskaya OB, Smirnova SV, Kuzovlev AN, Moroz VV, Golubev AM, Pabalan NA, Salnikova LE.

Sci Rep. 2016 Oct 11;6:35021. doi: 10.1038/srep35021.


Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.

Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE.

Cell. 2016 Aug 25;166(5):1269-1281.e19. doi: 10.1016/j.cell.2016.07.049.


Assembly PCR synthesis of optimally designed, compact, multi-responsive promoters suited to gene therapy application.

Mohamed H, Chernajovsky Y, Gould D.

Sci Rep. 2016 Jul 8;6:29388. doi: 10.1038/srep29388.


Probing chromatin landscape reveals roles of endocardial TBX20 in septation.

Boogerd CJ, Aneas I, Sakabe N, Dirschinger RJ, Cheng QJ, Zhou B, Chen J, Nobrega MA, Evans SM.

J Clin Invest. 2016 Aug 1;126(8):3023-35. doi: 10.1172/JCI85350. Epub 2016 Jun 27.


Heterogeneity of transcription factor binding specificity models within and across cell lines.

Sharmin M, Bravo HC, Hannenhalli S.

Genome Res. 2016 Aug;26(8):1110-23. doi: 10.1101/gr.199166.115. Epub 2016 Jun 16.


Interactions between pluripotency factors specify cis-regulation in embryonic stem cells.

Fiore C, Cohen BA.

Genome Res. 2016 Jun;26(6):778-86. doi: 10.1101/gr.200733.115. Epub 2016 Apr 15.


How motif environment influences transcription factor search dynamics: Finding a needle in a haystack.

Dror I, Rohs R, Mandel-Gutfreund Y.

Bioessays. 2016 Jul;38(7):605-12. doi: 10.1002/bies.201600005. Epub 2016 May 19. Review.


Identification and Validation of Novel Hedgehog-Responsive Enhancers Predicted by Computational Analysis of Ci/Gli Binding Site Density.

Gurdziel K, Lorberbaum DS, Udager AM, Song JY, Richards N, Parker DS, Johnson LA, Allen BL, Barolo S, Gumucio DL.

PLoS One. 2015 Dec 28;10(12):e0145225. doi: 10.1371/journal.pone.0145225. eCollection 2015.


DNA-Binding Motif of the Imprinted Transcription Factor PEG3.

Lee S, Ye A, Kim J.

PLoS One. 2015 Dec 21;10(12):e0145531. doi: 10.1371/journal.pone.0145531. eCollection 2015.


Lynx: a knowledge base and an analytical workbench for integrative medicine.

Sulakhe D, Xie B, Taylor A, D'Souza M, Balasubramanian S, Hashemifar S, White S, Dave UJ, Agam G, Xu J, Wang S, Gilliam TC, Maltsev N.

Nucleic Acids Res. 2016 Jan 4;44(D1):D882-7. doi: 10.1093/nar/gkv1257. Epub 2015 Nov 20.

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