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High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation.

Ozdemir A, Fisher-Aylor KI, Pepke S, Samanta M, Dunipace L, McCue K, Zeng L, Ogawa N, Wold BJ, Stathopoulos A.

Genome Res. 2011 Apr;21(4):566-77. doi: 10.1101/gr.104018.109. Epub 2011 Mar 7.


The distribution and evolution of Arabidopsis thaliana cis natural antisense transcripts.

Bouchard J, Oliver C, Harrison PM.

BMC Genomics. 2015 Jun 9;16:444. doi: 10.1186/s12864-015-1587-0.


DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.

Wilken MS, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen RS, Bender MA, Stamatoyannopoulos J, Reh TA.

Epigenetics Chromatin. 2015 Feb 28;8:8. doi: 10.1186/1756-8935-8-8. eCollection 2015.


Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.

Naval-Sánchez M, Potier D, Hulselmans G, Christiaens V, Aerts S.

Mol Biol Evol. 2015 May 4. pii: msv107. [Epub ahead of print]


Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila.

Carl SH, Russell S.

BMC Genomics. 2015 Apr 13;16:292. doi: 10.1186/s12864-015-1495-3.


Supramolecular sensing: Enzyme activity with a twist.

Amabilino DB.

Nat Chem. 2015 Apr;7(4):275-7. doi: 10.1038/nchem.2208. No abstract available.


Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.

Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EE, Taipale J.

Elife. 2015 Mar 17;4. doi: 10.7554/eLife.04837.


Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

Denas O, Sandstrom R, Cheng Y, Beal K, Herrero J, Hardison RC, Taylor J.

BMC Genomics. 2015 Feb 14;16:87. doi: 10.1186/s12864-015-1245-6.


ChIP-nexus enables improved detection of in vivo transcription factor binding footprints.

He Q, Johnston J, Zeitlinger J.

Nat Biotechnol. 2015 Apr;33(4):395-401. doi: 10.1038/nbt.3121. Epub 2015 Mar 9.


Definition of the transcription factor TdIF1 consensus-binding sequence through genomewide mapping of its binding sites.

Koiwai K, Kubota T, Watanabe N, Hori K, Koiwai O, Masai H.

Genes Cells. 2015 Mar;20(3):242-54. doi: 10.1111/gtc.12216. Epub 2015 Jan 26.


Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.

Potier D, Davie K, Hulselmans G, Naval Sanchez M, Haagen L, Huynh-Thu VA, Koldere D, Celik A, Geurts P, Christiaens V, Aerts S.

Cell Rep. 2014 Dec 24;9(6):2290-303. doi: 10.1016/j.celrep.2014.11.038. Epub 2014 Dec 18.


cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila.

Yang TH, Wang CC, Hung PC, Wu WS.

BMC Syst Biol. 2014;8 Suppl 4:S8. doi: 10.1186/1752-0509-8-S4-S8. Epub 2014 Dec 8.


De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.

Niu M, Tabari ES, Su Z.

BMC Genomics. 2014 Dec 2;15:1047. doi: 10.1186/1471-2164-15-1047.


Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts.

Kratochwil CF, Meyer A.

Mol Ecol Resour. 2015 Jul;15(4):761-71. doi: 10.1111/1755-0998.12350. Epub 2014 Dec 6.


Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.

Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.

Elife. 2014 Oct 3;3:e02626. doi: 10.7554/eLife.02626.


Genome-wide Twist1 occupancy in endocardial cushion cells, embryonic limb buds, and peripheral nerve sheath tumor cells.

Lee MP, Ratner N, Yutzey KE.

BMC Genomics. 2014 Sep 28;15:821. doi: 10.1186/1471-2164-15-821.


A Twist and New Observation in a Case of Persistent Neonatal Hyperuricosuria.

Purandare AV, Broom MA.

Clin Pediatr (Phila). 2014 Sep 19. pii: 0009922814551136. [Epub ahead of print] No abstract available.


Genome-wide computational analysis reveals cardiomyocyte-specific transcriptional Cis-regulatory motifs that enable efficient cardiac gene therapy.

Rincon MY, Sarcar S, Danso-Abeam D, Keyaerts M, Matrai J, Samara-Kuko E, Acosta-Sanchez A, Athanasopoulos T, Dickson G, Lahoutte T, De Bleser P, VandenDriessche T, Chuah MK.

Mol Ther. 2015 Jan;23(1):43-52. doi: 10.1038/mt.2014.178. Epub 2014 Sep 8.


Evidence for deep regulatory similarities in early developmental programs across highly diverged insects.

Kazemian M, Suryamohan K, Chen JY, Zhang Y, Samee MA, Halfon MS, Sinha S.

Genome Biol Evol. 2014 Sep;6(9):2301-20. doi: 10.1093/gbe/evu184.


cgChIP: a cell type- and gene-specific method for chromatin analysis.

Agelopoulos M, McKay DJ, Mann RS.

Methods Mol Biol. 2014;1196:291-306. doi: 10.1007/978-1-4939-1242-1_18.

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