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Items: 1 to 20 of 37

1.

A map of direct TF-DNA interactions in the human genome.

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A.

Nucleic Acids Res. 2018 Dec 4. doi: 10.1093/nar/gky1210. [Epub ahead of print]

PMID:
30517703
2.

Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers.

Khan A, Mathelier A, Zhang X.

Epigenetics. 2018;13(9):910-922. doi: 10.1080/15592294.2018.1514231. Epub 2018 Oct 11.

PMID:
30169995
3.

Computational Analysis of Transcriptional Regulation Sites at the HTT Gene Locus.

De Souza RAG, Kosior N, Thomson SB, Mathelier A, Zhang AW, Bečanović K, Wasserman WW, Leavitt BR.

J Huntingtons Dis. 2018;7(3):223-237. doi: 10.3233/JHD-170272.

PMID:
30103339
4.

New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina.

Simpson EM, Korecki AJ, Fornes O, McGill TJ, Cueva-Vargas JL, Agostinone J, Farkas RA, Hickmott JW, Lam SL, Mathelier A, Renner LM, Stoddard J, Zhou M, Di Polo A, Neuringer M, Wasserman WW.

Hum Gene Ther. 2018 Oct 2. doi: 10.1089/hum.2018.118. [Epub ahead of print]

PMID:
30062914
5.

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations.

Fornes O, Gheorghe M, Richmond PA, Arenillas DJ, Wasserman WW, Mathelier A.

Sci Data. 2018 Jul 24;5:180141. doi: 10.1038/sdata.2018.141.

6.

Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response.

Lecellier CH, Wasserman WW, Mathelier A.

Genetics. 2018 Aug;209(4):1055-1071. doi: 10.1534/genetics.118.301116. Epub 2018 Jun 5.

PMID:
29871881
7.

Put science first and formatting later.

Khan A, Montenegro-Montero A, Mathelier A.

EMBO Rep. 2018 May;19(5). pii: e45731. doi: 10.15252/embr.201845731. Epub 2018 Apr 12. No abstract available.

PMID:
29650529
8.

Characterization of the human RFX transcription factor family by regulatory and target gene analysis.

Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P.

BMC Genomics. 2018 Mar 6;19(1):181. doi: 10.1186/s12864-018-4564-6.

9.

JASPAR RESTful API: accessing JASPAR data from any programming language.

Khan A, Mathelier A.

Bioinformatics. 2018 May 1;34(9):1612-1614. doi: 10.1093/bioinformatics/btx804.

PMID:
29253085
10.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1284. doi: 10.1093/nar/gkx1188. No abstract available.

11.

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Khan A, Fornes O, Stigliani A, Gheorghe M, Castro-Mondragon JA, van der Lee R, Bessy A, Chèneby J, Kulkarni SR, Tan G, Baranasic D, Arenillas DJ, Sandelin A, Vandepoele K, Lenhard B, Ballester B, Wasserman WW, Parcy F, Mathelier A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D260-D266. doi: 10.1093/nar/gkx1126.

12.

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.

Chèneby J, Gheorghe M, Artufel M, Mathelier A, Ballester B.

Nucleic Acids Res. 2018 Jan 4;46(D1):D267-D275. doi: 10.1093/nar/gkx1092.

13.

DNA methylation at enhancers identifies distinct breast cancer lineages.

Fleischer T, Tekpli X, Mathelier A, Wang S, Nebdal D, Dhakal HP, Sahlberg KK, Schlichting E; Oslo Breast Cancer Research Consortium (OSBREAC), Børresen-Dale AL, Borgen E, Naume B, Eskeland R, Frigessi A, Tost J, Hurtado A, Kristensen VN.

Nat Commun. 2017 Nov 9;8(1):1379. doi: 10.1038/s41467-017-00510-x.

14.

An integrated expression atlas of miRNAs and their promoters in human and mouse.

de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, de Hoon MJL.

Nat Biotechnol. 2017 Sep;35(9):872-878. doi: 10.1038/nbt.3947. Epub 2017 Aug 21.

15.

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets.

Khan A, Mathelier A.

BMC Bioinformatics. 2017 May 31;18(1):287. doi: 10.1186/s12859-017-1708-7.

16.

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.

Chen CY, Shi W, Balaton BP, Matthews AM, Li Y, Arenillas DJ, Mathelier A, Itoh M, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR, Brown CJ, Wasserman WW.

Sci Rep. 2016 Nov 18;6:37324. doi: 10.1038/srep37324.

17.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H.

Nucleic Acids Res. 2017 Jan 4;45(D1):D737-D743. doi: 10.1093/nar/gkw995. Epub 2016 Oct 27.

18.

PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina.

Hickmott JW, Chen CY, Arenillas DJ, Korecki AJ, Lam SL, Molday LL, Bonaguro RJ, Zhou M, Chou AY, Mathelier A, Boye SL, Hauswirth WW, Molday RS, Wasserman WW, Simpson EM.

Mol Ther Methods Clin Dev. 2016 Aug 10;3:16051. doi: 10.1038/mtm.2016.51. eCollection 2016.

19.

DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.

Mathelier A, Xin B, Chiu TP, Yang L, Rohs R, Wasserman WW.

Cell Syst. 2016 Sep 28;3(3):278-286.e4. doi: 10.1016/j.cels.2016.07.001. Epub 2016 Aug 18.

20.

Evaluating the impact of single nucleotide variants on transcription factor binding.

Shi W, Fornes O, Mathelier A, Wasserman WW.

Nucleic Acids Res. 2016 Dec 1;44(21):10106-10116. Epub 2016 Aug 4.

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