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Items: 20

1.

RSAT 2018: regulatory sequence analysis tools 20th anniversary.

Nguyen NTT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, van Helden J, Medina-Rivera A, Thomas-Chollier M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W209-W214. doi: 10.1093/nar/gky317.

2.

Widespread Enhancer Activity from Core Promoters.

Medina-Rivera A, Santiago-Algarra D, Puthier D, Spicuglia S.

Trends Biochem Sci. 2018 Jun;43(6):452-468. doi: 10.1016/j.tibs.2018.03.004. Epub 2018 Apr 16. Review.

PMID:
29673772
3.

Genome-wide characterization of mammalian promoters with distal enhancer functions.

Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, Charbonnier G, Griffon A, Vanhille L, Stephen T, Alomairi J, Martin D, Torres M, Fernandez N, Soler E, van Helden J, Puthier D, Spicuglia S.

Nat Genet. 2017 Jul;49(7):1073-1081. doi: 10.1038/ng.3884. Epub 2017 Jun 5.

PMID:
28581502
4.

Sex-specific effect of CPB2 Ala147Thr but not Thr325Ile variants on the risk of venous thrombosis: A comprehensive meta-analysis.

Zwingerman N, Medina-Rivera A, Kassam I, Wilson MD, Morange PE, Trégouët DA, Gagnon F.

PLoS One. 2017 May 26;12(5):e0177768. doi: 10.1371/journal.pone.0177768. eCollection 2017.

5.

Dynamic regulation of VEGF-inducible genes by an ERK/ERG/p300 transcriptional network.

Fish JE, Cantu Gutierrez M, Dang LT, Khyzha N, Chen Z, Veitch S, Cheng HS, Khor M, Antounians L, Njock MS, Boudreau E, Herman AM, Rhyner AM, Ruiz OE, Eisenhoffer GT, Medina-Rivera A, Wilson MD, Wythe JD.

Development. 2017 Jul 1;144(13):2428-2444. doi: 10.1242/dev.146050. Epub 2017 May 23.

6.

Leveraging cell type specific regulatory regions to detect SNPs associated with tissue factor pathway inhibitor plasma levels.

Dennis J, Medina-Rivera A, Truong V, Antounians L, Zwingerman N, Carrasco G, Strug L, Wells P, Trégouët DA, Morange PE, Wilson MD, Gagnon F.

Genet Epidemiol. 2017 Jul;41(5):455-466. doi: 10.1002/gepi.22049. Epub 2017 Apr 18.

PMID:
28421636
7.

Single nucleotide polymorphisms in an intergenic chromosome 2q region associated with tissue factor pathway inhibitor plasma levels and venous thromboembolism.

Dennis J, Truong V, Aïssi D, Medina-Rivera A, Blankenberg S, Germain M, Lemire M, Antounians L, Civelek M, Schnabel R, Wells P, Wilson MD, Morange PE, Trégouët DA, Gagnon F.

J Thromb Haemost. 2016 Oct;14(10):1960-1970. doi: 10.1111/jth.13431. Epub 2016 Sep 17.

8.

Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders.

Uusküla-Reimand L, Hou H, Samavarchi-Tehrani P, Rudan MV, Liang M, Medina-Rivera A, Mohammed H, Schmidt D, Schwalie P, Young EJ, Reimand J, Hadjur S, Gingras AC, Wilson MD.

Genome Biol. 2016 Aug 31;17(1):182. doi: 10.1186/s13059-016-1043-8.

9.

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond.

Gama-Castro S, Salgado H, Santos-Zavaleta A, Ledezma-Tejeida D, Muñiz-Rascado L, García-Sotelo JS, Alquicira-Hernández K, Martínez-Flores I, Pannier L, Castro-Mondragón JA, Medina-Rivera A, Solano-Lira H, Bonavides-Martínez C, Pérez-Rueda E, Alquicira-Hernández S, Porrón-Sotelo L, López-Fuentes A, Hernández-Koutoucheva A, Del Moral-Chávez V, Rinaldi F, Collado-Vides J.

Nucleic Acids Res. 2016 Jan 4;44(D1):D133-43. doi: 10.1093/nar/gkv1156. Epub 2015 Nov 2.

10.

RSAT 2015: Regulatory Sequence Analysis Tools.

Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J.

Nucleic Acids Res. 2015 Jul 1;43(W1):W50-6. doi: 10.1093/nar/gkv362. Epub 2015 Apr 22.

11.

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.

12.

MACE: model based analysis of ChIP-exo.

Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W.

Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23.

13.

In silico identification and experimental characterization of regulatory elements controlling the expression of the Salmonella csrB and csrC genes.

Martínez LC, Martínez-Flores I, Salgado H, Fernández-Mora M, Medina-Rivera A, Puente JL, Collado-Vides J, Bustamante VH.

J Bacteriol. 2014 Jan;196(2):325-36. doi: 10.1128/JB.00806-13. Epub 2013 Nov 1.

14.

Evidence classification of high-throughput protocols and confidence integration in RegulonDB.

Weiss V, Medina-Rivera A, Huerta AM, Santos-Zavaleta A, Salgado H, Morett E, Collado-Vides J.

Database (Oxford). 2013 Jan 17;2013:bas059. doi: 10.1093/database/bas059. Print 2013.

15.

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D203-13. doi: 10.1093/nar/gks1201. Epub 2012 Nov 29.

16.

RSAT 2011: regulatory sequence analysis tools.

Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W86-91. doi: 10.1093/nar/gkr377.

17.

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. doi: 10.1093/nar/gkq1110. Epub 2010 Nov 4.

18.

Theoretical and empirical quality assessment of transcription factor-binding motifs.

Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J.

Nucleic Acids Res. 2011 Feb;39(3):808-24. doi: 10.1093/nar/gkq710. Epub 2010 Oct 4.

19.

Structural and functional map of a bacterial nucleoid.

Martínez-Antonio A, Medina-Rivera A, Collado-Vides J.

Genome Biol. 2009;10(12):247. doi: 10.1186/gb-2009-10-12-247. Epub 2009 Dec 11. Review.

20.

Bioinformatics resources for the study of gene regulation in bacteria.

Collado-Vides J, Salgado H, Morett E, Gama-Castro S, Jiménez-Jacinto V, Martínez-Flores I, Medina-Rivera A, Muñiz-Rascado L, Peralta-Gil M, Santos-Zavaleta A.

J Bacteriol. 2009 Jan;191(1):23-31. doi: 10.1128/JB.01017-08. Epub 2008 Oct 31. Review. No abstract available.

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