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Items: 29

1.

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.

Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka-Katayama T, Nakano H, Rowe ML, Elphick MR, Thomas-Chollier M, Hankeln T, Mertes F, Wallberg A, Rast JP, Copley RR, Martinez P, Telford MJ.

Curr Biol. 2019 Jun 3;29(11):1818-1826.e6. doi: 10.1016/j.cub.2019.04.009. Epub 2019 May 16.

PMID:
31104936
2.

Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation.

Rodríguez-Jorge O, Kempis-Calanis LA, Abou-Jaoudé W, Gutiérrez-Reyna DY, Hernandez C, Ramirez-Pliego O, Thomas-Chollier M, Spicuglia S, Santana MA, Thieffry D.

Sci Signal. 2019 Apr 16;12(577). pii: eaar3641. doi: 10.1126/scisignal.aar3641.

PMID:
30992399
3.

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise.

Schöne S, Bothe M, Einfeldt E, Borschiwer M, Benner P, Vingron M, Thomas-Chollier M, Meijsing SH.

PLoS Genet. 2018 Nov 14;14(11):e1007793. doi: 10.1371/journal.pgen.1007793. eCollection 2018 Nov.

4.

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.

5.

Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements.

Thierion E, Le Men J, Collombet S, Hernandez C, Coulpier F, Torbey P, Thomas-Chollier M, Noordermeer D, Charnay P, Gilardi-Hebenstreit P.

PLoS Genet. 2017 Jul 27;13(7):e1006903. doi: 10.1371/journal.pgen.1006903. eCollection 2017 Jul.

6.

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M, van Helden J.

Nucleic Acids Res. 2017 Jul 27;45(13):e119. doi: 10.1093/nar/gkx314.

7.

Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.

Collombet S, van Oevelen C, Sardina Ortega JL, Abou-Jaoudé W, Di Stefano B, Thomas-Chollier M, Graf T, Thieffry D.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5792-5799. doi: 10.1073/pnas.1610622114.

8.

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.

Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH.

Nucleic Acids Res. 2017 Feb 28;45(4):1805-1819. doi: 10.1093/nar/gkw1163.

9.

Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

Schöne S, Jurk M, Helabad MB, Dror I, Lebars I, Kieffer B, Imhof P, Rohs R, Vingron M, Thomas-Chollier M, Meijsing SH.

Nat Commun. 2016 Nov 22;7:13784. doi: 10.1038/ncomms13784. No abstract available.

10.

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity.

Schöne S, Jurk M, Helabad MB, Dror I, Lebars I, Kieffer B, Imhof P, Rohs R, Vingron M, Thomas-Chollier M, Meijsing SH.

Nat Commun. 2016 Sep 1;7:12621. doi: 10.1038/ncomms12621. Erratum in: Nat Commun. 2016 Nov 22;7:13784.

11.

Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation.

Hossan T, Nagarajan S, Baumgart SJ, Xie W, Magallanes RT, Hernandez C, Chiaroni PM, Indenbirken D, Spitzner M, Thomas-Chollier M, Grade M, Thieffry D, Grundhoff A, Wegwitz F, Johnsen SA.

Stem Cells. 2016 May;34(5):1369-76. doi: 10.1002/stem.2287. Epub 2016 Feb 13.

12.

Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements.

Telorac J, Prykhozhij SV, Schöne S, Meierhofer D, Sauer S, Thomas-Chollier M, Meijsing SH.

Nucleic Acids Res. 2016 Jul 27;44(13):6142-56. doi: 10.1093/nar/gkw203. Epub 2016 Mar 25.

13.

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.

14.

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors.

Starick SR, Ibn-Salem J, Jurk M, Hernandez C, Love MI, Chung HR, Vingron M, Thomas-Chollier M, Meijsing SH.

Genome Res. 2015 Jun;25(6):825-35. doi: 10.1101/gr.185157.114. Epub 2015 Feb 26.

15.

Molecular insights into the origin of the Hox-TALE patterning system.

Hudry B, Thomas-Chollier M, Volovik Y, Duffraisse M, Dard A, Frank D, Technau U, Merabet S.

Elife. 2014 Mar 18;3:e01939. doi: 10.7554/eLife.01939.

16.

A naturally occurring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms.

Thomas-Chollier M, Watson LC, Cooper SB, Pufall MA, Liu JS, Borzym K, Vingron M, Yamamoto KR, Meijsing SH.

Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17826-31. doi: 10.1073/pnas.1316235110. Epub 2013 Oct 14.

17.

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J.

Nat Protoc. 2012 Jul 26;7(8):1551-68. doi: 10.1038/nprot.2012.088.

PMID:
22836136
18.

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.

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

Nucleic Acids Res. 2012 Feb;40(4):e31. doi: 10.1093/nar/gkr1104. Epub 2011 Dec 8.

19.

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.

Thomas-Chollier M, Hufton A, Heinig M, O'Keeffe S, Masri NE, Roider HG, Manke T, Vingron M.

Nat Protoc. 2011 Nov 3;6(12):1860-9. doi: 10.1038/nprot.2011.409.

PMID:
22051799
20.

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.

21.

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.

22.

A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution.

Thomas-Chollier M, Ledent V, Leyns L, Vervoort M.

BMC Evol Biol. 2010 Mar 11;10:73. doi: 10.1186/1471-2148-10-73.

23.

Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl.

Sand O, Thomas-Chollier M, van Helden J.

Bioinformatics. 2009 Oct 15;25(20):2739-40. doi: 10.1093/bioinformatics/btp519. Epub 2009 Aug 31.

PMID:
19720677
24.

Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services: an example with ChIP-chip data.

Sand O, Thomas-Chollier M, Vervisch E, van Helden J.

Nat Protoc. 2008;3(10):1604-15. doi: 10.1038/nprot.2008.99.

PMID:
18802441
25.

Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules.

Turatsinze JV, Thomas-Chollier M, Defrance M, van Helden J.

Nat Protoc. 2008;3(10):1578-88. doi: 10.1038/nprot.2008.97.

PMID:
18802439
26.

RSAT: regulatory sequence analysis tools.

Thomas-Chollier M, Sand O, Turatsinze JV, Janky R, Defrance M, Vervisch E, Brohée S, van Helden J.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W119-27. doi: 10.1093/nar/gkn304. Epub 2008 May 21.

27.
28.

HoxPred: automated classification of Hox proteins using combinations of generalised profiles.

Thomas-Chollier M, Leyns L, Ledent V.

BMC Bioinformatics. 2007 Jul 12;8:247.

29.

Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics.

Simionato E, Ledent V, Richards G, Thomas-Chollier M, Kerner P, Coornaert D, Degnan BM, Vervoort M.

BMC Evol Biol. 2007 Mar 2;7:33.

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