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Assessing computational tools for the discovery of transcription factor binding sites.
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Tompa M, et al. Among authors: van helden j. Nat Biotechnol. 2005 Jan;23(1):137-44. doi: 10.1038/nbt1053. Nat Biotechnol. 2005. PMID: 15637633 Free article.
Transcriptional regulation of protein complexes in yeast.
Simonis N, van Helden J, Cohen GN, Wodak SJ. Simonis N, et al. Among authors: van helden j. Genome Biol. 2004;5(5):R33. doi: 10.1186/gb-2004-5-5-r33. Epub 2004 Apr 30. Genome Biol. 2004. PMID: 15128447 Free PMC article.
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project; Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Stark A, et al. Among authors: van helden j. Nature. 2007 Nov 8;450(7167):219-32. doi: 10.1038/nature06340. Nature. 2007. PMID: 17994088 Free PMC article.
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. Medina-Rivera A, et al. Among authors: van helden j. Nucleic Acids Res. 2015 Jul 1;43(W1):W50-6. doi: 10.1093/nar/gkv362. Epub 2015 Apr 22. Nucleic Acids Res. 2015. PMID: 25904632 Free PMC article.
Redefining fundamental concepts of transcription initiation in bacteria.
Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Mejía-Almonte C, et al. Among authors: van helden j. Nat Rev Genet. 2020 Nov;21(11):699-714. doi: 10.1038/s41576-020-0254-8. Epub 2020 Jul 14. Nat Rev Genet. 2020. PMID: 32665585 Free PMC article. Review.
147 results