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Items: 1 to 20 of 72

1.

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M.

Methods. 2016 Jul 15;104:204-205. doi: 10.1016/j.ymeth.2015.12.016. Epub 2016 Jan 13. No abstract available.

2.

The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells.

Salatino S, Kupr B, Baresic M, van Nimwegen E, Handschin C.

Mol Endocrinol. 2016 Jul;30(7):809-25. doi: 10.1210/me.2016-1036. Epub 2016 May 16.

PMID:
27182621
3.

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

van Nimwegen E.

PLoS Comput Biol. 2016 May 12;12(5):e1004726. doi: 10.1371/journal.pcbi.1004726. eCollection 2016 May. No abstract available.

4.

ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data.

Pemberton-Ross PJ, Pachkov M, van Nimwegen E.

Methods. 2015 Sep 1;85:62-74. doi: 10.1016/j.ymeth.2015.06.024. Epub 2015 Jul 8.

PMID:
26164700
5.

Expression noise facilitates the evolution of gene regulation.

Wolf L, Silander OK, van Nimwegen E.

Elife. 2015 Jun 17;4. doi: 10.7554/eLife.05856.

6.

Quantifying the strength of miRNA-target interactions.

Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M.

Methods. 2015 Sep 1;85:90-9. doi: 10.1016/j.ymeth.2015.04.012. Epub 2015 Apr 16.

7.

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development.

Schertel C, Albarca M, Rockel-Bauer C, Kelley NW, Bischof J, Hens K, van Nimwegen E, Basler K, Deplancke B.

Genome Res. 2015 Apr;25(4):514-23. doi: 10.1101/gr.181305.114. Epub 2015 Jan 7.

8.

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells.

Gruber AR, Martin G, Müller P, Schmidt A, Gruber AJ, Gumienny R, Mittal N, Jayachandran R, Pieters J, Keller W, van Nimwegen E, Zavolan M.

Nat Commun. 2014 Nov 21;5:5465. doi: 10.1038/ncomms6465.

PMID:
25413384
9.

Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program.

Baresic M, Salatino S, Kupr B, van Nimwegen E, Handschin C.

Mol Cell Biol. 2014 Aug;34(16):2996-3012. doi: 10.1128/MCB.01710-13. Epub 2014 Jun 9.

10.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

11.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

12.

Automated reconstruction of whole-genome phylogenies from short-sequence reads.

Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E.

Mol Biol Evol. 2014 May;31(5):1077-88. doi: 10.1093/molbev/msu088. Epub 2014 Mar 5.

13.

Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation.

Dill MT, Makowska Z, Trincucci G, Gruber AJ, Vogt JE, Filipowicz M, Calabrese D, Krol I, Lau DT, Terracciano L, van Nimwegen E, Roth V, Heim MH.

J Clin Invest. 2014 Apr;124(4):1568-81. doi: 10.1172/JCI70408. Epub 2014 Feb 24.

14.

Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition.

Diepenbruck M, Waldmeier L, Ivanek R, Berninger P, Arnold P, van Nimwegen E, Christofori G.

J Cell Sci. 2014 Apr 1;127(Pt 7):1523-36. doi: 10.1242/jcs.139865. Epub 2014 Feb 19.

15.

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.

Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E.

Genome Res. 2014 May;24(5):869-84. doi: 10.1101/gr.169508.113. Epub 2014 Feb 10.

16.

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion.

Luisier R, Unterberger EB, Goodman JI, Schwarz M, Moggs J, Terranova R, van Nimwegen E.

Nucleic Acids Res. 2014 Apr;42(7):4180-95. doi: 10.1093/nar/gkt1415. Epub 2014 Jan 23.

17.

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.

Vigano MA, Ivanek R, Balwierz P, Berninger P, van Nimwegen E, Karjalainen K, Rolink A.

Eur J Immunol. 2014 Apr;44(4):1181-93. doi: 10.1002/eji.201344022. Epub 2014 Feb 1.

18.

Timescales and bottlenecks in miRNA-dependent gene regulation.

Hausser J, Syed AP, Selevsek N, van Nimwegen E, Jaskiewicz L, Aebersold R, Zavolan M.

Mol Syst Biol. 2013 Dec 3;9:711. doi: 10.1038/msb.2013.68.

19.

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

Ozonov EA, van Nimwegen E.

PLoS Comput Biol. 2013;9(8):e1003181. doi: 10.1371/journal.pcbi.1003181. Epub 2013 Aug 22.

20.

Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming.

Tiwari N, Tiwari VK, Waldmeier L, Balwierz PJ, Arnold P, Pachkov M, Meyer-Schaller N, Schübeler D, van Nimwegen E, Christofori G.

Cancer Cell. 2013 Jun 10;23(6):768-83. doi: 10.1016/j.ccr.2013.04.020.

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