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Results: 1 to 20 of 65

1.

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
[PubMed - in process]
2.

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.

PMID:
24912679
[PubMed - indexed for MEDLINE]
3.

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.

PMID:
24792157
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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, Lassman 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.

PMID:
24670764
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
24600054
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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 1;124(4):1568-81. doi: 10.1172/JCI70408. Epub 2014 Feb 24.

PMID:
24569457
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
24554433
[PubMed - in process]
Free Article
8.

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.

PMID:
24515121
[PubMed - in process]
Free PMC Article
9.

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.

PMID:
24464994
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
24374622
[PubMed - indexed for MEDLINE]
11.

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.

PMID:
24301800
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23990766
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23764001
[PubMed - indexed for MEDLINE]
Free Article
14.

Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium.

Meier-Abt F, Milani E, Roloff T, Brinkhaus H, Duss S, Meyer DS, Klebba I, Balwierz PJ, van Nimwegen E, Bentires-Alj M.

Breast Cancer Res. 2013 Apr 29;15(2):R36. doi: 10.1186/bcr3419.

PMID:
23621987
[PubMed - in process]
Free PMC Article
15.

Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8).

Tiwari N, Meyer-Schaller N, Arnold P, Antoniadis H, Pachkov M, van Nimwegen E, Christofori G.

PLoS One. 2013;8(2):e57329. doi: 10.1371/journal.pone.0057329. Epub 2013 Feb 25. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/121b04a1-0cbb-4e24-8a63-fc9cdd31ec76.

PMID:
23451207
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli.

Hofsteenge N, van Nimwegen E, Silander OK.

BMC Microbiol. 2013 Feb 4;13:25. doi: 10.1186/1471-2180-13-25.

PMID:
23379956
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets.

Khorshid M, Hausser J, Zavolan M, van Nimwegen E.

Nat Methods. 2013 Mar;10(3):253-5. doi: 10.1038/nmeth.2341. Epub 2013 Jan 20.

PMID:
23334102
[PubMed - indexed for MEDLINE]
18.

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.

Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E.

Nucleic Acids Res. 2013 Jan;41(Database issue):D214-20. doi: 10.1093/nar/gks1145. Epub 2012 Nov 24.

PMID:
23180783
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The corepressor NCoR1 antagonizes PGC-1α and estrogen-related receptor α in the regulation of skeletal muscle function and oxidative metabolism.

Pérez-Schindler J, Summermatter S, Salatino S, Zorzato F, Beer M, Balwierz PJ, van Nimwegen E, Feige JN, Auwerx J, Handschin C.

Mol Cell Biol. 2012 Dec;32(24):4913-24. doi: 10.1128/MCB.00877-12. Epub 2012 Oct 1.

PMID:
23028049
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.

Arnold P, Schöler A, Pachkov M, Balwierz PJ, Jørgensen H, Stadler MB, van Nimwegen E, Schübeler D.

Genome Res. 2013 Jan;23(1):60-73. doi: 10.1101/gr.142661.112. Epub 2012 Sep 10.

PMID:
22964890
[PubMed - indexed for MEDLINE]
Free PMC Article

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