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Items: 1 to 50 of 78

1.

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.

Berger S, Pachkov M, Arnold P, Omidi S, Kelley N, Salatino S, van Nimwegen E.

Genome Res. 2019 Jul;29(7):1164-1177. doi: 10.1101/gr.239319.118. Epub 2019 May 28.

2.

Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction.

Rzepiela AJ, Ghosh S, Breda J, Vina-Vilaseca A, Syed AP, Gruber AJ, Eschbach K, Beisel C, van Nimwegen E, Zavolan M.

Mol Syst Biol. 2018 Aug 27;14(8):e8266. doi: 10.15252/msb.20188266.

3.

Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC.

Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M.

Genome Biol. 2018 Mar 28;19(1):44. doi: 10.1186/s13059-018-1415-3.

4.

Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software.

Kaiser M, Jug F, Julou T, Deshpande S, Pfohl T, Silander OK, Myers G, van Nimwegen E.

Nat Commun. 2018 Jan 15;9(1):212. doi: 10.1038/s41467-017-02505-0.

5.

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.

Omidi S, Zavolan M, Pachkov M, Breda J, Berger S, van Nimwegen E.

PLoS Comput Biol. 2017 Jul 28;13(7):e1005176. doi: 10.1371/journal.pcbi.1005176. eCollection 2017 Jul.

6.

The ISMARA client.

Artimo P, Duvaud S, Pachkov M, Ioannidis V, van Nimwegen E, Stockinger H.

F1000Res. 2016 Dec 15;5. pii: ELIXIR-2851. doi: 10.12688/f1000research.9794.1. eCollection 2016.

7.

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.

8.

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

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

Mol Endocrinol. 2016 Jul;30(7):809-25. doi: 10.1210/me.2016-1036. Epub 2016 May 16. Erratum in: Endocrinology. 2018 Jul 1;159(7):2703.

9.

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.

10.

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
11.

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.

12.

Quantifying the strength of miRNA-target interactions.

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

Methods. 2015 Sep 1;85:90-99. doi: 10.1016/j.ymeth.2015.04.012. Epub 2015 Apr 16.

13.

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.

14.

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
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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
31.

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.

32.

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.

33.

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.

34.

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels.

Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D.

Mol Syst Biol. 2012 Jul 17;8:593. doi: 10.1038/msb.2012.23.

35.

Adipose tissue microRNAs as regulators of CCL2 production in human obesity.

Arner E, Mejhert N, Kulyté A, Balwierz PJ, Pachkov M, Cormont M, Lorente-Cebrián S, Ehrlund A, Laurencikiene J, Hedén P, Dahlman-Wright K, Tanti JF, Hayashizaki Y, Rydén M, Dahlman I, van Nimwegen E, Daub CO, Arner P.

Diabetes. 2012 Aug;61(8):1986-93. doi: 10.2337/db11-1508. Epub 2012 Jun 11.

36.

Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop.

Aceto N, Sausgruber N, Brinkhaus H, Gaidatzis D, Martiny-Baron G, Mazzarol G, Confalonieri S, Quarto M, Hu G, Balwierz PJ, Pachkov M, Elledge SJ, van Nimwegen E, Stadler MB, Bentires-Alj M.

Nat Med. 2012 Mar 4;18(4):529-37. doi: 10.1038/nm.2645.

PMID:
22388088
37.

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.

Arnold P, Erb I, Pachkov M, Molina N, van Nimwegen E.

Bioinformatics. 2012 Feb 15;28(4):487-94. doi: 10.1093/bioinformatics/btr695.

PMID:
22334039
38.

DNA-binding factors shape the mouse methylome at distal regulatory regions.

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D.

Nature. 2011 Dec 14;480(7378):490-5. doi: 10.1038/nature10716. Erratum in: Nature. 2012 Apr 26;484(7395):550. van Nimwegen, Erik [added].

PMID:
22170606
39.

Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

Erb I, van Nimwegen E.

PLoS One. 2011;6(9):e24279. doi: 10.1371/journal.pone.0024279. Epub 2011 Sep 9.

40.

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

Kawaji H, Severin J, Lizio M, Forrest AR, van Nimwegen E, Rehli M, Schroder K, Irvine K, Suzuki H, Carninci P, Hayashizaki Y, Daub CO.

Nucleic Acids Res. 2011 Jan;39(Database issue):D856-60. doi: 10.1093/nar/gkq1112. Epub 2010 Nov 12.

41.

Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae.

Chen K, van Nimwegen E, Rajewsky N, Siegal ML.

Genome Biol Evol. 2010;2:697-707. doi: 10.1093/gbe/evq054. Epub 2010 Sep 9.

42.

Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome.

Summers KM, Raza S, van Nimwegen E, Freeman TC, Hume DA.

Eur J Hum Genet. 2010 Nov;18(11):1209-15. doi: 10.1038/ejhg.2010.91. Epub 2010 Jun 16.

43.

An atlas of combinatorial transcriptional regulation in mouse and man.

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y.

Cell. 2010 Mar 5;140(5):744-52. doi: 10.1016/j.cell.2010.01.044. Erratum in: Cell. 2010 Apr 16;141(2):369. Kamburov, Atanas [added]; Kaur, Mandeep [added]; MacPherson, Cameron Ross [added]; Radovanovic, Aleksandar [added]; Schwartz, Ariel [added].

44.

Disentangling direct from indirect co-evolution of residues in protein alignments.

Burger L, van Nimwegen E.

PLoS Comput Biol. 2010 Jan;6(1):e1000633. doi: 10.1371/journal.pcbi.1000633. Epub 2010 Jan 1.

45.

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.

Genome Biol. 2009;10(7):R79. doi: 10.1186/gb-2009-10-7-r79. Epub 2009 Jul 22.

46.

Scaling laws in functional genome content across prokaryotic clades and lifestyles.

Molina N, van Nimwegen E.

Trends Genet. 2009 Jun;25(6):243-7. doi: 10.1016/j.tig.2009.04.004. Epub 2009 May 18.

PMID:
19457568
47.

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.

Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19.

PMID:
19377474
48.

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.

Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR.

Genome Biol. 2009;10(4):R39. doi: 10.1186/gb-2009-10-4-r39. Epub 2009 Apr 19.

49.

The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion.

Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM.

Genome Res. 2009 Apr;19(4):611-25. doi: 10.1101/gr.083881.108. Epub 2009 Jan 29.

50.

MicroRNA-221-222 regulate the cell cycle in mast cells.

Mayoral RJ, Pipkin ME, Pachkov M, van Nimwegen E, Rao A, Monticelli S.

J Immunol. 2009 Jan 1;182(1):433-45.

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