Items where Author is "van Nimwegen, Erik"

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Omidi, Saeed and Zavolan, Mihaela and Pachkov, Mikhail and Breda, Jeremie and Berger, Severin and van Nimwegen, Erik. (2017) Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13 (7). e1005176.

van Nimwegen, Erik. (2016) Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PLoS Computational Biology, 12 (5). e1004726.

Salatino, Silvia and Kupr, Barbara and Baresic, Mario and van Nimwegen, Erik and Handschin, Christoph. (2016) The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells. Molecular Endocrinology, 30 (7). pp. 809-825.

Artimo, Panu and Duvaud, Séverine and Pachkov, Mikhail and Ioannidis, Vassilios and van Nimwegen, Erik and Stockinger, Heinz. (2016) The ISMARA client. F1000Research, 5 (Elixir). p. 2851.

Schertel, Claus and Albarca, Monica and Rockel-Bauer, Claudia and Kelley, Nicholas W. and Bischof, Johannes and Hens, Korneel and van Nimwegen, Erik and Basler, Konrad and Deplancke, Bart. (2015) A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome research, Vol.25, H. 4. pp. 514-523.

Pemberton-Ross, Peter J. and Pachkov, Mikhail and van Nimwegen, Erik. (2015) ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data. Methods, Vol. 85. pp. 62-74.

Breda, Jeremie and Rzepiela, Andrzej J. and Gumienny, Rafal and van Nimwegen, Erik and Zavolan, Mihaela. (2015) Quantifying the strength of miRNA-target interactions. Methods, Vol. 85. pp. 90-99.

Vigano, M. Alessandra and Ivanek, Robert and Balwierz, Piotr and Berninger, Philipp and van Nimwegen, Erik and Karjalainen, Klaus and Rolink, Antonius. (2014) An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. European journal of immunology, Vol. 44, H. 4. pp. 1181-1193.

Bertels, Frederic and Silander, Olin K. and Pachkov, Mikhail and Rainey, Paul B. and van Nimwegen, Erik. (2014) Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular biology and evolution, Vol. 31, no. 5. pp. 1077-1088.

Luisier, Raphaëlle and Unterberger, Elif B. and Goodman, Jay I. and Schwarz, Michael and Moggs, Jonathan and Terranova, Rémi and van Nimwegen, Erik. (2014) Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic Acids Research, 42 (7). pp. 4180-4195.

Gruber, Andreas J. and Grandy, William A. and Balwierz, Piotr J. and Dimitrova, Yoana A. and Pachkov, Mikhail and Ciaudo, Constance and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42 (14). pp. 9313-9326.

Balwierz, Piotr J. and Pachkov, Mikhail and Arnold, Phild and Gruber, Andreas J. and Zavolan, Mihaela and van Nimwegen, Erik. (2014) ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, Vol. 24, H. 5. pp. 869-884.

Jug, Florian and Pietzsch, Tobias and Kainmüller, Dagmar and Funke, Jan and Kaiser, Matthias and van Nimwegen, Erik and Rother, Carsten and Myers, Gene. (2014) Optimal joint segmentation and tracking of Escherichia coli in the mother machine. In: Bayesian and grAphical models for biomedical imaging : First International Workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers. Cham, pp. 25-36.

Dill, Michael T. and Makowska, Zuzanna and Trincucci, Gaia and Gruber, Andreas J. and Vogt, Julia E. and Filipowicz, Magdalena and Calabrese, Diego and Krol, Ilona and Lau, Daryl T. and Terracciano, Luigi and van Nimwegen, Erik and Roth, Volker and Heim, Markus H.. (2014) Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation. Journal of Clinical Investigation, Vol. 124, H. 4. pp. 1568-1581.

Diepenbruck, Maren and Waldmeier, Lorenz and Ivanek, Robert and Berninger, Philipp and Arnold, Phil and van Nimwegen, Erik and Christofori, Gerhard. (2014) Tead2 expression levels control Yap/Taz subcellular distribution, zyxin expression, and epithelial-mesenchymal transition. Journal of Cell Science, 127 (7). pp. 1523-1536.

Diepenbruck, Maren and Waldmeier, Lorenz and Ivanek, Robert and Berninger, Philipp and Arnold, Phil and van Nimwegen, Erik and Christofori, Gerhard. (2014) Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition. Journal of Cell Science, 127 (7). pp. 1523-1536.

Baresic, Mario and Salatino, Silvia and Kupr, Barbara and van Nimwegen, Erik and Handschin, Christoph. (2014) Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program. Molecular and cellular biology, Vol. 34, H. 16. pp. 2996-3012.

Khorshid, Mohsen and Hausser, Jean and Zavolan, Mihaela and van Nimwegen, Erik. (2013) A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nature methods, Vol. 10, H. 3. pp. 253-255.

Tiwari, Neha and Meyer-Schaller, Nathalie and Arnold, Phil and Antoniadis, Helena and Pachkov, Mikhail and van Nimwegen, Erik and Christofori, Gerhard. (2013) Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8). PLoS one, Vol. 8, H. 10 , nn.

Arnold, Phil and Schöler, Anne and Pachkov, Mikhail and Balwierz, Piotr J. and Jørgensen, Helle and Stadler, Michael B. and van Nimwegen, Erik and Schübeler, Dirk. (2013) Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome research, Vol. 23. pp. 60-73.

Ozonov, Evgeniy A. and van Nimwegen, Erik. (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Computational Biology, Vol. 9, H. 8 , e1003181.

Meier-Abt, Fabienne and Milani, Emanuela and Roloff, Tim and Brinkhaus, Heike and Duss, Stephan and Meyer, Dominique S. and Klebba, Ina and Balwierz, Piotr J. and van Nimwegen, Erik and Bentires-Alj, Mohamed. (2013) Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium. Breast cancer research, Vol. 15, H. 2 , R36.

Hofsteenge, Niels and van Nimwegen, Erik and Silander, Olin K.. (2013) Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC microbiology, Vol. 13, 25.

Hausser, Jean and Syed, Afzal Pasha and Selevsek, Nathalie and van Nimwegen, Erik and Jaskiewicz, Lukasz and Aebersold, Ruedi and Zavolan, Mihaela. (2013) Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular systems biology, Vol. 9 , 711.

Arner, Erik and Mejhert, Niklas and Kulyté, Agné and Balwierz, Piotr J. and Pachkov, Mikhail and Cormont, Mireille and Lorente-Cebrián, Silvia and Ehrlund, Anna and Laurencikiene, Jurga and Hedén, Per and Dahlman-Wright, Karin and Tanti, Jean-François and Hayashizaki, Yoshihide and Rydén, Mikael and Dahlman, Ingrid and van Nimwegen, Erik and Daub, Carsten O. and Arner, Peter. (2012) Adipose tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes, Vol. 61, H. 8. pp. 1986-1993.

Tippmann, Sylvia C. and Ivanek, Robert and Gaidatzis, Dimos and Schöler, Anne and Hoerner, Leslie and van Nimwegen, Erik and Stadler, Peter F. and Stadler, Michael B. and Schübeler, Dirk. (2012) Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Molecular systems biology, Vol. 8. p. 593.

Arnold, Phil and Erb, Ionas and Pachkov, Mikhail and Molina, Nacho and van Nimwegen, Erik. (2012) MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics, Vol. 28, H. 4. pp. 487-494.

Pachkov, Mikhail and Balwierz, Piotr J. and Arnold, Phil and Ozonov, Evgeniy and van Nimwegen, Erik. (2012) SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Research, 41 (D1). D214-D220.

Pérez-Schindler, Joaquín and Summermatter, Serge and Salatino, Silvia and Zorzato, Francesco and Beer, Markus and Balwierz, Piotr J. and van Nimwegen, Erik and Feige, Jérôme N. and Auwerx, Johan and Handschin, Christoph. (2012) The Corepressor NCoR1 Antagonizes PGC-1α and Estrogen-Related Receptor α in the Regulation of Skeletal Muscle Function and Oxidative Metabolism. Molecular and cellular biology, Vol. 32, H. 24. pp. 4913-4924.

Aceto, Nicola and Sausgruber, Nina and Brinkhaus, Heike and Gaidatzis, Dimos and Martiny-Baron, Georg and Mazzarol, Giovanni and Confalonieri, Stefano and Quarto, Micaela and Hu, Guang and Balwierz, Piotr J. and Pachkov, Mikhail and Elledge, Stephen J. and van Nimwegen, Erik and Stadler, Michael B. and Bentires-Alj, Mohamed. (2012) Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop. Nature medicine, Vol. 18, H. 4. pp. 529-537.

Stadler, Michael B. and Murr, Rabih and Burger, Lukas and Ivanek, Robert and Lienert, Florian and Schöler, Anne and van Nimwegen, Erik and Wirbelauer, Christiane and Oakeley, Edward J. and Gaidatzis, Dimos and Tiwari, Vijay K. and Schübeler, Dirk. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, Vol. 480, H. 7378. pp. 490-495.

Erb, Ionas and van Nimwegen, Erik. (2011) Transcription Factor Binding Site Positioning in Yeast : Proximal Promoter Motifs Characterize TATA-Less Promoters. PLoS one, Vol. 6, H. 9 , e24279.

Siddharthan, Rahul and van Nimwegen, Erik. (2007) Detecting regulatory sites using PhyloGibbs. Methods in Molecular Biology, 395. pp. 381-402.

Oprea, Mihaela and van Nimwegen, Erik and Perelson, Alan S.. (2000) Dynamics of one-pass germinal center models: implications for affinity maturation. Bulletin of Mathematical Biology, 62 (1). pp. 121-153.