Items where Division is "05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)"
Number of items at this level: 85. 2017Omidi, 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. May 2016van Nimwegen, Erik. (2016) Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PLoS Computational Biology, 12 (5). e1004726. 4 January 2016Swiss Institute of Bioinformatics Members, SIB. (2016) The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1). D27-D37. 2016Artimo, 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. 14 December 2015Carbajo, Daniel and Magi, Shigeyuki and Itoh, Masayoshi and Kawaji, Hideya and Lassmann, Timo and Arner, Erik and Forrest, Alistair R. R. and Carninci, Piero and Hayashizaki, Yoshihide and Daub, Carsten O. and Fantom Consortium, and Okada-Hatakeyama, Mariko and Mar, Jessica C.. (2015) Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PLoS one, 10 (12). e0144176. December 2015Hurst, Laurence D. and Ghanbarian, Avazeh T. and Forrest, Alistair R. R. and Fantom Consortium, and Huminiecki, Lukasz. (2015) The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biology, 13 (12). e1002315. 2015Breda, 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. Klishami, Saeed Omidi. Computational methods for dissecting transcription regulatory networks. 2015, Doctoral Thesis, University of Basel, Faculty of Science. Liang, Cong and Fantom Consortium, and Forrest, Alistair R. R. and Wagner, Günter P.. (2015) The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nature communications, Vol. 6 , Article Nr. 6066. 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. 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. Wolf, Luise and Silander, Olin K. and van Nimwegen, Erik J.. (2015) Expression noise facilitates the evolution of gene regulation. eLife, 2015, H. 4, e05856. Yoshihara, Masahito and Ohmiya, Hiroko and Hara, Susumu and Kawasaki, Satoshi and Fantom consortium, and Hayashizaki, Yoshihide and Itoh, Masayoshi and Kawaji, Hideya and Tsujikawa, Motokazu and Nishida, Kohji. (2015) Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PLoS one, Vol. 10, H. 3 , e0117581. 2014Andersson, Robin and Gebhard, Claudia and Miguel-Escalada, Irene and Hoof, Ilka and Bornholdt, Jette and Boyd, Mette and Chen, Yun and Zhao, Xiaobei and Schmidl, Christian and Suzuki, Takahiro and Ntini, Evgenia and Arner, Erik and Valen, Eivind and Li, Kang and Schwarzfischer, Lucia and Glatz, Dagmar and Raithel, Johanna and Lilje, Berit and Rapin, Nicolas and Bagger, Frederik Otzen and Jørgensen, Mette and Andersen, Peter Refsing and Bertin, Nicolas and Rackham, Owen and Burroughs, A. Maxwell and Baillie, J. Kenneth and Ishizu, Yuri and Shimizu, Yuri and Furuhata, Erina and Maeda, Shiori and Negishi, Yutaka and Mungall, Christopher J. and Meehan, Terrence F. and Lassmann, Timo and Itoh, Masayoshi and Kawaji, Hideya and Kondo, Naoto and Kawai, Jun and Lennartsson, Andreas and Daub, Carsten O. and Heutink, Peter and Hume, David A. and Jensen, Torben Heick and Suzuki, Harukazu and Hayashizaki, Yoshihide and Müller, Ferenc and Fantom Consortium, and Forrest, Alistair R. R. and Carninci, Piero and Rehli, Michael and Sandelin, Albin. (2014) An atlas of active enhancers across human cell types and tissues. Nature, Vol. 507, H. 7493. pp. 455-461. Arner, Erik and Forrest, Alistair R. R. and Ehrlund, Anna and Mejhert, Niklas and Itoh, Masayoshi and Kawaji, Hideya and Lassmann, Timo and Laurencikiene, Jurga and Rydén, Mikael and Arner, Peter and Fantom Consortium, . (2014) Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS one, Vol. 9, H. 3 , e80274. 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. 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. 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. Blank, Diana and Wolf, Luise and Ackermann, Martin and Silander, Olin K.. (2014) The predictability of molecular evolution during functional innovation. Proceedings of the National Academy of Sciences, 111 (8). pp. 3044-3049. 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. 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. Fantom Consortium, and the Riken P. M. I., and Clst, . (2014) A promoter-level mammalian expression atlas. Nature, Vol. 507, H. 7493. pp. 462-470. 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. Gruber, Andreas R. and Martin, Georges and Müller, Philipp and Schmidt, Alexander and Gruber, Andreas J. and Gumienny, Rafal and Mittal, Nitish and Jayachandran, Rajesh and Pieters, Jean and Keller, Walter. (2014) Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nature Communications, 5 (5465). pp. 1-10. Hasegawa, Yuki and Tang, Dave and Takahashi, Naoko and Hayashizaki, Yoshihide and Forrest, Alistair R. R. and Fantom Consortium, and Suzuki, Harukazu. (2014) CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Scientific Reports, 4. p. 5228. 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. Luisier, Raphaëlle. Towards a better understanding of early drug-induced regulatory mechanisms of liver tumorigenesis. 2014, Doctoral Thesis, University of Basel, Faculty of Science. 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. Morikawa, Hiromasa and Ohkura, Naganari and Vandenbon, Alexis and Itoh, Masayoshi and Nagao-Sato, Sayaka and Kawaji, Hideya and Lassmann, Timo and Carninci, Piero and Hayashizaki, Yoshihide and Forrest, Alistair R. R. and Standley, Daron M. and Date, Hiroshi and Sakaguchi, Shimon and Fantom Consortium, . (2014) Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, H. 14. pp. 5289-5294. 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. Wolf, Luise. Evolution of transcriptional regulation in "Escherichia coli". 2014, Doctoral Thesis, University of Basel, Faculty of Science. 2013Arnold, Phil. A framework to identify epigenome and transcription factor crosstalk. 2013, Doctoral Thesis, University of Basel, Faculty of Science. 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. 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. 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. 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. 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. Ozonov, Evgeniy Andreevich. Modeling nucleosome mediated mechanisms of gene regulation. 2013, Doctoral Thesis, University of Basel, Faculty of Science. Tiwari, N. and Meyer-Schaller, N. and Arnold, P. and Antoniadis, H. and Pachkov, M. and van Nimwegen, E. and Christofori, G.. (2013) Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS one, Vol. 8, H. 2 , e57329. Tiwari, N. and Tiwari, V. K. and Waldmeier, L. and Balwierz, P. J. and Arnold, P. and Pachkov, M. and Meyer-Schaller, N. and Schubeler, D. and van Nimwegen, E. and Christofori, G.. (2013) Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer cell, Vol. 23, H. 6. pp. 768-783. 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. 2012Aceto, 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. 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. 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. Balwierz, Piotr J.. Inference of gene regulatory interactions from deep sequencing data. 2012, Doctoral Thesis, University of Basel, Faculty of Science. 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. 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. 2011Erb, 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. Kawaji, H. and Severin, J. and Lizio, M. and Forrest, A. R. and van Nimwegen, E. and Rehli, M. and Schroder, K. and Irvine, K. and Suzuki, H. and Carninci, P. and Hayashizaki, Y. and Daub, C. O.. (2011) Update of the FANTOM web resource : from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39 (1 Supplement). D856-D860. 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. 2010Burger, L. and van Nimwegen, E.. (2010) Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Computational Biology, 61 (1). e1000633. Burger, Lukas Johannes. Inference of biomolecular interactions from sequence data. 2010, Doctoral Thesis, University of Basel, Faculty of Science. Chen, K. and van Nimwegen, E. and Rajewsky, N. and Siegal, M. L.. (2010) Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome biology and evolution, Vol. 2. pp. 697-707. Molina, Nacho. Genome evolution and regulatory network structure in bacteria. 2010, Doctoral Thesis, University of Basel, Faculty of Science. Ravasi, T. and Suzuki, H. and Cannistraci, C. V. and Katayama, S. and Bajic, V. B. and Tan, K. and Akalin, A. and Schmeier, S. and Kanamori-Katayama, M. and Bertin, N. and Carninci, P. and Daub, C. O. and Forrest, A. R. R. and Gough, J. and Grimmond, S. and Han, J. -H. and Hashimoto, T. and Hide, W. and Hofmann, O. and Kamburov, A. and Kaur, M. and Kawaji, H. and Kubosaki, A. and Lassmann, T. and van Nimwegen, E. and MacPherson, C. R. and Ogawa, C. and Radovanovic, A. and Schwartz, A. and Teasdale, R. D. and Tegner, J. and Lenhard, B. and Teichmann, S. A. and Arakawa, T. and Ninomiya, N. and Murakami, K. and Tagami, M. and Fukuda, S. and Imamura, K. and Kai, C. and Ishihara, R. and Kitazume, Y. and Kawai, J. and Hume, D. A. and Ideker, T. and Hayashizaki, Y.. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, Vol. 140, H. 5. pp. 744-752. Summers, K. M. and Raza, S. and van Nimwegen, E. and Freeman, T. C. and Hume, D. A.. (2010) Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines : implications for phenotypic variability in Marfan syndrome. European journal of human genetics, Vol. 18, H. 11. pp. 1209-1215. 2009Balwierz, P. J. and Carninci, P. and Daub, C. O. and Kawai, J. and Hayashizaki, Y. and Van Belle, W. and Beisel, C. and van Nimwegen, E. J.. (2009) Methods for analyzing deep sequencing expression data : constructing the human and mouse promoterome with deepCAGE data. Genome biology, Vol. 10, H. 7 , R79. Mayoral, R. J. and Pipkin, M. E. and Pachkov, M. and van Nimwegen, E. and Rao, A. and Monticelli, S.. (2009) MicroRNA-221-222 regulate the cell cycle in mast cells. Journal of immunology, Vol. 182, H. 1. pp. 433-445. Molina, N. and van Nimwegen, E.. (2009) Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends in genetics, Vol. 25, H. 6. pp. 243-247. Severin, J. and Waterhouse, A. M. and Kawaji, H. and Lassmann, T. and van Nimwegen, E. and Balwierz, P. J. and de Hoon, M. J. and Hume, D. A. and Carninci, P. and Hayashizaki, Y. and Suzuki, H. and Daub, C. O. and Forrest, A. R.. (2009) FANTOM4 EdgeExpressDB: : an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome biology, Vol. 10, H. 4 , R39. Suzuki, H. and Forrest, A. R. and van Nimwegen, E. and Daub, C. O. and Balwierz, P. J. and Irvine, K. M. and Lassmann, T. and Ravasi, T. and Hasegawa, Y. and de Hoon, M. J. and Katayama, S. and Schroder, K. and Carninci, P. and Tomaru, Y. and Kanamori-Katayama, M. and Kubosaki, A. and Akalin, A. and Ando, Y. and Arner, E. and Asada, M. and Asahara, H. and Bailey, T. and Bajic, V. B. and Bauer, D. and Beckhouse, A. G. and Bertin, N. and Bjorkegren, J. and Brombacher, F. and Bulger, E. and Chalk, A. M. and Chiba, J. and Cloonan, N. and Dawe, A. and Dostie, J. and Engstrom, P. G. and Essack, M. and Faulkner, G. J. and Fink, J. L. and Fredman, D. and Fujimori, K. and Furuno, M. and Gojobori, T. and Gough, J. and Grimmond, S. M. and Gustafsson, M. and Hashimoto, M. and Hashimoto, T. and Hatakeyama, M. and Heinzel, S. and Hide, W. and Hofmann, O. and Hornquist, M. and Huminiecki, L. and Ikeo, K. and Imamoto, N. and Inoue, S. and Inoue, Y. and Ishihara, R. and Iwayanagi, T. and Jacobsen, A. and Kaur, M. and Kawaji, H. and Kerr, M. C. and Kimura, R. and Kimura, S. and Kimura, Y. and Kitano, H. and Koga, H. and Kojima, T. and Kondo, S. and Konno, T. and Krogh, A. and Kruger, A. and Kumar, A. and Lenhard, B. and Lennartsson, A. and Lindow, M. and Lizio, M. and Macpherson, C. and Maeda, N. and Maher, C. A. and Maqungo, M. and Mar, J. and Matigian, N. A. and Matsuda, H. and Mattick, J. S. and Meier, S. and Miyamoto, S. and Miyamoto-Sato, E. and Nakabayashi, K. and Nakachi, Y. and Nakano, M. and Nygaard, S. and Okayama, T. and Okazaki, Y. and Okuda-Yabukami, H. and Orlando, V. and Otomo, J. and Pachkov, M. and Petrovsky, N. and Plessy, C. and Quackenbush, J. and Radovanovic, A. and Rehli, M. and Saito, R. and Sandelin, A. and Schmeier, S. and Schonbach, C. and Schwartz, A. S. and Semple, C. A. and Sera, M. and Severin, J. and Shirahige, K. and Simons, C. and St Laurent, G. and Suzuki, M. and Suzuki, T. and Sweet, M. J. and Taft, R. J. and Takeda, S. and Takenaka, Y. and Tan, K. and Taylor, M. S. and Teasdale, R. D. and Tegner, J. and Teichmann, S. and Valen, E. and Wahlestedt, C. and Waki, K. and Waterhouse, A. and Wells, C. A. and Winther, O. and Wu, L. and Yamaguchi, K. and Yanagawa, H. and Yasuda, J. and Zavolan, M. and Hume, D. A. and Arakawa, T. and Fukuda, S. and Imamura, K. and Kai, C. and Kaiho, A. and Kawashima, T. and Kawazu, C. and Kitazume, Y. and Kojima, M. and Miura, H. and Murakami, K. and Murata, M. and Ninomiya, N. and Nishiyori, H. and Noma, S. and Ogawa, C. and Sano, T. and Simon, C. and Tagami, M. and Takahashi, Y. and Kawai, J. and Hayashizaki, Y.. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics, Vol. 41, H. 5. pp. 553-562. Taddei, A. and Van Houwe, G. and Nagai, S. and Erb, I. and van Nimwegen, E. and Gasser, S. M.. (2009) The functional importance of telomere clustering : Global changes in gene expression result from SIR factor dispersion. Genome research, Vol. 19, H. 4. pp. 611-625. 2008Berninger, P. and Gaidatzis, D. and van Nimwegen, E. and Zavolan, M.. (2008) Computational analysis of small RNA cloning data. Methods, Vol. 44, no. 1. pp. 13-21. Burger, L. and van Nimwegen, E.. (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular systems biology, Vol. 4 , 165. Chern, T. -M. and Paul, N. and van Nimwegen, E. and Zavolan, M.. (2008) Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA research, Vol. 15, H. 2. pp. 63-72. Molina, N. and van Nimwegen, E.. (2008) The evolution of domain-content in bacterial genomes. Biology Direct, Vol. 3. p. 51. Molina, N. and van Nimwegen, E.. (2008) Universal patterns of purifying selection at noncoding positions in bacteria. Genome research, Vol. 18, H. 1. pp. 148-160. Schlecht, U. and Erb, I. and Demougin, P. and Robine, N. and Borde, V. and van Nimwegen, E. and Nicolas, A. and Primig, M.. (2008) Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Molecular Biology of the Cell, 19 (5). pp. 2193-2207. 2007Gaidatzis, D. and van Nimwegen, E. and Hausser, J. and Zavolan, M.. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics, Vol. 8 , 69. Pachkov, M. and Erb, I. and Molina, N. and van Nimwegen, E.. (2007) SwissRegulon : a database of genome-wide annotations of regulatory sites. Nucleic Acids Research, 35 (1 Supplement). D127-D131. Siddharthan, Rahul and van Nimwegen, Erik. (2007) Detecting regulatory sites using PhyloGibbs. Methods in Molecular Biology, 395. pp. 381-402. van Nimwegen, E.. (2007) Finding regulatory elements and regulatory motifs : a general probabilistic framework. BMC Bioinformatics, Vol. 8, Suppl 6 , S4. 2006Chern, T. -M. and van Nimwegen, E. and Kai, C. and Kawai, J. and Carninci, P. and Hayashizaki, Y. and Zavolan, M.. (2006) A simple physical model predicts small exon length variations. PLoS genetics, Vol. 2, H. 4 , e45. Zavolan, M. and van Nimwegen, E.. (2006) The types and prevalence of alternative splice forms. Current opinion in structural biology, Vol. 16, H. 3. pp. 362-367. van Nimwegen, E.. (2006) Influenza escapes immunity along neutral networks. Science, Vol. 314, no. 5807. pp. 1884-1886. van Nimwegen, E. and Paul, N. and Sheridan, R. and Zavolan, M.. (2006) SPA : a probabilistic algorithm for spliced alignment. PLoS genetics, Vol. 2, H. 4 , e24. 2005Carninci, P. and Kasukawa, T. and Katayama, S. and Gough, J. and Frith, M. 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