Prof. Dr. Erik van Nimwegen

Biozentrum
University of Basel
Klingelbergstrasse 50 / 70
CH - 4056 Basel
KLB61, Room 905 Phone: +41 61 207 15 76
Email: erik.vannimwegen-at-unibas.ch
Curriculum Vitae

Administrative Assistant

Yvonne Steger
KLB61, Room 916
Phone: +41 61 207 15 86
Fax: +41 61 207 15 85
Email: yvonne.steger-at-unibas.ch

Research group Erik van Nimwegen

Articles

2016
Artimo, Panu; Duvaud, Séverine; Pachkov, Mikhail; Ioannidis, Vassilios; van Nimwegen, Erik; Stockinger, Heinz (2016). The ISMARA client. F1000Research, 5(Elixir), 2851.
Salatino, Silvia; Kupr, Barbara; Baresic, Mario; van Nimwegen, Erik; Handschin, Christoph (2016). The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells. Molecular Endocrinology, 30(7), 809-825.
van Nimwegen, Erik (2016). Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?. PLoS computational biology, 12(5), e1004726.
Swiss Institute of Bioinformatics Members, SIB (2016). The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44(D1), D27-D37.
2015
Hurst, Laurence D.; Ghanbarian, Avazeh T.; Forrest, Alistair R. R.; Fantom Consortium; Huminiecki, Lukasz (2015). The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biology, 13(12), e1002315.
Carbajo, Daniel; Magi, Shigeyuki; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Arner, Erik; Forrest, Alistair R R; Carninci, Piero; Hayashizaki, Yoshihide; Daub, Carsten O; FANTOM consortium; Okada-Hatakeyama, Mariko; 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.
Pemberton-Ross, Peter J; Pachkov, Mikhail; van Nimwegen, Erik (2015). ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data. Methods, 85, 62-74.
Breda, Jeremie; Rzepiela, Andrzej J; Gumienny, Rafal; van Nimwegen, Erik; Zavolan, Mihaela (2015). Quantifying the strength of miRNA-target interactions. Methods, 85, 90-9.
Yoshihara, Masahito; Ohmiya, Hiroko; Hara, Susumu; Kawasaki, Satoshi; FANTOM consortium; Hayashizaki, Yoshihide; Itoh, Masayoshi; Kawaji, Hideya; Tsujikawa, Motokazu; Nishida, Kohji (2015). Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PLoS one, 10(3), e0117581.
Liang, Cong; Forrest, Alistair R. R.; Wagner, Guenter P.; FANTOM Consortium (2015). The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nature communications, 6, 6066.
Wolf, Luise; Silander, Olin K; van Nimwegen, Erik (2015). Expression noise facilitates the evolution of gene regulation. eLife, 4(4), e05856.
Schertel, Claus; Albarca, Monica; Rockel-Bauer, Claudia; Kelley, Nicholas W.; Bischof, Johannes; Hens, Korneel; van Nimwegen, Erik; Basler, Konrad; 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, 25(4), 514-523.
2014
Gruber, Andreas R; Martin, Georges; Müller, Philipp; Schmidt, Alexander; Gruber, Andreas J; Gumienny, Rafal; Mittal, Nitish; Jayachandran, Rajesh; Pieters, Jean; Keller, Walter; van Nimwegen, Erik; Zavolan, Mihaela (2014). Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nature communications, 5(5465), 5465.
Gruber, Andreas J; Grandy, William A; Balwierz, Piotr J; Dimitrova, Yoana A; Pachkov, Mikhail; Ciaudo, Constance; Nimwegen, Erik van; Zavolan, Mihaela (2014). Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic acids research, 42(14), 9313-26.
Hasegawa, Yuki; Tang, Dave; Takahashi, Naoko; Hayashizaki, Yoshihide; Forrest, Alistair R R; FANTOM Consortium; Suzuki, Harukazu (2014). CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Scientific reports, 4, 5228.
Baresic, Mario; Salatino, Silvia; Kupr, Barbara; van Nimwegen, Erik; 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, 34(16), 2996-3012.
Stockinger, Heinz; Altenhoff, Adrian M; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Le Mercier, Philippe; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M; Rougemont, Jacques; Schwede, Torsten; von Mering, Christian; van Nimwegen, Erik; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M; Zoete, Vincent; Appel, Ron D (2014). Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support. Nucleic acids research, 42(Web Server issue), W436-41.
Morikawa, Hiromasa; Ohkura, Naganari; Vandenbon, Alexis; Itoh, Masayoshi; Nagao-Sato, Sayaka; Kawaji, Hideya; Lassmann, Timo; Carninci, Piero; Hayashizaki, Yoshihide; Forrest, Alistair R R; Standley, Daron M; Date, Hiroshi; Sakaguchi, Shimon; 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, 111(14), 5289-94.
Arner, Erik; Forrest, Alistair R R; Ehrlund, Anna; Mejhert, Niklas; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Laurencikiene, Jurga; Rydén, Mikael; Arner, Peter; 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, 9(3), e80274.
FANTOM Consortium and the RIKEN PMI and CLST (DGT) (2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462-470.
Andersson, Robin; Gebhard, Claudia; Miguel-Escalada, Irene; Hoof, Ilka; Bornholdt, Jette; Boyd, Mette; Chen, Yun; Zhao, Xiaobei; Schmidl, Christian; Suzuki, Takahiro; Ntini, Evgenia; Arner, Erik; Valen, Eivind; Li, Kang; Schwarzfischer, Lucia; Glatz, Dagmar; Raithel, Johanna; Lilje, Berit; Rapin, Nicolas; Bagger, Frederik Otzen; Jørgensen, Mette; Andersen, Peter Refsing; Bertin, Nicolas; Rackham, Owen; Burroughs, A Maxwell; Baillie, J Kenneth; Ishizu, Yuri; Shimizu, Yuri; Furuhata, Erina; Maeda, Shiori; Negishi, Yutaka; Mungall, Christopher J; Meehan, Terrence F; Lassmann, Timo; Itoh, Masayoshi; Kawaji, Hideya; Kondo, Naoto; Kawai, Jun; Lennartsson, Andreas; Daub, Carsten O; Heutink, Peter; Hume, David A; Jensen, Torben Heick; Suzuki, Harukazu; Hayashizaki, Yoshihide; Müller, Ferenc; FANTOM Consortium; Forrest, Alistair R R; Carninci, Piero; Rehli, Michael; Sandelin, Albin (2014). An atlas of active enhancers across human cell types and tissues. Nature, 507(7493), 455-61.
Bertels, Frederic; Silander, Olin K; Pachkov, Mikhail; Rainey, Paul B; van Nimwegen, Erik (2014). Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular biology and evolution, 31(5), 1077-88.
Dill, Michael T; Makowska, Zuzanna; Trincucci, Gaia; Gruber, Andreas J; Vogt, Julia E; Filipowicz, Magdalena; Calabrese, Diego; Krol, Ilona; Lau, Daryl T; Terracciano, Luigi; van Nimwegen, Erik; Roth, Volker; Heim, Markus H (2014). Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation. The Journal of clinical investigation, 124(4), 1568-81.
Diepenbruck, Maren; Waldmeier, Lorenz; Ivanek, Robert; Berninger, Philipp; Arnold, Phil; van Nimwegen, Erik; 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(Pt 7), 1523-36.
Balwierz, Piotr J; Pachkov, Mikhail; Arnold, Phil; Gruber, Andreas J; Zavolan, Mihaela; van Nimwegen, Erik (2014). ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, 24(5), 869-84.
Luisier, Raphaëlle; Unterberger, Elif B; Goodman, Jay I; Schwarz, Michael; Moggs, Jonathan; Terranova, Rémi; van Nimwegen, Erik (2014). Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic acids research, 42(7), 4180-95.
Vigano, Maria Alessandra; Ivanek, Robert; Balwierz, Piotr; Berninger, Philipp; van Nimwegen, Erik; Karjalainen, Klaus; Rolink, Antonius (2014). An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. European journal of immunology, 44(4), 1181-93.
Jug, Florian; Pietzsch, Tobias; Kainmüller, Dagmar; Funke, Jan; Kaiser, Matthias; van Nimwegen, Erik; Rother, Carsten; Myers, Gene: Optimal joint segmentation and tracking of Escherichia coli in the mother machine, in: Cardoso, JM; Simpson, I; Arbel, T; Precup, D; Ribbens, A (Ed.). (2014). Bayesian and grAphical models for biomedical imaging : First International Workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers, Cham: Springer , S. S. 25-36.
2013
Hausser, Jean; Syed, Afzal Pasha; Selevsek, Nathalie; van Nimwegen, Erik; Jaskiewicz, Lukasz; Aebersold, Ruedi; Zavolan, Mihaela (2013). Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular systems biology, 9, 711.
Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8). PLoS one, 8(10), nn.
Ozonov, Evgeniy A; 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, 9(8), e1003181.
Tiwari, Neha; Tiwari, Vijay K; Waldmeier, Lorenz; Balwierz, Piotr J; Arnold, Phil; Pachkov, Mikhail; Meyer-Schaller, Nathalie; Schübeler, Dirk; van Nimwegen, Erik; Christofori, Gerhard (2013). Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer cell, 23(6), 768-83.
Meier-Abt, Fabienne; Milani, Emanuela; Roloff, Tim; Brinkhaus, Heike; Duss, Stephan; Meyer, Dominique S; Klebba, Ina; Balwierz, Piotr J; van Nimwegen, Erik; 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, 15(2), R36.
Tiwari, Neha; Meyer-Schaller, Nathalie; Arnold, Phil; Antoniadis, Helena; Pachkov, Mikhail; van Nimwegen, Erik; Christofori, Gerhard (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS one, 8(2), e57329.
Hofsteenge, Niels; van Nimwegen, Erik; Silander, Olin K (2013). Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC microbiology, 13(1), 25.
Khorshid, Mohsen; Hausser, Jean; Zavolan, Mihaela; van Nimwegen, Erik (2013). A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nature methods, 10(3), 253-5.
Arnold, Phil; Schöler, Anne; Pachkov, Mikhail; Balwierz, Piotr J; Jørgensen, Helle; Stadler, Michael B; van Nimwegen, Erik; Schübeler, Dirk (2013). Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome research, 23(1), 60-73.
2012
Pachkov, Mikhail; Balwierz, Piotr J; Arnold, Phil; Ozonov, Evgeniy; van Nimwegen, Erik (2012). SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates. Nucleic acids research, 41(Database issue), D214-20.
Pérez-Schindler, Joaquín; Summermatter, Serge; Salatino, Silvia; Zorzato, Francesco; Beer, Markus; Balwierz, Piotr J; van Nimwegen, Erik; Feige, Jérôme N; Auwerx, Johan; 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, 32(24), 4913-24.
Tippmann, Sylvia C; Ivanek, Robert; Gaidatzis, Dimos; Schöler, Anne; Hoerner, Leslie; van Nimwegen, Erik; Stadler, Peter F; Stadler, Michael B; Schübeler, Dirk (2012). Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Molecular systems biology, 8, 593.
Arner, Erik; Mejhert, Niklas; Kulyté, Agné; Balwierz, Piotr J; Pachkov, Mikhail; Cormont, Mireille; Lorente-Cebrián, Silvia; Ehrlund, Anna; Laurencikiene, Jurga; Hedén, Per; Dahlman-Wright, Karin; Tanti, Jean-François; Hayashizaki, Yoshihide; Rydén, Mikael; Dahlman, Ingrid; van Nimwegen, Erik; Daub, Carsten O; Arner, Peter (2012). Adipose tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes, 61(8), 1986-93.
Aceto, Nicola; Sausgruber, Nina; Brinkhaus, Heike; Gaidatzis, Dimos; Martiny-Baron, Georg; Mazzarol, Giovanni; Confalonieri, Stefano; Quarto, Micaela; Hu, Guang; Balwierz, Piotr J; Pachkov, Mikhail; Elledge, Stephen J; van Nimwegen, Erik; Stadler, Michael B; 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, 18(4), 529-37.
Arnold, Phil; Erb, Ionas; Pachkov, Mikhail; Molina, Nacho; van Nimwegen, Erik (2012). MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics, 28(4), 487-94.
2011
Stadler, Michael B; Murr, Rabih; Burger, Lukas; Ivanek, Robert; Lienert, Florian; Schöler, Anne; van Nimwegen, Erik; Wirbelauer, Christiane; Oakeley, Edward J; Gaidatzis, Dimos; Tiwari, Vijay K; Schübeler, Dirk (2011). DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, 480(7378), 490-5.
Kawaji, Hideya; Severin, Jessica; Lizio, Marina; Forrest, Alistair R R; van Nimwegen, Erik; Rehli, Michael; Schroder, Kate; Irvine, Katharine; Suzuki, Harukazu; Carninci, Piero; Hayashizaki, Yoshihide; Daub, Carsten O (2011). Update of the FANTOM web resource : from mammalian transcriptional landscape to its dynamic regulation. Nucleic acids research, 39(Database issue), D856-60.
Erb, Ionas; van Nimwegen, Erik (2011). Transcription Factor Binding Site Positioning in Yeast : Proximal Promoter Motifs Characterize TATA-Less Promoters. PLoS one, 6(9), e24279.
2010
Chen, Kevin; van Nimwegen, Erik; Rajewsky, Nikolaus; Siegal, Mark L (2010). Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome biology and evolution, 2, 697-707.
Summers, Kim M; Raza, Sobia; van Nimwegen, Erik; Freeman, Thomas C; Hume, David 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, 18(11), 1209-15.
Ravasi, Timothy; Suzuki, Harukazu; Cannistraci, Carlo Vittorio; Katayama, Shintaro; Bajic, Vladimir B; Tan, Kai; Akalin, Altuna; Schmeier, Sebastian; Kanamori-Katayama, Mutsumi; Bertin, Nicolas; Carninci, Piero; Daub, Carsten O; Forrest, Alistair R R; Gough, Julian; Grimmond, Sean; Han, Jung-Hoon; Hashimoto, Takehiro; Hide, Winston; Hofmann, Oliver; Kamburov, Atanas; Kaur, Mandeep; Kawaji, Hideya; Kubosaki, Atsutaka; Lassmann, Timo; van Nimwegen, Erik; MacPherson, Cameron Ross; Ogawa, Chihiro; Radovanovic, Aleksandar; Schwartz, Ariel; Teasdale, Rohan D; Tegnér, Jesper; Lenhard, Boris; Teichmann, Sarah A; Arakawa, Takahiro; Ninomiya, Noriko; Murakami, Kayoko; Tagami, Michihira; Fukuda, Shiro; Imamura, Kengo; Kai, Chikatoshi; Ishihara, Ryoko; Kitazume, Yayoi; Kawai, Jun; Hume, David A; Ideker, Trey; Hayashizaki, Yoshihide (2010). An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140(5), 744-52.
Burger, Lukas; van Nimwegen, Erik (2010). Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Computational Biology, 6(1), e1000633.
2009
Molina, Nacho; van Nimwegen, Erik (2009). Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends in genetics, 25(6), 243-7.
Taddei, Angela; Van Houwe, Griet; Nagai, Shigeki; Erb, Ionas; van Nimwegen, Erik; Gasser, Susan M (2009). The functional importance of telomere clustering : Global changes in gene expression result from SIR factor dispersion. Genome research, 19(4), 611-25.
FANTOM Consortium; Suzuki, Harukazu; Forrest, Alistair R R; van Nimwegen, Erik; Daub, Carsten O; Balwierz, Piotr J; Irvine, Katharine M; Lassmann, Timo; Ravasi, Timothy; Hasegawa, Yuki; de Hoon, Michiel J L; Katayama, Shintaro; Schroder, Kate; Carninci, Piero; Tomaru, Yasuhiro; Kanamori-Katayama, Mutsumi; Kubosaki, Atsutaka; Akalin, Altuna; Ando, Yoshinari; Arner, Erik; Asada, Maki; Asahara, Hiroshi; Bailey, Timothy; Bajic, Vladimir B; Bauer, Denis; Beckhouse, Anthony G; Bertin, Nicolas; Björkegren, Johan; Brombacher, Frank; Bulger, Erika; Chalk, Alistair M; Chiba, Joe; Cloonan, Nicole; Dawe, Adam; Dostie, Josee; Engström, Pär G; Essack, Magbubah; Faulkner, Geoffrey J; Fink, J Lynn; Fredman, David; Fujimori, Ko; Furuno, Masaaki; Gojobori, Takashi; Gough, Julian; Grimmond, Sean M; Gustafsson, Mika; Hashimoto, Megumi; Hashimoto, Takehiro; Hatakeyama, Mariko; Heinzel, Susanne; Hide, Winston; Hofmann, Oliver; Hörnquist, Michael; Huminiecki, Lukasz; Ikeo, Kazuho; Imamoto, Naoko; Inoue, Satoshi; Inoue, Yusuke; Ishihara, Ryoko; Iwayanagi, Takao; Jacobsen, Anders; Kaur, Mandeep; Kawaji, Hideya; Kerr, Markus C; Kimura, Ryuichiro; Kimura, Syuhei; Kimura, Yasumasa; Kitano, Hiroaki; Koga, Hisashi; Kojima, Toshio; Kondo, Shinji; Konno, Takeshi; Krogh, Anders; Kruger, Adele; Kumar, Ajit; Lenhard, Boris; Lennartsson, Andreas; Lindow, Morten; Lizio, Marina; Macpherson, Cameron; Maeda, Norihiro; Maher, Christopher A; Maqungo, Monique; Mar, Jessica; Matigian, Nicholas A; Matsuda, Hideo; Mattick, John S; Meier, Stuart; Miyamoto, Sei; Miyamoto-Sato, Etsuko; Nakabayashi, Kazuhiko; Nakachi, Yutaka; Nakano, Mika; Nygaard, Sanne; Okayama, Toshitsugu; Okazaki, Yasushi; Okuda-Yabukami, Haruka; Orlando, Valerio; Otomo, Jun; Pachkov, Mikhail; Petrovsky, Nikolai; Plessy, Charles; Quackenbush, John; Radovanovic, Aleksandar; Rehli, Michael; Saito, Rintaro; Sandelin, Albin; Schmeier, Sebastian; Schönbach, Christian; Schwartz, Ariel S; Semple, Colin A; Sera, Miho; Severin, Jessica; Shirahige, Katsuhiko; Simons, Cas; St Laurent, George; Suzuki, Masanori; Suzuki, Takahiro; Sweet, Matthew J; Taft, Ryan J; Takeda, Shizu; Takenaka, Yoichi; Tan, Kai; Taylor, Martin S; Teasdale, Rohan D; Tegnér, Jesper; Teichmann, Sarah; Valen, Eivind; Wahlestedt, Claes; Waki, Kazunori; Waterhouse, Andrew; Wells, Christine A; Winther, Ole; Wu, Linda; Yamaguchi, Kazumi; Yanagawa, Hiroshi; Yasuda, Jun; Zavolan, Mihaela; Hume, David A; Riken Omics Science Center; Arakawa, Takahiro; Fukuda, Shiro; Imamura, Kengo; Kai, Chikatoshi; Kaiho, Ai; Kawashima, Tsugumi; Kawazu, Chika; Kitazume, Yayoi; Kojima, Miki; Miura, Hisashi; Murakami, Kayoko; Murata, Mitsuyoshi; Ninomiya, Noriko; Nishiyori, Hiromi; Noma, Shohei; Ogawa, Chihiro; Sano, Takuma; Simon, Christophe; Tagami, Michihira; Takahashi, Yukari; Kawai, Jun; Hayashizaki, Yoshihide (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics, 41(5), 553-62.
Severin, Jessica; Waterhouse, Andrew M; Kawaji, Hideya; Lassmann, Timo; van Nimwegen, Erik; Balwierz, Piotr J; de Hoon, Michiel Jl; Hume, David A; Carninci, Piero; Hayashizaki, Yoshihide; Suzuki, Harukazu; Daub, Carsten O; Forrest, Alistair Rr (2009). FANTOM4 EdgeExpressDB: : an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome biology, 10(4), R39.
Mayoral, Ramon J; Pipkin, Matthew E; Pachkov, Mikhail; van Nimwegen, Erik; Rao, Anjana; Monticelli, Silvia (2009). MicroRNA-221-222 regulate the cell cycle in mast cells. Journal of immunology, 182(1), 433-45.
Balwierz, Piotr J; Carninci, Piero; Daub, Carsten O; Kawai, Jun; Hayashizaki, Yoshihide; Van Belle, Werner; Beisel, Christian; van Nimwegen, Erik (2009). Methods for analyzing deep sequencing expression data : constructing the human and mouse promoterome with deepCAGE data. Genome biology, 10(7), R79.
2008
Berninger, Philipp; Gaidatzis, Dimos; van Nimwegen, Erik; Zavolan, Mihaela (2008). Computational analysis of small RNA cloning data. Methods, 44(1), 13-21.
Molina, Nacho; van Nimwegen, Erik (2008). The evolution of domain-content in bacterial genomes. Biology Direct, 3, 51.
Burger, Lukas; van Nimwegen, Erik (2008). Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular systems biology, 4, 165.
Molina, Nacho; van Nimwegen, Erik (2008). Universal patterns of purifying selection at noncoding positions in bacteria. Genome research, 18(1), 148-60.
Chern, Tzu-Ming; Paul, Nicodeme; van Nimwegen, Erik; Zavolan, Mihaela (2008). Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA research, 15(2), 63-72.
Schlecht, Ulrich; Erb, Ionas; Demougin, Philippe; Robine, Nicolas; Borde, Valérie; van Nimwegen, Erik; Nicolas, Alain; Primig, Michael (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), 2193-207.
2007
van Nimwegen, Erik (2007). Finding regulatory elements and regulatory motifs : a general probabilistic framework. BMC Bioinformatics, 8, S4.
Gaidatzis, Dimos; van Nimwegen, Erik; Hausser, Jean; Zavolan, Mihaela (2007). Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics, 8, 69.
Pachkov, Mikhail; Erb, Ionas; Molina, Nacho; van Nimwegen, Erik (2007). SwissRegulon : a database of genome-wide annotations of regulatory sites. Nucleic acids research, 35(Database issue), D127-31.
Siddharthan, Rahul; van Nimwegen, Erik (2007). Detecting regulatory sites using PhyloGibbs. Methods in molecular biology (Humana Press), 395, 381-402.
2006
van Nimwegen, Erik (2006). Influenza escapes immunity along neutral networks. Science, 314(5807), 1884-1886.
van Nimwegen, Erik; Paul, Nicodeme; Sheridan, Robert; Zavolan, Mihaela (2006). SPA : a probabilistic algorithm for spliced alignment. PLoS genetics, 2(4), e24.
Chern, Tzu-Ming; van Nimwegen, Erik; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Zavolan, Mihaela (2006). A simple physical model predicts small exon length variations. PLoS genetics, 2(4), e45.
Zavolan, Mihaela; van Nimwegen, Erik (2006). The types and prevalence of alternative splice forms. Current opinion in structural biology, 16(3), 362-7.
2005
Sewer, Alain; Paul, Nicodème; Landgraf, Pablo; Aravin, Alexei; Pfeffer, Sébastien; Brownstein, Michael J; Tuschl, Thomas; van Nimwegen, Erik; Zavolan, Mihaela (2005). Identification of clustered microRNAs using an ab initio prediction method. BMC bioinformatics, 6, 267.
Carninci, P; Kasukawa, T; Katayama, S; Gough, J; Frith, M C; Maeda, N; Oyama, R; Ravasi, T; Lenhard, B; Wells, C; Kodzius, R; Shimokawa, K; Bajic, V B; Brenner, S E; Batalov, S; Forrest, A R R; Zavolan, M; Davis, M J; Wilming, L G; Aidinis, V; Allen, J E; Ambesi-Impiombato, A; Apweiler, R; Aturaliya, R N; Bailey, T L; Bansal, M; Baxter, L; Beisel, K W; Bersano, T; Bono, H; Chalk, A M; Chiu, K P; Choudhary, V; Christoffels, A; Clutterbuck, D R; Crowe, M L; Dalla, E; Dalrymple, B P; de Bono, B; Della Gatta, G; di Bernardo, D; Down, T; Engstrom, P; Fagiolini, M; Faulkner, G; Fletcher, C F; Fukushima, T; Furuno, M; Futaki, S; Gariboldi, M; Georgii-Hemming, P; Gingeras, T R; Gojobori, T; Green, R E; Gustincich, S; Harbers, M; Hayashi, Y; Hensch, T K; Hirokawa, N; Hill, D; Huminiecki, L; Iacono, M; Ikeo, K; Iwama, A; Ishikawa, T; Jakt, M; Kanapin, A; Katoh, M; Kawasawa, Y; Kelso, J; Kitamura, H; Kitano, H; Kollias, G; Krishnan, S P T; Kruger, A; Kummerfeld, S K; Kurochkin, I V; Lareau, L F; Lazarevic, D; Lipovich, L; Liu, J; Liuni, S; McWilliam, S; Madan Babu, M; Madera, M; Marchionni, L; Matsuda, H; Matsuzawa, S; Miki, H; Mignone, F; Miyake, S; Morris, K; Mottagui-Tabar, S; Mulder, N; Nakano, N; Nakauchi, H; Ng, P; Nilsson, R; Nishiguchi, S; Nishikawa, S; Nori, F; Ohara, O; Okazaki, Y; Orlando, V; Pang, K C; Pavan, W J; Pavesi, G; Pesole, G; Petrovsky, N; Piazza, S; Reed, J; Reid, J F; Ring, B Z; Ringwald, M; Rost, B; Ruan, Y; Salzberg, S L; Sandelin, A; Schneider, C; Schönbach, C; Sekiguchi, K; Semple, C A M; Seno, S; Sessa, L; Sheng, Y; Shibata, Y; Shimada, H; Shimada, K; Silva, D; Sinclair, B; Sperling, S; Stupka, E; Sugiura, K; Sultana, R; Takenaka, Y; Taki, K; Tammoja, K; Tan, S L; Tang, S; Taylor, M S; Tegner, J; Teichmann, S A; Ueda, H R; van Nimwegen, E; Verardo, R; Wei, C L; Yagi, K; Yamanishi, H; Zabarovsky, E; Zhu, S; Zimmer, A; Hide, W; Bult, C; Grimmond, S M; Teasdale, R D; Liu, E T; Brusic, V; Quackenbush, J; Wahlestedt, C; Mattick, J S; Hume, D A; Kai, C; Sasaki, D; Tomaru, Y; Fukuda, S; Kanamori-Katayama, M; Suzuki, M; Aoki, J; Arakawa, T; Iida, J; Imamura, K; Itoh, M; Kato, T; Kawaji, H; Kawagashira, N; Kawashima, T; Kojima, M; Kondo, S; Konno, H; Nakano, K; Ninomiya, N; Nishio, T; Okada, M; Plessy, C; Shibata, K; Shiraki, T; Suzuki, S; Tagami, M; Waki, K; Watahiki, A; Okamura-Oho, Y; Suzuki, H; Kawai, J; Hayashizaki, Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) (2005). The transcriptional landscape of the mammalian genome. Science, 309(5740), 1559-63.
Speirs, Christina; van Nimwegen, Erik; Bolton, Diane; Zavolan, Mihaela; Duvall, Melody; Angleman, Sara; Siegel, Richard; Perelson, Alan S; Lenardo, Michael J (2005). Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture. Journal of virology, 79(7), 4025-32.
2003
Yang, Edward; van Nimwegen, Erik; Zavolan, Mihaela; Rajewsky, Nikolaus; Schroeder, Mark; Magnasco, Marcelo; Darnell, James E (2003). Decay rates of human mRNAs : correlation with functional characteristics and sequence attributes. Genome research, 13(8), 1863-72.
2002
van Nimwegen, Erik; Zavolan, Mihaela; Rajewsky, Nikolaus; Siggia, Eric D (2002). Probabilistic clustering of sequences : inferring new bacterial regulons by comparative genomics. Proceedings of the National Academy of Sciences of the United States of America, 99(11), 7323-8.
Zavolan, Mihaela; van Nimwegen, Erik; Gaasterland, Terry (2002). Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome research, 12(9), 1377-85.

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