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Prof. Dr. Erik van Nimwegen

Department Biozentrum
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Publications

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Galbusera, Luca, Bellement, Gwendoline, Julou, Thomas, & van Nimwegen, Erik. (2024). Transient transcription factor depletions explain diverse single-cell responses of LexA target promoters to mild DNA damage [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.11.28.625836

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Grobecker, Pascal, Sakoparnig, Thomas, & van Nimwegen, Erik. (2024). Identifying cell states in single-cell RNA-seq data at statistically maximal resolution [Journal-article]. PLOS Computational Biology, 20(7). https://doi.org/10.1371/journal.pcbi.1012224

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Bak, Maciej, van Nimwegen, Erik, Kouzel, Ian U., Gur, Tamer, Schmidt, Ralf, Zavolan, Mihaela, & Gruber, Andreas J. (2024). MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer [Journal-article]. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-48046-1

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Bak, Maciej, van Nimwegen, Erik, Kouzel, Ian U., Gur, Tamer, Schmidt, Ralf, Zavolan, Mihaela, & Gruber, Andreas J. (2024, March 21). Supplementary Results. https://doi.org/10.5281/zenodo.10849750

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Bak, Maciej, van Nimwegen, Erik, Kouzel, Ian U., Gur, Tamer, Schmidt, Ralf, Zavolan, Mihaela, & Gruber, Andreas J. (2024). MAPP. Nature Communications, 15(1). https://doi.org/10.5281/zenodo.10845501

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Gervais, Théo, Kscheschinski, Bjoern, Mell, Michael, Goepfert, Nevil, van Nimwegen, Erik, & Julou, Thomas. (2024). E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.02.29.582700

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Sollier, Julie, Basler, Marek, Broz, Petr, Dittrich, Petra S., Drescher, Knut, Egli, Adrian, Harms, Alexander, Hierlemann, Andreas, Hiller, Sebastian, King, Carolyn G., McKinney, John D., Moran-Gilad, Jacob, Neher, Richard A., Page, Malcolm G. P., Panke, Sven, Persat, Alexandre, Picotti, Paola, Rentsch, Katharina M., Rivera-Fuentes, Pablo, et al. (2024). Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions. Nature Microbiology, 9(1), 1–3. https://doi.org/10.1038/s41564-023-01566-w

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Grobecker, P., & van Nimwegen, E. (2023). Identifying cell states in single-cell RNA-seq data at statistically maximal resolution [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.10.31.564980

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de Groot, Daan H., Tjalma, Age J., Bruggeman, Frank J., & van Nimwegen, Erik. (2023). Effective bet-hedging through growth rate dependent stability. Proceedings of the National Academy of Sciences of the United States of America, 120(8), e2211091120. https://doi.org/10.1073/pnas.2211091120

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Katsantoni, Maria, van Nimwegen, Erik, & Zavolan, Mihaela. (2023). Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs. Genome Biology, 24(1), 77. https://doi.org/10.1186/s13059-023-02913-0

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Grison, Alice, Karimaddini, Zahra, Breda, Jeremie, Mukhtar, Tanzila, Boareto, Marcelo, Eschbach, Katja, Beisel, Christian, Iber, Dagmar, van Nimwegen, Erik, Taylor, Verdon, & Atanasoski, Suzana. (2022). The protooncogene Ski regulates the neuron-glia switch during development of the mammalian cerebral cortex [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.12.16.520470

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Kruglyak, L., Beyer, A., Bloom, J. S., Grossbach, J., Lieberman, T. D., Mancuso, C. P., Rich, M. S., Sherlock, G., van Nimwegen, E., & Kaplan, C. D. (2022). No evidence that synonymous mutations in yeast genes are mostly deleterious. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.07.14.500130

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de Groot, D. H., Tjalma, A. J., Bruggeman, F. J., & van Nimwegen, E. (2022). Coupling phenotype stability to growth rate overcomes limitations of bet-hedging strategies [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.04.12.488059

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Julou, T., Gervais, T., & van Nimwegen, E. (2022). Growth rate controls the sensitivity of gene regulatory circuits [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.04.03.486858

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Baranasic, Damir, Hörtenhuber, Matthias, Balwierz, Piotr J., Zehnder, Tobias, Mukarram, Abdul Kadir, Nepal, Chirag, Várnai, Csilla, Hadzhiev, Yavor, Jimenez-Gonzalez, Ada, Li, Nan, Wragg, Joseph, D’Orazio, Fabio M., Relic, Dorde, Pachkov, Mikhail, Díaz, Noelia, Hernández-Rodríguez, Benjamín, Chen, Zelin, Stoiber, Marcus, Dong, Michaël, et al. (2022). Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics, 54(7), 1037–1050. https://doi.org/10.1038/s41588-022-01089-w

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Mukhtar, Tanzila, Breda, Jeremie, Adam, Manal A., Boareto, Marcelo, Grobecker, Pascal, Karimaddini, Zahra, Grison, Alice, Eschbach, Katja, Chandrasekhar, Ramakrishnan, Vermeul, Swen, Okoniewski, Michal, Pachkov, Mikhail, Harwell, Corey C., Atanasoski, Suzana, Beisel, Christian, Iber, Dagmar, van Nimwegen, Erik, & Taylor, Verdon. (2022). Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis. The EMBO Journal, 41(24), e111132. https://doi.org/10.15252/embj.2022111132

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Bloom, Jesse D., Chan, Yujia Alina, Baric, Ralph S., Bjorkman, Pamela J., Cobey, Sarah, Deverman, Benjamin E., Fisman, David N., Gupta, Ravindra, Iwasaki, Akiko, Lipsitch, Marc, Medzhitov, Ruslan, Neher, Richard A., Nielsen, Rasmus, Patterson, Nick, Stearns, Tim, van Nimwegen, Erik, Worobey, Michael, & Relman, David A. (2021). Investigate the origins of COVID-19. Science, 372(6543), 694. https://doi.org/10.1126/science.abj0016

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Breda, Jérémie, Zavolan, Mihaela, & van Nimwegen, Erik. (2021). Bayesian inference of gene expression states from single-cell RNA-seq data. Nature Biotechnology, 39(8), 1008–1016. https://doi.org/10.1038/s41587-021-00875-x

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Sakoparnig, Thomas, Field, Chris, & van Nimwegen, Erik. (2021). Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife, 10, e65366. https://doi.org/10.7554/elife.65366

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Urchueguía, Arantxa, Galbusera, Luca, Chauvin, Dany, Bellement, Gwendoline, Julou, Thomas, & van Nimwegen, Erik. (2021). Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network. PLoS Biology, 19(12), e3001491. https://doi.org/10.1371/journal.pbio.3001491

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Galbusera, Luca, Bellement-Theroue, Gwendoline, Urchueguia, Arantxa, Julou, Thomas, & van Nimwegen, Erik. (2020). Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria. PLoS ONE, 15(10), e0240233. https://doi.org/10.1371/journal.pone.0240233

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Julou, Thomas, & vanNimwegen, Erik. (2020). Single-cell data on lac operon induction by lactose in E. coli (Julou, Thomas; vanNimwegen, Erik;, Ed.) [dataset]. https://doi.org/10.5281/zenodo.3894719

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Julou, Thomas, Zweifel, Ludovit, Blank, Diana, Fiori, Athos, & van Nimwegen, Erik. (2020). Subpopulations of sensorless bacteria drive fitness in fluctuating environments. PLoS Biology, 18(12), e3000952. https://doi.org/10.1371/journal.pbio.3000952

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Mukhtar, Tanzila, Breda, Jeremie, Grison, Alice, Karimaddini, Zahra, Grobecker, Pascal, Iber, Dagmar, Beisel, Christian, van Nimwegen, Erik, & Taylor, Verdon. (2020). Tead transcription factors differentially regulate cortical development. Scientific Reports, 10(1), 4625. https://doi.org/10.1038/s41598-020-61490-5

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Witz, Guillaume, Julou, Thomas, & an Nimwegen, Erik. (2020). Response to comment on textquoteleftInitiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanismtextquoteright. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.08.04.227694

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Urchueguía, A., Galbusera, L., Bellement, G., Julou, T., & Nimwegen, E. v. (2019). Noise propagation shapes condition-dependent gene expression noise in Escherichia coli [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/795369

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Galbusera, L., Bellement-Theroue, G., Urchueguia, A., Julou, T., & Nimwegen, E. v. (2019). Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/793976

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Berger, Severin, Pachkov, Mikhail, Arnold, Phil, Omidi, Saeed, Kelley, Nicholas, Salatino, Silvia, & van Nimwegen, Erik. (2019). Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs. Genome Research, 29(7), 1164–1177. https://doi.org/10.1101/gr.239319.118

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Witz, Guillaume, van Nimwegen, Erik, & Julou, Thomas. (2019). Initiation of chromosome replication controls both division and replication cycles in; E. coli; through a double-adder mechanism. eLife, 8, e48063. https://doi.org/10.7554/elife.48063

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Gruber, Andreas J., Schmidt, Ralf, Ghosh, Souvik, Martin, Georges, Gruber, Andreas R., van Nimwegen, Erik, & Zavolan, Mihaela. (2018). Discovery of physiological and cancer-related regulators of 3′ UTR processing with KAPAC. Genome Biology, 19(1), 44. https://doi.org/10.1186/s13059-018-1415-3

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Kaiser, Matthias, Jug, Florian, Julou, Thomas, Deshpande, Siddharth, Pfohl, Thomas, Silander, Olin K., Myers, Gene, & van Nimwegen, Erik. (2018). Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software. Nature Communications, 9(1), 212. https://doi.org/10.1038/s41467-017-02505-0

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Rzepiela, Andrzej J., Ghosh, Souvik, Breda, Jeremie, Vina-Vilaseca, Arnau, Syed, Afzal P., Gruber, Andreas J., Eschbach, Katja, Beisel, Christian, van Nimwegen, Erik, & Zavolan, Mihaela. (2018). Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction. Molecular Systems Biology, 14(8), e8266. https://doi.org/10.15252/msb.20188266

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Kaiser, Matthias, Jug, Florian, Julou, Thomas, Deshpande, Siddharth, Pfohl, Thomas, Silander, Olin, Myers, Gene, & vanNimwegen, Erik. (2017). Analysis of lac operon induction with single cell resolution using the DIMM microfluidics chip and the MoMA software (Kaiser, Matthias; Jug, Florian; Julou, Thomas; Deshpande, Siddharth; Pfohl, Thomas; Silander, Olin; Myers, Gene; van Nimwegen, Erik, Ed.) [dataset]. https://doi.org/10.5281/zenodo.746230

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Omidi, Saeed, Zavolan, Mihaela, Pachkov, Mikhail, Breda, Jeremie, Berger, Severin, & 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. https://doi.org/10.1371/journal.pcbi.1005176

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Artimo, Panu, Duvaud, Séverine, Pachkov, Mikhail, Ioannidis, Vassilios, van Nimwegen, Erik, & Stockinger, Heinz. (2016). The ISMARA client. F1000Research, 5(Elixir), 2851. https://doi.org/10.12688/f1000research.9794.1

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Berger, Severin, Omidi, Saeed, Pachkov, Mikhail, Arnold, Phil, Kelley, Nicholas, Salatino, Silvia, & van Nimwegen, Erik. (2016). Crunch: Completely Automated Analysis of ChIP-seq Data. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/042903

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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. https://doi.org/10.1210/me.2016-1036

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van Nimwegen, Erik. (2016). Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PLoS Computational Biology, 12(5), e1004726. https://doi.org/10.1371/journal.pcbi.1004726

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Breda, Jeremie, Rzepiela, Andrzej J, Gumienny, Rafal, van Nimwegen, Erik, & Zavolan, Mihaela. (2015). Quantifying the strength of miRNA-target interactions. Methods, 85, 90–99. https://doi.org/10.1016/j.ymeth.2015.04.012

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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. https://doi.org/10.1016/j.ymeth.2015.06.024

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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. https://doi.org/10.1101/gr.181305.114

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Wolf, Luise, Silander, Olin K, & van Nimwegen, Erik. (2015). Expression noise facilitates the evolution of gene regulation. eLife, 4(4), e05856. https://doi.org/10.7554/elife.05856

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Wolf, L., Silander, O. K., & van Nimwegen, E. J. (2014). Expression noise facilitates the evolution of gene regulation [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/007237

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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), 869–884. https://doi.org/10.1101/gr.169508.113

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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. https://doi.org/10.1128/mcb.01710-13

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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), 1077–1088. https://doi.org/10.1093/molbev/msu088

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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), 1523–1536. https://doi.org/10.1242/jcs.139865

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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. Journal of Clinical Investigation, 124(4), 1568–1581. https://doi.org/10.1172/jci70408

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Dill, M.T., Makowska, Z., Trincucci, G., Gruber, A.J., Vogt, J.E., Filipowicz, M., Calabrese, D., Krol, I., Lau, D.T., Terracciano, L., van Nimwegen, E., Roth, V., & Heim, M.H. (2014). O47 PEGYLATED INTERFERON-ALPHA INDUCES SUSTAINED TRANSCRIPTIONAL RESPONSE IN LIVER INFILTRATING IMMUNE CELLS BUT NOT IN HEPATOCYTES IN THE LIVER OF PATIENTS WITH CHRONIC HEPATITIS C. Journal of Hepatology, 60, S1–S22. https://doi.org/10.1016/s0168-8278(14)60049-0

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Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jorgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, et al. (2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462–470. https://doi.org/10.1038/nature13182

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Gruber, Andreas J., Grandy, William A., Balwierz, Piotr J., Dimitrova, Yoana A., Pachkov, Mikhail, Ciaudo, Constance, van Nimwegen, Erik, & Zavolan, Mihaela. (2014). Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42(14), 9313–9326. https://doi.org/10.1093/nar/gku544

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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. https://doi.org/10.1038/ncomms6465

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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), 4180–4195. https://doi.org/10.1093/nar/gkt1415

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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), 5289–5294. https://doi.org/10.1073/pnas.1312717110

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Stockinger, Heinz, Altenhoff, Adrian M., Arnold, Konstantin, Bairoch, Amos, Bastian, Frederic, Bergmann, Sven, Bougueleret, Lydie, Bucher, Philipp, Delorenzi, Mauro, Lane, Lydie, Mercier, Philippe Le, Lisacek, Frédérique, Michielin, Olivier, Palagi, Patricia M., Rougemont, Jacques, Schwede, Torsten, Mering, Christian von, Nimwegen, Erik van, Walther, Daniel, et al. (2014). Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support. Nucleic Acids Research, 42(Web Server issue), W436–41. https://doi.org/10.1093/nar/gku380

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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), 1181–1193. https://doi.org/10.1002/eji.201344022

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Jug, Florian, Pietzsch, Tobias, Kainmüller, Dagmar, Funke, Jan, Kaiser, Matthias, van Nimwegen, Erik, Rother, Carsten, & Myers, Gene. (2014). Optimal joint segmentation and tracking of Escherichia coli in the mother machine. In Cardoso, M. Jorge; Simpson, Ivor; Arbel, Tal; Precup, Doina; Ribbens, Annemie (Ed.), Bayesian and grAphical models for biomedical imaging : First International Workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers (pp. 25–36). Springer. https://doi.org/10.1007/978-3-319-12289-2_3

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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. https://doi.org/10.1101/gr.142661.112

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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. https://doi.org/10.1038/msb.2013.68

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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. https://doi.org/10.1186/1471-2180-13-25

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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), 253–255. https://doi.org/10.1038/nmeth.2341

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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. https://doi.org/10.1186/bcr3419

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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. https://doi.org/10.1371/journal.pcbi.1003181

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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), 768–783. https://doi.org/10.1016/j.ccr.2013.04.020

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Tiwari, N., Meyer-Schaller, N., Arnold, P., Antoniadis, H., Pachkov, M., van Nimwegen, E., & Christofori, G. (2013). Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, 8(2), e57329. https://doi.org/10.1371/journal.pone.0057329

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Stadler, M. B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Schöler, A., Van Nimwegen, E., Wirbelauer, C., Oakeley, E. J., Gaidatzis, D., Tiwari, V. K., & Schübeler, D. (2012). Erratum: DNA-binding factors shape the mouse methylome at distal regulatory regions (Nature (2011) 480 (490-495)). Nature, 484(7395). https://doi.org/10.1038/nature11086

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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), 529–537. https://doi.org/10.1038/nm.2645

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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), 1986–1993. https://doi.org/10.2337/db11-1508

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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), 487–494. https://doi.org/10.1093/bioinformatics/btr695

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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. https://doi.org/10.1093/nar/gks1145

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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), 4913–4924. https://doi.org/10.1128/mcb.00877-12

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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. https://doi.org/10.1038/msb.2012.23

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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. https://doi.org/10.1371/journal.pone.0024279

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Kawaji, H., Severin, J., Lizio, M., Forrest, A. R., van Nimwegen, E., Rehli, M., Schroder, K., Irvine, K., Suzuki, H., Carninci, P., Hayashizaki, Y., & Daub, C. O. (2011). Update of the FANTOM web resource : from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39(Database issue), D856–60. https://doi.org/10.1093/nar/gkq1112

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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), 490–495. https://doi.org/10.1038/nature10716

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Burger, L., & van Nimwegen, E. (2010). Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Computational Biology, 6(1), e1000633. https://doi.org/10.1371/journal.pcbi.1000633

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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. https://doi.org/10.1093/gbe/evq054

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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, et al. (2010). An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140(5), 744–752. https://doi.org/10.1016/j.cell.2010.01.044

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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), 1209–1215. https://doi.org/10.1038/ejhg.2010.91

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van Nimwegen, Erik. (2010). Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39. https://doi.org/ 10.1093/nar/gkq1112

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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. https://doi.org/10.1186/gb-2009-10-7-r79

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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, et al. (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41(5), 553–562. https://doi.org/10.1038/ng.375

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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), 433–445. https://doi.org/10.4049/jimmunol.182.1.433

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Molina, Nacho, & van Nimwegen, Erik. (2009). Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends in Genetics, 25(6), 243–247. https://doi.org/10.1016/j.tig.2009.04.004

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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. https://doi.org/10.1186/gb-2009-10-4-r39

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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), 611–625. https://doi.org/10.1101/gr.083881.108

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Berninger, Philipp, Gaidatzis, Dimos, van Nimwegen, Erik, & Zavolan, Mihaela. (2008). Computational analysis of small RNA cloning data. Methods, 44(1), 13–21. https://doi.org/10.1016/j.ymeth.2007.10.002

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Burger, Lukas, & van Nimwegen, Erik. (2008). Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular Systems Biology, 4, 165. https://doi.org/10.1038/msb4100203

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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. https://doi.org/10.1093/dnares/dsm036

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Molina, Nacho, & van Nimwegen, Erik. (2008). The evolution of domain-content in bacterial genomes. Biology Direct, 3, 51. https://doi.org/10.1186/1745-6150-3-51

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Molina, Nacho, & van Nimwegen, Erik. (2008). Universal patterns of purifying selection at noncoding positions in bacteria. Genome Research, 18(1), 148–160. https://doi.org/10.1101/gr.6759507

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Schlecht, U., Erb, I., Demougin, P., Robine, N., Borde, V., van Nimwegen, E., Nicolas, A., & 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), 2193–2207. https://doi.org/10.1091/mbc.e07-12-1242

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Gaidatzis, D., van Nimwegen, E., Hausser, J., & Zavolan, M. (2007). Erratum: Inference of miRNA targets using evolutionary conservation and pathway analysis (BMC Bioinformatics). BMC Bioinformatics, 8. https://doi.org/10.1186/1471-2105-8-248

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Gaidatzis, Dimos, van Nimwegen, Erik, Hausser, Jean, & Zavolan, Mihaela. (2007). Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics, 8, 69. https://doi.org/10.1186/1471-2105-8-69

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Gaidatzis, D, van Nimwegen, E, Hausser, J, & Zavolan, M. (2007). Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics , 8. https://doi.org/10.1186/1471-2105-8-69

Pachkov, M., Erb, I., Molina, N., & van Nimwegen, E. (2007). SwissRegulon : a database of genome-wide annotations of regulatory sites. Nucleic Acids Research, 35(Database issue), D127–31. https://doi.org/10.1093/nar/gkl857

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Siddharthan, Rahul, & van Nimwegen, Erik. (2007). Detecting regulatory sites using PhyloGibbs. Methods in Molecular Biology, 395, 381–402. https://doi.org/10.1007/978-1-59745-514-5_24

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van Nimwegen, Erik. (2007). Finding regulatory elements and regulatory motifs : a general probabilistic framework. BMC Bioinformatics, 8, S4. https://doi.org/10.1186/1471-2105-8-s6-s4

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Zavolan, M., & van Nimwegen, E. (2006). The types and prevalence of alternative splice forms [Current Opinion in Structural Biology 2006, 16:362-367] (DOI:10.1016/j.sbi.2006.05.002). Current Opinion in Structural Biology, 16(4). https://doi.org/10.1016/j.sbi.2006.06.010

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Burger, L., & Van Nimwegen, E. (2006). A Bayesian algorithm for reconstructing two-component signaling networks. 4175 LNBI, 44–55. https://doi.org/10.1007/11851561_5

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