Prof. Dr. Erik van Nimwegen

Luca Galbusera, Gwendoline Bellement-Theroue, Thomas Julou, & Erik van Nimwegen. (2025). Data for the figures of the article “Transient transcription factor depletions explain diverse single-cell responses of LexA target promoters to mild DNA damage” (v1 ed.) [dataset]. https://doi.org/10.5281/zenodo.15547214

Galbusera, Luca, Bellement-Theroue, Gwendoline, Julou, Thomas, & van Nimwegen, Erik. (2025). Rapid Transcription Factor Fluctuations Drive Nonequilibrium Gene Regulatory Dynamics in Bacteria [Journal-article]. PRX Life, 3(3). https://doi.org/10.1103/nvk3-jsvm

de Groot, Daan Hugo, Leonardo, Sarah X Morillo, Pachkov, Mikhail, & van Nimwegen, Erik. (2025). Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data [Posted-content]. In bioRxiv . Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.05.08.652944

Julou, Thomas, Gervais, Théo, de Groot, Daan, & van Nimwegen, Erik. (2025). Growth rate controls the sensitivity of gene regulatory circuits [Journal-article]. Science Advances, 11(17). https://doi.org/10.1126/sciadv.adu9279

Erik van Nimwegen. (2025, April 16). Why is it so hard to analyze single-cell RNA-seq data? https://doi.org/10.5281/zenodo.15230282

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Breda, Jeremie, Rzepiela, Andrzej J, Gumienny, Rafal, van Nimwegen, Erik, & Zavolan, Mihaela. (2015). Quantifying the strength of miRNA-target interactions. Methods, 85, 9–90. https://doi.org/10.1016/j.ymeth.2015.04.012

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

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

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

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

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

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), 84–869. https://doi.org/10.1101/gr.169508.113

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

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), 88–1077. https://doi.org/10.1093/molbev/msu088

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), 36–1523. https://doi.org/10.1242/jcs.139865

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), 81–1568. https://doi.org/10.1172/jci70408

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

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

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), 26–9313. https://doi.org/10.1093/nar/gku544

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

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), 95–4180. https://doi.org/10.1093/nar/gkt1415

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), 94–5289. https://doi.org/10.1073/pnas.1312717110

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

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), 93–1181. https://doi.org/10.1002/eji.201344022

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

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

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

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), 5–253. https://doi.org/10.1038/nmeth.2341

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

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

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), 83–768. https://doi.org/10.1016/j.ccr.2013.04.020

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

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

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), 37–529. https://doi.org/10.1038/nm.2645

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), 93–1986. https://doi.org/10.2337/db11-1508

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), 94–487. https://doi.org/10.1093/bioinformatics/btr695

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

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), 24–4913. https://doi.org/10.1128/mcb.00877-12

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

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

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

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), 5–490. https://doi.org/10.1038/nature10716

van Nimwegen, Erik. (2011). Update of the FANTOM web resource: From mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39(SUPPL. 1). https://doi.org/10.1093/nar/gkq1112

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

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

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), 52–744. https://doi.org/10.1016/j.cell.2010.01.044

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), 15–1209. https://doi.org/10.1038/ejhg.2010.91

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

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), 62–553. https://doi.org/10.1038/ng.375

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), 45–433. https://doi.org/10.4049/jimmunol.182.1.433

Molina, Nacho, & van Nimwegen, Erik. (2009). Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends in Genetics, 25(6), 7–243. https://doi.org/10.1016/j.tig.2009.04.004

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

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), 25–611. https://doi.org/10.1101/gr.083881.108

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

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

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

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

Molina, Nacho, & van Nimwegen, Erik. (2008). Universal patterns of purifying selection at noncoding positions in bacteria. Genome Research, 18(1), 60–148. https://doi.org/10.1101/gr.6759507

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), 207–2193. https://doi.org/10.1091/mbc.e07-12-1242

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

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

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