Items where Author is "van Nimwegen, Erik"
Number of items: 63. 2023de Groot, Daan H. and Tjalma, Age J. and Bruggeman, Frank J. and 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. Katsantoni, Maria and van Nimwegen, Erik and 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 (77). pp. 1-25. 2022Baranasic, Damir and Hörtenhuber, Matthias and Balwierz, Piotr J. and Zehnder, Tobias and Mukarram, Abdul Kadir and Nepal, Chirag and Várnai, Csilla and Hadzhiev, Yavor and Jimenez-Gonzalez, Ada and Li, Nan and Wragg, Joseph and D'Orazio, Fabio M. and Relic, Dorde and Pachkov, Mikhail and Díaz, Noelia and Hernández-Rodríguez, Benjamín and Chen, Zelin and Stoiber, Marcus and Dong, Michaël and Stevens, Irene and Ross, Samuel E. and Eagle, Anne and Martin, Ryan and Obasaju, Oluwapelumi and Rastegar, Sepand and McGarvey, Alison C. and Kopp, Wolfgang and Chambers, Emily and Wang, Dennis and Kim, Hyejeong R. and Acemel, Rafael D. and Naranjo, Silvia and Łapiński, Maciej and Chong, Vanessa and Mathavan, Sinnakaruppan and Peers, Bernard and Sauka-Spengler, Tatjana and Vingron, Martin and Carninci, Piero and Ohler, Uwe and Lacadie, Scott Allen and Burgess, Shawn M. and Winata, Cecilia and van Eeden, Freek and Vaquerizas, Juan M. and Gómez-Skarmeta, José Luis and Onichtchouk, Daria and Brown, Ben James and Bogdanovic, Ozren and van Nimwegen, Erik and Westerfield, Monte and Wardle, Fiona C. and Daub, Carsten O. and Lenhard, Boris and Müller, Ferenc. (2022) Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics, 54 (7). pp. 1037-1050. Mukhtar, Tanzila and Breda, Jeremie and Adam, Manal A. and Boareto, Marcelo and Grobecker, Pascal and Karimaddini, Zahra and Grison, Alice and Eschbach, Katja and Chandrasekhar, Ramakrishnan and Vermeul, Swen and Okoniewski, Michal and Pachkov, Mikhail and Harwell, Corey C. and Atanasoski, Suzana and Beisel, Christian and Iber, Dagmar and van Nimwegen, Erik and Taylor, Verdon. (2022) Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis. The EMBO Journal. e111132. 2021Breda, Jérémie and Zavolan, Mihaela and van Nimwegen, Erik. (2021) Bayesian inference of gene expression states from single-cell RNA-seq data. Nature Biotechnology, 39 (8). pp. 1008-1016. Urchueguía, Arantxa and Galbusera, Luca and Chauvin, Dany and Bellement, Gwendoline and Julou, Thomas and 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. Bloom, Jesse D. and Chan, Yujia Alina and Baric, Ralph S. and Bjorkman, Pamela J. and Cobey, Sarah and Deverman, Benjamin E. and Fisman, David N. and Gupta, Ravindra and Iwasaki, Akiko and Lipsitch, Marc and Medzhitov, Ruslan and Neher, Richard A. and Nielsen, Rasmus and Patterson, Nick and Stearns, Tim and van Nimwegen, Erik and Worobey, Michael and Relman, David A.. (2021) Investigate the origins of COVID-19. Science, 372 (6543). p. 694. Sakoparnig, Thomas and Field, Chris and van Nimwegen, Erik. (2021) Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species. eLife, 10. e65366. 2020Julou, Thomas and Zweifel, Ludovit and Blank, Diana and Fiori, Athos and van Nimwegen, Erik. (2020) Subpopulations of sensorless bacteria drive fitness in fluctuating environments. PLoS biology, 18 (12). e3000952. Mukhtar, Tanzila and Breda, Jeremie and Grison, Alice and Karimaddini, Zahra and Grobecker, Pascal and Iber, Dagmar and Beisel, Christian and van Nimwegen, Erik and Taylor, Verdon. (2020) Tead transcription factors differentially regulate cortical development. Scientific Reports, 10 (1). p. 4625. Galbusera, Luca and Bellement-Theroue, Gwendoline and Urchueguia, Arantxa and Julou, Thomas and van Nimwegen, Erik. (2020) Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria. PLoS ONE, 15 (10). e0240233. 2019Berger, Severin and Pachkov, Mikhail and Arnold, Phil and Omidi, Saeed and Kelley, Nicholas and Salatino, Silvia and van Nimwegen, Erik. (2019) Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs. Genome Research, 29 (7). pp. 1164-1177. Witz, Guillaume and van Nimwegen, Erik and Julou, Thomas. (2019) Initiation of chromosome replication controls both division and replication cycles in; E. coli; through a double-adder mechanism. eLife, 8. e48063. 2018Gruber, Andreas J. and Schmidt, Ralf and Ghosh, Souvik and Martin, Georges and Gruber, Andreas R. and van Nimwegen, Erik and Zavolan, Mihaela. (2018) Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. Genome biology, 19 (1). p. 44. Kaiser, Matthias and Jug, Florian and Julou, Thomas and Deshpande, Siddharth and Pfohl, Thomas and Silander, Olin K. and Myers, Gene and van Nimwegen, Erik. (2018) Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software. Nature Communications, 9 (1). p. 212. Rzepiela, Andrzej J. and Ghosh, Souvik and Breda, Jeremie and Vina-Vilaseca, Arnau and Syed, Afzal P. and Gruber, Andreas J. and Eschbach, Katja and Beisel, Christian and van Nimwegen, Erik and Zavolan, Mihaela. (2018) Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction. Molecular systems biology, 14 (8). e8266. 2017Omidi, Saeed and Zavolan, Mihaela and Pachkov, Mikhail and Breda, Jeremie and Berger, Severin and van Nimwegen, Erik. (2017) Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13 (7). e1005176. May 2016van Nimwegen, Erik. (2016) Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean? PLoS Computational Biology, 12 (5). e1004726. 2016Breda, Jeremie and Rzepiela, Andrzej J. and Gumienny, Rafal and van Nimwegen, Erik and Zavolan, Mihaela. (2016) Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99]. Methods, 104. pp. 204-205. Salatino, Silvia and Kupr, Barbara and Baresic, Mario and van Nimwegen, Erik and Handschin, Christoph. (2016) The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells. Molecular Endocrinology, 30 (7). pp. 809-825. Artimo, Panu and Duvaud, Séverine and Pachkov, Mikhail and Ioannidis, Vassilios and van Nimwegen, Erik and Stockinger, Heinz. (2016) The ISMARA client. F1000Research, 5 (Elixir). p. 2851. 2015Schertel, Claus and Albarca, Monica and Rockel-Bauer, Claudia and Kelley, Nicholas W. and Bischof, Johannes and Hens, Korneel and van Nimwegen, Erik and Basler, Konrad and Deplancke, Bart. (2015) A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome research, Vol.25, H. 4. pp. 514-523. Pemberton-Ross, Peter J. and Pachkov, Mikhail and van Nimwegen, Erik. (2015) ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data. Methods, Vol. 85. pp. 62-74. Breda, Jeremie and Rzepiela, Andrzej J. and Gumienny, Rafal and van Nimwegen, Erik and Zavolan, Mihaela. (2015) Quantifying the strength of miRNA-target interactions. Methods, Vol. 85. pp. 90-99. 2014Vigano, M. Alessandra and Ivanek, Robert and Balwierz, Piotr and Berninger, Philipp and van Nimwegen, Erik and Karjalainen, Klaus and Rolink, Antonius. (2014) An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. European journal of immunology, Vol. 44, H. 4. pp. 1181-1193. Bertels, Frederic and Silander, Olin K. and Pachkov, Mikhail and Rainey, Paul B. and van Nimwegen, Erik. (2014) Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular biology and evolution, Vol. 31, no. 5. pp. 1077-1088. Luisier, Raphaëlle and Unterberger, Elif B. and Goodman, Jay I. and Schwarz, Michael and Moggs, Jonathan and Terranova, Rémi and van Nimwegen, Erik. (2014) Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic Acids Research, 42 (7). pp. 4180-4195. Gruber, Andreas J. and Grandy, William A. and Balwierz, Piotr J. and Dimitrova, Yoana A. and Pachkov, Mikhail and Ciaudo, Constance and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42 (14). pp. 9313-9326. Gruber, Andreas R. and Martin, Georges and Müller, Philipp and Schmidt, Alexander and Gruber, Andreas J. and Gumienny, Rafal and Mittal, Nitish and Jayachandran, Rajesh and Pieters, Jean and Keller, Walter and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nature Communications, 5 (5465). pp. 1-10. Balwierz, Piotr J. and Pachkov, Mikhail and Arnold, Phild and Gruber, Andreas J. and Zavolan, Mihaela and van Nimwegen, Erik. (2014) ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, Vol. 24, H. 5. pp. 869-884. Jug, Florian and Pietzsch, Tobias and Kainmüller, Dagmar and Funke, Jan and Kaiser, Matthias and van Nimwegen, Erik and Rother, Carsten and Myers, Gene. (2014) Optimal joint segmentation and tracking of Escherichia coli in the mother machine. In: Bayesian and grAphical models for biomedical imaging : First International Workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers. Cham, pp. 25-36. Dill, Michael T. and Makowska, Zuzanna and Trincucci, Gaia and Gruber, Andreas J. and Vogt, Julia E. and Filipowicz, Magdalena and Calabrese, Diego and Krol, Ilona and Lau, Daryl T. and Terracciano, Luigi and van Nimwegen, Erik and Roth, Volker and Heim, Markus H.. (2014) Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation. Journal of Clinical Investigation, Vol. 124, H. 4. pp. 1568-1581. Diepenbruck, Maren and Waldmeier, Lorenz and Ivanek, Robert and Berninger, Philipp and Arnold, Phil and van Nimwegen, Erik and Christofori, Gerhard. (2014) Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition. Journal of Cell Science, 127 (7). pp. 1523-1536. Baresic, Mario and Salatino, Silvia and Kupr, Barbara and van Nimwegen, Erik and Handschin, Christoph. (2014) Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program. Molecular and cellular biology, Vol. 34, H. 16. pp. 2996-3012. 2013Khorshid, Mohsen and Hausser, Jean and Zavolan, Mihaela and van Nimwegen, Erik. (2013) A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nature methods, Vol. 10, H. 3. pp. 253-255. Tiwari, Neha and Meyer-Schaller, Nathalie and Arnold, Phil and Antoniadis, Helena and Pachkov, Mikhail and van Nimwegen, Erik and Christofori, Gerhard. (2013) Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8). PLoS ONE, Vol. 8, H. 10 , nn. Arnold, Phil and Schöler, Anne and Pachkov, Mikhail and Balwierz, Piotr J. and Jørgensen, Helle and Stadler, Michael B. and van Nimwegen, Erik and Schübeler, Dirk. (2013) Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome research, Vol. 23. pp. 60-73. Ozonov, Evgeniy A. and van Nimwegen, Erik. (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Computational Biology, Vol. 9, H. 8 , e1003181. Meier-Abt, Fabienne and Milani, Emanuela and Roloff, Tim and Brinkhaus, Heike and Duss, Stephan and Meyer, Dominique S. and Klebba, Ina and Balwierz, Piotr J. and van Nimwegen, Erik and Bentires-Alj, Mohamed. (2013) Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium. Breast cancer research, Vol. 15, H. 2 , R36. Hofsteenge, Niels and van Nimwegen, Erik and Silander, Olin K.. (2013) Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC microbiology, Vol. 13, 25. Hausser, Jean and Syed, Afzal Pasha and Selevsek, Nathalie and van Nimwegen, Erik and Jaskiewicz, Lukasz and Aebersold, Ruedi and Zavolan, Mihaela. (2013) Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular systems biology, Vol. 9 , 711. 2012Arner, Erik and Mejhert, Niklas and Kulyté, Agné and Balwierz, Piotr J. and Pachkov, Mikhail and Cormont, Mireille and Lorente-Cebrián, Silvia and Ehrlund, Anna and Laurencikiene, Jurga and Hedén, Per and Dahlman-Wright, Karin and Tanti, Jean-François and Hayashizaki, Yoshihide and Rydén, Mikael and Dahlman, Ingrid and van Nimwegen, Erik and Daub, Carsten O. and Arner, Peter. (2012) Adipose tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes, Vol. 61, H. 8. pp. 1986-1993. Tippmann, Sylvia C. and Ivanek, Robert and Gaidatzis, Dimos and Schöler, Anne and Hoerner, Leslie and van Nimwegen, Erik and Stadler, Peter F. and Stadler, Michael B. and Schübeler, Dirk. (2012) Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Molecular systems biology, Vol. 8. p. 593. Arnold, Phil and Erb, Ionas and Pachkov, Mikhail and Molina, Nacho and van Nimwegen, Erik. (2012) MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics, Vol. 28, H. 4. pp. 487-494. Pachkov, Mikhail and Balwierz, Piotr J. and Arnold, Phil and Ozonov, Evgeniy and van Nimwegen, Erik. (2012) SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Research, 41 (D1). D214-D220. Pérez-Schindler, Joaquín and Summermatter, Serge and Salatino, Silvia and Zorzato, Francesco and Beer, Markus and Balwierz, Piotr J. and van Nimwegen, Erik and Feige, Jérôme N. and Auwerx, Johan and Handschin, Christoph. (2012) The Corepressor NCoR1 Antagonizes PGC-1α and Estrogen-Related Receptor α in the Regulation of Skeletal Muscle Function and Oxidative Metabolism. Molecular and cellular biology, Vol. 32, H. 24. pp. 4913-4924. Aceto, Nicola and Sausgruber, Nina and Brinkhaus, Heike and Gaidatzis, Dimos and Martiny-Baron, Georg and Mazzarol, Giovanni and Confalonieri, Stefano and Quarto, Micaela and Hu, Guang and Balwierz, Piotr J. and Pachkov, Mikhail and Elledge, Stephen J. and van Nimwegen, Erik and Stadler, Michael B. and Bentires-Alj, Mohamed. (2012) Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop. Nature medicine, Vol. 18, H. 4. pp. 529-537. 2011Stadler, Michael B. and Murr, Rabih and Burger, Lukas and Ivanek, Robert and Lienert, Florian and Schöler, Anne and van Nimwegen, Erik and Wirbelauer, Christiane and Oakeley, Edward J. and Gaidatzis, Dimos and Tiwari, Vijay K. and Schübeler, Dirk. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, Vol. 480, H. 7378. pp. 490-495. Erb, Ionas and van Nimwegen, Erik. (2011) Transcription Factor Binding Site Positioning in Yeast : Proximal Promoter Motifs Characterize TATA-Less Promoters. PLoS ONE, Vol. 6, H. 9 , e24279. 2007Siddharthan, Rahul and van Nimwegen, Erik. (2007) Detecting regulatory sites using PhyloGibbs. Methods in Molecular Biology, 395. pp. 381-402. 2006van Nimwegen, Erik. (2006) Scaling laws in the functional content of genomes: Fundamental constants of evolution? In: Power Law, Scale-Free Networks and Genome Biology. Boston, pp. 236-253. 2005Siddharthan, Rahul and Siggia, Eric D. and van Nimwegen, Erik. (2005) PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Computational Biology, 1 (7). e67. 2004Paz, Keren and Socci, Nicholas D. and van Nimwegen, Erik and Viale, Agnes and Darnell, James E.. (2004) Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNA. Oncogene, 23 (52). pp. 8455-8463. 2003Sinha, Saurabh and van Nimwegen, Erik and Siggia, Eric D.. (2003) A probabilistic method to detect regulatory modules. Bioinformatics, 19 (Supplement 1). i292-i301. van Nimwegen, Erik. (2003) Scaling laws in the functional content of genomes. Trends in Genetics, 19 (9). pp. 479-484. 2002Crutchfield, James P. and van Nimwegen, Erik. (2002) The evolutionary unfolding of complexity. In: Evolution as Computation. Berlin, pp. 67-94. 2001van Nimwegen, Erik and Crutchfield, James P.. (2001) Optimizing epochal evolutionary search: Population-size dependent theory. Machine Learning, 45 (1). pp. 77-114. 2000Oprea, Mihaela and van Nimwegen, Erik and Perelson, Alan S.. (2000) Dynamics of one-pass germinal center models: implications for affinity maturation. Bulletin of Mathematical Biology, 62 (1). pp. 121-153. van Nimwegen, Erik and Crutchfield, James P.. (2000) Metastable evolutionary dynamics: Crossing fitness barriers or escaping via neutral paths? Bulletin of Mathematical Biology, 62 (5). pp. 799-848. van Nimwegen, Erik and Crutchfield, James P.. (2000) Optimizing epochal evolutionary search: population-size independent theory. Computer Methods in Applied Mechanics and Engineering, 186 (2-4). pp. 171-194. 1999van Nimwegen, Erik and Crutchfield, James P. and Huynen, Martijn. (1999) Neutral evolution of mutational robustness. Proceedings of the National Academy of Sciences of the United States of America, 96 (17). pp. 9716-9720. van Nimwegen, Erik and Crutchfield, James P. and Mitchell, Melanie. (1999) Statistical dynamics of the royal road genetic algorithm. Theoretical Computer Science, 229 (1-2). pp. 41-102. 1998Huynen, Martijn A. and van Nimwegen, Erik. (1998) The frequency distribution of gene family sizes in complete genomes. Molecular Biology and Evolution , 15 (5). pp. 583-589. |
