Items where Division is "05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)"

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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.

de 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.

Baranasic, 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.

Grapotte, Mathys and Saraswat, Manu and Bessière, Chloé and Menichelli, Christophe and Ramilowski, Jordan A. and Severin, Jessica and Hayashizaki, Yoshihide and Itoh, Masayoshi and Tagami, Michihira and Murata, Mitsuyoshi and Kojima-Ishiyama, Miki and Noma, Shohei and Noguchi, Shuhei and Kasukawa, Takeya and Hasegawa, Akira and Suzuki, Harukazu and Nishiyori-Sueki, Hiromi and Frith, Martin C. and Carninci, Piero and Chatelain, Clément and de Hoon, Michiel J. L. and Wasserman, Wyeth W. and Bréhélin, Laurent and Lecellier, Charles-Henri and Fantom consortium, . (2022) Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature communications, 13 (1). p. 1200.

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.

Breda, 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.

Grapotte, Mathys and Saraswat, Manu and Bessière, Chloé and Menichelli, Christophe and Ramilowski, Jordan A. and Severin, Jessica and Hayashizaki, Yoshihide and Itoh, Masayoshi and Tagami, Michihira and Murata, Mitsuyoshi and Kojima-Ishiyama, Miki and Noma, Shohei and Noguchi, Shuhei and Kasukawa, Takeya and Hasegawa, Akira and Suzuki, Harukazu and Nishiyori-Sueki, Hiromi and Frith, Martin C. and Fantom consortium, and Chatelain, Clément and Carninci, Piero and de Hoon, Michiel J. L. and Wasserman, Wyeth W. and Bréhélin, Laurent and Lecellier, Charles-Henri. (2021) Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1). p. 3297.

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.

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.

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.

Julou, 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.

Berger, 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.

Gruber, 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.

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.

Omidi, 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.

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.

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.

Carbajo, Daniel and Magi, Shigeyuki and Itoh, Masayoshi and Kawaji, Hideya and Lassmann, Timo and Arner, Erik and Forrest, Alistair R. R. and Carninci, Piero and Hayashizaki, Yoshihide and Daub, Carsten O. and Fantom Consortium, and Okada-Hatakeyama, Mariko and Mar, Jessica C.. (2015) Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PLoS ONE, 10 (12). e0144176.

Hurst, Laurence D. and Ghanbarian, Avazeh T. and Forrest, Alistair R. R. and Fantom Consortium, and Huminiecki, Lukasz. (2015) The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biology, 13 (12). e1002315.

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.

Liang, Cong and Fantom Consortium, and Forrest, Alistair R. R. and Wagner, Günter P.. (2015) The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nature communications, Vol. 6 , Article Nr. 6066.

Pemberton-Ross, Peter J. and Pachkov, Mikhail and van Nimwegen, Erik. (2015) ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data. Methods, Vol. 85. pp. 62-74.

Schertel, Claus and Albarca, Monica and Rockel-Bauer, Claudia and Kelley, Nicholas W. and Bischof, Johannes and Hens, Korneel and van Nimwegen, Erik and Basler, Konrad and Deplancke, Bart. (2015) A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development. Genome research, Vol.25, H. 4. pp. 514-523.

Wolf, Luise and Silander, Olin K. and van Nimwegen, Erik J.. (2015) Expression noise facilitates the evolution of gene regulation. eLife, 2015, H. 4, e05856.

Yoshihara, Masahito and Ohmiya, Hiroko and Hara, Susumu and Kawasaki, Satoshi and Fantom consortium, and Hayashizaki, Yoshihide and Itoh, Masayoshi and Kawaji, Hideya and Tsujikawa, Motokazu and Nishida, Kohji. (2015) Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PLoS ONE, Vol. 10, H. 3 , e0117581.

Andersson, Robin and Gebhard, Claudia and Miguel-Escalada, Irene and Hoof, Ilka and Bornholdt, Jette and Boyd, Mette and Chen, Yun and Zhao, Xiaobei and Schmidl, Christian and Suzuki, Takahiro and Ntini, Evgenia and Arner, Erik and Valen, Eivind and Li, Kang and Schwarzfischer, Lucia and Glatz, Dagmar and Raithel, Johanna and Lilje, Berit and Rapin, Nicolas and Bagger, Frederik Otzen and Jørgensen, Mette and Andersen, Peter Refsing and Bertin, Nicolas and Rackham, Owen and Burroughs, A. Maxwell and Baillie, J. Kenneth and Ishizu, Yuri and Shimizu, Yuri and Furuhata, Erina and Maeda, Shiori and Negishi, Yutaka and Mungall, Christopher J. and Meehan, Terrence F. and Lassmann, Timo and Itoh, Masayoshi and Kawaji, Hideya and Kondo, Naoto and Kawai, Jun and Lennartsson, Andreas and Daub, Carsten O. and Heutink, Peter and Hume, David A. and Jensen, Torben Heick and Suzuki, Harukazu and Hayashizaki, Yoshihide and Müller, Ferenc and Fantom Consortium, and Forrest, Alistair R. R. and Carninci, Piero and Rehli, Michael and Sandelin, Albin. (2014) An atlas of active enhancers across human cell types and tissues. Nature, Vol. 507, H. 7493. pp. 455-461.

Arner, Erik and Forrest, Alistair R. R. and Ehrlund, Anna and Mejhert, Niklas and Itoh, Masayoshi and Kawaji, Hideya and Lassmann, Timo and Laurencikiene, Jurga and Rydén, Mikael and Arner, Peter and Fantom Consortium, . (2014) Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS ONE, Vol. 9, H. 3 , e80274.

Balwierz, Piotr J. and Pachkov, Mikhail and Arnold, Phild and Gruber, Andreas J. and Zavolan, Mihaela and van Nimwegen, Erik. (2014) ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, Vol. 24, H. 5. pp. 869-884.

Baresic, Mario and Salatino, Silvia and Kupr, Barbara and van Nimwegen, Erik and Handschin, Christoph. (2014) Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program. Molecular and cellular biology, Vol. 34, H. 16. pp. 2996-3012.

Bertels, Frederic and Silander, Olin K. and Pachkov, Mikhail and Rainey, Paul B. and van Nimwegen, Erik. (2014) Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular biology and evolution, Vol. 31, no. 5. pp. 1077-1088.

Blank, Diana and Wolf, Luise and Ackermann, Martin and Silander, Olin K.. (2014) The predictability of molecular evolution during functional innovation. Proceedings of the National Academy of Sciences, 111 (8). pp. 3044-3049.

Denoth Lippuner, Annina and Julou, Thomas and Barral, Yves. (2014) Budding yeast as a model organism to study the effects of age. FEMS microbiology reviews, 38 (2). pp. 300-325.

Diepenbruck, Maren and Waldmeier, Lorenz and Ivanek, Robert and Berninger, Philipp and Arnold, Phil and van Nimwegen, Erik and Christofori, Gerhard. (2014) Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition. Journal of Cell Science, 127 (7). pp. 1523-1536.

Dill, Michael T. and Makowska, Zuzanna and Trincucci, Gaia and Gruber, Andreas J. and Vogt, Julia E. and Filipowicz, Magdalena and Calabrese, Diego and Krol, Ilona and Lau, Daryl T. and Terracciano, Luigi and van Nimwegen, Erik and Roth, Volker and Heim, Markus H.. (2014) Pegylated IFN-α regulates hepatic gene expression through transient Jak/STAT activation. Journal of Clinical Investigation, Vol. 124, H. 4. pp. 1568-1581.

Fantom Consortium, and the Riken P. M. I., and Clst, . (2014) A promoter-level mammalian expression atlas. Nature, Vol. 507, H. 7493. pp. 462-470.

Gruber, Andreas J. and Grandy, William A. and Balwierz, Piotr J. and Dimitrova, Yoana A. and Pachkov, Mikhail and Ciaudo, Constance and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42 (14). pp. 9313-9326.

Gruber, Andreas R. and Martin, Georges and Müller, Philipp and Schmidt, Alexander and Gruber, Andreas J. and Gumienny, Rafal and Mittal, Nitish and Jayachandran, Rajesh and Pieters, Jean and Keller, Walter 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.

Hasegawa, Yuki and Tang, Dave and Takahashi, Naoko and Hayashizaki, Yoshihide and Forrest, Alistair R. R. and Fantom Consortium, and Suzuki, Harukazu. (2014) CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Scientific Reports, 4. p. 5228.

Jug, Florian and Pietzsch, Tobias and Kainmüller, Dagmar and Funke, Jan and Kaiser, Matthias and van Nimwegen, Erik and Rother, Carsten and Myers, Gene. (2014) Optimal joint segmentation and tracking of Escherichia coli in the mother machine. In: Bayesian and grAphical models for biomedical imaging : First International Workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers. Cham, pp. 25-36.

Luisier, Raphaëlle and Unterberger, Elif B. and Goodman, Jay I. and Schwarz, Michael and Moggs, Jonathan and Terranova, Rémi and van Nimwegen, Erik. (2014) Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic Acids Research, 42 (7). pp. 4180-4195.

Morikawa, Hiromasa and Ohkura, Naganari and Vandenbon, Alexis and Itoh, Masayoshi and Nagao-Sato, Sayaka and Kawaji, Hideya and Lassmann, Timo and Carninci, Piero and Hayashizaki, Yoshihide and Forrest, Alistair R. R. and Standley, Daron M. and Date, Hiroshi and Sakaguchi, Shimon and Fantom Consortium, . (2014) Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, H. 14. pp. 5289-5294.

Vigano, M. Alessandra and Ivanek, Robert and Balwierz, Piotr and Berninger, Philipp and van Nimwegen, Erik and Karjalainen, Klaus and Rolink, Antonius. (2014) An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. European journal of immunology, Vol. 44, H. 4. pp. 1181-1193.

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.

Coquel, Anne-Sophie and Jacob, Jean-Pascal and Primet, Mael and Demarez, Alice and Dimiccoli, Mariella and Julou, Thomas and Moisan, Lionel and Lindner, Ariel B. and Berry, Hugues. (2013) Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect. PLoS Computational Biology, 9 (4). e1003038.

Hausser, Jean and Syed, Afzal Pasha and Selevsek, Nathalie and van Nimwegen, Erik and Jaskiewicz, Lukasz and Aebersold, Ruedi and Zavolan, Mihaela. (2013) Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular systems biology, Vol. 9 , 711.

Hofsteenge, Niels and van Nimwegen, Erik and Silander, Olin K.. (2013) Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli. BMC microbiology, Vol. 13, 25.

Julou, Thomas and Mora, Thierry and Guillon, Laurent and Croquette, Vincent and Schalk, Isabelle J. and Bensimon, David and Desprat, Nicolas. (2013) Cell-cell contacts confine public goods diffusion inside Pseudomonas aeruginosa clonal microcolonies. Proceedings of the National Academy of Sciences of the United States of America, 110 (31). pp. 12577-12582.

Meier-Abt, Fabienne and Milani, Emanuela and Roloff, Tim and Brinkhaus, Heike and Duss, Stephan and Meyer, Dominique S. and Klebba, Ina and Balwierz, Piotr J. and van Nimwegen, Erik and Bentires-Alj, Mohamed. (2013) Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium. Breast cancer research, Vol. 15, H. 2 , R36.

Ozonov, Evgeniy A. and van Nimwegen, Erik. (2013) Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers. PLoS Computational Biology, Vol. 9, H. 8 , e1003181.

Tiwari, N. and Meyer-Schaller, N. and Arnold, P. and Antoniadis, H. and Pachkov, M. and van Nimwegen, E. and Christofori, G.. (2013) Klf4 is a transcriptional regulator of genes critical for EMT, including Jnk1 (Mapk8). PLoS ONE, Vol. 8, H. 2 , e57329.

Tiwari, N. and Tiwari, V. K. and Waldmeier, L. and Balwierz, P. J. and Arnold, P. and Pachkov, M. and Meyer-Schaller, N. and Schubeler, D. and van Nimwegen, E. and Christofori, G.. (2013) Sox4 is a master regulator of epithelial-mesenchymal transition by controlling ezh2 expression and epigenetic reprogramming. Cancer cell, Vol. 23, H. 6. pp. 768-783.

Tiwari, Neha and Meyer-Schaller, Nathalie and Arnold, Phil and Antoniadis, Helena and Pachkov, Mikhail and van Nimwegen, Erik and Christofori, Gerhard. (2013) Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8). PLoS ONE, Vol. 8, H. 10 , nn.

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.

Arner, Erik and Mejhert, Niklas and Kulyté, Agné and Balwierz, Piotr J. and Pachkov, Mikhail and Cormont, Mireille and Lorente-Cebrián, Silvia and Ehrlund, Anna and Laurencikiene, Jurga and Hedén, Per and Dahlman-Wright, Karin and Tanti, Jean-François and Hayashizaki, Yoshihide and Rydén, Mikael and Dahlman, Ingrid and van Nimwegen, Erik and Daub, Carsten O. and Arner, Peter. (2012) Adipose tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes, Vol. 61, H. 8. pp. 1986-1993.

Arnold, Phil and Erb, Ionas and Pachkov, Mikhail and Molina, Nacho and van Nimwegen, Erik. (2012) MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics, Vol. 28, H. 4. pp. 487-494.

Julou, Thomas and Desprat, Nicolas and Bensimon, David and Croquette, Vincent. (2012) Monitoring microbial population dynamics at low densities. Review of Scientific Instruments, 83 (7). 074301.

Pachkov, Mikhail and Balwierz, Piotr J. and Arnold, Phil and Ozonov, Evgeniy and van Nimwegen, Erik. (2012) SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Research, 41 (D1). D214-D220.

Pérez-Schindler, Joaquín and Summermatter, Serge and Salatino, Silvia and Zorzato, Francesco and Beer, Markus and Balwierz, Piotr J. and van Nimwegen, Erik and Feige, Jérôme N. and Auwerx, Johan and Handschin, Christoph. (2012) The Corepressor NCoR1 Antagonizes PGC-1α and Estrogen-Related Receptor α in the Regulation of Skeletal Muscle Function and Oxidative Metabolism. Molecular and cellular biology, Vol. 32, H. 24. pp. 4913-4924.

Tippmann, Sylvia C. and Ivanek, Robert and Gaidatzis, Dimos and Schöler, Anne and Hoerner, Leslie and van Nimwegen, Erik and Stadler, Peter F. and Stadler, Michael B. and Schübeler, Dirk. (2012) Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Molecular systems biology, Vol. 8. p. 593.

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.

Kawaji, H. and Severin, J. and Lizio, M. and Forrest, A. R. and van Nimwegen, E. and Rehli, M. and Schroder, K. and Irvine, K. and Suzuki, H. and Carninci, P. and Hayashizaki, Y. and Daub, C. O.. (2011) Update of the FANTOM web resource : from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39 (1 Supplement). D856-D860.

Stadler, Michael B. and Murr, Rabih and Burger, Lukas and Ivanek, Robert and Lienert, Florian and Schöler, Anne and van Nimwegen, Erik and Wirbelauer, Christiane and Oakeley, Edward J. and Gaidatzis, Dimos and Tiwari, Vijay K. and Schübeler, Dirk. (2011) DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature, Vol. 480, H. 7378. pp. 490-495.

Burger, L. and van Nimwegen, E.. (2010) Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Computational Biology, 61 (1). e1000633.

Chen, K. and van Nimwegen, E. and Rajewsky, N. and Siegal, M. L.. (2010) Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome biology and evolution, Vol. 2. pp. 697-707.

Ravasi, T. and Suzuki, H. and Cannistraci, C. V. and Katayama, S. and Bajic, V. B. and Tan, K. and Akalin, A. and Schmeier, S. and Kanamori-Katayama, M. and Bertin, N. and Carninci, P. and Daub, C. O. and Forrest, A. R. R. and Gough, J. and Grimmond, S. and Han, J. -H. and Hashimoto, T. and Hide, W. and Hofmann, O. and Kamburov, A. and Kaur, M. and Kawaji, H. and Kubosaki, A. and Lassmann, T. and van Nimwegen, E. and MacPherson, C. R. and Ogawa, C. and Radovanovic, A. and Schwartz, A. and Teasdale, R. D. and Tegner, J. and Lenhard, B. and Teichmann, S. A. and Arakawa, T. and Ninomiya, N. and Murakami, K. and Tagami, M. and Fukuda, S. and Imamura, K. and Kai, C. and Ishihara, R. and Kitazume, Y. and Kawai, J. and Hume, D. A. and Ideker, T. and Hayashizaki, Y.. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, Vol. 140, H. 5. pp. 744-752.

Summers, K. M. and Raza, S. and van Nimwegen, E. and Freeman, T. C. and Hume, D. A.. (2010) Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines : implications for phenotypic variability in Marfan syndrome. European journal of human genetics, Vol. 18, H. 11. pp. 1209-1215.

Balwierz, P. J. and Carninci, P. and Daub, C. O. and Kawai, J. and Hayashizaki, Y. and Van Belle, W. and Beisel, C. and van Nimwegen, E. J.. (2009) Methods for analyzing deep sequencing expression data : constructing the human and mouse promoterome with deepCAGE data. Genome biology, Vol. 10, H. 7 , R79.

Mayoral, R. J. and Pipkin, M. E. and Pachkov, M. and van Nimwegen, E. and Rao, A. and Monticelli, S.. (2009) MicroRNA-221-222 regulate the cell cycle in mast cells. Journal of immunology, Vol. 182, H. 1. pp. 433-445.

Molina, N. and van Nimwegen, E.. (2009) Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends in genetics, Vol. 25, H. 6. pp. 243-247.

Severin, J. and Waterhouse, A. M. and Kawaji, H. and Lassmann, T. and van Nimwegen, E. and Balwierz, P. J. and de Hoon, M. J. and Hume, D. A. and Carninci, P. and Hayashizaki, Y. and Suzuki, H. and Daub, C. O. and Forrest, A. R.. (2009) FANTOM4 EdgeExpressDB: : an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome biology, Vol. 10, H. 4 , R39.

Suzuki, H. and Forrest, A. R. and van Nimwegen, E. and Daub, C. O. and Balwierz, P. J. and Irvine, K. M. and Lassmann, T. and Ravasi, T. and Hasegawa, Y. and de Hoon, M. J. and Katayama, S. and Schroder, K. and Carninci, P. and Tomaru, Y. and Kanamori-Katayama, M. and Kubosaki, A. and Akalin, A. and Ando, Y. and Arner, E. and Asada, M. and Asahara, H. and Bailey, T. and Bajic, V. B. and Bauer, D. and Beckhouse, A. G. and Bertin, N. and Bjorkegren, J. and Brombacher, F. and Bulger, E. and Chalk, A. M. and Chiba, J. and Cloonan, N. and Dawe, A. and Dostie, J. and Engstrom, P. G. and Essack, M. and Faulkner, G. J. and Fink, J. L. and Fredman, D. and Fujimori, K. and Furuno, M. and Gojobori, T. and Gough, J. and Grimmond, S. M. and Gustafsson, M. and Hashimoto, M. and Hashimoto, T. and Hatakeyama, M. and Heinzel, S. and Hide, W. and Hofmann, O. and Hornquist, M. and Huminiecki, L. and Ikeo, K. and Imamoto, N. and Inoue, S. and Inoue, Y. and Ishihara, R. and Iwayanagi, T. and Jacobsen, A. and Kaur, M. and Kawaji, H. and Kerr, M. C. and Kimura, R. and Kimura, S. and Kimura, Y. and Kitano, H. and Koga, H. and Kojima, T. and Kondo, S. and Konno, T. and Krogh, A. and Kruger, A. and Kumar, A. and Lenhard, B. and Lennartsson, A. and Lindow, M. and Lizio, M. and Macpherson, C. and Maeda, N. and Maher, C. A. and Maqungo, M. and Mar, J. and Matigian, N. A. and Matsuda, H. and Mattick, J. S. and Meier, S. and Miyamoto, S. and Miyamoto-Sato, E. and Nakabayashi, K. and Nakachi, Y. and Nakano, M. and Nygaard, S. and Okayama, T. and Okazaki, Y. and Okuda-Yabukami, H. and Orlando, V. and Otomo, J. and Pachkov, M. and Petrovsky, N. and Plessy, C. and Quackenbush, J. and Radovanovic, A. and Rehli, M. and Saito, R. and Sandelin, A. and Schmeier, S. and Schonbach, C. and Schwartz, A. S. and Semple, C. A. and Sera, M. and Severin, J. and Shirahige, K. and Simons, C. and St Laurent, G. and Suzuki, M. and Suzuki, T. and Sweet, M. J. and Taft, R. J. and Takeda, S. and Takenaka, Y. and Tan, K. and Taylor, M. S. and Teasdale, R. D. and Tegner, J. and Teichmann, S. and Valen, E. and Wahlestedt, C. and Waki, K. and Waterhouse, A. and Wells, C. A. and Winther, O. and Wu, L. and Yamaguchi, K. and Yanagawa, H. and Yasuda, J. and Zavolan, M. and Hume, D. A. and Arakawa, T. and Fukuda, S. and Imamura, K. and Kai, C. and Kaiho, A. and Kawashima, T. and Kawazu, C. and Kitazume, Y. and Kojima, M. and Miura, H. and Murakami, K. and Murata, M. and Ninomiya, N. and Nishiyori, H. and Noma, S. and Ogawa, C. and Sano, T. and Simon, C. and Tagami, M. and Takahashi, Y. and Kawai, J. and Hayashizaki, Y.. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics, Vol. 41, H. 5. pp. 553-562.

Taddei, A. and Van Houwe, G. and Nagai, S. and Erb, I. and van Nimwegen, E. and Gasser, S. M.. (2009) The functional importance of telomere clustering : Global changes in gene expression result from SIR factor dispersion. Genome research, Vol. 19, H. 4. pp. 611-625.

Berninger, P. and Gaidatzis, D. and van Nimwegen, E. and Zavolan, M.. (2008) Computational analysis of small RNA cloning data. Methods, Vol. 44, no. 1. pp. 13-21.

Burger, L. and van Nimwegen, E.. (2008) Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Molecular systems biology, Vol. 4 , 165.

Chern, T. -M. and Paul, N. and van Nimwegen, E. and Zavolan, M.. (2008) Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA research, Vol. 15, H. 2. pp. 63-72.

Molina, N. and van Nimwegen, E.. (2008) The evolution of domain-content in bacterial genomes. Biology Direct, Vol. 3. p. 51.

Molina, N. and van Nimwegen, E.. (2008) Universal patterns of purifying selection at noncoding positions in bacteria. Genome research, Vol. 18, H. 1. pp. 148-160.

Mosconi, Francesco and Julou, Thomas and Desprat, Nicolas and Sinha, Deepak Kumar and Allemand, Jean-François and Croquette, Vincent and Bensimon, David. (2008) Some nonlinear challenges in biology. Nonlinearity, 21 (8). T131-T147.

Schlecht, U. and Erb, I. and Demougin, P. and Robine, N. and Borde, V. and van Nimwegen, E. and Nicolas, A. and Primig, M.. (2008) Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Molecular Biology of the Cell, 19 (5). pp. 2193-2207.

Gaidatzis, D. and van Nimwegen, E. and Hausser, J. and Zavolan, M.. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics, Vol. 8 , 69.

Pachkov, M. and Erb, I. and Molina, N. and van Nimwegen, E.. (2007) SwissRegulon : a database of genome-wide annotations of regulatory sites. Nucleic Acids Research, 35 (1 Supplement). D127-D131.

Siddharthan, Rahul and van Nimwegen, Erik. (2007) Detecting regulatory sites using PhyloGibbs. Methods in Molecular Biology, 395. pp. 381-402.

van Nimwegen, E.. (2007) Finding regulatory elements and regulatory motifs : a general probabilistic framework. BMC Bioinformatics, Vol. 8, Suppl 6 , S4.

Chern, T. -M. and van Nimwegen, E. and Kai, C. and Kawai, J. and Carninci, P. and Hayashizaki, Y. and Zavolan, M.. (2006) A simple physical model predicts small exon length variations. PLoS genetics, Vol. 2, H. 4 , e45.

Zavolan, M. and van Nimwegen, E.. (2006) The types and prevalence of alternative splice forms. Current opinion in structural biology, Vol. 16, H. 3. pp. 362-367.

van Nimwegen, E.. (2006) Influenza escapes immunity along neutral networks. Science, Vol. 314, no. 5807. pp. 1884-1886.

van Nimwegen, E. and Paul, N. and Sheridan, R. and Zavolan, M.. (2006) SPA : a probabilistic algorithm for spliced alignment. PLoS genetics, Vol. 2, H. 4 , e24.

van 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.

Carninci, P. and Kasukawa, T. and Katayama, S. and Gough, J. and Frith, M. C. and Maeda, N. and Oyama, R. and Ravasi, T. and Lenhard, B. and Wells, C. and Kodzius, R. and Shimokawa, K. and Bajic, V. B. and Brenner, S. E. and Batalov, S. and Forrest, A. R. R. and Zavolan, M. and Davis, M. J. and Wilming, L. G. and Aidinis, V. and Allen, J. E. and Ambesi-Impiombato, A. and Apweiler, R. and Aturaliya, R. N. and Bailey, T. L. and Bansal, M. and Baxter, L. and Beisel, K. W. and Bersano, T. and Bono, H. and Chalk, A. M. and Chiu, K. P. and Choudhary, V. and Christoffels, A. and Clutterbuck, D. R. and Crowe, M. L. and Dalla, E. and Dalrymple, B. P. and de Bono, B. and Della Gatta, G. and di Bernardo, D. and Down, T. and Engstrom, P. and Fagiolini, M. and Faulkner, G. and Fletcher, C. F. and Fukushima, T. and Furuno, M. and Futaki, S. and Gariboldi, M. and Georgii-Hemming, P. and Gingeras, T. R. and Gojobori, T. and Green, R. E. and Gustincich, S. and Harbers, M. and Hayashi, Y. and Hensch, T. K. and Hirokawa, N. and Hill, D. and Huminiecki, L. and Iacono, M. and Ikeo, K. and Iwama, A. and Ishikawa, T. and Jakt, M. and Kanapin, A. and Katoh, M. and Kawasawa, Y. and Kelso, J. and Kitamura, H. and Kitano, H. and Kollias, G. and Krishnan, S. P. T. and Kruger, A. and Kummerfeld, S. K. and Kurochkin, I. V. and Lareau, L. F. and Lazarevic, D. and Lipovich, L. and Liu, J. and Liuni, S. and McWilliam, S. and Madan Babu, M. and Madera, M. and Marchionni, L. and Matsuda, H. and Matsuzawa, S. and Miki, H. and Mignone, F. and Miyake, S. and Morris, K. and Mottagui-Tabar, S. and Mulder, N. and Nakano, N. and Nakauchi, H. and Ng, P. and Nilsson, R. and Nishiguchi, S. and Nishikawa, S. and Nori, F. and Ohara, O. and Okazaki, Y. and Orlando, V. and Pang, K. C. and Pavan, W. J. and Pavesi, G. and Pesole, G. and Petrovsky, N. and Piazza, S. and Reed, J. and Reid, J. F. and Ring, B. Z. and Ringwald, M. and Rost, B. and Ruan, Y. and Salzberg, S. L. and Sandelin, A. and Schneider, C. and Schonbach, C. and Sekiguchi, K. and Semple, C. A. M. and Seno, S. and Sessa, L. and Sheng, Y. and Shibata, Y. and Shimada, H. and Shimada, K. and Silva, D. and Sinclair, B. and Sperling, S. and Stupka, E. and Sugiura, K. and Sultana, R. and Takenaka, Y. and Taki, K. and Tammoja, K. and Tan, S. L. and Tang, S. and Taylor, M. S. and Tegner, J. and Teichmann, S. A. and Ueda, H. R. and van Nimwegen, E. and Verardo, R. and Wei, C. L. and Yagi, K. and Yamanishi, H. and Zabarovsky, E. and Zhu, S. and Zimmer, A. and Hide, W. and Bult, C. and Grimmond, S. M. and Teasdale, R. D. and Liu, E. T. and Brusic, V. and Quackenbush, J. and Wahlestedt, C. and Mattick, J. S. and Hume, D. A. and Kai, C. and Sasaki, D. and Tomaru, Y. and Fukuda, S. and Kanamori-Katayama, M. and Suzuki, M. and Aoki, J. and Arakawa, T. and Iida, J. and Imamura, K. and Itoh, M. and Kato, T. and Kawaji, H. and Kawagashira, N. and Kawashima, T. and Kojima, M. and Kondo, S. and Konno, H. and Nakano, K. and Ninomiya, N. and Nishio, T. and Okada, M. and Plessy, C. and Shibata, K. and Shiraki, T. and Suzuki, S. and Tagami, M. and Waki, K. and Watahiki, A. and Okamura-Oho, Y. and Suzuki, H. and Kawai, J. and Hayashizaki, Y.. (2005) The transcriptional landscape of the mammalian genome. Science, Vol. 309, no. 5740. pp. 1559-1563.

Julou, Thomas and Burghardt, Bastian and Gebauer, Gerhard and Berveiller, Daniel and Damesin, Claire and Selosse, Marc-André. (2005) Mixotrophy in orchids: insights from a comparative study of green individuals and nonphotosynthetic individuals of Cephalanthera damasonium. New Phytologist, 166 (2). pp. 639-653.

Sewer, A. and Paul, N. and Landgraf, P. and Aravin, A. and Pfeffer, S. and Brownstein, M. J. and Tuschl, T. and van Nimwegen, E. and Zavolan, M.. (2005) Identification of clustered microRNAs using an ab initio prediction method. BMC bioinformatics, Vol. 6, , 267.

Siddharthan, 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.

Speirs, C. and van Nimwegen, E. and Bolton, D. and Zavolan, M. and Duvall, M. and Angleman, S. and Siegel, R. and Perelson, A. S. and Lenardo, M. J.. (2005) Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture. Journal of virology, Vol. 79, H. 7. pp. 4025-4032.

Paz, 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.

Sinha, Saurabh and van Nimwegen, Erik and Siggia, Eric D.. (2003) A probabilistic method to detect regulatory modules. Bioinformatics, 19 (Supplement 1). i292-i301.

Yang, E. and van Nimwegen, E. and Zavolan, M. and Rajewsky, N. and Schroeder, M. and Magnasco, M. and Darnell, J. E. J.. (2003) Decay rates of human mRNAs : correlation with functional characteristics and sequence attributes. Genome research, Vol. 13, H. 8. pp. 1863-1872.

van Nimwegen, Erik. (2003) Scaling laws in the functional content of genomes. Trends in Genetics, 19 (9). pp. 479-484.

Crutchfield, James P. and van Nimwegen, Erik. (2002) The evolutionary unfolding of complexity. In: Evolution as Computation. Berlin, pp. 67-94.

Zavolan, M. and van Nimwegen, E. and Gaasterland, T.. (2002) Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome research, Vol. 12, H. 9. pp. 1377-1385.

van Nimwegen, E. and Zavolan, M. and Rajewsky, N. and Siggia, E. 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, Vol. 99, No. 11. pp. 7323-7328.

van Nimwegen, Erik and Crutchfield, James P.. (2001) Optimizing epochal evolutionary search: Population-size dependent theory. Machine Learning, 45 (1). pp. 77-114.

Oprea, 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.

van 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.

Huynen, 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.

No

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.

Klishami, Saeed Omidi. Computational methods for dissecting transcription regulatory networks. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

Luisier, Raphaëlle. Towards a better understanding of early drug-induced regulatory mechanisms of liver tumorigenesis. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

Wolf, Luise. Evolution of transcriptional regulation in "Escherichia coli". 2014, Doctoral Thesis, University of Basel, Faculty of Science.

Arnold, Phil. A framework to identify epigenome and transcription factor crosstalk. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

Ozonov, Evgeniy Andreevich. Modeling nucleosome mediated mechanisms of gene regulation. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

Balwierz, Piotr J.. Inference of gene regulatory interactions from deep sequencing data. 2012, Doctoral Thesis, University of Basel, Faculty of Science.

Burger, Lukas Johannes. Inference of biomolecular interactions from sequence data. 2010, Doctoral Thesis, University of Basel, Faculty of Science.

Molina, Nacho. Genome evolution and regulatory network structure in bacteria. 2010, Doctoral Thesis, University of Basel, Faculty of Science.

Wojnowska-Boudier, Kamila. The role of AgRax1p, AgRax2p, AgBud7p and AgBud10p in mycelial development of the filamentous fungus "Ashbya gossypii". 2005, Doctoral Thesis, University of Basel, Faculty of Science.