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Baranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D’Orazio, F. M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S. E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A. C., Kopp, W., Chambers, E., Wang, D., Kim, H. R., Acemel, R. D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S. A., Burgess, S. M., Winata, C., van Eeden, F., Vaquerizas, J. M., Gómez-Skarmeta, J. L., Onichtchouk, D., Brown, B. J., Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F. C., Daub, C. O., Lenhard, B. and Müller, F. (2022) ‘Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements’, Nature Genetics, 54(7), pp. 1037–1050. 10.1038/s41588-022-01089-w.   edoc | Open Access
Urchueguía, A., Galbusera, L., Chauvin, D., Bellement, G., Julou, T. and van Nimwegen, E. (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), p. e3001491. 10.1371/journal.pbio.3001491.   edoc | Open Access
Bloom, J. D., Chan, Y. A., Baric, R. S., Bjorkman, P. J., Cobey, S., Deverman, B. E., Fisman, D. N., Gupta, R., Iwasaki, A., Lipsitch, M., Medzhitov, R., Neher, R. A., Nielsen, R., Patterson, N., Stearns, T., van Nimwegen, E., Worobey, M. and Relman, D. A. (2021) ‘Investigate the origins of COVID-19’, Science, 372(6543), p. 694. 10.1126/science.abj0016.   edoc
Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Fantom consortium, Chatelain, C., Carninci, P., de Hoon, M. J. L., Wasserman, W. W., Bréhélin, L. and Lecellier, C.-H. (2021) ‘Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network’, Nature Communications, 12(1), p. 3297. 10.1038/s41467-021-23143-7.   edoc
Breda, J., Zavolan, M. and van Nimwegen, E. (2021) ‘Bayesian inference of gene expression states from single-cell RNA-seq data’, Nature Biotechnology, 39(8), pp. 1008–1016. 10.1038/s41587-021-00875-x.   edoc
Sakoparnig, T., Field, C. and van Nimwegen, E. (2021) ‘Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species’, eLife, 10, p. e65366. 10.7554/eLife.65366.   edoc
Julou, T., Zweifel, L., Blank, D., Fiori, A. and van Nimwegen, E. (2020) ‘Subpopulations of sensorless bacteria drive fitness in fluctuating environments’, PLoS biology, 18(12), p. e3000952. 10.1371/journal.pbio.3000952.   edoc | Open Access
Galbusera, L., Bellement-Theroue, G., Urchueguia, A., Julou, T. and van Nimwegen, E. (2020) ‘Using fluorescence flow cytometry data for single-cell gene expression analysis in bacteria’, PLoS ONE, 15(10), p. e0240233. 10.1371/journal.pone.0240233.   edoc | Open Access
Mukhtar, T., Breda, J., Grison, A., Karimaddini, Z., Grobecker, P., Iber, D., Beisel, C., van Nimwegen, E. and Taylor, V. (2020) ‘Tead transcription factors differentially regulate cortical development’, Scientific Reports, 10(1), p. 4625. 10.1038/s41598-020-61490-5.   edoc
Witz, G., van Nimwegen, E. and Julou, T. (2019) ‘Initiation of chromosome replication controls both division and replication cycles in; E. coli; through a double-adder mechanism’, eLife, 8, p. e48063. 10.7554/eLife.48063.   edoc
Berger, S., Pachkov, M., Arnold, P., Omidi, S., Kelley, N., Salatino, S. and van Nimwegen, E. (2019) ‘Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs’, Genome Research, 29(7), pp. 1164–1177. 10.1101/gr.239319.118.   edoc
Gruber, A. J., Schmidt, R., Ghosh, S., Martin, G., Gruber, A. R., van Nimwegen, E. and Zavolan, M. (2018) ‘Discovery of physiological and cancer-related regulators of 3’ UTR processing with KAPAC’, Genome biology, 19(1), p. 44. 10.1186/s13059-018-1415-3.   edoc
Rzepiela, A. J., Ghosh, S., Breda, J., Vina-Vilaseca, A., Syed, A. P., Gruber, A. J., Eschbach, K., Beisel, C., van Nimwegen, E. and Zavolan, M. (2018) ‘Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction’, Molecular systems biology, 14(8), p. e8266. 10.15252/msb.20188266.   edoc
Kaiser, M., Jug, F., Julou, T., Deshpande, S., Pfohl, T., Silander, O. K., Myers, G. and van Nimwegen, E. (2018) ‘Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software’, Nature Communications, 9(1), p. 212. 10.1038/s41467-017-02505-0.   edoc | Open Access
Omidi, S., Zavolan, M., Pachkov, M., Breda, J., Berger, S. and van Nimwegen, E. (2017) ‘Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors’, PLoS Computational Biology, 13(7), p. e1005176. 10.1371/journal.pcbi.1005176.   edoc
van Nimwegen, E. (2016) ‘Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?’, PLoS Computational Biology, 12(5), p. e1004726. 10.1371/journal.pcbi.1004726.   edoc
Swiss Institute of Bioinformatics Members, S. (2016) ‘The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases’, Nucleic acids research, 44(D1), pp. D27-D37. 10.1093/nar/gkv1310.   edoc | Open Access
Artimo, P., Duvaud, S., Pachkov, M., Ioannidis, V., van Nimwegen, E. and Stockinger, H. (2016) ‘The ISMARA client’, F1000Research, 5(Elixir), p. 2851. 10.12688/f1000research.9794.1.   edoc
Carbajo, D., Magi, S., Itoh, M., Kawaji, H., Lassmann, T., Arner, E., Forrest, A. R. R., Carninci, P., Hayashizaki, Y., Daub, C. O., Fantom Consortium, Okada-Hatakeyama, M. and Mar, J. C. (2015) ‘Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage’, PLoS ONE, 10(12), p. e0144176. 10.1371/journal.pone.0144176.   edoc
Hurst, L. D., Ghanbarian, A. T., Forrest, A. R. R., Fantom Consortium and Huminiecki, L. (2015) ‘The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome’, PLoS Biology, 13(12), p. e1002315. 10.1371/journal.pbio.1002315.   edoc
Yoshihara, M., Ohmiya, H., Hara, S., Kawasaki, S., Fantom consortium, Hayashizaki, Y., Itoh, M., Kawaji, H., Tsujikawa, M. and Nishida, K. (2015) ‘Discovery of molecular markers to discriminate corneal endothelial cells in the human body’, PLoS ONE, Vol. 10, H. 3 , e0117581. 10.1371/journal.pone.0117581.   edoc
Wolf, L., Silander, O. K. and van Nimwegen, E. J. (2015) ‘Expression noise facilitates the evolution of gene regulation’, eLife, 2015, H. 4, e05856. 10.7554/eLife.05856.002.   edoc
Breda, J., Rzepiela, A. J., Gumienny, R., van Nimwegen, E. and Zavolan, M. (2015) ‘Quantifying the strength of miRNA-target interactions’, Methods, Vol. 85, pp. 90–99. 10.1016/j.ymeth.2015.04.012.   edoc
Liang, C., Fantom Consortium, Forrest, A. R. R. and Wagner, G. P. (2015) ‘The statistical geometry of transcriptome divergence in cell-type evolution and cancer’, Nature communications, Vol. 6 , Article Nr. 6066. 10.1038/ncomms7066.   edoc
Pemberton-Ross, P. J., Pachkov, M. and van Nimwegen, E. (2015) ‘ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data’, Methods, Vol. 85, pp. 62–74. 10.1016/j.ymeth.2015.06.024.   edoc
Schertel, C., Albarca, M., Rockel-Bauer, C., Kelley, N. W., Bischof, J., Hens, K., van Nimwegen, E., Basler, K. and Deplancke, B. (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. 10.1101/gr.181305.114.   edoc
Denoth Lippuner, A., Julou, T. and Barral, Y. (2014) ‘Budding yeast as a model organism to study the effects of age’, FEMS microbiology reviews, 38(2), pp. 300–325. 10.1111/1574-6976.12060.   edoc
Blank, D., Wolf, L., Ackermann, M. and Silander, O. K. (2014) ‘The predictability of molecular evolution during functional innovation’, Proceedings of the National Academy of Sciences, 111(8), pp. 3044–3049. 10.1073/pnas.1318797111.   edoc
Diepenbruck, M., Waldmeier, L., Ivanek, R., Berninger, P., Arnold, P., van Nimwegen, E. and Christofori, G. (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. 10.1242/jcs.139865.   edoc | Open Access
Jug, F., Pietzsch, T., Kainmüller, D., Funke, J., Kaiser, M., van Nimwegen, E., Rother, C. and Myers, G. (2014) ‘Optimal joint segmentation and tracking of Escherichia coli in the mother machine’, in Cardoso, M. J., Simpson, I., Arbel, T., Precup, D., and Ribbens, A. (eds) Bayesian and grAphical models for biomedical imaging : First International Workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers. Cham: Springer, pp. 25–36. 10.1007/978-3-319-12289-2_3.   edoc
Gruber, A. R., Martin, G., Müller, P., Schmidt, A., Gruber, A. J., Gumienny, R., Mittal, N., Jayachandran, R., Pieters, J., Keller, W., van Nimwegen, E. and Zavolan, M. (2014) ‘Global 3’ UTR shortening has a limited effect on protein abundance in proliferating T cells’, Nature Communications, 5(5465), pp. 1–10. 10.1038/ncomms6465.   edoc | Open Access
Hasegawa, Y., Tang, D., Takahashi, N., Hayashizaki, Y., Forrest, A. R. R., Fantom Consortium and Suzuki, H. (2014) ‘CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes’, Scientific Reports, 4, p. 5228. 10.1038/srep05228.   edoc | Open Access
Gruber, A. J., Grandy, W. A., Balwierz, P. J., Dimitrova, Y. A., Pachkov, M., Ciaudo, C., van Nimwegen, E. and Zavolan, M. (2014) ‘Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways’, Nucleic Acids Research, 42(14), pp. 9313–9326. 10.1093/nar/gku544.   edoc | Open Access
Baresic, M., Salatino, S., Kupr, B., van Nimwegen, E. and Handschin, C. (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.   edoc | Open Access
Balwierz, P. J., Pachkov, M., Arnold, P., Gruber, A. J., Zavolan, M. and van Nimwegen, E. (2014) ‘ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs’, Genome research, Vol. 24, H. 5, pp. 869–884. 10.1101/gr.169508.113.   edoc
Arner, E., Forrest, A. R. R., Ehrlund, A., Mejhert, N., Itoh, M., Kawaji, H., Lassmann, T., Laurencikiene, J., Rydén, M., Arner, P. 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. 10.1371/journal.pone.0080274.   edoc
Vigano, M. A., Ivanek, R., Balwierz, P., Berninger, P., van Nimwegen, E., Karjalainen, K. and Rolink, A. (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. 10.1002/eji.201344022.   edoc
Bertels, F., Silander, O. K., Pachkov, M., Rainey, P. B. and van Nimwegen, E. (2014) ‘Automated reconstruction of whole genome phylogenies from short sequence reads’, Molecular biology and evolution, Vol. 31, no. 5, pp. 1077–1088. 10.1093/molbev/msu088.   edoc
Fantom Consortium, the Riken P. M. I. and Clst (2014) ‘A promoter-level mammalian expression atlas’, Nature, Vol. 507, H. 7493, pp. 462–470. 10.1038/nature13182.   edoc
Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., Suzuki, T., Ntini, E., Arner, E., Valen, E., Li, K., Schwarzfischer, L., Glatz, D., Raithel, J., Lilje, B., Rapin, N., Bagger, F. O., Jørgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Müller, F., Fantom Consortium, Forrest, A. R. R., Carninci, P., Rehli, M. and Sandelin, A. (2014) ‘An atlas of active enhancers across human cell types and tissues’, Nature, Vol. 507, H. 7493, pp. 455–461. 10.1038/nature12787.   edoc
Morikawa, H., Ohkura, N., Vandenbon, A., Itoh, M., Nagao-Sato, S., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A. R. R., Standley, D. M., Date, H., Sakaguchi, S. 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. 10.1073/pnas.1312717110.   edoc
Luisier, R., Unterberger, E. B., Goodman, J. I., Schwarz, M., Moggs, J., Terranova, R. and van Nimwegen, E. (2014) ‘Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion’, Nucleic Acids Research, 42(7), pp. 4180–4195. 10.1093/nar/gkt1415.   edoc | Open Access
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. and Heim, M. 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. 10.1172/JCI70408.   edoc
Coquel, A.-S., Jacob, J.-P., Primet, M., Demarez, A., Dimiccoli, M., Julou, T., Moisan, L., Lindner, A. B. and Berry, H. (2013) ‘Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect’, PLoS Computational Biology, 9(4), p. e1003038. 10.1371/journal.pcbi.1003038.   edoc | Open Access
Julou, T., Mora, T., Guillon, L., Croquette, V., Schalk, I. J., Bensimon, D. and Desprat, N. (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. 10.1073/pnas.1301428110.   edoc | Open Access
Tiwari, N., Meyer-Schaller, N., Arnold, P., Antoniadis, H., Pachkov, M., van Nimwegen, E. and Christofori, G. (2013) ‘Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)’, PLoS ONE. Public Library of Science. 10.1371/annotation/121b04a1-0cbb-4e24-8a63-fc9cdd31ec76.   edoc
Hausser, J., Syed, A. P., Selevsek, N., van Nimwegen, E., Jaskiewicz, L., Aebersold, R. and Zavolan, M. (2013) ‘Timescales and bottlenecks in miRNA-dependent gene regulation’, Molecular systems biology, Vol. 9 , 711. 10.1038/msb.2013.68.   edoc
Ozonov, E. A. and van Nimwegen, E. (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. 10.1371/journal.pcbi.1003181.   edoc
Tiwari, N., Tiwari, V. K., Waldmeier, L., Balwierz, P. J., Arnold, P., Pachkov, M., Meyer-Schaller, N., Schubeler, D., 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. 10.1016/j.ccr.2013.04.020.   edoc
Meier-Abt, F., Milani, E., Roloff, T., Brinkhaus, H., Duss, S., Meyer, D. S., Klebba, I., Balwierz, P. J., van Nimwegen, E. and Bentires-Alj, M. (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. 10.1186/bcr3419.   edoc
Tiwari, N., Meyer-Schaller, N., Arnold, P., Antoniadis, H., Pachkov, M., 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. 10.1371/journal.pone.0057329.   edoc
Hofsteenge, N., van Nimwegen, E. and Silander, O. K. (2013) ‘Quantitative analysis of persister fractions suggests different mechanisms of formation among environmental isolates of E. coli’, BMC microbiology, Vol. 13, 25. 10.1186/1471-2180-13-25.   edoc
Arnold, P., Schöler, A., Pachkov, M., Balwierz, P. J., Jørgensen, H., Stadler, M. B., van Nimwegen, E. and Schübeler, D. (2013) ‘Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting’, Genome research, Vol. 23, pp. 60–73. 10.1101/gr.142661.112.   edoc
Julou, T., Desprat, N., Bensimon, D. and Croquette, V. (2012) ‘Monitoring microbial population dynamics at low densities’, Review of Scientific Instruments, 83(7), p. 74301. 10.1063/1.4729796.   edoc
Pachkov, M., Balwierz, P. J., Arnold, P., Ozonov, E. and van Nimwegen, E. (2012) ‘SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates’, Nucleic Acids Research, 41(D1), pp. D214-D220. 10.1093/nar/gks1145.   edoc | Open Access
Pérez-Schindler, J., Summermatter, S., Salatino, S., Zorzato, F., Beer, M., Balwierz, P. J., van Nimwegen, E., Feige, J. N., Auwerx, J. and Handschin, C. (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. 10.1128/MCB.00877-12.   edoc | Open Access
Tippmann, S. C., Ivanek, R., Gaidatzis, D., Schöler, A., Hoerner, L., van Nimwegen, E., Stadler, P. F., Stadler, M. B. and Schübeler, D. (2012) ‘Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels’, Molecular systems biology, Vol. 8, p. 593. 10.1038/msb.2012.23.   edoc
Arnold, P., Erb, I., Pachkov, M., Molina, N. and van Nimwegen, E. (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. 10.1093/bioinformatics/btr695.   edoc
Aceto, N., Sausgruber, N., Brinkhaus, H., Gaidatzis, D., Martiny-Baron, G., Mazzarol, G., Confalonieri, S., Quarto, M., Hu, G., Balwierz, P. J., Pachkov, M., Elledge, S. J., van Nimwegen, E., Stadler, M. B. and Bentires-Alj, M. (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. 10.1038/nm.2645.   edoc
Arner, E., Mejhert, N., Kulyté, A., Balwierz, P. J., Pachkov, M., Cormont, M., Lorente-Cebrián, S., Ehrlund, A., Laurencikiene, J., Hedén, P., Dahlman-Wright, K., Tanti, J.-F., Hayashizaki, Y., Rydén, M., Dahlman, I., van Nimwegen, E., Daub, C. O. and Arner, P. (2012) ‘Adipose tissue microRNAs as regulators of CCL2 production in human obesity’, Diabetes, Vol. 61, H. 8, pp. 1986–1993. 10.2337/db11-1508.   edoc
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. and Schübeler, D. (2011) ‘DNA-binding factors shape the mouse methylome at distal regulatory regions’, Nature, Vol. 480, H. 7378, pp. 490–495. 10.1038/nature10716.   edoc
Erb, I. and van Nimwegen, E. (2011) ‘Transcription Factor Binding Site Positioning in Yeast : Proximal Promoter Motifs Characterize TATA-Less Promoters’, PLoS ONE, Vol. 6, H. 9 , e24279. 10.1371/journal.pone.0024279.   edoc
Kawaji, H., Severin, J., Lizio, M., Forrest, A. R., van Nimwegen, E., Rehli, M., Schroder, K., Irvine, K., Suzuki, H., Carninci, P., 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), pp. D856-D860. 10.1093/nar/gkq1112.   edoc | Open Access
Burger, L. and van Nimwegen, E. (2010) ‘Disentangling direct from indirect co-evolution of residues in protein alignments’, PLoS Computational Biology, 61(1), p. e1000633. 10.1371/journal.pcbi.1000633.   edoc
Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., Carninci, P., Daub, C. O., Forrest, A. R. R., Gough, J., Grimmond, S., Han, J. .-H., Hashimoto, T., Hide, W., Hofmann, O., Kamburov, A., Kaur, M., Kawaji, H., Kubosaki, A., Lassmann, T., van Nimwegen, E., MacPherson, C. R., Ogawa, C., Radovanovic, A., Schwartz, A., Teasdale, R. D., Tegner, J., Lenhard, B., Teichmann, S. A., Arakawa, T., Ninomiya, N., Murakami, K., Tagami, M., Fukuda, S., Imamura, K., Kai, C., Ishihara, R., Kitazume, Y., Kawai, J., Hume, D. A., Ideker, T. and Hayashizaki, Y. (2010) ‘An atlas of combinatorial transcriptional regulation in mouse and man’, Cell, Vol. 140, H. 5, pp. 744–752. 10.1016/j.cell.2010.01.044.   edoc
Summers, K. M., Raza, S., van Nimwegen, E., 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. 10.1038/ejhg.2010.91.   edoc
Chen, K., van Nimwegen, E., 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. 10.1093/gbe/evq054.   edoc
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.   edoc
Taddei, A., Van Houwe, G., Nagai, S., Erb, I., 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.   edoc
Suzuki, H., Forrest, A. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Bjorkegren, J., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engstrom, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hornquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M. C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., Macpherson, C., Maeda, N., Maher, C. A., Maqungo, M., Mar, J., Matigian, N. A., Matsuda, H., Mattick, J. S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schonbach, C., Schwartz, A. S., Semple, C. A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M. J., Taft, R. J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M. S., Teasdale, R. D., Tegner, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C. A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D. A., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., 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. 10.1038/ng.375.   edoc
Balwierz, P. J., Carninci, P., Daub, C. O., Kawai, J., Hayashizaki, Y., Van Belle, W., 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.   edoc
Mayoral, R. J., Pipkin, M. E., Pachkov, M., van Nimwegen, E., 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.   edoc
Severin, J., Waterhouse, A. M., Kawaji, H., Lassmann, T., van Nimwegen, E., Balwierz, P. J., de Hoon, M. J., Hume, D. A., Carninci, P., Hayashizaki, Y., Suzuki, H., 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.   edoc
Mosconi, F., Julou, T., Desprat, N., Sinha, D. K., Allemand, J.-F., Croquette, V. and Bensimon, D. (2008) ‘Some nonlinear challenges in biology’, Nonlinearity, 21(8), pp. T131-T147. 10.1088/0951-7715/21/8/T03.   edoc
Berninger, P., Gaidatzis, D., van Nimwegen, E. and Zavolan, M. (2008) ‘Computational analysis of small RNA cloning data’, Methods, Vol. 44, no. 1, pp. 13–21. 10.1016/j.ymeth.2007.10.002.   edoc
Molina, N. and van Nimwegen, E. (2008) ‘The evolution of domain-content in bacterial genomes’, Biology Direct, Vol. 3, p. 51.   edoc
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.   edoc
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.   edoc
Chern, T. .-M., Paul, N., 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. 10.1093/dnares/dsm036.   edoc
Schlecht, U., Erb, I., Demougin, P., Robine, N., Borde, V., van Nimwegen, E., 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. 10.1091/mbc.E07-12-1242.   edoc | Open Access
Siddharthan, R. and van Nimwegen, E. (2007) ‘Detecting regulatory sites using PhyloGibbs’, Methods in Molecular Biology, 395, pp. 381–402.   edoc
Gaidatzis, D., van Nimwegen, E., Hausser, J. and Zavolan, M. (2007) ‘Inference of miRNA targets using evolutionary conservation and pathway analysis’, BMC bioinformatics, Vol. 8 , 69. 10.1186/1471-2105-8-69.   edoc
Pachkov, M., Erb, I., Molina, N. and van Nimwegen, E. (2007) ‘SwissRegulon : a database of genome-wide annotations of regulatory sites’, Nucleic Acids Research, 35(1 Supplement), pp. D127-D131. 10.1093/nar/gkl857.   edoc | Open Access
van Nimwegen, E. (2007) ‘Finding regulatory elements and regulatory motifs : a general probabilistic framework’, BMC Bioinformatics, Vol. 8, Suppl 6 , S4.   edoc
van Nimwegen, E. (2006) ‘Scaling laws in the functional content of genomes: Fundamental constants of evolution?’, in Koonin, E. V., Wolf, Y. I., and Karev, G. P. (eds) Power Law, Scale-Free Networks and Genome Biology. Boston: Springer (Molecular Biology Intelligence Unit), pp. 236–253. 10.1007/0-387-33916-7_14.   edoc
van Nimwegen, E., Paul, N., Sheridan, R. and Zavolan, M. (2006) ‘SPA : a probabilistic algorithm for spliced alignment’, PLoS genetics, Vol. 2, H. 4 , e24. 10.1371/journal.pgen.0020024.   edoc
van Nimwegen, E. (2006) ‘Influenza escapes immunity along neutral networks’, Science, Vol. 314, no. 5807, pp. 1884–1886.   edoc
Chern, T. .-M., van Nimwegen, E., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y. and Zavolan, M. (2006) ‘A simple physical model predicts small exon length variations’, PLoS genetics, Vol. 2, H. 4 , e45. 10.1371/journal.pgen.0020045.   edoc
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. 10.1016/   edoc
Siddharthan, R., Siggia, E. D. and van Nimwegen, E. (2005) ‘PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny’, PLoS Computational Biology, 1(7), p. e67. 10.1371/journal.pcbi.0010067.   edoc | Open Access
Julou, T., Burghardt, B., Gebauer, G., Berveiller, D., Damesin, C. and Selosse, M.-A. (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. 10.1111/j.1469-8137.2005.01364.x.   edoc
Sewer, A., Paul, N., Landgraf, P., Aravin, A., Pfeffer, S., Brownstein, M. J., Tuschl, T., van Nimwegen, E. and Zavolan, M. (2005) ‘Identification of clustered microRNAs using an ab initio prediction method’, BMC bioinformatics, Vol. 6, , 267. 10.1186/1471-2105-6-267.   edoc
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., Della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P. T., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schonbach, C., Sekiguchi, K., Semple, C. A. M., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J. and Hayashizaki, Y. (2005) ‘The transcriptional landscape of the mammalian genome’, Science, Vol. 309, no. 5740, pp. 1559–1563. 10.1126/science.1112014.   edoc
Speirs, C., van Nimwegen, E., Bolton, D., Zavolan, M., Duvall, M., Angleman, S., Siegel, R., 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. 10.1128/JVI.79.7.4025-4032.2005.   edoc
Paz, K., Socci, N. D., van Nimwegen, E., Viale, A. and Darnell, J. 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. 10.1038/sj.onc.1207803.   edoc
van Nimwegen, E. (2003) ‘Scaling laws in the functional content of genomes’, Trends in Genetics, 19(9), pp. 479–484. 10.1016/S0168-9525(03)00203-8.   edoc
Sinha, S., van Nimwegen, E. and Siggia, E. D. (2003) ‘A probabilistic method to detect regulatory modules’, Bioinformatics, 19(Supplement 1), pp. i292-i301. 10.1093/bioinformatics/btg1040.   edoc
Yang, E., van Nimwegen, E., Zavolan, M., Rajewsky, N., Schroeder, M., 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.   edoc
Crutchfield, J. P. and van Nimwegen, E. (2002) ‘The evolutionary unfolding of complexity’, in Landweber, L. F. and Winfree, E. (eds) Evolution as Computation. Berlin: Springer (Natural Computing Series), pp. 67–94. 10.1007/978-3-642-55606-7_4.   edoc
van Nimwegen, E., Zavolan, M., 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. 10.1073/pnas.112690399.   edoc
Zavolan, M., 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. 10.1101/gr.191702.   edoc
van Nimwegen, E. and Crutchfield, J. P. (2001) ‘Optimizing epochal evolutionary search: Population-size dependent theory’, Machine Learning, 45(1), pp. 77–114. 10.1023/A:1010928206141.   edoc
van Nimwegen, E. and Crutchfield, J. P. (2000) ‘Optimizing epochal evolutionary search: population-size independent theory’, Computer Methods in Applied Mechanics and Engineering, 186(2-4), pp. 171–194. 10.1016/S0045-7825(99)00383-7.   edoc
van Nimwegen, E. and Crutchfield, J. P. (2000) ‘Metastable evolutionary dynamics: Crossing fitness barriers or escaping via neutral paths?’, Bulletin of Mathematical Biology, 62(5), pp. 799–848. 10.1006/bulm.2000.0180.   edoc
Oprea, M., van Nimwegen, E. . and Perelson, A. S. (2000) ‘Dynamics of one-pass germinal center models: implications for affinity maturation’, Bulletin of Mathematical Biology, 62(1), pp. 121–153. 10.1006/bulm.1999.0144.   edoc
van Nimwegen, E., Crutchfield, J. P. and Huynen, M. (1999) ‘Neutral evolution of mutational robustness’, Proceedings of the National Academy of Sciences of the United States of America, 96(17), pp. 9716–9720. 10.1073/pnas.96.17.9716.   edoc
van Nimwegen, E., Crutchfield, J. P. and Mitchell, M. (1999) ‘Statistical dynamics of the royal road genetic algorithm’, Theoretical Computer Science, 229(1-2), pp. 41–102. 10.1016/S0304-3975(99)00119-X.   edoc
Huynen, M. A. and van Nimwegen, E. (1998) ‘The frequency distribution of gene family sizes in complete genomes’, Molecular Biology and Evolution , 15(5), pp. 583–589. 10.1093/oxfordjournals.molbev.a025959.   edoc