Erik van Nimwegen

According to our database, Erik van Nimwegen authored at least 23 papers between 1999 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Identifying cell states in single-cell RNA-seq data at statistically maximal resolution.

Pascal Grobecker, Thomas Sakoparnig, Erik van Nimwegen

PLoS Comput. Biol., 2024

2017

Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.

Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen

PLoS Comput. Biol., 2017

2016

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

Erik van Nimwegen

PLoS Comput. Biol., 2016

2014

A promoter-level mammalian expression atlas.

The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki

Nat., 2014

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

Heinz Stockinger, Adrian M. Altenhoff, Konstantin Arnold, Amos Bairoch, Frederic B. Bastian, Sven Bergmann, Lydie Bougueleret, Philipp Bucher, Mauro Delorenzi, Lydie Lane, Philippe Le Mercier, Frédérique Lisacek, Olivier Michielin, Patricia M. Palagi, Jacques Rougemont, Torsten Schwede, Christian von Mering, Erik van Nimwegen, Daniel Walther, Ioannis Xenarios, Mihaela Zavolan, Evgeny M. Zdobnov, Vincent Zoete, Ron D. Appel

Nucleic Acids Res., 2014

Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine.

Florian Jug, Tobias Pietzsch, Dagmar Kainmüller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers

Proceedings of the Bayesian and grAphical Models for Biomedical Imaging, 2014

2013

Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers.

Evgeniy A. Ozonov, Erik van Nimwegen

PLoS Comput. Biol., 2013

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.

Mikhail Pachkov, Piotr J. Balwierz, Phil Arnold, Evgeniy A. Ozonov, Erik van Nimwegen

Nucleic Acids Res., 2013

2012

Corrigendum: DNA-binding factors shape the mouse methylome at distal regulatory regions.

Michael B. Stadler, Rabih Murr, Lukas Burger, Robert Ivanek, Florian Lienert, Anne Schöler, Erik van Nimwegen, Christiane Wirbelauer, Edward J. Oakeley, Dimos Gaidatzis, Vijay K. Tiwari, Dirk Schübeler

Nat., 2012

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.

Phil Arnold, Ionas Erb, Mikhail Pachkov, Nacho Molina, Erik van Nimwegen

Bioinform., 2012

2011

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

Hideya Kawaji, Jessica Severin, Marina Lizio, Alistair R. R. Forrest, Erik van Nimwegen, Michael Rehli, Kate Schroder, Katharine M. Irvine, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub

Nucleic Acids Res., 2011

2010

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments.

Lukas Burger, Erik van Nimwegen

PLoS Comput. Biol., 2010

2007

SwissRegulon: a database of genome-wide annotations of regulatory sites.

Mikhail Pachkov, Ionas Erb, Nacho Molina, Erik van Nimwegen

Nucleic Acids Res., 2007

Finding regulatory elements and regulatory motifs: a general probabilistic framework.

Erik van Nimwegen

BMC Bioinform., 2007

Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis.

Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan

BMC Bioinform., 2007

Inference of miRNA targets using evolutionary conservation and pathway analysis.

Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan

BMC Bioinform., 2007

2006

A Bayesian Algorithm for Reconstructing Two-Component Signaling Networks.

Lukas Burger, Erik van Nimwegen

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

2005

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.

Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen

PLoS Comput. Biol., 2005

Identification of clustered microRNAs using an <i>ab initio </i>prediction method.

Alain Sewer, Nicodème Paul, Pablo Landgraf, Alexei Aravin, Sébastien Pfeffer, Michael J. Brownstein, Thomas Tuschl, Erik van Nimwegen, Mihaela Zavolan

BMC Bioinform., 2005

2004

PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information.

Rahul Siddharthan, Erik van Nimwegen, Eric D. Siggia

Proceedings of the Regulatory Genomics, 2004

2003

A probabilistic method to detect regulatory modules.

Saurabh Sinha, Erik van Nimwegen, Eric D. Siggia

Proceedings of the Eleventh International Conference on Intelligent Systems for Molecular Biology, June 29, 2003

2001

Optimizing Epochal Evolutionary Search: Population-Size Dependent Theory.

Erik van Nimwegen, James P. Crutchfield

Mach. Learn., 2001

1999

Statistical Dynamics of the Royal Road Genetic Algorithm.

Erik van Nimwegen, James P. Crutchfield, Melanie Mitchell

Theor. Comput. Sci., 1999