Publications by authors named "Erik van Nimwegen"

77Publications

Tead transcription factors differentially regulate cortical development.

Sci Rep 2020 03 13;10(1):4625. Epub 2020 Mar 13.

Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058, Basel, Switzerland.

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http://dx.doi.org/10.1038/s41598-020-61490-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070074PMC
March 2020

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.

Genome Res 2019 07 28;29(7):1164-1177. Epub 2019 May 28.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.239319.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6633267PMC
July 2019

Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC.

Genome Biol 2018 03 28;19(1):44. Epub 2018 Mar 28.

Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056, Basel, Switzerland.

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http://dx.doi.org/10.1186/s13059-018-1415-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5875010PMC
March 2018

Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software.

Nat Commun 2018 01 15;9(1):212. Epub 2018 Jan 15.

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056, Basel, Switzerland.

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http://www.nature.com/articles/s41467-017-02505-0
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http://dx.doi.org/10.1038/s41467-017-02505-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768764PMC
January 2018

The ISMARA client.

F1000Res 2016 15;5. Epub 2016 Dec 15.

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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https://f1000research.com/articles/5-2851/v1
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http://dx.doi.org/10.12688/f1000research.9794.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302150PMC
December 2016

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

Methods 2016 Jul 13;104:204-205. Epub 2016 Jan 13.

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.12.016DOI Listing
July 2016

The Genomic Context and Corecruitment of SP1 Affect ERRα Coactivation by PGC-1α in Muscle Cells.

Mol Endocrinol 2016 07 16;30(7):809-25. Epub 2016 May 16.

Focal Area Growth and Development (S.S., B.K., M.B., C.H.) and Focal Area Computational and Systems Biology (S.S., E.N.), Biozentrum, University of Basel, and Swiss Institute of Bioinformatics (S.S., E.N.), CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1210/me.2016-1036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4970653PMC
July 2016

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

PLoS Comput Biol 2016 05 12;12(5):e1004726. Epub 2016 May 12.

Biozentrum, University of Basel, Basel, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1004726DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4865087PMC
May 2016

ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data.

Methods 2015 Sep 8;85:62-74. Epub 2015 Jul 8.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10462023153000
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http://dx.doi.org/10.1016/j.ymeth.2015.06.024DOI Listing
September 2015

Expression noise facilitates the evolution of gene regulation.

Elife 2015 Jun 17;4. Epub 2015 Jun 17.

Biozentrum, University of Basel, Basel, Switzerland.

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http://dx.doi.org/10.7554/eLife.05856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468965PMC
June 2015

Quantifying the strength of miRNA-target interactions.

Methods 2015 Sep 16;85:90-99. Epub 2015 Apr 16.

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.04.012DOI Listing
September 2015

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development.

Genome Res 2015 Apr 7;25(4):514-23. Epub 2015 Jan 7.

Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;

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http://genome.cshlp.org/lookup/doi/10.1101/gr.181305.114
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http://dx.doi.org/10.1101/gr.181305.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381523PMC
April 2015

Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells.

Nat Commun 2014 Nov 21;5:5465. Epub 2014 Nov 21.

Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland.

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http://dx.doi.org/10.1038/ncomms6465DOI Listing
November 2014

Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program.

Mol Cell Biol 2014 Aug 9;34(16):2996-3012. Epub 2014 Jun 9.

Focal Area Growth and Development, Biozentrum, University of Basel, Basel, Switzerland

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http://dx.doi.org/10.1128/MCB.01710-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135604PMC
August 2014

A promoter-level mammalian expression atlas.

Authors:
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 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 C 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 Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas 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 Furni 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 C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L 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 Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya 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 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 Takaai 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 Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado 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

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Automated reconstruction of whole-genome phylogenies from short-sequence reads.

Mol Biol Evol 2014 May 5;31(5):1077-88. Epub 2014 Mar 5.

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msu088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995342PMC
May 2014

Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition.

J Cell Sci 2014 Apr 19;127(Pt 7):1523-36. Epub 2014 Feb 19.

Department of Biomedicine, University of Basel, 4058 Basel, Switzerland.

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http://dx.doi.org/10.1242/jcs.139865DOI Listing
April 2014

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.

Genome Res 2014 May 10;24(5):869-84. Epub 2014 Feb 10.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.169508.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009616PMC
May 2014

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion.

Nucleic Acids Res 2014 Apr 23;42(7):4180-95. Epub 2014 Jan 23.

Discovery and Investigative Safety, Novartis Institutes for Biomedical Research, 4057 Basel, Switzerland, Department of Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, University of Tübingen, 72074 Tübingen, Germany, Department of Pharmacology and Toxicology, Michigan State University, MI 48824, USA and Biozentrum, University of Basel and Swiss Institute of Bioinformatics, 4056 Basel, Switzerland.

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http://dx.doi.org/10.1093/nar/gkt1415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985636PMC
April 2014

An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants.

Eur J Immunol 2014 Apr 1;44(4):1181-93. Epub 2014 Feb 1.

Developmental and Molecular Immunology Group, Department of Biomedicine, University of Basel, Basel, Switzerland.

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http://doi.wiley.com/10.1002/eji.201344022
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http://dx.doi.org/10.1002/eji.201344022DOI Listing
April 2014

Timescales and bottlenecks in miRNA-dependent gene regulation.

Mol Syst Biol 2013 Dec 3;9:711. Epub 2013 Dec 3.

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.

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http://dx.doi.org/10.1038/msb.2013.68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3882800PMC
December 2013

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

PLoS Comput Biol 2013 22;9(8):e1003181. Epub 2013 Aug 22.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1003181DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749953PMC
February 2014

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets.

Nat Methods 2013 Mar 20;10(3):253-5. Epub 2013 Jan 20.

Biozentrum, University of Basel, Basel, Switzerland.

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http://dx.doi.org/10.1038/nmeth.2341DOI Listing
March 2013

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

Nucleic Acids Res 2013 Jan 24;41(Database issue):D214-20. Epub 2012 Nov 24.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1093/nar/gks1145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531101PMC
January 2013

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.

Genome Res 2013 Jan 10;23(1):60-73. Epub 2012 Sep 10.

Biozentrum of the University of Basel and Swiss Institute of Bioinformatics, CH 4056 Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.142661.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530684PMC
January 2013

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

Bioinformatics 2012 Feb;28(4):487-94

Biozentrum, University of Basel, Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btr695DOI Listing
February 2012

Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

PLoS One 2011 9;6(9):e24279. Epub 2011 Sep 9.

Bioinformatics and Genomics program, Center for Genomic Regulation and Pompeu Fabra University, Barcelona, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024279PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170328PMC
March 2012

Disentangling direct from indirect co-evolution of residues in protein alignments.

PLoS Comput Biol 2010 Jan 1;6(1):e1000633. Epub 2010 Jan 1.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland.

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http://dx.doi.org/10.1371/journal.pcbi.1000633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793430PMC
January 2010

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.

Genome Biol 2009 22;10(7):R79. Epub 2009 Jul 22.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland.

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http://dx.doi.org/10.1186/gb-2009-10-7-r79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728533PMC
January 2010

Scaling laws in functional genome content across prokaryotic clades and lifestyles.

Trends Genet 2009 Jun 18;25(6):243-7. Epub 2009 May 18.

Biozentrum, the University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland.

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http://dx.doi.org/10.1016/j.tig.2009.04.004DOI Listing
June 2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion.

Genome Res 2009 Apr 29;19(4):611-25. Epub 2009 Jan 29.

Friedrich Miescher Institute for Biomedical Research and National Center for Competence in Research "Frontiers in Genetics," CH-4058 Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.083881.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665780PMC
April 2009

MicroRNA-221-222 regulate the cell cycle in mast cells.

J Immunol 2009 Jan;182(1):433-45

Institute for Research in Biomedicine, Bellinzona, Switzerland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2610349PMC
http://dx.doi.org/10.4049/jimmunol.182.1.433DOI Listing
January 2009

The evolution of domain-content in bacterial genomes.

Biol Direct 2008 Dec 11;3:51. Epub 2008 Dec 11.

Biozentrum, Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland. Erik van Nimwegen

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http://dx.doi.org/10.1186/1745-6150-3-51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615428PMC
December 2008

Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method.

Mol Syst Biol 2008 12;4:165. Epub 2008 Feb 12.

Biozentrum, the University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland.

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http://dx.doi.org/10.1038/msb4100203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267735PMC
March 2008

Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs.

DNA Res 2008 Apr 14;15(2):63-72. Epub 2008 Feb 14.

Division of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel CH-4056, Switzerland.

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http://dx.doi.org/10.1093/dnares/dsm036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650624PMC
April 2008

Computational analysis of small RNA cloning data.

Methods 2008 Jan;44(1):13-21

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.

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http://dx.doi.org/10.1016/j.ymeth.2007.10.002DOI Listing
January 2008

Universal patterns of purifying selection at noncoding positions in bacteria.

Genome Res 2008 Jan 21;18(1):148-60. Epub 2007 Nov 21.

Biozentrum, the University of Basel, and Swiss Institute of Bioinformatics, 4056-CH, Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.6759507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134783PMC
January 2008

Detecting regulatory sites using PhyloGibbs.

Methods Mol Biol 2007 ;395:381-402

Institute of Mathematical Sciences, India.

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http://dx.doi.org/10.1007/978-1-59745-514-5_24DOI Listing
March 2008

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

BMC Bioinformatics 2007 Sep 27;8 Suppl 6:S4. Epub 2007 Sep 27.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, Basel, Switzerland.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-8-S6-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1995539PMC
September 2007

Inference of miRNA targets using evolutionary conservation and pathway analysis.

BMC Bioinformatics 2007 Mar 1;8:69. Epub 2007 Mar 1.

Biozentrum, University of Basel, Basel, Switzerland.

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http://dx.doi.org/10.1186/1471-2105-8-69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838429PMC
March 2007

Epidemiology. Influenza escapes immunity along neutral networks.

Science 2006 Dec;314(5807):1884-6

Division of Bioinformatics, Biozentrum, University of Basel, 4056 Basel, Switzerland.

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http://dx.doi.org/10.1126/science.1137300DOI Listing
December 2006

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

Nucleic Acids Res 2007 Jan 27;35(Database issue):D127-31. Epub 2006 Nov 27.

Biozentrum, The University of Basel, Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland.

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http://dx.doi.org/10.1093/nar/gkl857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716717PMC
January 2007

The types and prevalence of alternative splice forms.

Curr Opin Struct Biol 2006 Jun 18;16(3):362-7. Epub 2006 May 18.

Division of Bioinformatics, Biozentrum, University of Basel, Klingelberstrasse 50-70, Basel, CH-4056, Switzerland.

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http://dx.doi.org/10.1016/j.sbi.2006.05.002DOI Listing
June 2006

A simple physical model predicts small exon length variations.

PLoS Genet 2006 Apr 28;2(4):e45. Epub 2006 Apr 28.

Division of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland.

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https://dx.doi.org/10.1371/journal.pgen.0020045
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http://dx.doi.org/10.1371/journal.pgen.0020045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449888PMC
April 2006

SPA: a probabilistic algorithm for spliced alignment.

PLoS Genet 2006 Apr 28;2(4):e24. Epub 2006 Apr 28.

Biozentrum, University of Basel, Basel, Switzerland.

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http://dx.doi.org/10.1371/journal.pgen.0020024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449883PMC
April 2006

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

PLoS Comput Biol 2005 Dec 9;1(7):e67. Epub 2005 Dec 9.

Center for Studies in Physics and Biology, The Rockefeller University, New York, New York, United States of America.

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http://www.physics.rockefeller.edu/siggia/Publications/2000-
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http://dx.plos.org/10.1371/journal.pcbi.0010067
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http://dx.doi.org/10.1371/journal.pcbi.0010067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1309704PMC
December 2005

Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture.

J Virol 2005 Apr;79(7):4025-32

Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892, USA.

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http://dx.doi.org/10.1128/JVI.79.7.4025-4032.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1061548PMC
April 2005

Transformation fingerprint: induced STAT3-C, v-Src and Ha-Ras cause small initial changes but similar established profiles in mRNA.

Oncogene 2004 Nov;23(52):8455-63

Laboratory of Molecular Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://www.nature.com/articles/1207803
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November 2004

Scaling laws in the functional content of genomes.

Trends Genet 2003 Sep;19(9):479-84

Center for Studies in Physics and Biology, the Rockefeller University, 1230 York Avenue, New York, NY 12001, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S016895250300203
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September 2003

Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes.

Genome Res 2003 Aug;13(8):1863-72

Laboratory of Molecular Cell Biology, The Rockefeller University, New York, New York 10021-6399, USA.

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http://dx.doi.org/10.1101/gr.1272403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403777PMC
August 2003

A probabilistic method to detect regulatory modules.

Bioinformatics 2003 ;19 Suppl 1:i292-301

Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 0021, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1040DOI Listing
October 2004

Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome.

Genome Res 2002 Sep;12(9):1377-85

Laboratory for Computational Genomics, The Rockefeller University, New York, New York 10021, USA.

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http://dx.doi.org/10.1101/gr.191702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC186662PMC
September 2002

Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics.

Proc Natl Acad Sci U S A 2002 May;99(11):7323-8

Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1073/pnas.112690399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC124229PMC
May 2002