Methods Applications

Methods

The transcriptional landscape of the mammalian genome
P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells and others
Science, 2005, 309(5740), 1559--1563

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny
R. Siddharthan, E. Siggia and E. Van Nimwegen
PLoS computational biology, 2005, 1(7), e67

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

A probabilistic method to detect regulatory modules
S. Sinha, E. Van Nimwegen and E. Siggia
Bioinformatics, 2003, 19(suppl 1), i292--i301

Inference of miRNA targets using evolutionary conservation and pathway analysis
D. Gaidatzis, E. van Nimwegen, J. Hausser and M. Zavolan
BMC bioinformatics, 2007, 8(1), 69

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
H. Suzuki, A. Forrest, E. van Nimwegen, C. Daub, P. Balwierz, K. Irvine, T. Lassmann, T. Ravasi, Y. Hasegawa, M. Hoon and others
Nature genetics, 2009, 41(5), 553--562

Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics
E. van Nimwegen, M. Zavolan, N. Rajewsky and E. Siggia
Proceedings of the National Academy of Sciences, 2002, 99(11), 7323--7328

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

Accurate prediction of protein--protein interactions from sequence alignments using a Bayesian method
L. Burger and E. Van Nimwegen
Molecular systems biology, 2008, 4(1)

SwissRegulon: a database of genome-wide annotations of regulatory sites
M. Pachkov, I. Erb, N. Molina and E. Van Nimwegen
Nucleic acids research, 2007, 35(suppl 1), D127--D131

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

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

Disentangling direct from indirect co-evolution of residues in protein alignments
L. Burger and E. Van Nimwegen
PLoS computational biology, 2010, 6(1), e1000633

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

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

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

Statistical features of yeast’s transcriptional regulatory code
I. Erb and Van Nimwegen
IEEE Proceedings of the first International Conference on Computational Systems Biology (ICCSB), 111--118

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
U. Schlecht, I. Erb, P. Demougin, N. Robine, V. Borde, E. Van Nimwegen, A. Nicolas and M. Primig
Molecular biology of the cell, 2008, 19(5), 2193--2207

Detecting regulatory sites using PhyloGibbs
R. Siddharthan and E. van Nimwegen
, 381--402

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

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
H. Kawaji, J. Severin, M. Lizio, A. Forrest, E. van Nimwegen, M. Rehli, K. Schroder, K. Irvine, H. Suzuki, P. Carninci and others
Nucleic acids research, gkq1112

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences
P. Arnold, I. Erb, M. Pachkov, N. Molina and E. van Nimwegen
Bioinformatics, 2012, 28(4), 487--494

A bayesian algorithm for reconstructing two-component signaling networks
L. Burger and E. van Nimwegen
, 44--55

Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters
I. Erb and E. Van Nimwegen
PloS one, 2011, 6(9), e24279

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
P. Arnold, A.Schoeler, M. Pachkov, P. Balwierz, H. Joergensen, M. Stadler, E. van Nimwegen and D. Schuebeler
Genome research, 2013, 23(1), 60--73

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates
M. Pachkov, P. Balwierz, P. Arnold, E. Ozonov and E. van Nimwegen
Nucleic acids research, 2013, 41(D1), D214--D220

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets
M. Khorshid, J. Hausser, M. Zavolan and E. van Nimwegen
Nature methods, 2013, 10(3), 253--255

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers
E. Ozonov and E. van Nimwegen
PLoS computational biology, 2013, 9(8), e1003181

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
P. Balwierz, M. Pachkov, P. Arnold, A. Gruber, M. Zavolan and E. van Nimwegen
Genome research, 2014, 24(5), 869--884

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads
F. Bertels, O. Silander, M. Pachkov, P. Rainey and E. van Nimwegen
Molecular biology and evolution, 2014, 31(5), 1077--1088

A promoter-level mammalian expression atlas
Consortium, The FANTOM and others
Nature, 2014, 507(7493), 462--470

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support
H. Stockinger, A. Altenhoff, K. Arnold, A. Bairoch, F. Bastian, S. Bergmann, L. Bougueleret, P. Bucher, M. Delorenzi, L. Lane and others
Nucleic acids research, gku380

Applications

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
H. Suzuki, A. Forrest, E. van Nimwegen, C. Daub, P. Balwierz, K. Irvine, T. Lassmann, T. Ravasi, Y. Hasegawa, M. de Hoon and others
Nature genetics, 2009, 41(5), 553-562

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
U. Schlecht, I. Erb, P. Demougin, N. Robine, V. Borde, E. Van Nimwegen, A. Nicolas, M. Primig
Molecular biology of the cell, 2008, 19(5), 2193--2207

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

Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop
N. Aceto, N. Sausgruber, H. Brinkhaus, D. Gaidatzis, G. Martiny-Baron, G. Mazzarol, S. Confalonieri, M. Quarto, G. Hu, P. Balwierz and others
Nature medicine, 18(4), 529--537

Co-expression of FBN1 with mesenchyme-specific genes in mouse cell lines: implications for phenotypic variability in Marfan syndrome
K. Summers, S. Raza, E. van Nimwegen, T. Freeman and D. Hume
European Journal of Human Genetics, 2010, 18(11), 1209--1215

Adipose tissue microRNAs as regulators of CCL2 production in human obesity
E. Arner, N. Mejhert, A. Kulyte, P. Balwierz, M. Pachkov, M. Cormont, S. Lorente-Cebrian, A. Ehrlund, J. Laurencikiene, P. Heden and others
Diabetes, 2012, 61(8), 1986--1993

An atlas of combinatorial transcriptional regulation in mouse and man
T. Ravasi, H. Suzuki, C. Cannistraci, S. Katayama, V. Bajic, K. Tan, A. Akalin, S. Schmeier, M. Kanamori-Katayama, N. Bertin and others
Cell, 2010, 140(5), 744--752

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
P. Arnold, A. Schoeler, M. Pachkov, P. Balwierz, H. Jorgensen, M. Stadler, E. van Nimwegen and D. Schuebeler
Genome research, 2013, 23(1), 60--73

The corepressor NCoR1 antagonizes PGC-1alpha and estrogen-related receptor alpha in the regulation of skeletal muscle function and oxidative metabolism
J. Perez-Schindler, S. Summermatter, S. Salatino, F. Zorzato, M. Beer, P. Balwierz, E. van Nimwegen, J. Feige, J. Auwerx and C. Handschin
Molecular and cellular biology, 2012, 32(24), 4913--4924

The Corepressor NCoR1 Antagonizes PGC-1 and Estrogen-Related Receptor in the Regulation of Skeletal Muscle Function and Oxidative Metabolism
J. Prez-Schindler, S. Summermatter, S. Salatino, F. Zorzato, M. Beer, P. Balwierz, E. van Nimwegen, J. Feige, J. Auwerx and C. Handschin
Molecular and Cellular Biology, 2012, 32(24), 4913

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

Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium
F. Meier-Abt, E. Milani, T. Roloff, H. Brinkhaus, S. Duss, D. Meyer, I. Klebba, P. Balwierz, E. Van Nimwegen and M. Bentires-Alj
Breast Cancer Research, 2013, 15(2), R36

Sox4 is a master regulator of epithelial-mesenchymal transition by controlling Ezh2 expression and epigenetic reprogramming
N. Tiwari, V. Tiwari, L. Waldmeier, P. Balwierz, P. Arnold, M. Pachkov, N. Meyer-Schaller, D. Schuebeler, E. van Nimwegen and G. Christofori
Cancer Cell, 2013, 23(6), 768--783

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion
R. Luisier, E. Unterberger, J. Goodman, M. Schwarz, J. Moggs, R. Terranova and E. van Nimwegen
Nucleic acids research, 2014, gkt1415

Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial--mesenchymal transition
M. Diepenbruck, L. Waldmeier, R. Ivanek, P. Berninger, P. Arnold, E. van Nimwegen and G. Christofori
Journal of cell science, 2014, 127(7), 1523--1536

Pegylated IFN-alpha regulates hepatic gene expression through transient Jak/STAT activation
M. Dill, Z. Makowska, G. Trincucci, A. Gruber, J. Vogt, M. Filipowicz, D. Calabrese, I. Krol, D. Lau, L. Terracciano and others
The Journal of clinical investigation, 2014, 124(4),0--0

O47 PEGYLATED INTERFERON-ALPHA INDUCES SUSTAINED TRANSCRIPTIONAL RESPONSE IN LIVER INFILTRATING IMMUNE CELLS BUT NOT IN HEPATOCYTES IN THE LIVER OF PATIENTS WITH CHRONIC HEPATITIS C
M. Dill, Z. Makowska, G. Trincucci, A. Gruber, J. Vogt, M. Filipowicz, D. Calabrese, I. Krol, D. Lau, L. Terracciano and others
Journal of Hepatology, 2014, 60(1), S20

Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1alpha in the regulation of the hypoxic gene program
M. Baresic, S. Salatino, B. Kupr, E. van Nimwegen and C. Handschin
Molecular and cellular biology, 2014, 34(16), 2996--3012

Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways
A. Gruber, W. Grandy, P. Balwierz, Y. Dimitrova, M. Pachkov, C. Ciaudo, E. van Nimwegen and M. Zavolan
Nucleic acids research, 2014, 42(14), 9313--9326

A large-scale, in vivo transcription factor screen defines bivalent chromatin as a key property of regulatory factors mediating Drosophila wing development
C. Schertel, M. Albarca, C. Rockel-Bauer, N. Kelley, J. Bischof, K. Hens, E. van Nimwegen, K. Basler, Konrad and B. Deplancke
Genome Research, 2015, gr--181305