Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

G. Ambrosini; I. Vorontsov; D. Penzar; R. Groux; O. Fornes et al. 

The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche

D. Ataca; P. Aouad; C. Constantin; C. Laszlo; M. Beleut et al. 

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

P. Meylan; R. Dreos; G. Ambrosini; R. Groux; P. Bucher 

Common genetic variants associated with Parkinson’s disease display widespread signature of epigenetic plasticity

A. Sharma; N. Osato; H. Liu; S. Asthana; T. C. Dakal et al. 

SPar-K: a method to partition NGS signal data

R. Groux; P. Bucher 

Opposing chromatin remodelers control transcription initiation frequency and start site selection

S. Kubik; M. J. Bruzzone; D. Challal; R. Dreos; S. Mattarocci et al. 

Chromatin three-dimensional interactions mediate genetic effects on gene expression

O. Delaneau; M. Zazhytska; C. Borel; G. Giannuzzi; G. Rey et al. 

Chromatin 3D interactions mediate genetic effects on gene expression

O. Delaneau; M. Zazhytska; C. Borel; G. Giannuzzi; G. Rey et al. 

Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each

A. M. Dogar; R. Pauchard-Batschulat; B. Grisoni-Neupert; L. Richman; A. Paillusson et al. 

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

A. Coudray; A. M. Battenhouse; P. Bucher; V. R. Iyer 

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

G. Ambrosini; R. Groux; P. Bucher 

MGA repository: a curated data resource for ChIP-seq and other genome annotated data

R. Dréos; G. Ambrosini; R. Groux; R. C. Périer; P. Bucher 

Local regulatory networks across two tissues and applications to analyze rare non-coding variants

A. Reymond; O. Delaneau; M. Zazhytska; K. Popadin; S. Kumar et al. 

SNP2TFBS-a database of regulatory SNPs affecting predicted transcription factor binding site affinity

G. Ambrosini; S. Kumar; P. Bucher 

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

A. Isakova; R. Groux; M. Imbeault; P. Rainer; D. Alpern et al. 

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

R. Dreos; G. Ambrosini; R. Groux; R. Cavin Périer; P. Bucher 

SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity

S. Kumar; G. Ambrosini; P. Bucher 

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

G. Ambrosini; R. Dreos; S. Kumar; P. Bucher 

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

R. Dreos; G. Ambrosini; P. Bucher 

A maximum-likelihood approach for building cell-type trees by lifting

N. U. Nair; L. Hunter; M. Shao; P. Grnarova; Y. Lin et al. 

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features

S. Kumar; P. Bucher 

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

R. Dreos; G. Ambrosini; R. C. Perier; P. Bucher 

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data

N. U. Nair; S. Kumar; B. M. E. Moret; P. Bucher 

Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers

D. Polychronopoulos; E. Weitschek; S. Dimitrieva; P. Bucher; G. Felici et al. 

Study of cell differentiation by phylogenetic analysis using histone modification data

N. U. Nair; Y. Lin; A. Manasovska; J. Antic; P. Grnarova et al. 

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

S. Dimitrieva; M. Anisimova 

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

H. Stockinger; A. M. Altenhoff; K. Arnold; A. Bairoch; F. Bastian et al. 

Principles of ChIP-seq Data Analysis Illustrated with Examples

G. Ambrosini; R. Dreos; P. Bucher 

Computational studies in epigenomics using histone modification data

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

P. Meyer; G. Siwo; D. Zeevi; E. Sharon; R. Norel et al. 

Nuclear Factor I genomic binding associates with chromatin boundaries

M. Pjanic; C. D. Schmid; A. Gaussin; G. Ambrosini; J. Adamcik et al. 

Evaluation of methods for modeling transcription factor sequence specificity

M. T. Weirauch; A. Cote; R. Norel; M. Annala; Y. Zhao et al. 

Assessment of transcript reconstruction methods for RNA-seq

T. Steijger; J. F. Abril; P. G. Engstrom; F. Kokocinski; T. J. Hubbard et al. 

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

R. Dreos; G. Ambrosini; R. Cavin Perier; P. Bucher 

Critical assessment of automated flow cytometry data analysis techniques

N. Aghaeepour; G. Finak; D. Dougall; K. AH; P. Mah et al. 

UCNEbase – a database of ultra-conserved non-coding elements and genomic regulatory blocks

S. Dimitrieva; P. Bucher 

Phylogenetic Analysis of Cell Types Using Histone Modifications

N. U. Nair; Y. Lin; P. Bucher; B. M. E. Moret 

Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes

Genetic and physiological analysis of Rht8 in bread wheat: an alternative source of semi-dwarfism with a reduced sensitivity to brassinosteroids

D. Gasperini; A. Greenland; P. Hedden; R. Dreos; W. Harwood et al. 

ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries

N. Nair; A. Das Sahu; P. Bucher; B. Moret 

Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements

S. Dimitrieva; P. Bucher 

Practicality and time complexity of a sparsified RNA folding algorithm

S. Dimitrieva; P. Bucher 

RNA Profiling and Chromatin Immunoprecipitation-Sequencing Reveal that PTF1a Stabilizes Pancreas Progenitor Identity via the Control of MNX1/HLXB9 and a Network of Other Transcription Factors

N. Thompson; E. Gesina; P. Scheinert; P. Bucher; A. Grapin-Botton 

ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites

T. J. Cradick; G. Ambrosini; C. Iseli; P. Bucher; A. P. McCaffrey 

BlastR-fast and accurate database searches for non-coding RNAs

G. Bussotti; E. Raineri; I. Erb; M. Zytnicki; A. Wilm et al. 

A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing

S. Meylan; A. C. Groner; G. Ambrosini; N. Malani; S. Quenneville et al. 

Multichannel Sequence Analysis Applied To Social Science Data

J-A. Gauthier; E. D. Widmer; P. Bucher; C. Notredame 

The transcription factor Rfx3 regulates beta-cell differentiation, function, and glucokinase expression

A. Ait-Lounis; C. Bonal; Q. Seguín-Estévez; C. D. Schmid; P. Bucher et al. 

MER41 repeat sequences contain inducible STAT1 binding sites

C. D. Schmid; P. Bucher 

KRAB-Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

A. C. Groner; S. Meylan; A. Ciuffi; N. Zangger; G. Ambrosini et al. 

Prediction of Survival and Risk Assessment Using Joint Analysis of Microarray Gene Expression Data

CleanEx: new data extraction and merging tools based on MeSH term annotation

V. Praz; P. Bucher 

Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site

E. Leimgruber; Q. Seguín-Estévez; I. Dunand-Sauthier; N. Rybtsova; C. D. Schmid et al. 

Can survival prediction be improved by merging gene expression data sets?

H. Yasrebi; P. Sperisen; V. Praz; P. Bucher 

How much does it cost? Optimization of costs in sequence analysis of social science data

J-A. Gauthier; E. D. Widmer; P. Bucher; C. Notredame 

Methods for discovery and characterization of DNA sequence motifs

P. Bucher 

Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation

M. Krawczyk; Q. Seguín-Estévez; E. Leimgruber; P. Sperisen; C. Schmid et al. 

ChIP-Seq data reveal nucleosome architecture of human promoters

C. D. Schmid; P. Bucher 

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data

C. D. Schmid; T. Sengstag; P. Bucher; M. Delorenzi 

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time

D. Retelska; E. Beaudoing; C. Notredame; C. V. Jongeneel; P. Bucher 

Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data

D. Rambaldi; B. Felice; V. Praz; P. Bucher; D. Cittaro et al. 

Indexing strategies for rapid searches of short words in genome sequences

C. Iseli; G. Ambrosini; P. Bucher; C. V. Jongeneel 

Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells

P. A. Girod; D. Q. Nguyen; D. Calabrese; S. Puttini; M. Grandjean et al. 

EPD in its twentieth year: towards complete promoter coverage of selected model organisms

C. D. Schmid; R. Perier; V. Praz; P. Bucher 

Similarities and differences of polyadenylation signals in human and fly

D. Retelska; C. Iseli; P. Bucher; C. V. Jongeneel; F. Naef 

HTPSELEX–a database of high-throughput SELEX libraries for transcription factor binding sites

V. Jagannathan; E. Roulet; M. Delorenzi; P. Bucher 

APDB: a web server to evaluate the accuracy of sequence alignments using structural information

F. Armougom; O. Poirot; S. Moretti; D. G. Higgins; P. Bucher et al. 

Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus

F. Beermann; K. Kaloulis; D. Hofmann; F. Murisier; P. Bucher et al. 

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge

F. Armand; P. Bucher; C. V. Jongeneel; E. E. Farmer 

Stealth proteins: in silico identification of a novel protein family rendering bacterial pathogens invisible to host immune defense

P. Sperisen; C. D. Schmid; P. Bucher; O. Zilian 

InterPro, progress and status in 2005

N. J. Mulder; R. Apweiler; T. K. Attwood; A. Bairoch; A. Bateman et al. 

Promoter rearrangements cause species-specific hepatic regulation of the glyoxylate reductase/hydroxypyruvate reductase gene by the peroxisome proliferator-activated receptor alpha

R. Genolet; S. Kersten; O. Braissant; S. Mandard; N. S. Tan et al. 

Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts

T. Egener; E. Roulet; M. Zehnder; P. Bucher; N. Mermod 

trome, trEST and trGEN: databases of predicted protein sequences

P. Sperisen; C. Iseli; M. Pagni; B. J. Stevenson; P. Bucher et al. 

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension

C. D. Schmid; V. Praz; M. Delorenzi; R. Perier; P. Bucher 

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature

V. Praz; V. Jagannathan; P. Bucher 

Long distance control of MHC class II expression by multiple distal enhancers regulated by regulatory factor X complex and CIITA

M. Krawczyk; N. Peyraud; N. Rybtsova; K. Masternak; P. Bucher et al. 

Recent improvements to the PROSITE database

N. Hulo; C. J. Sigrist; V. Le Saux; P. S. Langendijk-Genevaux; L. Bordoli et al. 

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

O. O’Sullivan; M. Zehnder; D. Higgins; P. Bucher; A. Grosdidier et al. 

The InterPro Database, 2003 brings increased coverage and new features

N. J. Mulder; R. Apweiler; T. K. Attwood; A. Bairoch; D. Barrell et al. 

Modeling sequencing errors by combining Hidden Markov models

C. Lottaz; C. Iseli; C. V. Jongeneel; P. Bucher 

Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes

S. Godard; G. Getz; M. Delorenzi; P. Farmer; H. Kobayashi et al. 

Telomere maintenance in fission yeast requires an Est1 ortholog

H. T. Beernink; K. Miller; A. Deshpande; P. Bucher; J. P. Cooper 

Signal search analysis server

G. Ambrosini; V. Praz; V. Jagannathan; P. Bucher 

A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed

P. Reichenbach; M. Hoss; C. M. Azzalin; M. Nabholz; P. Bucher et al. 

PROSITE: a documented database using patterns and profiles as motif descriptors

C. J. Sigrist; L. Cerutti; N. Hulo; A. Gattiker; L. Falquet et al. 

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites

E. Roulet; S. Busso; A. A. Camargo; A. J. Simpson; N. Mermod et al. 

Nineteen additional unpredicted transcripts from human chromosome 21

A. Reymond; A. A. Camargo; S. Deutsch; B. J. Stevenson; R. B. Parmigiani et al. 

The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data

V. Praz; R. Perier; C. Bonnard; P. Bucher 

InterPro: an integrated documentation resource for protein families, domains and functional sites

N. J. Mulder; R. Apweiler; T. K. Attwood; A. Bairoch; A. Bateman et al. 

Long-range heterogeneity at the 3′ ends of human mRNAs

C. Iseli; B. J. Stevenson; S. J. de Souza; H. B. Samaia; A. A. Camargo et al. 

The PROSITE database, its status in 2002

L. Falquet; M. Pagni; P. Bucher; N. Hulo; C. J. Sigrist et al. 

Numerous potentially functional but non-genic conserved sequences on human chromosome 21

E. T. Dermitzakis; A. Reymond; R. Lyle; N. Scamuffa; C. Ucla et al. 

trEST, trGEN and Hits: access to databases of predicted protein sequences

M. Pagni; C. Iseli; T. Junier; L. Falquet; V. Jongeneel et al. 

Individuality of Ag-selected and preimmune TCR repertoires

J. L. Maryanski; V. Attuil; A. Hamrouni; M. Mutin; M. Rossi et al. 

mmsearch: a motif arrangement language and search program

T. Junier; M. Pagni; P. Bucher 

DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites

G. B. Ehret; P. Reichenbach; U. Schindler; C. M. Horvath; S. Fritz et al. 

A cSNP map and database for human chromosome 21

S. Deutsch; C. Iseli; P. Bucher; S. E. Antonarakis; H. S. Scott 

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

R. Apweiler; T. K. Attwood; A. Bairoch; A. Bateman; E. Birney et al. 

Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites

E. Roulet; P. Bucher; R. Schneider; E. Wingender; Y. Dusserre et al.