Publications

2018

Journal Articles

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

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

PeerJ. 2018-07-31. Vol. 6, p. e5362. DOI : 10.7717/peerj.5362.

Detailed record

Full text - View at publisher

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

G. Ambrosini; R. Groux; P. Bucher 

Bioinformatics. 2018-03-05.  p. bty127. DOI : 10.1093/bioinformatics/bty127.

Detailed record

Full text - View at publisher

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 

Nucleic Acids Research. 2018. Vol. 46, num. D1, p. D175-D180. DOI : 10.1093/nar/gkx995.

Detailed record

View at publisher

2017

Journal Articles

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

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

Nature methods. 2017. Vol. 14, p. 316-322. DOI : 10.1038/nmeth.4143.

Detailed record

View at publisher

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

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

Nucleic Acids Research. 2017. Vol. 45, num. D1, p. D51-D55. DOI : 10.1093/nar/gkw1069.

Detailed record

Full text - View at publisher

2016

Journal Articles

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

S. Kumar; G. Ambrosini; P. Bucher 

Nucleic acids research. 2016. Vol. 45, num. D1, p. D139-D144. DOI : 10.1093/nar/gkw1064.

Detailed record

Full text - View at publisher

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 

BMC genomics. 2016. Vol. 17, num. 1, p. 938. DOI : 10.1186/s12864-016-3288-8.

Detailed record

View at publisher

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

R. Dreos; G. Ambrosini; P. Bucher 

PLoS Comput Biol. 2016. Vol. 112, num. 10, p. e1005144. DOI : 10.1371/journal.pcbi.1005144.

Detailed record

Full text - View at publisher

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

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

BMC Genomics. 2016. Vol. 17, num. 1, 14, p. 14. DOI : 10.1186/s12864-015-2297-3.

Detailed record

View at publisher

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

S. Kumar; P. Bucher 

Bmc Bioinformatics. 2016. Vol. 17, p. 4. DOI : 10.1186/s12859-015-0846-z.

Detailed record

View at publisher

2015

Journal Articles

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

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

Nucleic Acids Research. 2015. Vol. 43, num. D1, p. D92-D96. DOI : 10.1093/nar/gku1111.

Detailed record

Full text - View at publisher

2014

Journal Articles

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

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

Bioinformatics. 2014. Vol. 30, num. 17, p. 2406-2413. DOI : 10.1093/bioinformatics/btu318.

Detailed record

Full text - View at publisher

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. 

Genomics. 2014. Vol. 104, num. 2, p. 79-86. DOI : 10.1016/j.ygeno.2014.07.004.

Detailed record

View at publisher

Study of cell differentiation by phylogenetic analysis using histone modification data

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

Bmc Bioinformatics. 2014. Vol. 15, num. 269. DOI : 10.1186/1471-2105-15-269.

Detailed record

View at publisher

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

S. Dimitrieva; M. Anisimova 

Plos One. 2014. Vol. 9, num. 6, p. e95034. DOI : 10.1371/journal.pone.0095034.

Detailed record

Full text - View at publisher

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. 

Nucleic Acids Research. 2014. Vol. 42, num. W1, p. W436-W441. DOI : 10.1093/nar/gku380.

Detailed record

Full text - View at publisher

Conference Papers

Principles of ChIP-seq Data Analysis Illustrated with Examples

G. Ambrosini; R. Dreos; P. Bucher 

2014. 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO), Granada, SPAIN, APR 07-09, 2014. p. 682-694.

Detailed record

Theses

Computational studies in epigenomics using histone modification data

N. U. Nair / B. Moret; P. Bucher (Dir.)  

Lausanne: EPFL, 2014. DOI : 10.5075/epfl-thesis-6327.

Detailed record

Full text - View at publisher

2013

Journal Articles

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

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

Genome research. 2013. Vol. 23, num. 11, p. 1928-37. DOI : 10.1101/gr.157420.113.

Detailed record

View at publisher

Nuclear Factor I genomic binding associates with chromatin boundaries

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

BMC Genomics. 2013. Vol. 14, p. 99. DOI : 10.1186/1471-2164-14-99.

Detailed record

Full text - View at publisher

Evaluation of methods for modeling transcription factor sequence specificity

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

Nature Biotechnology. 2013. Vol. 31, num. 2, p. 126-134. DOI : 10.1038/nbt.2486.

Detailed record

View at publisher

Assessment of transcript reconstruction methods for RNA-seq

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

Nature Methods. 2013. Vol. 10, num. 12, p. 1177-1184. DOI : 10.1038/NMETH.2714.

Detailed record

Full text - View at publisher

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

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

Nucleic Acids Research. 2013. Vol. 41, num. D1, p. D157-64. DOI : 10.1093/nar/gks1233.

Detailed record

Full text - View at publisher

Critical assessment of automated flow cytometry data analysis techniques

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

Nature Methods. 2013. DOI : 10.1038/nmeth.2365.

Detailed record

View at publisher

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

S. Dimitrieva; P. Bucher 

Nucleic Acids Research. 2013. Vol. 41, p. D101-9. DOI : 10.1093/nar/gks1092.

Detailed record

Full text - View at publisher

Conference Papers

Differentiation trees for cell developmental history based on histone modifications

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

2013. 13th Workshop on Algorithms in Bioinformatics (WABI '13). p. 326-337.

Detailed record

Theses

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

S. Dimitrieva Janeva / B. Moret; P. Bucher (Dir.)  

Lausanne: EPFL, 2013. DOI : 10.5075/epfl-thesis-5942.

Detailed record

Full text - View at publisher

2012

Journal Articles

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 

Plos One. 2012. Vol. 7, num. 8, p. e39573. DOI : 10.1371/journal.pone.0039573.

Detailed record

Full text - View at publisher

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

S. Dimitrieva; P. Bucher 

Bioinformatics. 2012. Vol. 28, num. 18, p. I395-I401. DOI : 10.1093/bioinformatics/bts400.

Detailed record

Full text - View at publisher

Practicality and time complexity of a sparsified RNA folding algorithm

S. Dimitrieva; P. Bucher 

Journal of Bioinformatics and Computational Biology. 2012. Vol. 10, num. 2, p. 1241007. DOI : 10.1142/S0219720012410077.

Detailed record

Full text - View at publisher

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 

Molecular And Cellular Biology. 2012. Vol. 32, num. 6, p. 1189-1199. DOI : 10.1128/MCB.06318-11.

Detailed record

View at publisher

2011

Journal Articles

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 

BMC Bioinformatics. 2011. Vol. 12, p. 152. DOI : 10.1186/1471-2105-12-152.

Detailed record

Full text - View at publisher

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

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

Nucleic Acids Research. 2011. Vol. 39, num. 16, p. 6886-6895. DOI : 10.1093/nar/gkr335.

Detailed record

Full text - View at publisher

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. 

BMC genomics. 2011. Vol. 12, num. 1, p. 378. DOI : 10.1186/1471-2164-12-378.

Detailed record

Full text - View at publisher

2010

Journal Articles

Multichannel Sequence Analysis Applied To Social Science Data

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

Sociological Methodology. 2010. Vol. 40, p. 1-38. DOI : 10.1111/j.1467-9531.2010.01227.x.

Detailed record

Full text - View at publisher

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. 

Diabetes. 2010. Vol. 59, num. 7, p. 1674-85. DOI : 10.2337/db09-0986.

Detailed record

View at publisher

MER41 repeat sequences contain inducible STAT1 binding sites

C. D. Schmid; P. Bucher 

PloS One. 2010. Vol. 5, num. 7, p. e11425. DOI : 10.1371/journal.pone.0011425.

Detailed record

Full text - View at publisher

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. 

PLoS genetics. 2010. Vol. 6, num. 3, p. e1000869. DOI : 10.1371/journal.pgen.1000869.

Detailed record

Full text - View at publisher

Theses

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

H. Yasrebi / P. Bucher; F. Naef (Dir.)  

Lausanne: EPFL, 2010. DOI : 10.5075/epfl-thesis-4494.

Detailed record

Full text - View at publisher

2009

Journal Articles

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

V. Praz; P. Bucher 

Nucleic acids research. 2009. Vol. 37, num. Suppl 1, p. D880-4. DOI : 10.1093/nar/gkn878.

Detailed record

Full text - View at publisher

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. 

Nucleic acids research. 2009. Vol. 37, num. 8, p. 2514-28. DOI : 10.1093/nar/gkp116.

Detailed record

Full text - View at publisher

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

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

PloS One. 2009. Vol. 4, num. 10, p. e7431. DOI : 10.1371/journal.pone.0007431.

Detailed record

Full text - View at publisher

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 

Sociological Methods & Research. 2009. Vol. 38, num. 1, p. 197-231. DOI : 10.1177/0049124109342065.

Detailed record

View at publisher

Book Chapters

Methods for discovery and characterization of DNA sequence motifs

P. Bucher 

Bioinformatics a swiss perspective; Singapore: World Scientific, 2009. p. 3-32.

Detailed record

2008

Journal Articles

Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation

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

Plos Genetics. 2008. Vol. 4, num. 4, p. e1000058. DOI : 10.1371/journal.pgen.1000058.

Detailed record

Full text - View at publisher

2007

Journal Articles

ChIP-Seq data reveal nucleosome architecture of human promoters

C. D. Schmid; P. Bucher 

Cell. 2007. Vol. 131, num. 5, p. 831-2. DOI : 10.1016/j.cell.2007.11.017.

Detailed record

View at publisher

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

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

Nucleic Acids Res. 2007. Vol. 35, num. Suppl 2, p. W201-5. DOI : 10.1093/nar/gkm343.

Detailed record

Full text - View at publisher

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 

BMC Genomics. 2007. Vol. 8, num. 1, p. 398. DOI : 10.1186/1471-2164-8-398.

Detailed record

View at publisher

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. 

BMC Bioinformatics. 2007. Vol. 8 Suppl 1, p. S17. DOI : 10.1186/1471-2105-8-S1-S17.

Detailed record

View at publisher

Indexing strategies for rapid searches of short words in genome sequences

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

PLoS ONE. 2007. Vol. 2, num. 6, p. e579. DOI : 10.1371/journal.pone.0000579.

Detailed record

Full text - View at publisher

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. 

Nat Methods. 2007. Vol. 4, num. 9, p. 747-753. DOI : 10.1038/nmeth1076.

Detailed record

View at publisher

2006

Journal Articles

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

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

Nucleic Acids Res. 2006. Vol. 34, num. Suppl 1, p. D82-5. DOI : 10.1093/nar/gkj146.

Detailed record

Full text - View at publisher

Similarities and differences of polyadenylation signals in human and fly

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

BMC Genomics. 2006. Vol. 7, num. 1, p. 176. DOI : 10.1186/1471-2164-7-176.

Detailed record

View at publisher

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

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

Nucleic Acids Res. 2006. Vol. 34, num. Suppl 1, p. D90-4. DOI : 10.1093/nar/gkj049.

Detailed record

Full text - View at publisher

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. 

Bioinformatics. 2006. Vol. 22, num. 19, p. 2439-40. DOI : 10.1093/bioinformatics/btl404.

Detailed record

View at publisher

Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus

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

Genesis. 2006. Vol. 44, num. 1, p. 1-6. DOI : 10.1002/gene.20177.

Detailed record

View at publisher

2005

Journal Articles

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge

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

Bioinformatics (Oxford, England). 2005. Vol. 21, num. 12, p. 2906-8. DOI : 10.1093/bioinformatics/bti435.

Detailed record

Full text - View at publisher

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 

PLoS Comput Biol. 2005. Vol. 1, num. 6, p. e63. DOI : 10.1371/journal.pcbi.0010063.

Detailed record

View at publisher

InterPro, progress and status in 2005

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

Nucleic Acids Res. 2005. Vol. 33, num. Suppl 1, p. D201-5. DOI : 10.1093/nar/gki106.

Detailed record

Full text - View at publisher

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. 

Journal of Biological Chemistry. 2005. Vol. 280, num. 25, p. 24143-52. DOI : 10.1074/jbc.M502649200.

Detailed record

View at publisher

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

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

Nucleic Acids Res. 2005. Vol. 33, num. 8, p. e79. DOI : 10.1093/nar/gni079.

Detailed record

Full text - View at publisher

2004

Journal Articles

trome, trEST and trGEN: databases of predicted protein sequences

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

Nucleic Acids Res. 2004. Vol. 32, num. Suppl 1, p. D509-11. DOI : 10.1093/nar/gkh067.

Detailed record

Full text - View at publisher

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

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

Nucleic Acids Res. 2004. Vol. 32, num. Suppl 1, p. D82-5. DOI : 10.1093/nar/gkh122.

Detailed record

Full text - View at publisher

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

V. Praz; V. Jagannathan; P. Bucher 

Nucleic Acids Res. 2004. Vol. 32, num. Suppl 1, p. D542-7. DOI : 10.1093/nar/gkh107.

Detailed record

Full text - View at publisher

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. 

Journal of Immunology. 2004. Vol. 173, num. 10, p. 6200-10.

Detailed record

Recent improvements to the PROSITE database

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

Nucleic Acids Res. 2004. Vol. 32, num. Suppl 1, p. D134-7. DOI : 10.1093/nar/gkh044.

Detailed record

Full text - View at publisher

2003

Journal Articles

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. 

Bioinformatics. 2003. Vol. 19 Suppl 1, p. i215-21. DOI : 10.1093/bioinformatics/btg1029.

Detailed record

View at publisher

The InterPro Database, 2003 brings increased coverage and new features

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

Nucleic Acids Res. 2003. Vol. 31, num. 1, p. 315-8. DOI : 10.1093/nar/gkg046.

Detailed record

Full text - View at publisher

Modeling sequencing errors by combining Hidden Markov models

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

Bioinformatics. 2003. Vol. 19 Suppl 2, p. ii103-12.

Detailed record

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. 

Cancer Res. 2003. Vol. 63, num. 20, p. 6613-25.

Detailed record

Telomere maintenance in fission yeast requires an Est1 ortholog

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

Curr Biol. 2003. Vol. 13, num. 7, p. 575-80. DOI : 10.1016/S0960-9822(03)00169-6.

Detailed record

View at publisher

Signal search analysis server

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

Nucleic Acids Res. 2003. Vol. 31, num. 13, p. 3618-20. DOI : 10.1093/nar/gkg611.

Detailed record

Full text - View at publisher

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. 

Curr Biol. 2003. Vol. 13, num. 7, p. 568-74. DOI : 10.1016/S0960-9822(03)00173-8.

Detailed record

View at publisher

2002

Journal Articles

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

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

Brief Bioinform. 2002. Vol. 3, num. 3, p. 265-74. DOI : 10.1093/bib/3.3.265.

Detailed record

View at publisher

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. 

Nat Biotechnol. 2002. Vol. 20, num. 8, p. 831-5.

Detailed record

Nineteen additional unpredicted transcripts from human chromosome 21

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

Genomics. 2002. Vol. 79, num. 6, p. 824-32. DOI : 10.1006/geno.2002.6781.

Detailed record

View at publisher

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

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

Nucleic Acids Res. 2002. Vol. 30, num. 1, p. 322-4. DOI : 10.1093/nar/30.1.322.

Detailed record

Full text - View at publisher

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. 

Brief Bioinform. 2002. Vol. 3, num. 3, p. 225-35. DOI : 10.1093/bib/3.3.225.

Detailed record

View at publisher

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. 

Genome Res. 2002. Vol. 12, num. 7, p. 1068-74.

Detailed record

The PROSITE database, its status in 2002

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

Nucleic Acids Res. 2002. Vol. 30, num. 1, p. 235-8. DOI : 10.1093/nar/30.1.235.

Detailed record

Full text - View at publisher

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. 

Nature. 2002. Vol. 420, num. 6915, p. 578-82. DOI : 10.1038/nature01251.

Detailed record

View at publisher

2001

Journal Articles

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

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

Nucleic Acids Res. 2001. Vol. 29, num. 1, p. 148-51. DOI : 10.1093/nar/29.1.148.

Detailed record

Full text - View at publisher

Individuality of Ag-selected and preimmune TCR repertoires

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

Immunol Res. 2001. Vol. 23, num. 1, p. 75-84. DOI : 10.1385/IR:23:1:75.

Detailed record

View at publisher

mmsearch: a motif arrangement language and search program

T. Junier; M. Pagni; P. Bucher 

Bioinformatics. 2001. Vol. 17, num. 12, p. 1234-5. DOI : 10.1093/bioinformatics/17.12.1234.

Detailed record

View at publisher

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. 

Journal of Biological Chemistry. 2001. Vol. 276, num. 9, p. 6675-88. DOI : 10.1074/jbc.M001748200.

Detailed record

View at publisher

A cSNP map and database for human chromosome 21

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

Genome Res. 2001. Vol. 11, num. 2, p. 300-7.

Detailed record

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. 

Nucleic Acids Res. 2001. Vol. 29, num. 1, p. 37-40. DOI : 10.1093/nar/29.1.37.

Detailed record

Full text - View at publisher

2000

Journal Articles

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. 

Journal of Molecular Biology. 2000. Vol. 297, num. 4, p. 833-48. DOI : 10.1006/jmbi.2000.3614.

Detailed record

View at publisher

The eukaryotic promoter database (EPD)

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

Nucleic Acids Res. 2000. Vol. 28, num. 1, p. 302-3. DOI : 10.1093/nar/28.1.302.

Detailed record

Full text - View at publisher

Shotgun sequencing of the human transcriptome with ORF expressed sequence tags

E. Dias Neto; R. G. Correa; S. Verjovski-Almeida; M. R. Briones; M. A. Nagai et al. 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2000. Vol. 97, num. 7, p. 3491-6. DOI : 10.1073/pnas.97.7.3491.

Detailed record

View at publisher

Comparative T cell receptor repertoire selection by antigen after adoptive transfer: a glimpse at an antigen-specific preimmune repertoire

V. Attuil; P. Bucher; M. Rossi; M. Mutin; J. L. Maryanski 

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2000. Vol. 97, num. 15, p. 8473-8. DOI : 10.1073/pnas.97.15.8473.

Detailed record

View at publisher

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

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

Bioinformatics. 2000. Vol. 16, num. 12, p. 1145-50. DOI : 10.1093/bioinformatics/16.12.1145.

Detailed record

View at publisher

1999

Journal Articles

ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences

C. Iseli; C. V. Jongeneel; P. Bucher 

Proc Int Conf Intell Syst Mol Biol. 1999.  p. 138-148.

Detailed record

The Eukaryotic Promoter Database (EPD): recent developments

R. C. Perier; T. Junier; C. Bonnard; P. Bucher 

Nucleic Acids Res. 1999. Vol. 27, num. 1, p. 307-9. DOI : 10.1093/nar/27.1.307.

Detailed record

Full text - View at publisher

A quantitative, single-cell PCR analysis of an antigen-specific TCR repertoire selected during an in vivo CD8 response: direct evidence for a wide range of clone sizes with uniform tissue distribution

J. L. Maryanski; V. Attuil; P. Bucher; P. R. Walker 

Mol Immunol. 1999. Vol. 36, num. 11-12, p. 745-53. DOI : 10.1016/S0161-5890(99)00088-7.

Detailed record

View at publisher

The PROSITE database, its status in 1999

K. Hofmann; P. Bucher; L. Falquet; A. Bairoch 

Nucleic Acids Res. 1999. Vol. 27, num. 1, p. 215-9. DOI : 10.1093/nar/27.1.215.

Detailed record

Full text - View at publisher

Reviews

Regulatory elements and expression profiles

P. Bucher 

Current opinion in structural biology. 1999. Vol. 9, num. 3, p. 400-7. DOI : 10.1016/S0959-440X(99)80054-2.

Detailed record

View at publisher

Book Chapters

Gene feature identification

P. Bucher 

Genetics databases; San Diego: Academic Press, 1999. p. 135-164.

Detailed record

1998

Journal Articles

Molecular models for the two discoidin domains of human blood coagulation factor V

B. O. Villoutreix; P. Bucher; K. Hofmann; S. Baumgartner; B. Dahlback 

J Mol Model. 1998. Vol. 4, num. 8, p. 268-275. DOI : 10.1007/s008940050084.

Detailed record

View at publisher

Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA

E. Roulet; I. Fisch; T. Junier; P. Bucher; N. Mermod 

In Silico Biol. 1998. Vol. 1, num. 1, p. 21-8.

Detailed record