Publications

2018

Journal Articles

[146]
A. Coudray; A. M. Battenhouse; P. Bucher; V. R. Iyer : Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data; PeerJ. 2018-07-31. DOI : 10.7717/peerj.5362.
[145]
G. Ambrosini; R. Groux; P. Bucher : PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix; Bioinformatics. 2018-03-05. DOI : 10.1093/bioinformatics/bty127.
[144]
R. Dréos; G. Ambrosini; R. Groux; R. C. Périer; P. Bucher : MGA repository: a curated data resource for ChIP-seq and other genome annotated data; Nucleic Acids Research. 2018. DOI : 10.1093/nar/gkx995.

2017

Journal Articles

[143]
A. Isakova; R. Groux; M. Imbeault; P. Rainer; D. Alpern et al. : SMiLE-seq identifies binding motifs of single and dimeric transcription factors; Nature methods. 2017. DOI : 10.1038/nmeth.4143.
[142]
R. Dreos; G. Ambrosini; R. Groux; R. Cavin Périer; P. Bucher : The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms; Nucleic Acids Research. 2017. DOI : 10.1093/nar/gkw1069.

2016

Journal Articles

[141]
S. Kumar; G. Ambrosini; P. Bucher : SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity; Nucleic acids research. 2016. DOI : 10.1093/nar/gkw1064.
[140]
G. Ambrosini; R. Dreos; S. Kumar; P. Bucher : The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data; BMC genomics. 2016. DOI : 10.1186/s12864-016-3288-8.
[139]
R. Dreos; G. Ambrosini; P. Bucher : Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters; PLoS Comput Biol. 2016. DOI : 10.1371/journal.pcbi.1005144.
[138]
N. U. Nair; L. Hunter; M. Shao; P. Grnarova; Y. Lin et al. : A maximum-likelihood approach for building cell-type trees by lifting; BMC Genomics. 2016. DOI : 10.1186/s12864-015-2297-3.
[137]
S. Kumar; P. Bucher : Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features; Bmc Bioinformatics. 2016. DOI : 10.1186/s12859-015-0846-z.

2015

Journal Articles

[136]
R. Dreos; G. Ambrosini; R. C. Perier; P. Bucher : The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools; Nucleic Acids Research. 2015. DOI : 10.1093/nar/gku1111.

2014

Journal Articles

[135]
G. Ambrosini; R. Dreos; P. Bucher : Principles of ChIP-seq Data Analysis Illustrated with Examples; Proceedings Iwbbio 2014: International Work-Conference On Bioinformatics And Biomedical Engineering, Vols 1 And 2. 2014.
[134]
N. U. Nair; S. Kumar; B. M. E. Moret; P. Bucher : Probabilistic partitioning methods to find significant patterns in ChIP-Seq data; Bioinformatics. 2014. DOI : 10.1093/bioinformatics/btu318.
[133]
D. Polychronopoulos; E. Weitschek; S. Dimitrieva; P. Bucher; G. Felici et al. : Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers; Genomics. 2014. DOI : 10.1016/j.ygeno.2014.07.004.
[132]
N. U. Nair; Y. Lin; A. Manasovska; J. Antic; P. Grnarova et al. : Study of cell differentiation by phylogenetic analysis using histone modification data; Bmc Bioinformatics. 2014. DOI : 10.1186/1471-2105-15-269.
[131]
S. Dimitrieva; M. Anisimova : Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families; Plos One. 2014. DOI : 10.1371/journal.pone.0095034.
[130]
H. Stockinger; A. M. Altenhoff; K. Arnold; A. Bairoch; F. Bastian et al. : Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support; Nucleic Acids Research. 2014. DOI : 10.1093/nar/gku380.

Theses

[129]
N. U. Nair / B. Moret; P. Bucher (Dir.) : Computational studies in epigenomics using histone modification data. Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6327.

2013

Journal Articles

[128]
P. Meyer; G. Siwo; D. Zeevi; E. Sharon; R. Norel et al. : Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach; Genome research. 2013. DOI : 10.1101/gr.157420.113.
[127]
M. Pjanic; C. D. Schmid; A. Gaussin; G. Ambrosini; J. Adamcik et al. : Nuclear Factor I genomic binding associates with chromatin boundaries; BMC Genomics. 2013. DOI : 10.1186/1471-2164-14-99.
[126]
M. T. Weirauch; A. Cote; R. Norel; M. Annala; Y. Zhao et al. : Evaluation of methods for modeling transcription factor sequence specificity; Nature Biotechnology. 2013. DOI : 10.1038/nbt.2486.
[125]
T. Steijger; J. F. Abril; P. G. Engstrom; F. Kokocinski; T. J. Hubbard et al. : Assessment of transcript reconstruction methods for RNA-seq; Nature Methods. 2013. DOI : 10.1038/NMETH.2714.
[124]
R. Dreos; G. Ambrosini; R. Cavin Perier; P. Bucher : EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era; Nucleic Acids Research. 2013. DOI : 10.1093/nar/gks1233.
[123]
N. Aghaeepour; G. Finak; D. Dougall; K. AH; P. Mah et al. : Critical assessment of automated flow cytometry data analysis techniques; Nature Methods. 2013. DOI : 10.1038/nmeth.2365.
[122]
S. Dimitrieva; P. Bucher : UCNEbase – a database of ultra-conserved non-coding elements and genomic regulatory blocks; Nucleic Acids Research. 2013. DOI : 10.1093/nar/gks1092.

Conference Papers

[121]
N. U. Nair; Y. Lin; P. Bucher; B. M. E. Moret : Differentiation trees for cell developmental history based on histone modifications. 2013. 13th Workshop on Algorithms in Bioinformatics (WABI '13). p. 326-337.

Theses

[120]
S. Dimitrieva Janeva / B. Moret; P. Bucher (Dir.) : Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes. Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5942.

2012

Journal Articles

[119]
N. Nair; A. Das Sahu; P. Bucher; B. Moret : ChIPnorm: a statistical method for normalizing and identifying differential regions in histone modification ChIP-seq libraries; Plos One. 2012. DOI : 10.1371/journal.pone.0039573.
[118]
S. Dimitrieva; P. Bucher : Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements; Bioinformatics. 2012. DOI : 10.1093/bioinformatics/bts400.
[117]
S. Dimitrieva; P. Bucher : Practicality and time complexity of a sparsified RNA folding algorithm; Journal of Bioinformatics and Computational Biology. 2012. DOI : 10.1142/S0219720012410077.
[116]
N. Thompson; E. Gesina; P. Scheinert; P. Bucher; A. Grapin-Botton : 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; Molecular And Cellular Biology. 2012. DOI : 10.1128/MCB.06318-11.

2011

Journal Articles

[115]
T. J. Cradick; G. Ambrosini; C. Iseli; P. Bucher; A. P. McCaffrey : ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites; BMC Bioinformatics. 2011. DOI : 10.1186/1471-2105-12-152.
[114]
G. Bussotti; E. Raineri; I. Erb; M. Zytnicki; A. Wilm et al. : BlastR-fast and accurate database searches for non-coding RNAs; Nucleic Acids Research. 2011. DOI : 10.1093/nar/gkr335.
[113]
S. Meylan; A. C. Groner; G. Ambrosini; N. Malani; S. Quenneville et al. : A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing; BMC genomics. 2011. DOI : 10.1186/1471-2164-12-378.

2010

Journal Articles

[112]
J.-A. Gauthier; E. D. Widmer; P. Bucher; C. Notredame : Multichannel Sequence Analysis Applied To Social Science Data; Sociological Methodology, Vol 40. 2010. DOI : 10.1111/j.1467-9531.2010.01227.x.
[111]
A. Ait-Lounis; C. Bonal; Q. Seguín-Estévez; C. D. Schmid; P. Bucher et al. : The transcription factor Rfx3 regulates beta-cell differentiation, function, and glucokinase expression; Diabetes. 2010. DOI : 10.2337/db09-0986.
[110]
C. D. Schmid; P. Bucher : MER41 repeat sequences contain inducible STAT1 binding sites; PloS one. 2010. DOI : 10.1371/journal.pone.0011425.
[109]
A. C. Groner; S. Meylan; A. Ciuffi; N. Zangger; G. Ambrosini et al. : KRAB-Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading; PLoS genetics. 2010. DOI : 10.1371/journal.pgen.1000869.

Theses

[108]
H. Yasrebi / P. Bucher; F. Naef (Dir.) : Prediction of Survival and Risk Assessment Using Joint Analysis of Microarray Gene Expression Data. Lausanne, EPFL, 2010. DOI : 10.5075/epfl-thesis-4494.

2009

Journal Articles

[107]
V. Praz; P. Bucher : CleanEx: new data extraction and merging tools based on MeSH term annotation; Nucleic acids research. 2009. DOI : 10.1093/nar/gkn878.
[106]
E. Leimgruber; Q. Seguín-Estévez; I. Dunand-Sauthier; N. Rybtsova; C. D. Schmid et al. : Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site; Nucleic acids research. 2009. DOI : 10.1093/nar/gkp116.
[105]
H. Yasrebi; P. Sperisen; V. Praz; P. Bucher : Can survival prediction be improved by merging gene expression data sets?; PloS one. 2009. DOI : 10.1371/journal.pone.0007431.
[104]
J.-A. Gauthier; E. D. Widmer; P. Bucher; C. Notredame : How much does it cost? Optimization of costs in sequence analysis of social science data; Sociological Methods & Research. 2009. DOI : 10.1177/0049124109342065.

Book Chapters

[103]
P. Bucher : Methods for discovery and characterization of DNA sequence motifs; Bioinformatics a swiss perspective; Singapore: World Scientific, 2009. p. 3-32.

2008

Journal Articles

[102]
M. Krawczyk; Q. Seguín-Estévez; E. Leimgruber; P. Sperisen; C. Schmid et al. : Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation; Plos Genetics. 2008. DOI : 10.1371/journal.pgen.1000058.

2007

Journal Articles

[101]
C. D. Schmid; P. Bucher : ChIP-Seq data reveal nucleosome architecture of human promoters; Cell. 2007. DOI : 10.1016/j.cell.2007.11.017.
[100]
C. D. Schmid; T. Sengstag; P. Bucher; M. Delorenzi : MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data; Nucleic Acids Res. 2007. DOI : 10.1093/nar/gkm343.
[99]
D. Retelska; E. Beaudoing; C. Notredame; C. V. Jongeneel; P. Bucher : Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time; BMC Genomics. 2007. DOI : 10.1186/1471-2164-8-398.
[98]
D. Rambaldi; B. Felice; V. Praz; P. Bucher; D. Cittaro et al. : Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data; BMC Bioinformatics. 2007. DOI : 10.1186/1471-2105-8-S1-S17.
[97]
C. Iseli; G. Ambrosini; P. Bucher; C. V. Jongeneel : Indexing strategies for rapid searches of short words in genome sequences; PLoS ONE. 2007. DOI : 10.1371/journal.pone.0000579.
[96]
P. A. Girod; D. Q. Nguyen; D. Calabrese; S. Puttini; M. Grandjean et al. : Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells; Nat Methods. 2007. DOI : 10.1038/nmeth1076.

2006

Journal Articles

[95]
C. D. Schmid; R. Perier; V. Praz; P. Bucher : EPD in its twentieth year: towards complete promoter coverage of selected model organisms; Nucleic Acids Res. 2006. DOI : 10.1093/nar/gkj146.
[94]
D. Retelska; C. Iseli; P. Bucher; C. V. Jongeneel; F. Naef : Similarities and differences of polyadenylation signals in human and fly; BMC Genomics. 2006. DOI : 10.1186/1471-2164-7-176.
[93]
V. Jagannathan; E. Roulet; M. Delorenzi; P. Bucher : HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sites; Nucleic Acids Res. 2006. DOI : 10.1093/nar/gkj049.
[92]
F. Armougom; O. Poirot; S. Moretti; D. G. Higgins; P. Bucher et al. : APDB: a web server to evaluate the accuracy of sequence alignments using structural information; Bioinformatics. 2006. DOI : 10.1093/bioinformatics/btl404.
[91]
F. Beermann; K. Kaloulis; D. Hofmann; F. Murisier; P. Bucher et al. : Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus; Genesis. 2006. DOI : 10.1002/gene.20177.

2005

Journal Articles

[90]
F. Armand; P. Bucher; C. V. Jongeneel; E. E. Farmer : Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge; Bioinformatics (Oxford, England). 2005. DOI : 10.1093/bioinformatics/bti435.
[89]
P. Sperisen; C. D. Schmid; P. Bucher; O. Zilian : Stealth proteins: in silico identification of a novel protein family rendering bacterial pathogens invisible to host immune defense; PLoS Comput Biol. 2005. DOI : 10.1371/journal.pcbi.0010063.
[88]
N. J. Mulder; R. Apweiler; T. K. Attwood; A. Bairoch; A. Bateman et al. : InterPro, progress and status in 2005; Nucleic Acids Res. 2005. DOI : 10.1093/nar/gki106.
[87]
R. Genolet; S. Kersten; O. Braissant; S. Mandard; N. S. Tan et al. : Promoter rearrangements cause species-specific hepatic regulation of the glyoxylate reductase/hydroxypyruvate reductase gene by the peroxisome proliferator-activated receptor alpha; J Biol Chem. 2005. DOI : 10.1074/jbc.M502649200.
[86]
T. Egener; E. Roulet; M. Zehnder; P. Bucher; N. Mermod : Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts; Nucleic Acids Res. 2005. DOI : 10.1093/nar/gni079.

2004

Journal Articles

[85]
P. Sperisen; C. Iseli; M. Pagni; B. J. Stevenson; P. Bucher et al. : trome, trEST and trGEN: databases of predicted protein sequences; Nucleic Acids Res. 2004. DOI : 10.1093/nar/gkh067.
[84]
C. D. Schmid; V. Praz; M. Delorenzi; R. Perier; P. Bucher : The Eukaryotic Promoter Database EPD: the impact of in silico primer extension; Nucleic Acids Res. 2004. DOI : 10.1093/nar/gkh122.
[83]
V. Praz; V. Jagannathan; P. Bucher : CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature; Nucleic Acids Res. 2004. DOI : 10.1093/nar/gkh107.
[82]
M. Krawczyk; N. Peyraud; N. Rybtsova; K. Masternak; P. Bucher et al. : Long distance control of MHC class II expression by multiple distal enhancers regulated by regulatory factor X complex and CIITA; J Immunol. 2004.
[81]
N. Hulo; C. J. Sigrist; V. Le Saux; P. S. Langendijk-Genevaux; L. Bordoli et al. : Recent improvements to the PROSITE database; Nucleic Acids Res. 2004. DOI : 10.1093/nar/gkh044.

2003

Journal Articles

[80]
O. O'Sullivan; M. Zehnder; D. Higgins; P. Bucher; A. Grosdidier et al. : APDB: a novel measure for benchmarking sequence alignment methods without reference alignments; Bioinformatics. 2003. DOI : 10.1093/bioinformatics/btg1029.
[79]
N. J. Mulder; R. Apweiler; T. K. Attwood; A. Bairoch; D. Barrell et al. : The InterPro Database, 2003 brings increased coverage and new features; Nucleic Acids Res. 2003. DOI : 10.1093/nar/gkg046.
[78]
C. Lottaz; C. Iseli; C. V. Jongeneel; P. Bucher : Modeling sequencing errors by combining Hidden Markov models; Bioinformatics. 2003.
[77]
S. Godard; G. Getz; M. Delorenzi; P. Farmer; H. Kobayashi et al. : 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; Cancer Res. 2003.
[76]
H. T. Beernink; K. Miller; A. Deshpande; P. Bucher; J. P. Cooper : Telomere maintenance in fission yeast requires an Est1 ortholog; Curr Biol. 2003. DOI : 10.1016/S0960-9822(03)00169-6.
[75]
G. Ambrosini; V. Praz; V. Jagannathan; P. Bucher : Signal search analysis server; Nucleic Acids Res. 2003. DOI : 10.1093/nar/gkg611.
[74]
P. Reichenbach; M. Hoss; C. M. Azzalin; M. Nabholz; P. Bucher et al. : A human homolog of yeast est1 associates with telomerase and uncaps chromosome ends when overexpressed; Curr Biol. 2003. DOI : 10.1016/S0960-9822(03)00173-8.

2002

Journal Articles

[73]
C. J. Sigrist; L. Cerutti; N. Hulo; A. Gattiker; L. Falquet et al. : PROSITE: a documented database using patterns and profiles as motif descriptors; Brief Bioinform. 2002. DOI : 10.1093/bib/3.3.265.
[72]
E. Roulet; S. Busso; A. A. Camargo; A. J. Simpson; N. Mermod et al. : High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites; Nat Biotechnol. 2002.
[71]
A. Reymond; A. A. Camargo; S. Deutsch; B. J. Stevenson; R. B. Parmigiani et al. : Nineteen additional unpredicted transcripts from human chromosome 21; Genomics. 2002. DOI : 10.1006/geno.2002.6781.
[70]
V. Praz; R. Perier; C. Bonnard; P. Bucher : The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data; Nucleic Acids Res. 2002. DOI : 10.1093/nar/30.1.322.
[69]
N. J. Mulder; R. Apweiler; T. K. Attwood; A. Bairoch; A. Bateman et al. : InterPro: an integrated documentation resource for protein families, domains and functional sites; Brief Bioinform. 2002. DOI : 10.1093/bib/3.3.225.
[68]
C. Iseli; B. J. Stevenson; S. J. de Souza; H. B. Samaia; A. A. Camargo et al. : Long-range heterogeneity at the 3' ends of human mRNAs; Genome Res. 2002.
[67]
L. Falquet; M. Pagni; P. Bucher; N. Hulo; C. J. Sigrist et al. : The PROSITE database, its status in 2002; Nucleic Acids Res. 2002. DOI : 10.1093/nar/30.1.235.
[66]
E. T. Dermitzakis; A. Reymond; R. Lyle; N. Scamuffa; C. Ucla et al. : Numerous potentially functional but non-genic conserved sequences on human chromosome 21; Nature. 2002. DOI : 10.1038/nature01251.

2001

Journal Articles

[65]
M. Pagni; C. Iseli; T. Junier; L. Falquet; V. Jongeneel et al. : trEST, trGEN and Hits: access to databases of predicted protein sequences; Nucleic Acids Res. 2001. DOI : 10.1093/nar/29.1.148.
[64]
J. L. Maryanski; V. Attuil; A. Hamrouni; M. Mutin; M. Rossi et al. : Individuality of Ag-selected and preimmune TCR repertoires; Immunol Res. 2001. DOI : 10.1385/IR:23:1:75.
[63]
T. Junier; M. Pagni; P. Bucher : mmsearch: a motif arrangement language and search program; Bioinformatics. 2001. DOI : 10.1093/bioinformatics/17.12.1234.
[62]
G. B. Ehret; P. Reichenbach; U. Schindler; C. M. Horvath; S. Fritz et al. : DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites; J Biol Chem. 2001. DOI : 10.1074/jbc.M001748200.
[61]
S. Deutsch; C. Iseli; P. Bucher; S. E. Antonarakis; H. S. Scott : A cSNP map and database for human chromosome 21; Genome Res. 2001.
[60]
R. Apweiler; T. K. Attwood; A. Bairoch; A. Bateman; E. Birney et al. : The InterPro database, an integrated documentation resource for protein families, domains and functional sites; Nucleic Acids Res. 2001. DOI : 10.1093/nar/29.1.37.

2000

Journal Articles

[59]
E. Roulet; P. Bucher; R. Schneider; E. Wingender; Y. Dusserre et al. : Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites; J Mol Biol. 2000. DOI : 10.1006/jmbi.2000.3614.
[58]
R. C. Perier; V. Praz; T. Junier; C. Bonnard; P. Bucher : The eukaryotic promoter database (EPD); Nucleic Acids Res. 2000. DOI : 10.1093/nar/28.1.302.
[57]
E. Dias Neto; R. G. Correa; S. Verjovski-Almeida; M. R. Briones; M. A. Nagai et al. : Shotgun sequencing of the human transcriptome with ORF expressed sequence tags; Proc Natl Acad Sci U S A. 2000. DOI : 10.1073/pnas.97.7.3491.
[56]
V. Attuil; P. Bucher; M. Rossi; M. Mutin; J. L. Maryanski : Comparative T cell receptor repertoire selection by antigen after adoptive transfer: a glimpse at an antigen-specific preimmune repertoire; Proc Natl Acad Sci U S A. 2000. DOI : 10.1073/pnas.97.15.8473.
[55]
R. Apweiler; T. K. Attwood; A. Bairoch; A. Bateman; E. Birney et al. : InterPro--an integrated documentation resource for protein families, domains and functional sites; Bioinformatics. 2000. DOI : 10.1093/bioinformatics/16.12.1145.

1999

Journal Articles

[54]
C. Iseli; C. V. Jongeneel; P. Bucher : ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences; Proc Int Conf Intell Syst Mol Biol. 1999.
[53]
R. C. Perier; T. Junier; C. Bonnard; P. Bucher : The Eukaryotic Promoter Database (EPD): recent developments; Nucleic Acids Res. 1999. DOI : 10.1093/nar/27.1.307.
[52]
J. L. Maryanski; V. Attuil; P. Bucher; P. R. Walker : 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; Mol Immunol. 1999. DOI : 10.1016/S0161-5890(99)00088-7.
[51]
K. Hofmann; P. Bucher; L. Falquet; A. Bairoch : The PROSITE database, its status in 1999; Nucleic Acids Res. 1999. DOI : 10.1093/nar/27.1.215.

Reviews

[50]
P. Bucher : Regulatory elements and expression profiles; Current opinion in structural biology. 1999. DOI : 10.1016/S0959-440X(99)80054-2.

Book Chapters

[49]
P. Bucher : Gene feature identification; Genetics databases; San Diego: Academic Press, 1999. p. 135-164.

1998

Journal Articles

[48]
B. O. Villoutreix; P. Bucher; K. Hofmann; S. Baumgartner; B. Dahlback : Molecular models for the two discoidin domains of human blood coagulation factor V; J Mol Model. 1998. DOI : 10.1007/s008940050084.
[47]
E. Roulet; I. Fisch; T. Junier; P. Bucher; N. Mermod : Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA; In Silico Biol. 1998.
[46]
M. Rehn; T. Pihlajaniemi; K. Hofmann; P. Bucher : The frizzled motif: in how many different protein families does it occur?; Trends Biochem Sci. 1998. DOI : 10.1016/S0968-0004(98)01290-0.
[45]
T. Junier; P. Bucher : SEView: a Java applet for browsing molecular sequence data; In Silico Biol. 1998.
[44]
K. Hofmann; P. Bucher; A. V. Kajava : A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain; J Mol Biol. 1998. DOI : 10.1006/jmbi.1998.1998.
[43]
K. Hofmann; P. Bucher : The PCI domain: a common theme in three multiprotein complexes; Trends Biochem Sci. 1998. DOI : 10.1016/S0968-0004(98)01217-1.
[42]
R. Cavin Perier; T. Junier; P. Bucher : The Eukaryotic Promoter Database EPD; Nucleic Acids Res. 1998. DOI : 10.1093/nar/26.1.353.
[41]
S. Baumgartner; K. Hofmann; R. Chiquet-Ehrismann; P. Bucher : The discoidin domain family revisited: new members from prokaryotes and a homology-based fold prediction; Protein Sci. 1998.

1997

Journal Articles

[40]
P. Lécine; M. Algarté; P. Rameil; C. Beadling; P. Bucher et al. : Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene; Molecular and cellular biology. 1997.
[39]
T. Weimbs; S. H. Low; S. J. Chapin; K. E. Mostov; P. Bucher et al. : A conserved domain is present in different families of vesicular fusion proteins: a new superfamily; Proc Natl Acad Sci U S A. 1997. DOI : 10.1073/pnas.94.7.3046.
[38]
K. Hofmann; P. Bucher; J. Tschopp : The CARD domain: a new apoptotic signalling motif; Trends Biochem Sci. 1997. DOI : 10.1016/S0968-0004(97)01043-8.
[37]
P. Bork; K. Hofmann; P. Bucher; A. F. Neuwald; S. F. Altschul et al. : A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins; Faseb J. 1997.
[36]
A. Bairoch; P. Bucher; K. Hofmann : The PROSITE database, its status in 1997; Nucleic Acids Res. 1997. DOI : 10.1093/nar/25.1.217.

Reviews

[35]
L. Duret; P. Bucher : Searching for regulatory elements in human noncoding sequences; Current opinion in structural biology. 1997.

1996

Journal Articles

[34]
P. R. Walker; A. Wilson; P. Bucher; J. L. Maryanski : Memory TCR repertoires analyzed long-term reflect those selected during the primary response; Int Immunol. 1996. DOI : 10.1093/intimm/8.7.1131.
[33]
J. L. Maryanski; C. V. Jongeneel; P. Bucher; J. L. Casanova; P. R. Walker : Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones; Immunity. 1996. DOI : 10.1016/S1074-7613(00)80297-6.
[32]
P. Lecine; M. Algarte; P. Rameil; C. Beadling; P. Bucher et al. : Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene; Mol Cell Biol. 1996.
[31]
K. Hofmann; P. Bucher : The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway; Trends Biochem Sci. 1996.
[30]
P. Emery; M. Strubin; K. Hofmann; P. Bucher; B. Mach et al. : A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity; Mol Cell Biol. 1996.
[29]
P. Bucher; J. W. Fickett; A. Hatzigeorgiou : Computational analysis of transcriptional regulatory elements: a field in flux; Comput Appl Biosci. 1996.
[28]
A. Bairoch; P. Bucher; K. Hofmann : The PROSITE database, its status in 1995; Nucleic Acids Res. 1996. DOI : 10.1093/nar/24.1.189.
[27]
P. Bucher; K. Karplus; N. Moeri; K. Hofmann : A flexible motif search technique based on generalized profiles; Computers Chem.. 1996. DOI : 10.1016/S0097-8485(96)80003-9.

Reviews

[26]
P. Bucher; K. Hofmann : A sequence similarity search algorithm based on a probabilistic interpretation of an alignment scoring system; Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology. 1996.

1995

Journal Articles

[25]
P. Sperisen; S. M. Wang; E. Soldaini; M. Pla; C. Rusterholz et al. : Mouse interleukin-2 receptor alpha gene expression. Interleukin-1 and interleukin-2 control transcription via distinct cis-acting elements; J Biol Chem. 1995. DOI : 10.1074/jbc.270.18.10743.
[24]
M. Nabholz; E. Soldaini; P. Sperisen; M. Pla; S. M. Wang et al. : The cis-acting elements controlling mouse IL-2R alpha transcription; Immunobiology. 1995.
[23]
K. Hofmann; P. Bucher : The rsp5-domain is shared by proteins of diverse functions; FEBS Lett. 1995. DOI : 10.1016/0014-5793(94)01415-W.
[22]
K. Hofmann; P. Bucher : The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors; Trends Biochem Sci. 1995. DOI : 10.1016/S0968-0004(00)89072-6.

1994

Journal Articles

[21]
P. Bucher; A. Bairoch : A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation; Proc Int Conf Intell Syst Mol Biol. 1994.
[20]
R. Luthy; I. Xenarios; P. Bucher : Improving the sensitivity of the sequence profile method; Protein Sci. 1994.
[19]
A. Bairoch; P. Bucher : PROSITE: recent developments; Nucleic Acids Res. 1994. DOI : 10.1093/nar/22.17.3626.

1992

Journal Articles

[18]
A. L. Lattion; E. Espel; P. Reichenbach; C. Fromental; P. Bucher et al. : Characterization of a new tissue-specific transcription factor binding to the simian virus 40 enhancer TC-II (NF-kappa B) element; Mol Cell Biol. 1992.
[17]
S. Karlin; P. Bucher : Correlation analysis of amino acid usage in protein classes; Proc Natl Acad Sci U S A. 1992. DOI : 10.1073/pnas.89.24.12165.
[16]
S. Karlin; V. Brendel; P. Bucher : Significant similarity and dissimilarity in homologous proteins; Mol Biol Evol. 1992.
[15]
S. Karlin; B. E. Blaisdell; P. Bucher : Quantile distributions of amino acid usage in protein classes; Protein Eng. 1992. DOI : 10.1093/protein/5.8.729.
[14]
V. Brendel; P. Bucher; I. R. Nourbakhsh; B. E. Blaisdell; S. Karlin : Methods and algorithms for statistical analysis of protein sequences; Proc Natl Acad Sci U S A. 1992. DOI : 10.1073/pnas.89.6.2002.

1991

Journal Articles

[13]
G. A. Schachtel; P. Bucher; E. S. Mocarski; B. E. Blaisdell; S. Karlin : Evidence for selective evolution in codon usage in conserved amino acid segments of human alphaherpesvirus proteins; J Mol Evol. 1991. DOI : 10.1007/BF02102801.
[12]
S. Karlin; P. Bucher; V. Brendel; S. F. Altschul : Statistical methods and insights for protein and DNA sequences; Annu Rev Biophys Biophys Chem. 1991.
[11]
P. Bucher; G. Yagil : Occurrence of oligopurine.oligopyrimidine tracts in eukaryotic and prokaryotic genes; DNA Seq. 1991. DOI : 10.3109/10425179109020767.

1990

Journal Articles

[10]
P. Bucher : Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences; J Mol Biol. 1990. DOI : 10.1016/0022-2836(90)90223-9.

1989

Theses

[9]
P. Bucher / E. N. Trifonov (Dir.) : Comparative analysis of eukaryotic promoters and development of computer algorithms to characterize nucleotide sequence patterns positionally correlated with a biological site. The Weizmann Institute of Science, 1989.

1988

Journal Articles

[8]
P. Bucher; E. N. Trifonov : CCAAT box revisited: bidirectionality, location and context; J Biomol Struct Dyn. 1988.

1987

Journal Articles

[7]
P. Bucher; E. N. Trifonov : On Nussinov's compilation of eukaryotic transcription initiation sites; J Theor Biol. 1987. DOI : 10.1016/S0022-5193(87)80243-6.

1986

Journal Articles

[6]
P. Bucher; E. N. Trifonov : Compilation and analysis of eukaryotic POL II promoter sequences; Nucleic Acids Res. 1986. DOI : 10.1093/nar/14.24.10009.

1984

Journal Articles

[5]
P. Bucher; B. Bryan : Signal search analysis: a new method to localize and characterize functionally important DNA sequences; Nucleic Acids Res. 1984. DOI : 10.1093/nar/12.1Part1.287.

1983

Journal Articles

[4]
S. Brahms; J. Vergne; J. G. Brahms; E. Di Capua; P. Bucher et al. : DNA formed by reassociation of complementary single-stranded circles from natural DNA is shown to contain left- and right-handed double helices; Cold Spring Harbor symposia on quantitative biology. 1983. DOI : 10.1101/SQB.1983.047.01.015.
[3]
R. G. Clerc; P. Bucher; K. Strub; M. L. Birnstiel : Transcription of a cloned Xenopus laevis H4 histone gene in the homologous frog oocyte system depends on an evolutionary conserved sequence motif in the -50 region; Nucleic Acids Res. 1983. DOI : 10.1093/nar/11.24.8641.

1982

Journal Articles

[2]
S. Brahms; J. Vergne; J. G. Brahms; E. Di Capua; P. Bucher et al. : Natural DNA sequences can form left-handed helices in low salt solution under conditions of topological constraint; J Mol Biol. 1982. DOI : 10.1016/0022-2836(82)90539-3.

1980

Journal Articles

[1]
C. Hentschel; J. C. Irminger; P. Bucher; M. L. Birnstiel : Sea urchin histone mRNA termini are located in gene regions downstream from putative regulatory sequences; Nature. 1980. DOI : 10.1038/285147a0.