P. Bucher

发表

Quantile distributions of amino acid usage in protein classes.

S. Karlin, B. Blaisdell, P. Bucher, 1992, Protein engineering.

Regulatory elements and expression profiles.

P. Bucher, Philipp Bucher, 1999, Current opinion in structural biology.

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites

Alex Bateman, Rolf Apweiler, Henning Hermjakob, 2002, Briefings Bioinform..

Searching for regulatory elements in human noncoding sequences.

P. Bucher, L. Duret, Philipp Bucher, 1997, Current opinion in structural biology.

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

Alex Bateman, Rolf Apweiler, Beate Marx, 2001, Nucleic Acids Res..

Occurrence of oligopurine.oligopyrimidine tracts in eukaryotic and prokaryotic genes.

P. Bucher, G. Yagil, Phillip Bucher, 1991, DNA sequence : the journal of DNA sequencing and mapping.

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences.

P. Bucher, 1990, Journal of molecular biology.

PROSITE: recent developments.

A. Bairoch, P. Bucher, Philip Bucher, 1994, Nucleic acids research.

The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway.

P. Bucher, K. Hofmann, K. Hofmann, 1996, Trends in biochemical sciences.

Can Survival Prediction Be Improved By Merging Gene Expression Data Sets?

P. Bucher, V. Praz, P. Sperisen, 2009, PloS one.

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

P. Bucher, G. Felici, D. Polychronopoulos, 2014, Genomics.

DNA Binding Specificity of Different STAT Proteins

P. Bucher, C. Horvath, U. Schindler, 2001, The Journal of Biological Chemistry.

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

P. Bucher, T. Werner, E. Wingender, 2000, Journal of molecular biology.

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

P. Bucher, A. Camargo, N. Mermod, 2002, Nature Biotechnology.

A cSNP map and database for human chromosome 21.

P. Bucher, S. Antonarakis, S. Deutsch, 2001, Genome research.

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

Philipp Bucher, Nadine Zangger, Nicolas Dénervaud, 2010, PLoS genetics.

The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors.

P Bucher, P. Bucher, K. Hofmann, 1995, Trends in biochemical sciences.

Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones.

C V Jongeneel, P Bucher, P. Bucher, 1996, Immunity.

A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins

Peer Bork, Philipp Bucher, S. Altschul, 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Nineteen additional unpredicted transcripts from human chromosome 21.

C. V. Jongeneel, Christian Iseli, Brian J. Stevenson, 2002, Genomics.

Chromatin three-dimensional interactions mediate genetic effects on gene expression

S. Kumar, D. Marbach, O. Delaneau, 2019, Science.

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

Philipp Bucher, René Dreos, P. Bucher, 2016, BMC Genomics.

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

F. Bushman, P. Bucher, J. Rougemont, 2011, BMC Genomics.

Opposing chromatin remodelers control transcription initiation frequency and start site selection

P. Bucher, D. Shore, D. Libri, 2019, Nature Structural & Molecular Biology.

Opposing chromatin remodelers control transcription initiation frequency and start site selection

P. Bucher, D. Shore, D. Libri, 2019, bioRxiv.

[Description of eukaryotic promoters in the EPD database].

P. Bucher, 1997, Molekuliarnaia biologiia.

DATA ON EUKARYOTIC PROMOTERS AS DESCRIBED IN THE EPD DATABASE

P. Bucher, 1997 .

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

Yu Lin, Bernard M. E. Moret, Mingfu Shao, 2016, BMC Genomics.

Gene Feature Identification

P. Bucher, 1999 .

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.

P. Bucher, P. Walker, J. Maryanski, 1999, Molecular immunology.

Methods for discovery and characterization of DNA sequence motifs

P. Bucher, 2009 .

Mmsearch: a Motif Arrangement Language and Search Program

Philipp Bucher, Marco Pagni, Thomas Junier, 2001, Bioinform..

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

P. Bucher, A. Grapin-Botton, Nancy Thompson, 2012, Molecular and Cellular Biology.

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

J. Beckmann, P. Bucher, N. Mermod, 2007, Nature Methods.

Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings

Bernard M. E. Moret, Philipp Bucher, P. Bucher, 2006, WABI.

Nuclear factor I revealed as family of promoter binding transcription activators

Christian Mazza, Nicolas Mermod, Philipp Bucher, 2011, BMC Genomics.

Computational Biology: Annotated Glossary of Terms

Graziano Pesole, William R. Taylor, M.J.C. Crabbe, 2004 .

The Transcription Factor Rfx3 Regulates β-Cell Differentiation, Function, and Glucokinase Expression

Philipp Bucher, Paolo Meda, Walter Reith, 2010, Diabetes.

The discoidin domain family revisited: New members from prokaryotes and a homology‐based fold prediction

Philipp Bucher, Kay Hofmann, P. Bucher, 1998, Protein science : a publication of the Protein Society.

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

Philipp Bucher, Vishwanath R Iyer, V. Iyer, 2018, PeerJ.

ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries

Bernard M. E. Moret, Avinash Das Sahu, Philipp Bucher, 2012, PloS one.

Proceedings of the 6th international conference on Algorithms in Bioinformatics

Bernard M. E. Moret, Philipp Bucher, P. Bucher, 2006 .

Nuclear Factor I genomic binding associates with chromatin boundaries

P. Bucher, N. Mermod, Jan Kerschgens, 2013, BMC Genomics.

Memory TCR repertoires analyzed long-term reflect those selected during the primary response.

P. Bucher, P. Walker, J. Maryanski, 1996, International immunology.

Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus

P. Bucher, A. Trumpp, F. Beermann, 2006, Genesis.

Telomere Maintenance in Fission Yeast Requires an Est1 Ortholog

P. Bucher, A. Deshpande, J. Cooper, 2003, Current Biology.

The PROSITE database, its status in 1997

A. Bairoch, P. Bucher, K. Hofmann, 1997, Nucleic Acids Res..

Influence of rotational nucleosome positioning on transcription start site selection in animals promoters

P. Bucher, R. Dreos, G. Ambrosini, 2016, bioRxiv.

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

V. Iyer, P. Bucher, Anna M. Battenhouse, 2018, bioRxiv.

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

Dmitry D. Penzar, Jan Grau, P. Bucher, 2020, Genome Biology.

receptor alpha gene. new enhancer of the human interleukin-2 Elf-1 and Stat5 bind to a critical element in a

P. Bucher, C. Beadling, J. Imbert, 2012 .

SMiLE-seq: Selective Microfluidics-based Ligand Enrichment followed by sequencing

P. Bucher, B. Deplancke, Alina Isakova, 2017 .

Characterization of a new tissue-specific transcription factor binding to the simian virus 40 enhancer TC-II (NF-kappa B) element

P. Bucher, A. Israël, P. Baeuerle, 1992, Molecular and cellular biology.

Characterization of a New Tissue-Specific Factor Binding to the Simian Virus 40 TC-II (NF-FB) Element Transcription Enhancer

Catherine, P. Bucher, P. Baeuerle, 2022 .

Long Distance Control of MHC Class II Expression by Multiple Distal Enhancers Regulated by Regulatory Factor X Complex and CIITA1

P. Bucher, W. Reith, M. Krawczyk, 2004, The Journal of Immunology.

A conserved domain is present in different families of vesicular fusion proteins: a new superfamily.

P. Bucher, T. Weimbs, K. Hofmann, 1997, Proceedings of the National Academy of Sciences of the United States of America.

On Nussinov's compilation of eukaryotic transcription initiation sites.

E. Trifonov, P. Bucher, 1987, Journal of theoretical biology.

CleanEx : a Gene Expression Reference Database

P. Bucher, V. Praz, 2003 .

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

Sunil Kumar, Philipp Bucher, P. Bucher, 2016, BMC Bioinformatics.

UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks

Philipp Bucher, Slavica Dimitrieva, P. Bucher, 2012, Nucleic Acids Res..

Philipp Bucher, Kay Hofmann, P. Bucher, 1996, ISMB.

A Flexible Motif Search Technique Based on Generalized Profiles

Kevin Karplus, Philipp Bucher, Nicolas Moeri, 1996, Comput. Chem..

Mouse interleukin-2 receptor alpha gene expression. Interleukin-1 and interleukin-2 control transcription via distinct cis-acting elements.

P. Bucher, P. Corthésy, M. Pla, 1995, The Journal of biological chemistry.

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

Philipp Bucher, Romain Groux, Bart Deplancke, 2017, Nature Methods.

DNA formed by reassociation of complementary single-stranded circles from natural DNA is shown to contain left- and right-handed double helices.

P. Bucher, J. Brahms, J. Vergne, 1983, Cold Spring Harbor symposia on quantitative biology.

Natural DNA sequences can form left-handed helices in low salt solution under conditions of topological constraint.

P. Bucher, J. Brahms, J. Vergne, 1982, Journal of molecular biology.

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

Aurélien Grosdidier, Desmond G. Higgins, Cédric Notredame, 2003, ISMB.

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

Giovanna Ambrosini, Philipp Bucher, René Dreos, 2012, Nucleic Acids Res..

ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences

C. V. Jongeneel, Christian Iseli, Philipp Bucher, 1999, ISMB.

Compilation and analysis of eukaryotic POL II promoter sequences.

P Bucher, E N Trifonov, E. Trifonov, 1986, Nucleic acids research.

Recent improvements to the PROSITE database

Amos Bairoch, Christian J. A. Sigrist, Edouard De Castro, 2004, Nucleic Acids Res..

PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors

Amos Bairoch, Christian J. A. Sigrist, Nicolas Hulo, 2002, Briefings Bioinform..

The PROSITE database, its status in 2002

Amos Bairoch, Christian J. A. Sigrist, Nicolas Hulo, 2002, Nucleic Acids Res..

InterPro : An integrated documentation resource for protein families , domains and functional sites The InterPro Consortium :

Alex Bateman, Rolf Apweiler, Beate Marx, 2005 .

Optimizing generalized profiles for enhanced discrimination of biomolecular sequences

Thomas M. Liebling, Philipp Bucher, Nicolas Moeri, 2000 .

The PROSITE database, its status in 1999

Amos Bairoch, Philipp Bucher, Kay Hofmann, 1999, Nucleic Acids Res..

The PROSITE database, its status in 1997

Amos Bairoch, Philipp Bucher, Kay Hofmann, 1997, Nucleic Acids Res..

Improving the sensitivity of the sequence profile method

P. Bucher, I. Xenarios, R. Lüthy, 1994, Protein science : a publication of the Protein Society.

A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation

Amos Bairoch, Philipp Bucher, A. Bairoch, 1994, ISMB.

Evidence for selective evolution in codon usage in conserved amino acid segments of human alphaherpesvirus proteins

S. Karlin, B. Blaisdell, P. Bucher, 1991, Journal of Molecular Evolution.

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

Giovanna Ambrosini, Philipp Bucher, Romain Groux, 2016, Nucleic Acids Res..

Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense

Philipp Bucher, Peter Sperisen, Christoph D. Schmid, 2005, PLoS Comput. Biol..

The Eukaryotic Promoter Database (EPD)

Philipp Bucher, Thomas Junier, Rouaïda Cavin Périer, 2000, Nucleic Acids Res..

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1

P. Bucher, C. Brisken, M. Fiche, 2021, EMBO molecular medicine.

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

Philipp Bucher, Slavica Dimitrieva, P. Bucher, 2012, Bioinform..

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

P. Bucher, N. Mermod, T. Egener, 2005, Nucleic acids research.

Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Pablo Meyer, Raquel Norel, Eran Segal, 2013, Genome research.

Computational identification and experimental characterization of preferred downstream positions in human core promoters

P. Bucher, T. Juven-Gershon, R. Dreos, 2021, bioRxiv.

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

Philipp Bucher, Christoph D. Schmid, Rouaïda Périer, 2005, Nucleic Acids Res..

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

C. V. Jongeneel, Philipp Bucher, Cédric Notredame, 2007, BMC Genomics.

Shotgun sequencing of the human transcriptome with ORF expressed sequence tags.

F F Costa, E Dias Neto, R G Correa, 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

Nicolas Mermod, Philipp Bucher, Thomas Junier, 1998, Silico Biol..

The rsp5‐domain is shared by proteins of diverse functions

P. Bucher, K. Hofmann, 1995, FEBS letters.

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

Philipp Bucher, Christoph D. Schmid, P. Bucher, 2010, PloS one.

The frizzled motif: in how many different protein families does it occur?

P. Bucher, K. Hofmann, T. Pihlajaniemi, 1998, Trends in biochemical sciences.

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

C. V. Jongeneel, Stylianos E. Antonarakis, Emmanouil T. Dermitzakis, 2002, Nature.

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

P. Bucher, Hongde Liu, N. Osato, 2019, Scientific Reports.

The PROSITE database, its status in 1995

Amos Bairoch, Philipp Bucher, Kay Hofmann, 1996, Nucleic Acids Res..

S Karlin, P Bucher, S. Karlin, 1992, Molecular biology and evolution.

A Human Homolog of Yeast Est1 Associates with Telomerase and Uncaps Chromosome Ends When Overexpressed

P. Bucher, C. Azzalin, J. Lingner, 2003, Current Biology.

Methods and algorithms for statistical analysis of protein sequences.

S Karlin, P Bucher, S. Karlin, 1992, Proceedings of the National Academy of Sciences of the United States of America.

C. V. Jongeneel, Christian Iseli, Felix Naef, 2006, BMC Genomics.

Indexing Strategies for Rapid Searches of Short Words in Genome Sequences

C. V. Jongeneel, P. Bucher, C. Iseli, 2007, PloS one.

The InterPro Database, 2003 brings increased coverage and new features

Alex Bateman, Rolf Apweiler, Nicola J. Mulder, 2003, Nucleic Acids Res..

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

Giovanna Ambrosini, Philipp Bucher, Romain Groux, 2018, Bioinform..

A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain.

P. Bucher, K. Hofmann, A. Kajava, 1998, Journal of molecular biology.

The CARD domain: a new apoptotic signalling motif.

P. Bucher, J. Tschopp, K. Hofmann, 1997, Trends in biochemical sciences.

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

Sunil Kumar, Giovanna Ambrosini, Philipp Bucher, 2016, Nucleic Acids Res..

trome, trEST and trGEN: databases of predicted protein sequences

C. V. Jongeneel, Christian Iseli, Brian J. Stevenson, 2004, Nucleic Acids Res..

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

C. V. Jongeneel, Christian Iseli, Philipp Bucher, 2001, Nucleic Acids Res..

The Eukaryotic Promoter Database EPD

Philipp Bucher, Rouaïda Périer, Thomas Junier, 1998, Nucleic Acids Res..

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

Philipp Bucher, Viviane Praz, Vidhya Jagannathan, 2004, Nucleic Acids Res..

Long-range heterogeneity at the 3' ends of human mRNAs.

C. V. Jongeneel, Kenneth H Buetow, Christian Iseli, 2002, Genome research.

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

Christian Iseli, Giovanna Ambrosini, Philipp Bucher, 2011, BMC Bioinformatics.

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

Philipp Bucher, Romain Groux, René Dreos, 2019, Nucleic Acids Res..

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

Giovanna Ambrosini, Philipp Bucher, René Dreos, 2014, Nucleic Acids Res..

The PCI domain: a common theme in three multiprotein complexes.

P Bucher, P. Bucher, K. Hofmann, 1998, Trends in biochemical sciences.

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

Matthias Zytnicki, Andreas Wilm, Philipp Bucher, 2011, Nucleic acids research.

Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene

P. Bucher, P. Lécine, C. Beadling, 1996, Molecular and cellular biology.

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

Philipp Bucher, Mauro Delorenzi, Christoph D. Schmid, 2004, Nucleic Acids Res..

Modeling sequencing errors by combining Hidden Markov models

C. V. Jongeneel, Christian Iseli, Claudio Lottaz, 2003, ECCB.

Practicality and Time Complexity of a Sparsified RNA Folding Algorithm

Philipp Bucher, Slavica Dimitrieva, P. Bucher, 2012, J. Bioinform. Comput. Biol..

Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene

P. Bucher, P. Lécine, C. Beadling, 1997, Molecular and cellular biology.

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

L. Kühn, P. Bucher, S. Pradervand, 2018, PloS one.

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

Giovanna Ambrosini, Philipp Bucher, René Dreos, 2016, bioRxiv.

Transcription factor binding and nucleosome positioning are alternative pathways for transcription start site selection in eukaryotic promoters

Giovanna Ambrosini, Philipp Bucher, René Dreos, 2014, IWBBIO.

Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation

P. Bucher, W. Reith, M. Krawczyk, 2008, PLoS genetics.

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

P. Bucher, C. Brisken, Csaba Laszlo, 2020, Nature Communications.

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

P. Bucher, J. Maryanski, V. Attuil, 2000, Proceedings of the National Academy of Sciences of the United States of America.

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

P. Bucher, W. Reith, I. Dunand-Sauthier, 2009, Nucleic acids research.

Promoter Rearrangements Cause Species-specific Hepatic Regulation of the Glyoxylate Reductase/Hydroxypyruvate Reductase Gene by the Peroxisome Proliferator-activated Receptor α*

P. Bucher, W. Wahli, N. Tan, 2005, Journal of Biological Chemistry.

Sea urchin histone mRNA termini are located in gene regions downstream from putative regulatory sequences

P. Bucher, M. Birnstiel, J. Irminger, 1980, Nature.

ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters

Philipp Bucher, Christoph D. Schmid, P. Bucher, 2007, Cell.

A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity

P. Bucher, P. Emery, W. Reith, 1996, Molecular and cellular biology.

altered specificity . domain and binding domain mutants with A consensus motif in the RFX DNA binding

P. Bucher, P. Emery, W. Reith, 1996 .

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Oliver Horlacher, Damian Szklarczyk, Christian von Mering, 2015, Nucleic Acids Res..

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.

P Bucher, P. Bucher, M. Birnstiel, 1983, Nucleic acids research.

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

Giovanna Ambrosini, Philipp Bucher, Romain Groux, 2017, Nucleic Acids Res..

Mouse Interleukin-2 Receptor Gene Expression

P. Bucher, P. Corthésy, S. Wang, 1995, Journal of Biological Chemistry.

The Eukaryotic Promoter Database (EPD): recent developments

Philipp Bucher, Thomas Junier, Rouaïda Périer, 1999, Nucleic Acids Res..

Statistical methods and insights for protein and DNA sequences.

S F Altschul, S Karlin, P Bucher, 1991, Annual review of biophysics and biophysical chemistry.

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

Philipp Bucher, Mauro Delorenzi, Thierry Sengstag, 2007, Nucleic Acids Res..

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

Philipp Bucher, Rouaïda Périer, Viviane Praz, 2002, Nucleic Acids Res..

A Conserved IL-2 Responsive Enhancer in the IL-2Rα Gene

P. Bucher, P. Corthésy, J. Imbert, 1997 .

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

Christian von Mering, Ron D. Appel, Evgeny M. Zdobnov, 2014, Nucleic Acids Res..

Signal search analysis: a new method to localize and characterize functionally important DNA sequences

Philipp Bucher, B. Bryan, P. Bucher, 1984, Nucleic Acids Res..

Compilation andanalysis ofeukaryotic POLIIpromoter sequences

P. Bucher, 1986 .

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

Jan Grau, P. Bucher, V. Makeev, 2020, Genome Biology.

Indexing Strategies for Rapid Searches of Short Words in Genome Sequences

C. V. Jongeneel, P. Bucher, C. Iseli, 2007, PloS one.

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

Philipp Bucher, Viviane Praz, P. Bucher, 2008, Nucleic Acids Res..

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

P. Bucher, R. Dreos, G. Ambrosini, 2016, BMC Genomics.

Study of cell differentiation by phylogenetic analysis using histone modification data

Yu Lin, Bernard M. E. Moret, Paulina Grnarova, 2014, BMC Bioinformatics.

Phylogenetic Analysis of Cell Types Using Histone Modifications

Yu Lin, Bernard M. E. Moret, Philipp Bucher, 2013, WABI.

Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation

P. Bucher, C. Brisken, Csaba Laszlo, 2021, EMBO molecular medicine.

Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks

O. Delaneau, C. Howald, A. Reymond, 2017, bioRxiv.

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

Bernard M. E. Moret, P. Bucher, Mingfu Shao, 2016, BMC Genomics.

Individuality of Ag-selected and preimmune TCR repertoires

P. Bucher, J. Maryanski, M. Mutin, 2001, Immunologic research.

Molecular Models for the two Discoidin Domains of Human Blood Coagulation Factor V

P. Bucher, K. Hofmann, B. Dahlbäck, 1998 .

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

Alessandro Guffanti, Davide Cittaro, Philipp Bucher, 2007, BMC Bioinformatics.

Principles of ChIP-seq Data Analysis Illustrated with Examples

Giovanna Ambrosini, Philipp Bucher, René Dreos, 2017, IWBBIO.

Computational analysis of transcriptional regulatory elements: a field in flux

Artemis G. Hatzigeorgiou, James W. Fickett, Philipp Bucher, 1996, Comput. Appl. Biosci..

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

P. Bucher, C. Brisken, Csaba Laszlo, 2020, Nature Communications.

Correlation analysis of amino acid usage in protein classes.

S Karlin, P Bucher, S. Karlin, 1992, Proceedings of the National Academy of Sciences of the United States of America.

The PROSITE database, its status in 1997

A. Bairoch, P. Bucher, K. Hofmann, 1997, Nucleic Acids Res..

The Cis-Acting Elements Controlling Mouse IL-2Rα Transcription

P. Bucher, H. Macdonald, S. Wang, 1995 .

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

Joshua L. Payne, Christian J. A. Sigrist, Brian J. Stevenson, 2015, Nucleic Acids Res..

The Eukaryotic Promoter Database (EPD)

P. Bucher, C. Bonnard, R. Périer, 2000, Nucleic Acids Res..

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

Christian J. A. Sigrist, R. Durbin, C. Ponting, 2000, Bioinform..

The PROSITE database, its status in 1995

A. Bairoch, P. Bucher, K. Hofmann, 1996, Nucleic Acids Res..

Signal search analysis server

Giovanna Ambrosini, Philipp Bucher, Viviane Praz, 2003, Nucleic Acids Res..