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Philipp Bucher

Cette personne n’est plus à l’EPFL

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Publications associées (54)

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

Philipp Bucher, Bernard Moret, Yu Lin, Nishanth Ulhas Nair, Mingfu Shao, Paulina Grnarova, Laura Madeleine Hunter

Background: In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modifications are known to play a significant r ...

2016

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

Philipp Bucher, Giovanna Ambrosini, Sunil Kumar

SNP2TFBS is a computational resource intended to support researchers investigating the molecular mechanisms underlying regulatory variation in the human genome. The database essentially consists of a collection of text files providing specific annotations ...

Oxford University Press2016

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

Philipp Bucher, Giovanna Ambrosini, René Dreos, Sunil Kumar

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrati ...

2016

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

Philipp Bucher, Sunil Kumar

Background: Understanding the mechanisms by which transcription factors (TF) are recruited to their physiological target sites is crucial for understanding gene regulation. DNA sequence intrinsic features such as predicted binding affinity are often not ve ...

Biomed Central Ltd2016

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

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, René Dreos

We present an update of EPDNew (http://epd. vital-it. ch), a recently introduced new part of the Eukaryotic Promoter Database (EPD) which has been described in more detail in a previous NAR Database Issue. EPD is an old database of experimentally character ...

Oxford University Press2015

Principles of ChIP-seq Data Analysis Illustrated with Examples

Philipp Bucher, Giovanna Ambrosini, René Dreos

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single C ...

Copicentro Granada S L2014

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

Philipp Bucher, Slavica Dimitrieva Janeva

Scarce work has been done in the analysis of the composition of conserved non-coding elements (CNEs) that are identified by comparisons of two or more genomes and are found to exist in all metazoan genomes. Here we present the analysis of CNEs with a metho ...

Academic Press Inc Elsevier Science2014

Study of cell differentiation by phylogenetic analysis using histone modification data

Philipp Bucher, Bernard Moret, Yu Lin, Nishanth Ulhas Nair, Paulina Grnarova, Jelena Antic, Ana Manasovska

Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in ...

BioMed Central2014

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

Philipp Bucher, Amos Bairoch, Olivier Michielin, Heinz Stockinger, Mauro Delorenzi, Jacques Rougemont, Ioannis Xenarios

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRI ...

Oxford University Press2014

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

Philipp Bucher, Bernard Moret, Nishanth Ulhas Nair, Sunil Kumar

Motivation: We have witnessed an enormous increase in ChIP-Seq data for histone modifications in the past few years. Discovering significant patterns in these data is an important problem for understanding biological mechanisms. Results: We propose probabi ...

Oxford University Press2014

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

Philipp Bucher, Slavica Dimitrieva Janeva

UCNEbase (http://ccg.vital-it.ch/UCNEbase) is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority ...

Oxford University Press2013

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

Rouayda Cavin Perier, Philipp Bucher, Giovanna Ambrosini, René Dreos

The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in th ...

Oxford University Press2013

Phylogenetic Analysis of Cell Types Using Histone Modifications

Philipp Bucher, Bernard Moret, Yu Lin, Nishanth Ulhas Nair

Springer Verlag2013

Critical assessment of automated flow cytometry data analysis techniques

Philipp Bucher, Pascal Meyer, Giovanna Ambrosini, Nima Aghaeepour, Slavica Dimitrieva Janeva, René Dreos

Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessm ...

Nature Publishing Group2013

Nuclear Factor I genomic binding associates with chromatin boundaries

Nicolas Mermod, Philipp Bucher, Giovanni Dietler, Jan Kerschgens, Armelle Gaussin, Giovanna Ambrosini, Petar Pjanic

Background: The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequenci ...

BioMed Central2013

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

Philipp Bucher, Bernard Moret, Nishanth Ulhas Nair

The advent of high-throughput technologies such as ChIP-seq has made possible the study of histone modifications. A problem of particular interest is the identification of regions of the genome where different cell types from the same organism exhibit diff ...

Public Library of Science2012

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

Philipp Bucher, Slavica Dimitrieva Janeva

Motivation: Genomic context analysis, also known as phylogenetic profiling, is widely used to infer functional interactions between proteins but rarely applied to non-coding cis-regulatory DNA elements. We were wondering whether this approach could provide ...

Oxford University Press2012

Practicality and time complexity of a sparsified RNA folding algorithm

Philipp Bucher, Slavica Dimitrieva Janeva

Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n^3). Recently, it has been claimed that RNA folding can be achie ...

2012

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

Philipp Bucher, Anne Grapin-Botton, Emilie Gesina, Nancy Thompson

Pancreas development is initiated by the specification and expansion of a small group of endodermal cells. Several transcription factors are crucial for progenitor maintenance and expansion, but their interactions and the downstream targets mediating their ...

American Society for Microbiology2012

Nuclear factor I revealed as family of promoter binding transcription activators

Nicolas Mermod, Philipp Bucher, Armelle Gaussin, Giovanna Ambrosini, Petar Pjanic

Background: Multiplex experimental assays coupled to computational predictions are being increasingly employed for the simultaneous analysis of many specimens at the genome scale, which quickly generates very large amounts of data. However, inferring valua ...

BioMed Central2011

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