Philipp Bucher

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

Bernard Moret, Philipp Bucher, Yu Lin, Mingfu Shao, Nishanth Ulhas Nair, 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 ...

Biomed Central Ltd2016

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

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

Giovanna Ambrosini, Philipp Bucher, René Dreos

The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription ...

Public Library Science2016

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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

Giovanna Ambrosini, Philipp Bucher, 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 ...

BioMed Central2016

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

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

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

Study of cell differentiation by phylogenetic analysis using histone modification data

Bernard Moret, Philipp Bucher, 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

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

Principles of ChIP-seq Data Analysis Illustrated with Examples

Giovanna Ambrosini, Philipp Bucher, 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

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

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

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

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