Publications by Philipp Bucher

Related publications (54)

Nuclear Factor I genomic binding associates with chromatin boundaries

Giovanni Dietler, Philipp Bucher, Giovanna Ambrosini, Nicolas Mermod, 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

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

Philipp Bucher

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

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge

Philipp Bucher, Florence Armand

Centrifuge is a user-friendly system to simultaneously access Arabidopsis gene annotations and intra- and inter-organism sequence comparison data. The tool allows rapid retrieval of user-selected data for each annotated Arabidopsis gene providing, in any c ...

Oxford University Press2005

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

Philipp Bucher, René Dreos

Author summary Transcription of genes by the RNA polymerase II enzyme initiates at a genomic region termed the core promoter. The core promoter is a regulatory region that may contain diverse short DNA sequence motifs/elements that confer specific properti ...

2021

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

Didier Trono, Philipp Bucher, Jacques Rougemont, Giovanna Ambrosini, Nadine Fournier, Adamantia Kapopoulou, Anna Claire Groner, Annamaria Kauzlaric

BACKGROUND: KRAB-ZFPs (Kruppel-associated box domain-zinc finger proteins) are vertebrate-restricted transcriptional repressors encoded in the hundreds by the mouse and human genomes. They act via an essential cofactor, KAP1, which recruits effectors respo ...

BioMed Central2011

How much does it cost? Optimization of costs in sequence analysis of social science data

Philipp Bucher

One major methodological problem in analysis of sequence data is the determination of costs from which distances between sequences are derived. Although this problem is currently not optimally dealt with in the social sciences, it has some similarity with ...

SAGE Publications2009

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

Philipp Bucher, Giovanna Ambrosini

Parkinson disease (PD) is characterized by a pivotal progressive loss of substantia nigra dopaminergic neurons and aggregation of alpha-synuclein protein encoded by the SNCA gene. Genome-wide association studies identified almost 100 sequence variants link ...

Springer Nature2019

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

Philipp Bucher

The CleanEx expression database (http://www.cleanex.isb-sib.ch) provides access to public gene expression data via unique gene names as well as via experiments biomedical characteristics. To reach this, a dual annotation of both sequences and experiments h ...

Oxford University Press2009

The transcription factor Rfx3 regulates beta-cell differentiation, function, and glucokinase expression

Philipp Bucher

OBJECTIVE: Pancreatic islets of perinatal mice lacking the transcription factor Rfx3 exhibit a marked reduction in insulin-producing beta-cells. The objective of this work was to unravel the cellular and molecular mechanisms underlying this deficiency. RES ...

American Diabetes Association2010

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

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

Philipp Bucher, Giovanna Ambrosini, René Dreos, Romain Fernand Pietro Groux

The Eukaryotic Promoter Database (EPD), available online at https://epd.epfl.ch, provides accurate transcription start site (TSS) information for promoters of 15 model organisms plus corresponding functional genomics data that can be viewed in a genome bro ...

2020

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

Philipp Bucher, Giovanna Ambrosini

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

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

Didier Trono, Philipp Bucher, Giovanna Ambrosini, Nadine Fournier, Anna Claire Groner, Nicolas Dénervaud

Krüppel-associated box domain-zinc finger proteins (KRAB-ZFPs) are tetrapod-specific transcriptional repressors encoded in the hundreds by the human genome. In order to explore their as yet ill-defined impact on gene expression, we developed an ectopic rep ...

Public Library of Science2010

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

Philipp Bucher, Giovanna Ambrosini, Romain Fernand Pietro Groux

BackgroundPositional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in a plethora of biological application ...

2020

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

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Rachel Marcone, Céline Berthe Constantin, Dalya Ataca, Marie Shamseddin, Csaba Ferenc László, Marian Caikovski, Patrik Aouad

Estrogens and progesterone control breast development and carcinogenesis via their cognate receptors expressed in a subset of luminal cells in the mammary epithelium. How they control the extracellular matrix, important to breast physiology and tumorigenes ...

Nature Research2020

SPar-K: a method to partition NGS signal data

Philipp Bucher, Romain Fernand Pietro Groux

We present SPar-K (Signal Partitioning with K-means), a method to search for archetypical chromatin architectures by partitioning a set of genomic regions characterized by chromatin signal profiles around ChIP-seq peaks and other kinds of functional sites. ...

Oxford University Press2019

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

Philipp Bucher

We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded ...

Oxford University Press2011

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

Philipp Bucher, Giovanna Ambrosini

Nucleosome depletion at transcription start sites (TSS) has been documented genome-wide in multiple eukaryotic organisms. However, the mechanisms that mediate this nucleosome depletion and its functional impact on transcription remain largely unknown. We h ...

Oxford University Press2009

Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation

Philipp Bucher, Cathrin Brisken, Giovanna Ambrosini, Valentina Scabia, Laura Battista, Fabio De Martino, Céline Berthe Constantin, Marie Shamseddin, Csaba Ferenc László

Hormonal contraception exposes women to synthetic progesterone receptor (PR) agonists, progestins, and transiently increases breast cancer risk. How progesterone and progestins affect the breast epithelium is poorly understood because we lack adequate mode ...

2021

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