Philipp Bucher

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

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

ABSTRACT: 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 effec ...

BioMed Central2011

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

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Background: Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model organisms. ZFN specificity is not a ...

BioMed Central2011

Nuclear factor I revealed as family of promoter binding transcription activators

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

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

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

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

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

MER41 repeat sequences contain inducible STAT1 binding sites

Philipp Bucher

Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences. At the example of public STAT1 ChIP-seq data sets, we ...

Public Library of Science2010

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

Multichannel Sequence Analysis Applied To Social Science Data

Philipp Bucher

Applications of optimal matching analysis in the social sciences are typically based on sequences of specific social statuses that model the residential, family, or occupational trajectories of individuals. Despite the broadly recognized interdependence of ...

2010

BACKGROUND: High-throughput gene expression profiling technologies generating a wealth of data, are increasingly used for characterization of tumor biopsies for clinical trials. By applying machine learning algorithms to such clinically documented data set ...

Public Library of Science2009

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

Giovanna Ambrosini, Philipp Bucher

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

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