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Philipp Bucher

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Related publications (54)

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

Christian Iseli, Philipp Bucher, Giovanna Ambrosini

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

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

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

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

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

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

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

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

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

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

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

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

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

Can survival prediction be improved by merging gene expression data sets?

Philipp Bucher, Haleh Yasrebi

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

Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation

Philipp Bucher

The class II trans-activator CIITA is a transcriptional co-activator required for the expression of Major Histocompatibility Complex (MHC) genes. Although the latter function is well established, the global target-gene specificity of CIITA had not been def ...

2008

ChIP-Seq data reveal nucleosome architecture of human promoters

Philipp Bucher

Elsevier2007

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

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