Philipp Bucher

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Related publications (158)

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Related publications (158)

Methods for discovery and characterization of DNA sequence motifs

Philipp Bucher

World Scientific2009

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

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

ABSTRACT: BACKGROUND: The comparison of complete genomes has revealed surprisingly large numbers of conserved non-protein-coding (CNC) DNA regions. However, the biological function of CNC remains elusive. CNC differ in two aspects from conserved protein-co ...

2007

Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells

Philipp Bucher, Stefania Puttini

Gene transfer in eukaryotic cells and organisms suffers from epigenetic effects that result in low or unstable transgene expression and high clonal variability. Use of epigenetic regulators such as matrix attachment regions (MARs) is a promising approach t ...

2007

Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data

Philipp Bucher

BACKGROUND: The Affymetrix technology is nowadays a well-established method for the analysis of gene expression profiles in cancer research studies. However, changes in gene expression levels are not the only way to link genes and disease. The existence of ...

2007

Indexing strategies for rapid searches of short words in genome sequences

Giovanna Ambrosini, Philipp Bucher

Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strateg ...

Public Library of Science2007

MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data

Philipp Bucher

A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcript ...

2007

Elsevier2007

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Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time

Philipp Bucher

Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells

Philipp Bucher, Stefania Puttini

2007

Indexing strategies for rapid searches of short words in genome sequences

Giovanna Ambrosini, Philipp Bucher

Public Library of Science2007

Elsevier2007

ChIP-Seq data reveal nucleosome architecture of human promoters

Philipp Bucher