Publications by Philipp Bucher

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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 ...

Motivation: We have witnessed an enormous increase in ChIP-Seq data for histone modifications in the past few years. Discovering significant patterns in these data is an important problem for understanding biological mechanisms. Results: We propose probabi ...

The Eukaryotic Promoter Database (EPD), available online at http://epd.vital-it.ch, is a collection of experimentally defined eukaryotic POL II promoters which has been maintained for more than 25 years. A promoter is represented by a single position in th ...

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 ...

Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessm ...

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 ...

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Philipp Bucher

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

Probabilistic partitioning methods to find significant patterns in ChIP-Seq data

EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era

Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation

ChIP-Seq data reveal nucleosome architecture of human promoters

Local regulatory networks across two tissues and applications to analyze rare non-coding variants

Phylogenetic Analysis of Cell Types Using Histone Modifications

Critical assessment of automated flow cytometry data analysis techniques

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

Chromatin 3D interactions mediate genetic effects on gene expression

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

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

Methods for discovery and characterization of DNA sequence motifs