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Philipp Bucher

Cette personne a quitté l’EPFL

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Publications associées (54)

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

Philipp Bucher, Jacques Rougemont, Mauro Delorenzi

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 ...

Oxford University Press2014

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

Bernard Moret, Philipp Bucher, Nishanth Ulhas Nair

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 ...

Oxford University Press2014

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

Philipp Bucher, Giovanna Ambrosini, René Dreos, Rouayda Cavin Perier

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 ...

Oxford University Press2013

Nuclear factor I revealed as family of promoter binding transcription activators

Giovanna Ambrosini, Philipp Bucher, Nicolas Mermod, Petar Pjanic

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

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

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

Philipp Bucher, Giovanna Ambrosini

NATURE PUBLISHING GROUP2018

Phylogenetic Analysis of Cell Types Using Histone Modifications

Bernard Moret, Philipp Bucher, Yu Lin, Nishanth Ulhas Nair

Springer Verlag2013

Critical assessment of automated flow cytometry data analysis techniques

Philipp Bucher, Giovanna Ambrosini, Pascal Meyer, Slavica Dimitrieva Janeva, René Dreos

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 ...

Nature Publishing Group2013

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

Philipp Bucher, Giovanna Ambrosini, René Dreos, Rouayda Cavin Perier

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 ...

Oxford University Press2015

Chromatin 3D interactions mediate genetic effects on gene expression

David Hacker, Philipp Bucher, Giovanna Ambrosini

NATURE PUBLISHING GROUP2019

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

Didier Trono, Bart Deplancke, Philipp Bucher, Giovanna Ambrosini, Riccardo Dainese, Daniel Alpern, Michaël Imbeault, Alina Isakova, Romain Fernand Pietro Groux, Pernille Yde Rainer

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 ...

Nature Publishing Group2017

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

Philipp Bucher, Giovanna Ambrosini

NATURE PUBLISHING GROUP2018

MGA repository: a curated data resource for ChIP-seq and other genome annotated data

Philipp Bucher, Giovanna Ambrosini, René Dreos, Rouayda Cavin Perier, Romain Fernand Pietro Groux

Oxford University Press2018