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Giovanna Ambrosini

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Publications associées (38)

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

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

Oxford University Press2018

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

Philipp Bucher, Giovanna Ambrosini, Sanjeev Kumar

NATURE PUBLISHING GROUP2018

Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each

Philipp Bucher, Lukas Kühn, Otto Hagenbüchle, Giovanna Ambrosini, Barbara Grisoni-Neupert, Ramona Pauchard-Batschulat

Regulation of mRNA stability by RNA-protein interactions contributes significantly to quantitative aspects of gene expression. We have identified potential mRNA targets of the AU-rich element binding protein AUF1. Myc-tagged AUF1 p42 was induced in mouse N ...

2018

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

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

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

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

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

We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next gene ...

2017

Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters

Philipp Bucher, Giovanna Ambrosini, René Dreos

The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription ...

Public Library Science2016

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

Philipp Bucher, Giovanna Ambrosini, Sunil Kumar

SNP2TFBS is a computational resource intended to support researchers investigating the molecular mechanisms underlying regulatory variation in the human genome. The database essentially consists of a collection of text files providing specific annotations ...

Oxford University Press2016

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

Philipp Bucher, Giovanna Ambrosini, René Dreos, Sunil Kumar

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrati ...

2016

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

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

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

Principles of ChIP-seq Data Analysis Illustrated with Examples

Philipp Bucher, Giovanna Ambrosini, René Dreos

Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single C ...

Copicentro Granada S L2014

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

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

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

Critical assessment of automated flow cytometry data analysis techniques

Philipp Bucher, Pascal Meyer, Giovanna Ambrosini, Nima Aghaeepour, 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

Nuclear Factor I genomic binding associates with chromatin boundaries

Nicolas Mermod, Philipp Bucher, Giovanni Dietler, Jan Kerschgens, Armelle Gaussin, Giovanna Ambrosini, Petar Pjanic

Background: The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequenci ...

BioMed Central2013

Nuclear factor I revealed as family of promoter binding transcription activators

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

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

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

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

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

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