Publications by Giovanna Ambrosini

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Studying the genetic basis of gene expression and chromatin organization is key to characterizing the effect of genetic variability on the function and structure of the human genome. Here we unravel how genetic variation perturbs gene regulation using a da ...

More than 70% of human breast cancers (BCs) are estrogen receptor α-positive (ER+). A clinical challenge of ER+ BC is that they can recur decades after initial treatments. Mechanisms governing latent disease remain elusive due to lack of adequate in vivo m ...

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 ...

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 ...

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 ...

Estrogen and progesterone receptor (ER, PR) signaling control breast development and impinge on breast carcinogenesis. ER is an established driver of ER + disease but the role of the PR, itself an ER target gene, is debated. We assess the issue in clinical ...

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 ...

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 relation of astrocytic endfeet to the vasculature plays a key functional role in the neuro‐glia‐vasculature unit. We characterize the spatial organization of astrocytes and the structural aspects that facilitate their involvement in molecular exchanges ...

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 ...

Giovanna Ambrosini

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Chromatin three-dimensional interactions mediate genetic effects on gene expression

Epithelial-mesenchymal plasticity determines estrogen receptor positive breast cancer dormancy and epithelial reconversion drives recurrence

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

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

Principles of ChIP-seq Data Analysis Illustrated with Examples

Estrogen receptor positive breast cancers have patient specific hormone sensitivities and rely on progesterone receptor

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

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

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

Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex

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