Giovanna Ambrosini

giovanna.ambrosini@epfl.ch +41 21 693 88 36

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Nationality: Italian and Swiss

EPFL SV PTECH BICC
AAB 1 19 (Bâtiment AAB)
Station 19
1015 Lausanne

+41 21 693 88 36
Office: AAB 1 21
EPFL › SV › PTECH › BICC

Website: https://bix.epfl.ch

Biography Publications

Current Position

Senior Scientist, School of Life Sciences, Bioinformatics Competence Center, école Polythechnique Fédérale de Lausanne, Lausanne.
Senior bioinformatician and software engineer with proven experience working in higher education institutions. Solid experience in scientific computing and web design. Proficient in physics and computational genomics, with a focus on high-throughput genomic sequencing data analysis (ChIP-seq, ATAC-seq, RNA-seq, scRNA-seq, and exome sequencing) and other types of data, statistical consulting, and supervision of data analysis pipelines. Good programming skills with C/C , Perl, Python, R, PHP, JavaScript and good working knowledge of Linux and other UNIX systems.

Honors

Admitted to the Ghislieri College in Pavia for my degree in Physics at the University of Pavia. The Ghislieri College is a centre of excellence and higher education, founded in 1567 by Pope Pius V in Pavia.

Education

Ph.D. in Physics

| High Energy Physics at CERN, Geneva, Switzerland

1995 – 1995 University of Pavia, Italy

Laurea, the italian equivalent of a BachelorÂ’s degree

| in Mathematical and Physical Sciences

1991 – 1991 University of Pavia, Italy

Professionals experiences

University Assistant

1995–1997

University of Bern, Switzerland CERN

Fellow in the EP Division ATD group at CERN

1998–1999

CERN

Software Engineer

1999–2000

Lightning Instrumentation SA, Lausanne

Systems Engineer

2000–2002

Creative Electronics Systems, Geneva

Bioinformatician

2002–2007

Swiss Institute for Experimental Cancer Research (ISREC), Lausanne/Epalinges

Senior Bioinformatician and software engineer

2007–2007

Ã‰cole Polytechnique FÃ©dÃ©rale de Lausanne (EPFL), Lausanne

Selected publications

Indexing strategies for rapid searches of short words in genome sequences

C. Iseli, G. Ambrosini, P. Bucher, and C. V. Jongeneel
Published in In PLoS ONE, volume 2, page e579, 2007. in

Signal search analysis server

G. Ambrosini, V. Praz, V. Jagannathan, and P. Bucher
Published in In Nucleic Acids Res, volume 31, number 13, pages 3618-20, 2003. in

PUBLICATIONS

Transcriptional dynamics and chromatin accessibility in the regulation of shade-responsive genes in Arabidopsis

S. Paulišić; A. Boccaccini; R. Dreos; G. Ambrosini; N. Guex et al.

Genome Biology. 2025. DOI : 10.1186/s13059-025-03901-2.

Giovanna Ambrosini

Current Position

Honors

Education

Ph.D. in Physics

Laurea, the italian equivalent of a BachelorÂ’s degree

Professionals experiences

Selected publications

Indexing strategies for rapid searches of short words in genome sequences

Signal search analysis server

PUBLICATIONS

Transcriptional dynamics and chromatin accessibility in the regulation of shade-responsive genes in Arabidopsis

Laccaria bicolor adapts to phosphate deficiency at the developmental, transcriptional and metabolic levels

Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors

A bioengineered human urothelial organoid model reveals the urine-urothelium interplay in tissue resilience and UPEC recurrence in urinary tract infections

biogrowleR: Enhancing Longitudinal Data Analysis

Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing

DNA methylation by CcrM contributes to genome maintenance in the Agrobacterium tumefaciens plant pathogen

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

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Inhibition of anti-tumor immunity by melanoma cell-derived Activin-A depends on STING

Integrating distribution kinetics and toxicodynamics to assess repeat dose neurotoxicity in vitro using human BrainSpheres: a case study on amiodarone

MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology

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

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

Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1

Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study

The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche

EPD in 2020: enhanced data visualization and extension to ncRNA promoters

Common genetic variants associated with Parkinson's disease display widespread signature of epigenetic plasticity

Chromatin 3D interactions mediate genetic effects on gene expression

Chromatin three-dimensional interactions mediate genetic effects on gene expression

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

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

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

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

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

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

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

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

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

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

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

Principles of ChIP-seq Data Analysis Illustrated with Examples

Nuclear Factor I genomic binding associates with chromatin boundaries

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

Critical assessment of automated flow cytometry data analysis techniques

A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing

ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites

KRAB-Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading

Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site

Indexing strategies for rapid searches of short words in genome sequences

Signal search analysis server

Infoscience