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About

Developing and evaluating bioinformatic tools for:
– next generation sequencing data
– genome analysis & comparison

Specialties:Genome & Transcriptome Bioinformatics

CV

Currently I am a bioinformatician research associate in the HUB team at institute Pasteur

Previous professional experience

03/13 – 11/15.

Postdoc at the European Bioinformatics Institute (EMBL-EBI)

Supervisor: Dr Anton J Enright

Analyzed both private and publicly available NGS data in the study of the human and mouse transcriptome, HPV virus integration in cervical cancer clones and the fly mesodermal development. Different library types included: RNA-Seq (PolyA+ enriched and Ribo-depleted), targeted sequencing, ChIP-Seq, CAGE, DNase-Seq and DNA Nextera mate-pairs. Used available tools to assemble gene models, established filtering pipelines to remove sequencing artifacts, integrated and visualized different data sources, interpreted the results, shortlisted candidates for functional validation. Conducted continuous technological watching and state of the art writing. Interacted weekly with bioinformaticians and experimental biologists for collaborative research work.

Cambridge, UK

09/08 – 03/13

PhD at the Comparative Bioinformatics Group, Bioinformatics and Genomics Programme, Center for Genomic Regulation (CRG)

Supervisor: Dr Cedric Notredame

Managed PhD research project in comparative genomics and collaborated with the ENCODE project. Developed pipeline for multi-species screenings. Established evaluation processes of multiple RNA structure alignments.

Barcelona, Spain

 

 

03/08 – 07/08

Researcher at the Department of Biochemistry, University of Zurich

Supervisor: Prof. Andreas Wagner

Growth of evolutionarily adapted yeast strains, DNA extractions, tiling arrays, single nucleotide polymorphism analysis.

Zurich, Switzerland

04/06 – 10/07

Trainee at the Department of Biochemical Sciences, Sapienza University of Rome

Supervisor: Prof. Anna Tramontano

Development of a method for the analysis of protein interaction networks, implementation of that method in a web server, server testing and addition of analysis tools.

Rome, Italy

04/05 – 10/05

Trainee at the Cellular Biotechnologies and Hematology Department,

Molecular Genetics Section, Sapienza University of Rome

Supervisor: Prof. Giuseppe Macino

Real Time PCR in the study of mammalian micro RNAs and circadian cycle.

Rome, Italy

Education

09/08 – 03/13

PhD in Biomedicine summa cum laude

University Pompeu Fabra

Barcelona, Spain

10/05 – 10/07

Master in Genomics Biotechnology summa cum laude

Sapienza University of Rome

Rome, Italy

10/02 – 10/05

Bachelor in biotechnology summa cum laude

Sapienza University of Rome

 

Rome, Italy

Computing:

Proficiently skilled in OS: Linux, Mac, Windows, development: perl, BASH, AWK, statistics: R

Languages:

  • Italian – native
  • English – fluent
  • Spanish – fluent
  • French – beginner.

 

Bioinformatics:

  • NGS data analysis (STAR, tophap-fusion, HTSeq, NextClip, Trinity, Tuxedo suite, deepTools, bioconductor DESeq and DEXSeq, bwa-mem, FastQC, Kraken, samtools, bamtools, bedtools, IGV, UCSC, ENSEMBL)
  • Multiple sequence alignments (T-Coffee, MAFFT)
  • Homology screenings (Exonerate, Blast, Blat, Covariance Models)
  • coding potential analyses (CPAT, PhyloCSF, BlastX, RPStBlastN)
  • network analysis (biolayout, cytoscape)
  • GO term enrichment (GOrilla, bioconductor GOstats)
  • motif analysis (MEME, MAST, GOMO)
  • clustering analysis (MCL, blastclust, K-means, graphClust, bioconductor EM clustering)

Laboratory techniques:

  • Basic practice of nucleotide extraction, quantification by spectrophotometry, electrophoresis, DNAse treatment for RNA, phenol purification, retrotranscription, real time PCR, tiling array.
  • Basic practice of microbiology techniques such as the growth and the selection of evolutionary adapted yeast strains.

COMMUNICATION                                                                                                                                                                                                

Presented research results in international journals and conferences, reported work progress in team meetings.

Published 24 peer-reviewed papers

Presentations:

  • Presented regularly work progress in team meetings and video conference calls.
  • Explained informally my research to the postdocs community at EBI.
  • Spoke about my research to informal “tea talk” at EBI.
  • Reported yearly work progress to fellowship institutions.
  • ISMB conference, 15-17 July 2012, Long Beach USA.
  • Invited speaker at a national science communication radio program, 11 September 2012, Italy.
  • IV CRG PhD Students Symposium 10-11 November 2010, Barcelona Spain.

 

OTHER RELEVANT INFORMATION

Awards:

  • December 2012: EMBL Interdisciplinary Postdocs (EIPOD) / Marie Curie research fellowship.
  • September 2008: La Caixa International PhD Program fellowship.
  • September 2006: joined B.E.S.T. (Bologna Experience for Superior Talents) with 50 graduates who had achieved first-class honors in humanities and technical subject, managed by Bologna University.
  • July 2006: fellowship of the Ministry of Foreign Affairs for a language course at Malta University.
  • December 2005: fellowship of the Faculty of Mathematical, Physical and Natural Sciences of the Sapienza University of Rome to help researchers and students in the bibliographic research.

Mentoring:

  • Mentored bioinformatics student at EBI summer school, Cambridge.
  • Appointed chair at the EMBL lab day, Heidelberg.
  • Supervised the bioinformatics undergraduate students at UPF’s School/Faculty of Biology.

Publications

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