User:Mariap3636
From Bioinformatics.Org Wiki
Contents |
About me
I am Maria Persico, a person with a great enthusiam for computational biology, free software, travelling, swimming and slow food; my current research is in the field of metagenomics and in the analysis of 16S rDNA datasets.
Biography
Since the end of 2017 I have joined the [1] Eva Budinska's group at the RECETOX (REsearch CEntre for TOXic compounds in the environment).
Since February 2015 I have joined the [2] Corrado Priami's group inside COSBI - Centre for Computational and Systems Biology in Rovereto, working on data analysis.
Since January 2014 I have joined the [3] Sandro Banfi's group inside Tigem Institute in Naples, working on smallRNAseq data analysis and some months later I have obtained another part time contract to collaborate with also the [4] Antonella De Matteis group, usind data mining and data integration approaches to study the signalling in membrane-trafficking. More in details, working as postdoc inside the Sandro Banfi's group at the Telethon Institute of Genetics and Medicine, I had the possibility to handle small RNA seq data generated and processed by the NGS facility of Tigem; biological samples of human retina have been derived from a collaboration with Eye Bank of Venice and this gave us the possibility to analyze human mirnome in physiological conditions as described here: http://www.ncbi.nlm.nih.gov/pubmed/26819412
Since July 2012 I have joined the [5]Alberto Luini's group in Naples;
as postdoc inside the Luini's group, I have participated to the development of the FIT analysis aimed at extracting probe sets having the tendency to respond consistently to a group of drugs (in the published paper drugs are CFTR correctors but the analysis together with the associated pathways
reconstruction efforts ,are applicable to other similar setting).
In the same year, I have developed a pipeline involving promoter analysis and an ordination technique applied to gene groups derived from a microarrays analysis. This approach has allowed to decipher a portion of a signaling pathway involved in lipid signaling.
from August 2009 to spring 2011 I worked as Postdoc at BIOTEC Technical University of Dresden in the Applied Bioinformatics group;
from December 2007 to July 2008 I was a consultant for the microarrays analysis at the lab.of pharmacogenomics in the onlus E.Tempia, Biella, Italy; In March 2007 I joined the CRS4 Bioinformatics SRL as consultant for a project related to protein network inferences.
In May 2003 I joined the [6] MINT group in the University of Tor Vergata, Rome, Italy led by G. Cesareni; due to my enrolement in the [7] Ph.D Programme in complexity in post-genomic biology ( University of Torino) , I was hosted for some time as visiting Ph.D. student at the LMU Department of Statistics where I joined the Information Theory and Bioinformatics research group led by [8]Korbinian Strimmer and subsequently at the Smurfit Institute of Genetics, University of Dublin, Trinity College, where I joined the [9]Evolutionary Genetics and Bioinformatics Laboratory led by professor Mario Fares . Among the coordinators of my PhD program it is of some worth to mention prof. M. Caselle, R. Calogero, F. Bussolino with which I have interacted during my PhD. For my Ph.D. thesis defence (December 2007) I developed some Computational Frameworks for wiring human and yeast proteomes Media:mythesis.pdf.gz. The work was carried out at the Dep. of Biology of the University of Tor Vergata from December 2004 to February 2007 (advisor Prof.G. Cesareni ) and elsewhere (CRS4 and Fondo Tempia) for the other 10 months, given my status of PhD student without ministerial fellowship.
My first experiences in Bioinformatics date back to March 1999, in the University of Milano Bicocca and in the company Pharmacia (2002). In the University of Milano Bicocca I was involved in a project related to modeling by homology the cold-active lipase of Pseudomonas fragili (advisor Prof. P. Fantucci and L.De Gioia) ; in the company Pharmacia I was involved in evaluating softwares for structural bioinformatics. In the same period I was also involved in projects related to microarrays analysis carried on in the Immunoly group led by prof.ssa P. Ricciardi-Castagnoli, always in the University of Milano Bicocca. For my Master in Bioinformatics thesis (2003) I developed some computational frameworks to link differential expression genes with the presence of functional motifs in its related upstream regions (advisor prof. R. Calogero).
For my Master in Biological Science thesis (1999) at the Department of Plant Molecular Biology, Universita degli studi di Milano http://www.unimi.it/, I worked on molecular markers in the characterization of cultivar of vitis vinifera (advisor prof. F. Sala and M.Labra).
Interests
My work is related to Bioinformatics and Computational Biology in general. I work on the development and exploration of computational methods to analyze and interpret data from a variety of cutting-edge high-throughput experimental technologies. In particular, my research interests are: Statistical properties of protein interactomes; Data integration; Machine learning. System biology and modeling of biological pathways; Co-evolution in protein networks. Synthetic biology DIY Biology; Fablab; Biohacking Microfluidics
In my Ph.D thesis I studied some approaches to model and to reconstruct protein interactomes from the available experimental data. Some spin off projects of that work were related to decoding evolutionary signals in protein networks and to identifying features associated to the different types of protein interactions (physical and functional, promiscuous and selective, permanent and transient) including also the no interaction category.
Web sites
- https://www.researchgate.net/profile/Maria_Persico/contributions
- https://tigem.academia.edu/MariaPersico
- http://www.google.com/codesearch?hl=it
- http://www.google.com/webhp?hl=en
- http://www.biomedexperts.com/Portal.aspx
- http://conceptwiki.org/
- http://www.labome.org/expert/italy/university/persico/maria-persico-875994.html
- http://www.r-project.org/
- http://www.faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_Programming.html
- http://www.bioconductor.org/
Selected Publications
"Systematic Analysis of Interactomes in Sequence Properties Space" Maria Persico Current Bioinformatics, Volume 8, 5 Issues, 2013 http://eurekaselect.com/111139/article
"A combinatorics based solution for input generation in the context of classification frameworks aimed to learning Interacting Protein Class"
Maria Persico.
Proceedings of ACMBCB10 Conference, 2-4 August 2010, Niagara Falls, New York USA.
http://portal.acm.org/citation.cfm?id=1854911
or
http://bioinfws27.biotec.tu-dresden.de/phpe/ACMBCB2010_Proceedings.pdf
or
http://localhost/phpe/ACMBCB2010_Proceedings.pdf
"HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms" Maria Persico, Arnaud Ceol, Caius Gavrila, Robert Hoffmann, Arnaldo Florio Gianni Cesareni. BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S21. http://www.biomedcentral.com/1471-2105/6?issue=S4&page=2 Supplemetary material available at: http://www.biomedcentral.com/1471-2105/6/S4/S21/additional/
"Comparative interactomics"
Cesareni G*, Ceol A, Gavrila C, Palazzi LM, Persico M, Schneider MV.* All the authors have contributed equally to this review.
FEBS Lett. 2005 Mar 21;579(8):1828-33.
"Inducible IL-2 production by dendritic cells revealed by global gene expression analysis."
Francesca Granucci, Caterina Vizzardelli, Norman Pavelka, Sonia Feau, Maria Persico, Ettore Virzi, Maria Rescigno, Giorgio Moro and Paola Castagnoli.
Nat Immunol. 2001 Sep;2(9):882-8.
My favourite places
Island of Lampedusa and Linosa
