Universitą degli studi di Pavia
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Cremaschi's cv
PhD student in Genetics, Molecular and Cellular Biology- Cycle XXVIII.
Scientific Supervisor: Dr. Silvia Bione
Phone: ++39 0382 546362
E-mail: paolo.cremaschi01@universitadipavia.it
Curriculum
Education
2012 - Oggi UNIVERSITĄ DEGLI STUDI DI PAVIA PhD student in Genetics, Molecular and Cellular Biology
Supervisor: Dr. Silvia Bione
2012 - Master’s degree in Biological Sciences - University of Pavia Graduated with a GPA of 103 on a 110 scale
1990 – 1996 UNIVERSITĄ DEGLI STUDI DI PAVIA Student Biological Sciences – University of Pavia.
Professional experience in the research field
2012 Institute of Molecular Genetics - CNR, Fellow and PhD student at the Laboratory of Computational Biology headed by Dr. Silvia Bione. Main research activities: Development of a tool for the bioinformatic analysis of gene co-expression data.
2011 - 2012 Institute of Molecular Genetics - CNR, Student at the Laboratory of Computational Biology headed by Dr. Silvia Bione. Main research activities: Creation of a model for the analysis of gene co-expression.
Professional experience as consultant
2011 evris Italy, in the Industry Division. Main activity: coordinator of a development group for business intelligence applications.
2010 - 2011 evris Italy, independent consultant in the Industry Division. Main activity: coordinator of a group developing a distributed application for customer management and organization of the sales force.
2003 - 2010 ZeroUno computer consultant. Main activity: analyst for the development of multidimensional database for the analysis of financial data and coordinator of its support group.
2001 - 2003 ZeroUno computer consultant. Main activity: analyst and developer for several projects for the Marketing department.
2000 - 2003 I.T.I. Information Technology Italy, senior developer. Main activity: analyst and developer for several projects for the Marketing and Sales departments.
2000 - 2003 RS R & D, systems analyst and developer. Main activity: network installations and developer in projects for the integration of multiplatform environment in many industries.
Laboratory skills
Construction of mutants for expression of recombinant proteins: PCR, transfection, Miniprep, DNA extraction, purification of DNA in cesium gradients, gel sequence, selection of mutants by ampicillin
Cell cultures: human cells (HeLa) and murine (3T3)
Immunofluorescence microscopy and confocal microscopy
Technical skills
• Operative systems
LINUX: RedHat, Fedora, Ubuntu
Microsoft: MS-DOS, Windows NT / 95 / 98 / XP / 2000 / 2003 / Windows 7
Mac OS: from version X
• Programming languages
Visual Studio: Visual Basic: from 3.0 to .NET 2008, C#.Net
Office Automation: VBA, VB Script
Java: Java, JScript
Lisp: common lisp, Allegro Common Lisp
SQL: T-SQL, PL/SQL
R: (from version 2.9 to 2.14) working with the following packages base, xtable, stat, Rcurl, RJSON, XML, plyr, arules, Rweka, lattice, VennDiagram, plotrix, splines, RSQLite, RODBC, RPostgreSQL, RMySQL, multicore, snow
R/Bioconductor: ho lavorato con i package GEOquery, ArrayExpress, MADAM, genefilter, Biobase, geneplotter, AnnotationDbi, puma, affyQCReport, limma, multtest, PGSEA, GSEABase, GenePattern, DAVIDQuery, affycoretools, GOSim, igraph
HTML
XML: XML, DTD, XSL
• Relational databases
Sybase
SQL Server: from version 6.5 to 2008
SS Analysis Server: from version 2000
Access: from version 2.0 a 2010
Oracle: version 11
MySQL: version 5
PostgreSQL: from version 8.1 a 9.1.3
SQLite: version 3
• Biological repositories
DAVID Web Site: Functional Annotation Clustering, Functional Annotation Chart, Functional Annotation Table, Gene Functional Classification, Gene name batch viewer and Gene ID conversion
DAVID Application Program Interface: access to the application trough the DAVIDQuery and Rcurl R packages
Gene Expression Omnibus (GEO) web site: query for Dataset, Gene profile and Platform, differentially expressed genes, gene cluster and data quality analysis
Gene Expression Omnibus (GEO) Application Program Interface: access to the application trough the GEOquery R package
ArrayExpress web site: query for Dataset, Gene profile and Platform, differentially expressed genes
ArrayExpress Application Program Interface: access to the application trough the ArrayExpress and Rcurl R packages
Gene Ontology (GO) web site: query with the AmiGO search engine and graph analysis
Gene Ontology (GO) Application Program Interface: access to the application trough the GOSim R package and graph analysis trough informatics algorithms
Kyoto Enciclopedia of Genes and Genomes (KEGG) web site: Functional pathway analysis
NetView web site: graph analysis
Molecular Signatures Database (MSigDB) Application Program Interface: gene list annotation trough PGSEA and GSEABase R packages
GRAIL e GraphWiz: gene list annotation
Cytoscape: graph analysis
• Development and configuration of parallel calculus environments
SQL Server: ETL processes (SSIS) parallelization and optimization of parallel queries trough the Execution Plan configuration
SS Analysis Server: OLAP loading processes optimization
Windows: multithread application development and optimization
• R: development and optimiztion of multhitread applications with the “multicore” and “snow” R packages
Research Project
Analysis of the biological signals in high-throughput experiment data
I'm doing a PhD in the computational biology laboratory of the Institute of Molecular Genetics IGM - CNR under the supervision of Dr. Silvia Bione.
My research activities is on the integration of data resulting from various "omics technologies" publicly available. In particular, I work on the analysis of data from high-throughput experiment through the developments of "machine learning" and "data mining" algorithms.
Currently my activity concerns the development of a bioinformatic tool for the co-expression analysis for the identification of functional pathways. We plan to make this tool available in the local CNR network as a first step and, as final target, publicly available in Internet.
The development of this tool include:
- development of an ETL process (Extract Transform and Load)
- development of a structured database
- creation and optimization of an algorithm for data analysis
- development of a web interface for public access to the instrument
- process optimization through the process parallelization
As part of this project I am collaborating with the Institute of Applied Mathematics and Information Technologies IMATI - CNR in order to implement the algorithm for the analysis of co-expression in languages that make it possible to take full advantage of architectures for parallel computing (Fortran and C + + ).
Publications
Abstracts
Cremaschi P, Rovida S, Sacchi L, Lisa A, Montecucco A, Biamonti G, Bione S, Sacchi G – 2012 Inside complex disorder pathways through gene expression analysis (oral comunication)
ATTI Convegno Intelligence Data Analysis in Biomedicine and Pharmacology IDAMAP Pavia (PV) in stampa
Cremaschi P, Rovida S, Sacchi L, Lisa A, Montecucco A, Biamonti G, Bione S, Sacchi G – 2012 CorrelaGenes: a new tool for the interpretation of the human transcriptome (poster)
ATTI Convegno NETTAB Como (CO) in stampa
R. Rossi, E. Savini, P. Cremaschi, F. Weighardt, G. Biamonti, G. Ciarrocchi e A. Montecucco - 1995 Dissezione funzionale della DNA ligasi I di mammifero: identificazione dei segnali coinvolti nella localizzazione nucleare e subnucleare della proteina (oral comunication)
ATTI Convegno Congiunto ABCD-AGI-SIBBM-SIMGBM, Montesilvano Lido (PE), 5.25, pag. 91.
Scientific Supervisor: Dr. Silvia Bione
Phone: ++39 0382 546362
E-mail: paolo.cremaschi01@universitadipavia.it
Curriculum
Education
2012 - Oggi UNIVERSITĄ DEGLI STUDI DI PAVIA PhD student in Genetics, Molecular and Cellular Biology
Supervisor: Dr. Silvia Bione
2012 - Master’s degree in Biological Sciences - University of Pavia Graduated with a GPA of 103 on a 110 scale
1990 – 1996 UNIVERSITĄ DEGLI STUDI DI PAVIA Student Biological Sciences – University of Pavia.
Professional experience in the research field
2012 Institute of Molecular Genetics - CNR, Fellow and PhD student at the Laboratory of Computational Biology headed by Dr. Silvia Bione. Main research activities: Development of a tool for the bioinformatic analysis of gene co-expression data.
2011 - 2012 Institute of Molecular Genetics - CNR, Student at the Laboratory of Computational Biology headed by Dr. Silvia Bione. Main research activities: Creation of a model for the analysis of gene co-expression.
Professional experience as consultant
2011 evris Italy, in the Industry Division. Main activity: coordinator of a development group for business intelligence applications.
2010 - 2011 evris Italy, independent consultant in the Industry Division. Main activity: coordinator of a group developing a distributed application for customer management and organization of the sales force.
2003 - 2010 ZeroUno computer consultant. Main activity: analyst for the development of multidimensional database for the analysis of financial data and coordinator of its support group.
2001 - 2003 ZeroUno computer consultant. Main activity: analyst and developer for several projects for the Marketing department.
2000 - 2003 I.T.I. Information Technology Italy, senior developer. Main activity: analyst and developer for several projects for the Marketing and Sales departments.
2000 - 2003 RS R & D, systems analyst and developer. Main activity: network installations and developer in projects for the integration of multiplatform environment in many industries.
Laboratory skills
Construction of mutants for expression of recombinant proteins: PCR, transfection, Miniprep, DNA extraction, purification of DNA in cesium gradients, gel sequence, selection of mutants by ampicillin
Cell cultures: human cells (HeLa) and murine (3T3)
Immunofluorescence microscopy and confocal microscopy
Technical skills
• Operative systems
LINUX: RedHat, Fedora, Ubuntu
Microsoft: MS-DOS, Windows NT / 95 / 98 / XP / 2000 / 2003 / Windows 7
Mac OS: from version X
• Programming languages
Visual Studio: Visual Basic: from 3.0 to .NET 2008, C#.Net
Office Automation: VBA, VB Script
Java: Java, JScript
Lisp: common lisp, Allegro Common Lisp
SQL: T-SQL, PL/SQL
R: (from version 2.9 to 2.14) working with the following packages base, xtable, stat, Rcurl, RJSON, XML, plyr, arules, Rweka, lattice, VennDiagram, plotrix, splines, RSQLite, RODBC, RPostgreSQL, RMySQL, multicore, snow
R/Bioconductor: ho lavorato con i package GEOquery, ArrayExpress, MADAM, genefilter, Biobase, geneplotter, AnnotationDbi, puma, affyQCReport, limma, multtest, PGSEA, GSEABase, GenePattern, DAVIDQuery, affycoretools, GOSim, igraph
HTML
XML: XML, DTD, XSL
• Relational databases
Sybase
SQL Server: from version 6.5 to 2008
SS Analysis Server: from version 2000
Access: from version 2.0 a 2010
Oracle: version 11
MySQL: version 5
PostgreSQL: from version 8.1 a 9.1.3
SQLite: version 3
• Biological repositories
DAVID Web Site: Functional Annotation Clustering, Functional Annotation Chart, Functional Annotation Table, Gene Functional Classification, Gene name batch viewer and Gene ID conversion
DAVID Application Program Interface: access to the application trough the DAVIDQuery and Rcurl R packages
Gene Expression Omnibus (GEO) web site: query for Dataset, Gene profile and Platform, differentially expressed genes, gene cluster and data quality analysis
Gene Expression Omnibus (GEO) Application Program Interface: access to the application trough the GEOquery R package
ArrayExpress web site: query for Dataset, Gene profile and Platform, differentially expressed genes
ArrayExpress Application Program Interface: access to the application trough the ArrayExpress and Rcurl R packages
Gene Ontology (GO) web site: query with the AmiGO search engine and graph analysis
Gene Ontology (GO) Application Program Interface: access to the application trough the GOSim R package and graph analysis trough informatics algorithms
Kyoto Enciclopedia of Genes and Genomes (KEGG) web site: Functional pathway analysis
NetView web site: graph analysis
Molecular Signatures Database (MSigDB) Application Program Interface: gene list annotation trough PGSEA and GSEABase R packages
GRAIL e GraphWiz: gene list annotation
Cytoscape: graph analysis
• Development and configuration of parallel calculus environments
SQL Server: ETL processes (SSIS) parallelization and optimization of parallel queries trough the Execution Plan configuration
SS Analysis Server: OLAP loading processes optimization
Windows: multithread application development and optimization
• R: development and optimiztion of multhitread applications with the “multicore” and “snow” R packages
Research Project
Analysis of the biological signals in high-throughput experiment data
I'm doing a PhD in the computational biology laboratory of the Institute of Molecular Genetics IGM - CNR under the supervision of Dr. Silvia Bione.
My research activities is on the integration of data resulting from various "omics technologies" publicly available. In particular, I work on the analysis of data from high-throughput experiment through the developments of "machine learning" and "data mining" algorithms.
Currently my activity concerns the development of a bioinformatic tool for the co-expression analysis for the identification of functional pathways. We plan to make this tool available in the local CNR network as a first step and, as final target, publicly available in Internet.
The development of this tool include:
- development of an ETL process (Extract Transform and Load)
- development of a structured database
- creation and optimization of an algorithm for data analysis
- development of a web interface for public access to the instrument
- process optimization through the process parallelization
As part of this project I am collaborating with the Institute of Applied Mathematics and Information Technologies IMATI - CNR in order to implement the algorithm for the analysis of co-expression in languages that make it possible to take full advantage of architectures for parallel computing (Fortran and C + + ).
Publications
Abstracts
Cremaschi P, Rovida S, Sacchi L, Lisa A, Montecucco A, Biamonti G, Bione S, Sacchi G – 2012 Inside complex disorder pathways through gene expression analysis (oral comunication)
ATTI Convegno Intelligence Data Analysis in Biomedicine and Pharmacology IDAMAP Pavia (PV) in stampa
Cremaschi P, Rovida S, Sacchi L, Lisa A, Montecucco A, Biamonti G, Bione S, Sacchi G – 2012 CorrelaGenes: a new tool for the interpretation of the human transcriptome (poster)
ATTI Convegno NETTAB Como (CO) in stampa
R. Rossi, E. Savini, P. Cremaschi, F. Weighardt, G. Biamonti, G. Ciarrocchi e A. Montecucco - 1995 Dissezione funzionale della DNA ligasi I di mammifero: identificazione dei segnali coinvolti nella localizzazione nucleare e subnucleare della proteina (oral comunication)
ATTI Convegno Congiunto ABCD-AGI-SIBBM-SIMGBM, Montesilvano Lido (PE), 5.25, pag. 91.
