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Daniel D'Andrea


Personal Informations
Name -- D'Andrea Daniel
Address 16, Via P.L. Cattolica, 80124, Naples, Italy
Telephone +393477611374
E-mail daniel(dot)dandrea(at)gmail(dot)com
Nationality Italian
Date of birth 16, October, 1980


My background consists of strong programming skills as well as significant training in genomics and molecular biology, which place me well to contribute in multidisciplinary areas such as bioinformatics and computational biology. My research focuses on the new sequencing techniques, the study of metabolic networks and the investigation of the structural and regulatory differences of the isozymes.
In the last three years, in Biocomputing group at Sapeinza University, I had the possibility to analyze several experiments produced by Next Generation Sequencing technologies dealing with different biomedical problems such as the identification of molecules involved in HBV replications, the contribution of long non coding RNAs in muscle differentiation or the generation of a high-resolution profile of antigen-specific antibody repertoires.
These experiences have also presented the opportunity for the development of tools able to improve some critical steps of the analyses, solve problems derived by system complexity and provide user friendly results. Some examples are FIDEA, a web server for the functional interpretation of differential expression analysis; IsomirT, a tool for the small RNA-Seq analysis and isomiR identification; Phagotto, a tool for analysing deep sequencing data derived from phage-displayed libraries.
In the previous two years, working at the Department of Biology and Cellular and Molecular Pathology at University of Naples Federico II, I have gained experience in the development and management of biobanks as well as in the statistical analysis on observational studies. Meanwhile I continued my thesis work on gene-environment interactions in populations affected by complex diseases investigating the behavior of Pattern Recognition methods through simulated models.


Dates (from) -- 2010 - 2014
Position PhD in Bioinformatics and Computational Biology (Pasteurian Sciences School).
Institution Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", P.le Aldo Moro, 5 -- 00185 Rome –Italy.
Supervisor Prof. Anna Tramontano
Thesis From gene to function: using new technologies for solving old problems.
Main activities and responsibilities

Development of tools and algorithms for Next Generation Sequencing analysis to improve some crucial steps and to solve problems derived by the complexity of the system. Development of routines for visualization and reporting of the results derived by Next Generation Sequeencing experiments. Analysis of data produced by Next Generation Sequencing technologies, in particular ChIP-seq, RNA-seq and miR-seq.
Partecipation at the assessment of the intra-molecular residue-residue contact predictions submitted during the 10th round of the Critical Assessment of protein Structure Prediction (CASP) experiment.
In the lab of Life-Nanoscience at Sapienza - University of Rome: providing the research labs with primary bioinformatics support regarding the Next Generation Sequencing technology: setting of the informatics infrastructures, active monitoring of system, data security, updating software.

Dates (from-to) September 1999 - March 2008.
Title of qualification awarded Degree in Computer Science of the School of Mathematics, Physics and  Natural Sciences; grade: 110/110.
Institution University of Naples, Federico II, Italy.
Dissertation "Bioinformatics methods for analysis of gene-environment interactions in populations with complex diseases".
Supervisor Mario Nicodemi,  Department of Physic Science, University of Naples “Federico II”, Naples.
Practical training From March 2007 to March 2008, researcher in the laboratory of Prof. S.Cocozza in Department of Biology and Cellular and Molecular Pathology, University of Naples “Federico II”.
Main topics: data mining (in particular on genetic databases), machine learning, feature selection methods for analysis of complex disease data, development of new methods for data analysis, statistic analysis on genetic data.
Name "Gruppo Interdipartimentale di Bioinformatica e Biologia Computazionale"(Interdepartmental Group of Bioinformatics and Computational Biology) (G.I.B.B.), University of Naples “Federico II” - University of Salerno.
Dates (from) March 2008
Main activities Complex disease, gene-environment interaction
Modeling and simulation of gene-environment interaction in complex diseases;
Data mining: feature selection, multivariate statistical methods
Implementation of a workbench where several feature selection methods, have been challenged versus case/control populations provided by GENS, a biologically realistic simulator;
Implementation of a tool, Gene-Environment iNteraction Exploration System (GENTES), that implements an ensemble of feature selection methods aimed to identify relevant genetic and non-genetic features involved in a given complex disease.
Dates (from-to) March, 2009 – March, 2010
Name and address of employer OncoTech consortium, via Pansini 5, Naples; Department of Endocrinology and Molecular and Clinical Oncology, University of Naples “Federico II”.
Type of business or sector University of Naples “Federico II”; Clinical Research Technology s.r.l.
Occupation or position held Database manager
Main activities and responsibilities Implementation of a informatics infrastructure to complement and execute activities of biorepository: collection, classification, storage and retrieval of data about patients and biological samples; development of tools to perform quality control and statistic analysis on data to answer requests from internal users and outside organizations (such as the Department of Biology and Cellular and Molecular Pathology “L.Califano”, University of Naples “Federico II”).
Dates (from-to) July, 2009 – September,2009
Name and address of employer Istituto tecnico industriale statale (Industrial Technical State Institute, High School) “F.Giordani”, via M.Caravaggio 184, Naples.
Type of business or sector Public high school.
Occupation or position held Teacher.
Main activities and responsibilities Teacher of "Computer Science".
Dates(from-to) April, 2008 – January,2009
Name and address of employer Department of Biology and Cellular and Molecular Pathology “L.Califano”, University of Naples “Federico II”, Naples.
Type of business or sector University of Naples “Federico II”.
Occupation or position held Project manager.
Main activities and responsibilities Planning, implementation and management of a specialized database of heterogeneous data (patients, tissue, cells, experiments): active monitoring of system, data security, quality control, query interfaces, backup and recovery, statistical analysis on data.
Dates (from-to) April, 2008 – July,2008
Name and address of employer Istituto tecnico industriale statale (Industrial Technical State Institute, High School) “F.Giordani”, via M.Caravaggio 184, Naples.
Type of business or sector Public high school.
Occupation or position held Teacher.
Main activities and responsibilities Teacher of "Computer Science".


Monastyrskyy B., D’Andrea D., Fidelis K., Tramontano A., Kryshtafovych A., Evaluation of residue-residue contact prediction in CASP10. Proteins, in press.

D'Andrea D., Grassi L., Mazzapioda M., Tramontano A., FIDEA: a server for the Functional Interpretation of Differential Expression Analysis. Nucleic Acids Research, Nucleic Acids Research, 2013, 41(W1):W84-W88. [doi:10.1093/nar/gkt516]

Nardone A., Corvigno S., Brescia A., D'Andrea D., Limite G., Veneziani BM., Long-term cultures of stem/progenitor cells from lobular and ductal breast carcinomas under non-adherent conditions. Cytotechnology 2011 Jan;63(1):67-80.

Amato R., Pinelli M., D'Andrea D., Miele G., Nicodemi M., Raiconi G. and Cocozza S., A novel approach to simulate gene-environment interactions in complex diseases. BMC Bioinformatics 2010, 11:8.

CONFERENCES AND POSTERS Guerrieri F., Belloni L., D'Andrea D., Le Pera L., Pediconi N., Tramontano A., Levrero M. (2013). Identification of HBx target miRNAs that regulate HBV replication by ChIP-Seq. In: International Liver Congress™ 2013 – 48th Annual meeting of the European Association for the Study of the Liver (EASL). Amsterdam, The Netherlands, April 24 - 28 2013. Abstract published in: Journal of Hepatology 2013 vol. 58 | S45–S61.
  Guerrieri F., Belloni L., D'Andrea D., Tramontano A., Levrero M. (2012). A genome wide chromatin-immunoprecipitation (ChIP-Seq) study identifies a broad repertoire of miRNAs as direct targets of HBx. In: 2012 Annual Meeting of the American Association for the Study of Liver Diseases (AASLD). Boston, Massachusetts, November 9-13 2012. Abstract published in: Hepatology, vol. 56, Issue Supplement S1.
  D’Andrea D.,  Amato R., Pinelli M., Tagliaferri R., Cocozza S. and Miele G (2010). Challenging an ensemble approach (GENTES) with the Gene-Environment iNteraction Simulator (GENS). In: BITS Annual Meeting 2010. Bari, Italy, April, 14-16  2008.
Amato R., Cocozza S., D’Andrea D., Miele G., Nicodemi M., Pinelli M., Raiconi G. and Tagliaferri R.(2008), Assessing the power of feature selection methods in complex diseases. In: 5th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics. IIASS – Vietri sul Mare (Sa), Italy, October, 3-4 2008.
Amato R., D’Andrea D.,  Miele G., Nicodemi M., Pinelli M., Raiconi G., Tagliaferri R. and Cocozza S. (2008). Gene-Environment iNteraction Simulator (GENS) for assessing the power of feature selection methods in complex disease. In: European Conference in Computational Biology (ECCB08). Cagliari, Italy, September, 22-26 2008.
Calabrese A., D’Andrea D., Ferella L., Mele F., Minei G., Sammartino G. and Sorgente A.(2005), A frame Logic based approach to build recommendation systems: an application to e-commerce domain, Proceeding of IADIS International conference WWW/Internet 2005, vol. 1, 143-150 ISBN: 972-8924-02-X.
Bioinformatics skills Analysis of Next Generation Sequencing data (ChIP-seq, RNA-seq, microRNA-seq, DNA-seq).
Development of algorithms and tools for analysis of Next Generation Sequencing data.
Data mining of bological data.
Statistical analysis on case-control and incidence studies.
Software development Programming languages: Perl, R, SQL, Java, Matlab, C, C++, Pascal.
Standard and application: JDBC, OCL, ODBC, UML.
Web development and CMS: Macromedia DreamWeaver, Joomla, JQuery, HTML, XML.
Software development tools: JBuilder, NetBeans, Poseidon.
Software engineering: requirements, design and development of the software;hardware and software documentation; systems integration; software configuration; user interface development.
Applications Informatics tools: Latex, Ms Office Package, Open Office.
Mathematical Software: SPSS, WEKA.
Administration and networks Operating systems: Linux, Windows, Unix.
Relational database management system: MySql, PostgresSQL, SQL Server.
Database management and administration: planning, upgrade and management. Data analysis, backup and recovery, data security.
Network management: administration, planning, implementation and configuration. 
Last Updated ( Thursday, 12 June 2014 15:28 )