PERSONAL DATA

Bioinformatics, Medical Informatics, Integrated Management and Analysis of Genomic Information with Patient Clinical and High-throughput Genomic Data, Information Systems and Databases in Bioinformatics, Biomedical Terminologies and Ontologies, Distributed Web Applications for Medicine and Biology, Biomedical Data Analysis and Knowledge Discovery, Image Processing.

Bioinformatics: a great Computer Engineering opportunity (with ethical relevance)

The extraordinary recent progresses in biotechnology and system biology make possible to quickly produce (few hours) at low cost (less than 1,000 $) the DNA sequence and the genetic and epigenetic activity profile of each individual in different conditions. This generates an amazing quantity of experimental data (about 0.3 TB for each individual and tested condition), which is shortly going to represent the biggest and most important “big data problem” of mankind.

Furthermore, the complexity of such data is not only in their sheer size, but also in the heterogeneity of underlying samples, conditions, biomolecular entities, etc., which is larger than in any other domain as it reflects the intrinsic biological complexity.

All these aspects and the largely public availability of these data make this domain a great challenge as well as a big opportunity for the Computer Engineering community, which can greatly contribute to unveil the nature laws through the reverse engineering of biological processes.

All main Computer Science centers in the world are investing many resources and personnel in Bioinformatics, with a medium/long term strategy to increase both their knowledge and critical mass in the domain, whose complexity requires both of them in order to aspire reaching relevant results of impact. They are paving the way to this aim by acquiring increasing domain expertise through on-the-field interdisciplinary activities, developed in collaboration also with top life science research centers, toward the ultimate goal of improving understanding, diagnosis and treatment of complex disorders (such as cancer, diabetes or several neurological pathologies) for the improvement of patients’ conditions and well-being. This can be done also at Politecnico di Milano.

Information extraction from the available big data and their interpretation towards knowledge discovery is a key aspect in bioinformatics. Several terminologies and ontologies are available to describe current biomedical knowledge and are broadly used to express biomedical facts (i.e., controlled annotations of biomedical entities). Increasingly numerous and heterogeneous biomedical controlled annotations are sparsely available in a variety of data sources; their integration and comprehensive analysis is a fundamental aspects of bioinformatics, which helps biologists’ evaluation and interpretation of experimental results fostering biomedical discoveries.

MAIN RELEVANT ASPECTS OF THE CURRICULUM VITAE (Top)

· Scientific National Qualifications to first level University Professor (Full Professor) in the sector 09/H1 – “Information Elaboration Systems” (ex scientific sector ING-INF/05) obtained at unanimity of the evaluation commission

· 3 Scientific National Qualifications to second level University Professor (Associate Professor) in the sectors 09/H1 – “Information Elaboration Systems”, 01/B1 – “Informatics” and 09/G2 – “Bioengineering” (ex scientific sectors ING-INF/05, INF/01 and ING-INF/06); in particular, the qualification in the sector 09/G2 has been obtained at unanimity of the evaluation commission

· 3 Distinct research areas: Bioinformatics, Medical Informatics and Image processing, always as methods and applications of Computer Engineering principles, technologies and methods)

· 352 Publications: from 1993 to 2024 (30 years) have been produced 4 curatorships and 2 editorial of international journal supplements and 346 publications (138 in the last 10 years (2013-2024), 68 in the last 5 years (2019-2024)), among which:

– 96 in International scientific journals (49 in the last 10 years, 28 in the last 5 years), besides 5 under evaluation; Class of relevance of the scientific journals: 66 in Class Q1 (best) of Scimago Journal Rank (SJR), 2 on IEEE Transactions on Information Technology in Biomedicine (of which 1 with single author), 9 on IEEE/ACM Transactions on Computational Biology and Bioinformatics, and 1 on IEEE Transactions on Knowledge and Data Engineering; first author in 29 and last author in 26 of such 96 publications (where author order matter)

– 3 in international (1) or national books (2)

– 37 as chapters of international books (19 in the last 12 years, 17 in the last 5 years) and 4 as chapters of national books

– 100 in proceedings of international congresses (26 in the last 10 years, 9 in the last 5 years) of which 22 in IEEE congresses, and 8 in proceedings of national congresses (4 in the last 10 years); 1 Best Paper award from the International Neural Networks Society

– 96 abstracts (44 in the last 10 years, 19 in the last 5 years)

– 2 research reports

The commission for the Scientific National Qualification to the role of University professor of first level in the Sector 09/H1 – “Information Elaboration Systems” evaluated “excellent” the scientific production within the national and international research scenario, based on originality, methodological rigor and innovation, and "very good" the relevance of the publications within the scientific disciplinary sector

The commission for the Scientific National Qualification to the role of University professor of second level in the Sector 09/H1 – “Information Elaboration Systems” evaluated “very good” the quality and editorial collocation of these scientific publications within the international research scenario

In the Evaluation of the Quality of the National Research (VQR) 2004-2010 I got the average evaluation 0.92 (Politecnico di Milano - Area 09: average DEI: 0.80; average ING-INF/05: 0.71; average ING-INF/06: 0.89), evaluated on 5 journal publications (over 5 maximum publications required), of which 3 were evaluated excellent

Given my interdisciplinary scientific activity, my bibliometric data are on more resources: DBLP: 131 papers (2000-2023) (https://dblp.org/pid/32/1035.html); PubMed: 102 papers (1993-2023) regarding bioinformatics applications (http://www.ncbi.nlm.nih.gov/pubmed?term=masseroli%20m); Google Scholar H-index 29 with 3572 citations (last 10 years, 156 papers with 1532 citations and H-index 21; last 5 years, 73 papers with 460 citations and H-index 11)

· Participation/Co-ordination of national and International projects: in 6 European (in 1 as co-responsible of research unit and in 1 as responsible and coordinator of the group for bio applications) and in 17 national projects (of which 13 as responsible or co-responsible of research unit);

· Evaluator for the European Commission: in FP7-HEALTH-2012-INNOVATION-1 and Horizon2020 H2020-PHC-2014, SC1-PM-02-2017, H2020-MSCA-IF-2017 and HORIZON-HLTH-2021-DISEASE_04-04, and ERC-2017-COG

· Participation in editorial or conference committees: Associate Editor of IEEE Transactions on Information Technologies in Biomedicine, of 3 supplements of the journal BMC Bioinformatics; and of 1 of EMBnet.journal. Chair of conferences NETTAB2012, BITS2015 and BioLom 2013; Chair of Sections in the ACM BCB, CIBB, DILS and BIBE conferences; Member of the scientific committee of many conferences: CIBCB, EvoBIO, DILS, IB, IWBBIO, IDAMAP, NETTAB, EMBC, MEDICON, BITS

· Experience at national or international scientific institutes: Research activity at: Politecnico di Milano; Universidad de Granada – Spain; Biomedical Engineering Department, The Cleveland Clinic Foundation, Cleveland, OH – US; European Institute of Oncology, Milano; Pharmacological Research Institute “Mario Negri”, Milano; San Raffaele Hospital, Milano. Visiting scholar at School of Computing and Mathematics, University of Ulster, UK, and Molecular Graphics Suite, School of Chemistry, Bath University, UK; Visiting faculty at National Library of Medicine, National Institute of Health, US; Visiting Professor at Departamento de Anatomía Patológica, Facultad de Medicina, Universidad de Granada – Spain

· Participation at the teaching and academic life of the institute: Since academic year 2019-2020 vice-coordinator of the Master Degree in Bioinformatics for Computational Genomics joint between Politecnico di Milano and Università Statale of Milan. From 2002 coordinator of 12 courses, of which: 5 of the Research Doctorate (Ph.D.) in Information Engineering, 3 of University Master, 3 of Superior Technical Education. From the academic year 2000-2001 official lecturer of 13 university courses of Politecnico di Milano, of which: 4 of the Research Doctorate in Information Engineering or Bioengineering, 3 of Master of I or II level, 3 of Laurea Magistrale or Laurea Specialistica (Master degree) in Information Engineering and/or in Bioengineering, 1 of Laurea. From 2001 Supervisor or Co-supervisor of 67 Laurea Theses and from 2010 Supervisor of 14 PhD students of the Research Doctorate in Information Engineering of Politecnico di Milano

· Systems development: Development of several systems for data integration and analysis and related Web applications, which I maintained publicly accessible and were actively used by the scientific community; among them:

o GMQL (since January 2017, more than 16,000 accesses from about 3,700 different IPs)

o MuSERA (since March 2016, nearly 6,500 accesses from about 1,000 different IPs)

o GPKB (since October 2012, more than 60,000 accesses from nearly 3,250 different IPs)

o Bio-SeCo (since August 2012, nearly 14,500 accesses from about 2,900 different IPs)

o GFINDer (since July 2004, more than 350,000 accesses from nearly 13,500 different IPs)

o MyWEST (since August 2003, about 95,000 accesses from about 15,800 different IPs, with more than 450 copies downloaded)

o MicroGen (da luglio 2005, quasi 13,500 accessi da circa 3,500 IP diversi)

o GAAS (since April 2003, more than 90,000 accesses from about 14,800 different IPs, with nearly 700 copies downloaded)

· Autonomy grade: Full: I opened and lead the research line in Bioinformatics at Politecnico di Milano; I lead almost all the publications, or the informatics computational part of the most applicative ones (the far majority of my coauthors are students, PhDs, post-docs or investigators of other scientific sector); 1 publication on IEEE T ITB is as single author

I practically always performer research activity in first person, mostly without being within a consolidated group performing such activity, or following a school founder in such activity

· 3 Patent: 1 regarding a package of informatics applications (1997), 2 regarding advanced computational oncogenomics methods for patient stratification (for colorectal or ovarian cancer)

HONORARY APPOINTMENTS (Top)

– Visiting scholar, School of Computing and Mathematics, University of Ulster at Jordanstown, Belfast, Great Britain in 2006,

– Visiting faculty, National Library of Medicine, National Institute of Health, US, for 6 months during 2004 and 2005.

– Visiting Professor, Pathology Department, School of Medicine, University of Granada, Granada – Spain, in 1992.

APPOINTMENTS (Top)

2019-today	Vice-coordinator of the Master Degree in Bioinformatics for Computational Genomics joint between Politecnico di Milano and Università Statale of Milan.
2015-today	Associate Professor (S.S.D. ING-INF/05) at Electronic, Information and Bioengineering Department, Politecnico di Milano, Milano - Italy
2011-today	Lecturer of University course “ICT for Health Care”, Master degree in Computer Science Engineering and Master degree in BioMedical Engineering, Politecnico di Milano, Milano - Italy
2010-today	Lecturer of University course “Informatics”, Laurea degree in Energy Engineering and Laurea degree in Mechanic and Transport Engineering, Politecnico di Milano, Milano - Italy
2008-today	Lecturer of University course “Bioinformatics and Computational Biology”, Master degree in Computer Science Engineering and Master degree in BioMedical Engineering, Politecnico di Milano, Milano - Italy
2006-2015	Researcher (S.S.D. ING-INF/05) at Electronic, Information and Bioengineering Department, Politecnico di Milano, Milano - Italy
2000-2010	Lecturer of University course “BioMedical Informatics”, Master degree in BioMedical Engineering, Politecnico di Milano, Milano - Italy
1999-2006	Research Assistant, Bioengineering Department, Politecnico di Milano, Milano - Italy
1999-2001	Researcher, Experimental Oncology Department, European Institute of Oncology, Milano - Italy
1996-1998	Post-Doctoral Fellow, Pathology Department, School of Medicine, University of Granada, Granada - Spain
1994-1995	Research Fellow, Biomedical Engineering Department, The Cleveland Clinic Foundation, Cleveland - OH, USA
1993-1996	PhD Student, Pathology Department, School of Medicine, University of Granada, Granada - Spain
1991-1993	Researcher, Pharmacological Research Institute " Mario Negri", Milano - Italy
1990-1991	Research Fellow, Molecular Graphics Suite, School of Chemistry, University of Bath, Bath - UK
1990	Research Fellow, Nuclear Medicine Department, San Raffaele Hospital, Milano - Italy

ACADEMIC DEGREES (Top)

2017	National Scientific Qualification to first level University Professor (Full Professor) in the area: - “Computer Science Engineering” (09/H1, ex. ING-INF/05), with "excellent" evaluation of the scientific production within the national and international research scenario, based on originality, methodological rigor and innovation, and with "very good" relevance of the publications within the scientific disciplinary sector
2013	National Scientific Qualification to second level University Professor (Associate Professor) in the areas: - “Computer Science Engineering” (09/H1, ex. ING-INF/05), with “very good” evaluation of quality and editorial location of the scientific publications within the research international scenario - “Computer Science” (01/B1, ex. ING-INF/06), with “fully adequate” evaluation of quality and editorial location of the scientific publications within the research international scenario - “BioMedical Engineering” (09/G2, ex. ING-INF/06), with “very good” evaluation at unanimity of quality and editorial location of the scientific publications within the research international scenario
2005	Specialization in "Power Scripting" (for using the genomics information provided by the National Center for Biotechnology Information databanks) at National Center for Biotechnology Information - National Library of Medicine, National Institute of Health Bethesda, MD - USA.
1998	Specialization in Digital Processing Techniques for Multimedia Images at Computational Science and Artificial Intelligence Department of Granada University, Granada - Spain (with mark 27/30).
1997	Specialization in Web Site Creation and Management at the Computer Science School of Granada University, Granada - Spain (with mark 30/30).
1996	PhD in Electronic Engineering at Granada University, Granada - Spain, (with maximum mark "cum laude").
1995	Post-graduate Specialization in Biomedical Engineering Research at Biomedical Engineering Department of the Research Institute of "The Cleveland Clinic Educational Foundation", Cleveland, OH - USA.
1991	Post-graduate Specialization in Business Management at the "XIII Corso Integrato Interdisciplinare Natale Toffoloni" organized by the "Fondazione Istituto Dirigenti Italiani" in Milan, Italy.
1990	Master degree in Electronic Engineering, speciality Bioengineering, at Politecnico di Milano, Milano – Italy (with mark 96/100). Thesis: "Bioimage processing: development of methods and programs on personal computer”.
1984	Diploma in humanistic Secondary School (with mark 54/60).

ACADEMIC TEACHING (Top)

2019-today	Vice-coordinator of the Master Degree in Bioinformatics for Computational Genomics joint between Politecnico di Milano and Università Statale of Milan.
2023	Lecturer of the module “GenoMetric Query Language (GMQL)” within the PhD course “Data Management and Analysis for Computational Biology”, PhD degree in Computer Science Engineering, Politecnico di Milano, Milano – Italy
2022	Lecturer of the module “AI challenges in onco-genomics” within the PhD course “AI Methods for Bioengineering Challenges”, PhD degree in Biomedical Engineering, Politecnico di Milano, Milano – Italy
2015, 2017, 2019	Coordinator and Lecturer of the course “Genomic Computing” within the PhD degree in Computer Science Engineering, Politecnico di Milano, Milano – Italy
2013	Coordinator of the course “Big Data Analysis Methods for Knowledge Discovery. Application on Challenging Life Science Data” within the PhD degree in Computer Science Engineering, Politecnico di Milano, Milano – Italy
2012	Lecturer of the course “Algorithms and methods for Bioinformatics” organized by the University of Cagliari, in collaboration with Regione Sardegna, consortium Sardegna Ricerche and Research Center CRS4.
2011-today	Lecturer of the course “ICT for Health Care and Life Sciences”, 5 CFU (S.S.D. ING-INF/05), Master degree in Computer Science Engineering and Master degree in Biomedical Engineering, Politecnico di Milano, Milano – Italy
2011	Coordinator of the course “Current Challenges in Bioinformatics” within the PhD degree in Computer Science Engineering, Politecnico di Milano, Milano – Italy
2010-today	Lecturer of the course “Informatics B”, 7 CFU (S.S.D. ING-INF/05), Degree in Energy Engineering, and Mechanic and Transport Engineering, Politecnico di Milano, Milano – Italy
2010, 2012, 2014, 2016, 2018	Lecturer of the course “Integration and Computational Analysis of Genomic and Proteomic Information”, PhD degree in Computer Science Engineering, Politecnico di Milano, Milano – Italy
2009	Coordinator of the course “Array Comparative Genomic Hybridization (aCGH) and its bioinformatic and statistical analysis” within the PhD degree in Computer Science Engineering, Politecnico di Milano, Milano – Italy
2008-today	Lecturer of the course “Bioinformatics and Computational Biology for Molecular Medicine”, 5 CFU (S.S.D. ING-INF/05), Master degree in Computer Science Engineering and Master degree in Biomedical Engineering, Politecnico di Milano, Milano – Italy
2004-2009	Lecturer of the course “Management of clinical data and international standards” of the ESF one year Master in “Informatics processing of biomedical data and telecontrol in Medicine”, University of Verona, Verona - Italy
2003-2010	Lecturer of the course “Laboratory of BioMedical Informatics and Distributed Systems”, Master degree in Biomedical Engineering, Politecnico di Milano, Milano - Italy
2003-2008	Lecturer of the course “Laboratory of Internet application building for medicine in healthcare” of the ESF one year course for the training of “Expert Technicians in Medical Informatics”, Politecnico di Milano, Milano - Italy
2002-2004	Coordinator of the module “Infrastructures for Telemedicine” within the ESF Telemedicine Master course of “Internet for Health Care and Medicine”, Cefriel - Politecnico di Milano, Milano - Italy
2002	Lecturer within the PhD course “Advanced Health Information Systems”, PhD in Biomedical Engineering, Politecnico di Milano, Milano - Italy
2002-2004	Lecturer of tutorials on Genomics data banks, Web access to remote databases, Software agents, Biomedical vocabularies and language systems, Bioimage archives, Medical image and Clinical data integration, within the ESF Telemedicine Master course “Internet for Health Care and Medicine”, Cefriel - Politecnico di Milano, Milano - Italy
2000-2003	Lecturer of the course “Medical Informatics III (laboratory)”, 5 CFU (S.S.D. ING-INF/05), Master degree in Biomedical Engineering, Politecnico di Milano, Milano - Italy
2000-2002	Lecturer and coordinator of the one week course "Seminars on Practical Clinical Informatics and on Basic Medical Statistics", International Academy of Bergamo for Advanced Medical Sciences and International Heart School, Bergamo - Italy
2000-2002	Lecturer of the practical lessons within the course “Medical Informatics”, Bachelor degree in Biomedical Engineering, Politecnico di Milano, Milano - Italy
2000	Lecturer within the module “Medical Informatics” of the ESF "Course for the training of Expert Technicians in Planning, Control, and Management of Sanitary Environments and Products", Politecnico di Milano, Milano - Italy
1999-2002	Lecturer of tutorial on Videomicroscopy and Image Processing within the course “Bioimaging”, Master degree in Biomedical Engineering, Politecnico di Milano, Milano - Italy

RESEARCH GRANTS (Top)

NRRP

· 2022- 2025 "MUSA – Multi-layered Urban Sustainability Action” – Spoke 2: Big Data-Open Data in Life Sciences", aimed at the development of an innovative digital platform for fast and secure storage and exchange of big data in life sciences, translate basic research into applications aiming to improve nutritional, healing and environmental conditions of citizens, organize data collection and processing with AI techniques; Responsible of Research Unit for Politecnico di Milano, Milano – Italy.

· 2022- 2025 Co-funding by the IRCCS Istituto Neurologico Carlo Besta for a fellowship in the PhD in Information Engineering of Politecnico di Milano to study computational approaches of data integration for the stratification of chronic pain patients; Responsible of Research Unit for Politecnico di Milano, Milano – Italy.

· 2022- 2025 Co-funding by the Pharmacological Research Institute Mario Negri - IRCCS for a fellowship in the PhD in Information Engineering of Politecnico di Milano to study computational genomics methods for the repurposing of valproic acid and simvastatin in the treatment of pancreatic carcinoma; Responsible of Research Unit for Politecnico di Milano, Milano – Italy.

ERC

· 2016- 2021 "GeCo: Data-Drieven Genomic Computing", aimed at efficient and easier genomic big data integration, management, querying and analysis; Co-responsible of the Bioinformatics Group Research Unit for Politecnico di Milano, Milano – Italy.

· 2008- 2013 "SECO: Search Computing", Responsible and Coordinator of the group bio applications of Research Unit for Politecnico di Milano, Milano – Italy.

EU

· 2007- 2010 STREP, FP6: "COOPER: Collaborative Open Environment for Project-Centered Learning", Member of Research Unit for Politecnico di Milano, Milano – Italy.

EIT

· 2020 "ViruSurf: System for searching and analyzing virus sequences", Member of Research Unit for Politecnico di Milano, Milano – Italy.

· 2015 "Connecting Digital Cities (3city)", Member of Research Unit for Politecnico di Milano, Milano – Italy.

· 2015 "ExpLorMI", Member of Research Unit for Politecnico di Milano, Milano – Italy.

PRIN

· 2023-2025 ARTUSI: "Computational analysis and functional validation of epithelial-mesenchymal interactions supporting tumour onset and progression using patient-derived models of colorectal cancer", aimed at performing a thorough computational analysis of RNA-seq data of colorectal cancer patient-derived and cell line-derived mouse xenografts, focused on ligand/receptor pairs and the “secretome”, to generate an interaction map depicting consistency, heterogeneity and significance of candidate paracrine interactions in colorectal cancer; Responsible of Research Unit for Politecnico di Milano, Milano – Italy.

· 2013-2015 "Data-Centric Genomic Computing (GenData 2020)", aimed at building abstractions, models and protocols for an informatics infrastructure able to efficiently support the organization, search and analysis of a network of genomic data, made available from servers located in the world main biological laboratories; Member Co-responsible of Research Unit for Politecnico di Milano, Milano – Italy.

· 2009- 2011 "EASE: Entity Aware Search Engine" aimed at developing novel methods and techniques for building large scale, “entity aware” search engines and for exploiting the retrieved information in an effective and efficient way; Member of Research Unit for Politecnico di Milano, Milano – Italy.

FSE

· 2007 "Elementi indicanti lo stato dell’arte della Cartella Clinica Informatizzata nelle Aziende Sanitarie e Ospedaliere Italiane", Collaborator for Università degli Studi di Verona, Verona – Italy.

REGIONE LOMBARDIA

· 2011 “BioProGenPlat: piattaforma integrata di biologia molecolare, genomica e proteomica correlata con le banche dati pubbliche”, for the development of a bioinformatica platform to support biotechnology SME activity; Responsible of Research Unit for Politecnico di Milano, Milano – Italy.

· 2007 "Virtual BioInformatics Lab: bioinformatics infrastructures and computational approaches supporting cancer diagnostics and biomarker discovery ", Co-responsible of Research Unit for Politecnico di Milano, Milano – Italy.

MURST

· 2003- 2005 "Information and Communication Technology for the management of prevention, care and rehabilitation processes", Collaborator for Politecnico di Milano, Milano – Italy.

· 1999-2000 "Development of Software Agents for Healthcare Information Systems", Collaborator for Politecnico di Milano, Milano – Italy.

FISS

· 1995-1998 "Immunehistochemical and digital image analysis study of the glomerulosclerosis and renal tubulointerstitial lesions associated with aging", Collaborator for the University of Granada, Granata – Spain.

CARIPLO

· 2024-2026 "DARIEN - Data Science Approaches for Representativeness and Inclusivity ENhancement in clinical trials", aimed at developing Data Science approaches to evaluate eligibility criteria and enhance representativeness and inclusivity in clinical trials, in order to bridge the gap between populations enrolled in clinical trials and broader populations affected by the same disease; Member of Research Unit for Politecnico di Milano, Milano – Italy. [Submitted – under evaluation]

TELETHON

· 2022-2025 "Computational Gene Therapy", funding of two three-year fellowships for the PhD in Computer Science Engineering of Politecnico di Milano for developing computational methods for the characterization of cell-free epigenome in human diseases and gene therapy treated patients, and for clonal tracking in patients under gene therapy and stem cell transplantation; Scientific responsible for Politecnico di Milano, Milano – Italy.

ONCOLOGY

· 2021-2023 "Feasibility study for the joint genomic diagnosis of genetic risk and sensitivity to new drugs in breast, ovary and colon cancer", three-year research agreement with Rete Oncologica Alleanza Contro il Cancro (ACC) for the development and application of analytical approaches of computational onco-genomics, through machine learning and deep learning techniques; Scientific responsible for Politecnico di Milano, Milano – Italy.

· 2020-2022 "Computational oncogenomics", three-year research agreement with Pharmacological Research Institute Mario Negri - IRCCS funding a fellowship in the PhD in Information Engineering of Politecnico di Milano to develop novel computational methods to characterize genomic and transcriptomic profiles of ovary tumours through NGS technology; Scientific responsible for Politecnico di Milano, Milano – Italy.

· 2019 "Machine learning techniques for the engineering of prognostic classifiers", one-year research contract with Fondazione del Piemonte per l’Oncologia - IRCCS to develop machine learning analysis techniques of genomic gene expression data, within the research project: “STRA-RNA” funded by the Italian Ministry of Health - Allianz Against Cancer (ACC) Oncologic Network IRCCS; Scientific responsible for Politecnico di Milano.

· 2000-2002 "Development of algorithms and tools for microarray data management and analysis", Collaborator for the European Institute of Oncology, Milano – Italy.

HONORS AND AWARDS (Top)

2011 Prize from the International Neural Networks Society for the best scientific paper: “Biomolecular annotation prediction through information integration”, by Chicco D, Tagliasacchi M, Masseroli M, presented by a young researcher at the conference Eighth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2011), Gargnano (BS) June 30^th - July 2^nd, 2011.

2006 “Visiting scholar program fellowship” from School of Computing and Mathematics of University of Ulster at Jordanstown, Belfast, for the evaluation of analysis algorithms of similarity among genes according to their functional annotation.

2004 e 2005 “Visiting faculty exchange program fellowship” of the National Library of Medicine, National Institute of Health, for six months, for the application of Natural Language Processing techniques on Medline abstract of scientific publications in order to automatically extract gene-gene and gene-disease semantic relations, and for the post-processing of extracted information with the aim of inferring unknown gene-gene and gene-disease relations.

2004 Selection, within the evaluation of Italian University Scientific Research, of the scientific publication Masseroli M, Cerveri P, Pelicci PG, Alcalay M. GAAS: “Gene Array Analyzer Software for management, analysis and visualization of gene expression data” Bioinformatics 2003;19(6):774-775 and the related web tool (http://www.bioinformatics.deib.polimi.it/GAAS/), as one of the best 7 research products of the Bioengineering Department of the Politecnico di Milano in the years 2001-2003.

2001 “Best scientific publication in basic investigation - year 2000”, from the "Fundación Hospital Clínico" of Granada - Spain, for the paper "Automatic quantification of liver fibrosis: design and validation of a new image analysis method. Comparison with semiquantitative indexes of fibrosis" published in Journal Hepatology 2000;32(3):453-64.

1997 "Premio Cesar LLamazares", from the journal "Nefrología" for the paper "Papel de los inhibidores de la enzima de conversión de la angiotensina en la prevención de las alteraciones renales asociadas al envejecimiento" published in Nefrología 1996;16(4):319-26.

1996-1998 European Post-Doctoral Fellowship from the Spanish board of science and technology "Comisión Interministerial de Ciencia y Tecnología (CICYT)" within the “Acciones de Formación de Personal Investigador - Estancias de Científicos y Tecnólogos Extranjeros en España” to develop research projects in the field of biomedical image processing.

1994 “Special fellowship” from “The Cleveland Clinic Educational Foundation”, as researcher for the development of image analysis programs for the automatic analysis of intravascular ultrasound images of human coronary arteries.

1993 “Best oral communication”, to the communication "Cuantificación automatizada de la fibrosis renal por análisis digital de imagen", presented at the "XVI National Congress of the Spanish Society of Pathology" held in Tenerife - Spain in May 1993.

1993 Doctoral fellowship from "Sandoz Pharma S.A.E." to develop image analysis programs for the quantification of renal fibrosis induced by Cyclosporin A pharmacological treatment.

1991 Post-graduate specialization fellowship from "Fondazione IDI" to attend the business management course "XIII Corso integrato interdisciplinare Natale Toffoloni".

PATENT (Top)

2024 EXA-CRIS: six-class predictor of ColoRectal tumor Intrinsic Subtypes, based on multi-label machine learning algorithm [under submission].

2024 HR3D: data-driven predictor of the Homologous Recombination Deficiency (HRD) status of ovarian cancer patients, in support to the precise best diagnosis and personalized treatment, based on machine learning algorithm [under submission].

ORGANIZATION AND BOARDS OF SCIENTIFIC EVENTS (Top)

Chair in Congresses

– Co-chair of the Special Session "Machine learning in health informatics and biological systems" within the 15th international Conference on Computational Intelligence methods for Bioinformatics and Biostatistcs - CIBB 2018, held in September 2018 at Almada (Lisboa), PT.

– Co-chair of the Track “Big Data in Bioinformatics”, within the 8^° ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2017), held in August 2017 at Boston, MA.

– Co-chair of the Special Session “Genomic big data management, modeling and computing”, within the international conference Intelligent Systems for Molecular Biology - ISMB 2016, held in July 2016 at Orando, FL.

– Chair of the Special Session “Genomic big data management, modeling and computing”, within the meeting “BITS 2016: Bioinformatics Italian Society Meeting”, held in June 2016 at University of Salerno, Fisciano (SA), Italy.

– Co-chair of the meeting “BITS 2015: Bioinformatics Italian Society Meeting”, held in June 2015 at University Milano “Bicocca”, Milan, Italy.

– Co-chair of the meeting “1° Bioinformatics, Computational Biology and System Biology Lombardy Day (BioLom 2013)”, held in November 2013 at Politecnico di Milano, Milan, Italy.

– Co-chair of the workshop “NETTAB 2012: Network Tools and Applications in Biology, focused on: Integrated BioSearch”, held in November 2012 at Politecnico di Milano in Como, Italy.

– Chair of the scientific session “Web Services” of the workshop “Data Integration in the Life Sciences (DILS 2010)”, held in August 2010.

– Chair of the scientific session “Graph-Based Modelling and Integration” of the workshop “Data Integration in the Life Sciences (DILS 2009)”, held in July 2009.

– Chair of the scientific session “Gene Expression Analysis” of the “Ninth IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2009)” held in June 2009.

Congresses Scientific Committees

– Member of the Technical Program Committee of the 11^th edition of the “IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2015) ”

– Member of the Program Committee of the 12^th edition of the “European Conference on Evolutionary Computation, Machine Learning and Data Mining in Computational Biology (EvoBIO 2014)”

– Member of the Technical Program Committee of the 10^th international conference “Beyond Databases, Architectures and Structures (BDAS’14)”

– Member of the Technical Program Committee of the “IEEE-EMBS International Conferences on Biomedical and Health Informatics (BHI)”

– Member of the Steering Committee of the “IWBBIO: International Work-Conference on Bioinformatics and Biomedical Engineering” since its foundation in 2013.

– Member of the International Scientific Committee of the “MEDICON2013: XIII Mediterranean Conference on Medical and Biological Engineering and Computing”.

– Member of the Scientific Committee of the workshop “International Symposium on Integrative Bioinformatics (IB)” in 2010, 2011, 2012 and 2013.

– Member of the Program Committee of the workshop “Data Integration in the Life Sciences (DILS)” in 2009, 2010 and 2012.

– Member of the Scientific Committee of the workshop “NETTAB: Network Tools and Applications in Biology”, focused on “A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications” (2007), “Clinical Bioinformatics” (2011), “Integrated BioSearch” (2012) and “Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories” (2013).

– Member of the Program Committee of the workshop “Intelligent Data Analysis in bioMedicine And Pharmacology (IDAMAP)” in 2007, 2008, 2009, 2010, 2011 and 2012.

– Reviewer of the “Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)” in its editions of 2007 and 2010.

– Member of the Scientific Committee of multiple editions of the Annual Meeting of the Bioinformatics Italian Society (BITS) in 2007, and from 2014 since today.

– Member of the Organizing Committee of the “First European Symposium on Current and Future directions for Clinical Flow Cytometry”, University of Granada, Granada – Spain in 1995.

EDITORIAL BOARDS, EVALUATION ACTIVITIES AND MEMBERSHIPS (Top)

Scientific Journal Committees

– Editor of supplement 12, volume 17, 2016, “BITS 2015: the annual meeting of the Italian Society of Bioinformatics” of the scientific journal BMC Bioinformatics.

– Associated Editor of the supplement 14, volume 15, 2014, “NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories” of the scientific journal BMC Bioinformatics.

– Editor of supplement 1, volume 15, 2014, “Integrated Bio-Search: selected works from the 12th International Workshop on Network Tools and Applications in Biology (NETTAB 2012)” of the scientific journal BMC Bioinformatics dedicated to Integrated Bio-Search.

– Editor of supplement B, volume 18, 2012, of the scientific journal EMBnet.journal dedicated to the workshop NETTAB 2012 on Integrated Bio-Search.

– Associated Editor of supplement 14, volume 13, 2012, “Research from the Eleventh International Workshop on Network Tools and Applications in Biology (NETTAB 2011)” of the scientific journal BMC Bioinformatics dedicated to Clinical Bioinformatics.

– Associate Editor of the scientific journal IEEE Transactions on Information Technologies in Biomedicine in 2004-2012.

– Reviewer of several the scientific journals since 2002, including IEEE Transactions on Information Technologies in Biomedicine, IEEE Transactions on Biomedical Engineering, IEEE Transactions on Medical Imaging, IEEE Transactions on Education, Bioinformatics, BMC Bioinformatics, BMC Genomics, Nucleic Acids Research, Computers in Biology and Medicine, Expert Reviews and VLDB Journal.

Scientific Evaluation Committees

– Independent evaluator for the European Research Council as expert for the evaluation of research proposals for the Horizon2020 call HORIZON-HLTH-2021-DISEASE_04-04 “Clinical validation of artificial intelligence (AI) solutions for treatment and care” in 2021.

– Independent evaluator for the European Research Council as expert for the evaluation of research proposals for the Marie Sklodowska-Curie Individual Fellowships call H2020-MSCA-IF-2017 in 2017.

– Independent evaluator for the European Research Council as expert for the evaluation of research proposals for the ERC Consolidator Grant call ERC-2017-COG “ICON-BIO-Integrated Connectedness for a New Representation of Biology” in 2016, in the Bioinformatics domain.

– Independent evaluator for the European Commission as expert for the evaluation of research proposals for the Horizon2020 call SC1-PM-02-2017 “New concepts in patient stratification” in 2015, in the domain of health care, demographic changes and well-being.

– Independent evaluator for the European Commission as expert for the evaluation of research proposals for the Horizon2020 call H2020-PHC-2014 “Advancing bioinformatics to meet biomedical and clinical needs” in 2014, in the domain of health care, demographic changes and well-being.

– Independent evaluator for the European Commission of research project proposals for the call FP7-HEALTH-2012-INNOVATION-1 in 2012, in the health care domain.

– Independent evaluator of research project proposals for the national PRIN and FIRB programs of the Italian Ministry of University and Research in 2011, in the informatics domain and of applications to the biomedical domain.

– Member of the Repertoire of Experts created for the delivery of specialized consulting and tutoring services, addressed to the beneficiaries of the facilities of the global grant INGENIO, promoted by the Lombardy Region and addressed to the new graduated selected for the development of a collaboration or applied research project in 2007.

Membership in Scientific Societies and Working Groups

– Member of the International Society for Computational Biology (ISCB) since 2015.

– Member of the Working Group on “Insurability of healthcare facilities and the medical and nursing staff”, promoted by the university consortium CINEAS “For a Risk Culture”, since 2013.

– Member of the Engineering in Medicine and Biology Society of the Institute of Electrical and Electronics Engineers (IEEE) in 2009-2010.

– Member of the Bioinformatics Italian Society (BITS) since 2002.

– Member of the American Medical Informatics Association (AMIA) in 2002-2005.

– Member of the Research Group CTS138 in Health Science and Technology of the Andalusian Board, Spain, in 1995-1998.

BIOINFORMATICS TOOLS DEVELOPED (Top)

(Use statistics on Marco 2024)

The highest impact bioinformatics applications that have been developed and maintained publicly accessible are:

– GMQL: GenoMetric Query Language (more than 16,000 accesses from about 3,700 different IPs)

– MuSERA: MuSERA: Multiple Sample Enriched Region Assessment (nearly 6,500 accesses from about 1,000 different IPs)

– GPKB: Genomic and Proteomic Knowledge Base (more than 60,000 accesses from nearly 3,250 distinct IPs)

– Bio-SeCo: Bio Search Computing (nearly 14,500 accesses from about 2,900 distinct IPs)

– GFINDer: Genome Function INtegrated Discoverer (more than 350,000 accesses from nearly 13,500 distinct IPs)

– MyWEST: My Web Extraction Software Tool (about 95,000 accesses from nearly 15,800 distinct IPs, with more than 450 downloaded copies)

– GAAS: Gene Array Analyzer Software (more than 90,000 accesses from about 14,800 distinct IPs, with nearly 700 downloaded copies)

– MicroGen: MIAME compliant microarray experiment information manager (nearly 13,500 accesses from more than 3,500 distinct IPs, with about 50 downloaded copies)

PUBLICATIONS (here the full publication list) (Top)

See the current list of my publications on:

– DBLP Bibliography Server

– IEEE Xplore Digital Library

– Collection of Computer Science Bibliographies

– PubMed

– Google Scholar page

A. Journals B. Books C. Chapters in Books

A. JOURNALS (Top)

106. Iudica C, Cascianelli S, Masseroli M. Uncovering genetic insights in triple negative breast cancer by exploring patient mutational profiles with novel machine learning strategies. Artificial Intelligence in Medicine 2025 (under review).

105. Mongardi S, Pengo MF, Lombardi C, Steca P, Masseroli M. Comparing LS7 and LE8 risk scores in Europe: Understanding the impact of sleep on cardiovascular health. European Heart Journal 2025. (under review).

104. Cascianelli S, Mainetti A, Medico E, Isella C, Masseroli M. Integrative approach for tumor class discovery and prediction applied to colorectal cancer. Briefings in Bioinformatics 2025 (under review).

103. Mongardi S, Tacca M, Cascianelli S, Masseroli M. Enhancing Tree-Based Machine Learning Models with Prior Biological Knowledge for Improved Interpretability. Artificial Intelligence in Medicine 2025. (under review).

102. Cascianelli S, Milojkovic I, Masseroli M. Multi-label characterization and classification for thorough gene expression-based stratification of cancer patients. Journal of Biomedical Informatics 2025 (in press).

101. Campi R, De Santis A, Colombo P, Scarpazza P, Masseroli M. Machine learning-based forecast of Helmet-CPAP therapy failure in acute respiratory distress syndrome patients. Computer Methods and Programs in Biomedicine 2025; 260: 108574, p. 1-9. DOI: 10.1016/j.cmpb.2024.108574

100. Mongardi S, Cascianelli S, Masseroli M. Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis. Bioinformatics 2024, 40(10): btae605, p. 1-8. DOI: 10.1093/bioinformatics/btae605

99. Sergi A, Beltrame L, Marchini S, Masseroli M. Integrated approach for low-fraction variant calling benchmarking using artificial data. BMC Bioinformatics 2024, 25: 180, p. 1-20. DOI: 10.1186/s12859-024-05793-8

98. Vergani AM, Bagnato A, Masseroli M. Predicting bovine daily milk yield by leveraging genomic breeding values. Computers and Electronics in Agriculture 2024, 219: 108777, p. 1-10. DOI: 10.1016/j.compag.2024.108777

97. Mannarino L, Ravasio N, D’Incalci M, Marchini S, Masseroli M. In-silico identification of novel pharmacological synergisms: the trabectedin case. International Journal of Molecular Sciences 2024; 25: 2059, p. 1-12. DOI: 10.3390/ijms25042059

96. Cascianelli S, Ceddia G, Marchesi A, Masseroli M. Identification of transcription factor high accumulation DNA zones. BMC Bioinformatics 2023; 24: 395, p. 1-20. DOI: 0.1186/s12859-023-05528-1

95. Cascianelli S, Galzerano A, Masseroli M. Supervised Relevance-Redundancy assessments for feature selection in omics-based classification scenarios. Journal of Biomedical Informatics 2023; 144: 104457. p. 1-11. DOI: 10.1016/j.jbi.2023.104457

94. Cascianelli S, Barbera C, Ulla AA, Grassi E, Lupo B, Pasini D, Bertotti A, Trusolino L, Medico E, Isella C, Masseroli M. Multi-label transcriptional classification of colorectal cancer reflects tumour cell population heterogeneity. Genome Medicine 2023; 15: 37, p. 1-17. DOI: 10.1186/s13073-023-01176-5

93. Schreiber J, Boix C, Lee JW, Li H, Guan Y, Chang C-C, Chang J-C, Hawkins-Hooker A, Schölkopf B, Schweikert G, Rojas Carulla M, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom R, Farrell N, Halow J, Lee K, Jiang L, Yang X, Epstein C, Strattan JS, Bernstein B, Snyder M, Kellis M, Stafford W, Kundaje A, ENCODE Imputation Challenge Participants. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biology 2023; 24(1): 79, p. 1-22. DOI: 0.1186/s13059-023-02915-y

92. Pinoli P, Ceddia G, Ceri S, Masseroli M. Predicting drug synergism by means of Non-negative Matrix Tri-Factorization. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022; 19(4): 1956-1967. DOI: 10.1109/TCBB.2021.3091814

91. Alfonsi T, Bernasconi A, Canakoglu A, Masseroli M. Genomic data integration and user-defined sample set extraction for population variant analysis. BMC Bioinformatics 2022; 23: 401, p. 1-33. DOI: 10.1186/s12859-022-04927-0

90. Frasca F, Matteucci M, Morelli M, Leone M, Masseroli M. ShallowChrome: Accurate and highly interpretable logistic classifiers for predicting gene expression from histone modifications. BMC Bioinformatics 2022; 23: 151, p. 1-17. DOI: 10.1186/s12859-022-04687-x

89. Pallotta S, Cascianelli S, Masseroli M. RGMQL: Scalable and interoperable computing of heterogeneous omic big data and metadata in R/Bioconductor. BMC Bioinformatics 2022; 23: 123, p. 1-28. DOI: 10.1186/s12859-022-04648-4

88. Leone M, Galeota E, Masseroli M, Pelizzola M. Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions. Bioinformatics 2022; 38(5): 1183–1190. DOI: 10.1093/bioinformatics/btab815

87. Cristovao F, Cascianelli S, Canakoglu A, Carman M, Nanni L, Pinoli P, Masseroli M. Investigating pan-cancer and multi-omic data for deep learning based breast cancer subtyping. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022; 19(1): 121-134. DOI: 10.1109/TCBB.2020.3042309

86. Bernasconi A, Canakoglu A, Masseroli M, Ceri S. META-BASE: a novel architecture for large-scale genomic metadata integration. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022; 19(1): 543-557. DOI: 10.1109/TCBB.2020.2998954

85. Regondi C, Fratelli M, Damia D, Matteucci M, Masseroli M. Predictive modeling of gene expression regulation. BMC Bioinformatics 2021; 22: 571, p. 1-21. DOI: 10.1186/s12859-021-04481-1

84. Ventrella P, Delgrossi G, Ferrario G, Righetti M, Masseroli M. Supervised machine learning for the assessment of chronic kidney disease advancement. Computer Methods and Programs in Biomedicine 2021; 209: 106329, p. 1-9. DOI: 10.1016/j.cmpb.2021.106329

83. Canakoglu A, Pinoli P, Gulino A, Nanni L, Masseroli M, Ceri S. Federated sharing and processing of genomic datasets for tertiary data analysis. Briefing in Bioinformatics 2021; 22(3): bbaa091, p. 1-11. DOI: 10.1093/bib/bbaa091

82. Bernasconi A, Canakoglu A, Masseroli M, Pinoli P, Ceri S. A review on viral data sources and integration methods for COVID-19 mitigation. Briefing in Bioinformatics 2021; 22(2): 664-675. DOI: 10.1109/TCBB.2020.3042309

81. Pidò S, Ceddia G, Masseroli M. Computational analysis of fused co-expression networks for the identification of candidate cancer gene biomarkers. npj Systems Biology and Applications 2021; 7(1): 17, p. 1-10. DOI: 10.1038/s41540-021-00175-9

80. Moro G, Masseroli M. Gene function finding through cross-organism ensemble learning. BioData Mining 2021; 14(1): 14, p. 1-21. DOI: 10.1186/s13040-021-00239-w

79. Bernasconi A, Canakoglu A, Masseroli M, Ceri S. The road towards data integration in human genomics: players, steps and interaction. Briefing in Bioinformatics 2021; 22(1): 30-44. DOI: 10.1093/bib/bbaa080

78. Martano G, Leone M, D’Oro P, Matafora V, Cattaneo A, Masseroli M, Bachi A. SMfinder: Small molecules finder for metabolomics and lipidomics analysis. Analytical Chemistry 2020; 92(13): 8874-8882. DOI: 10.1021/acs.analchem.0c00585

77. Ceddia G, Pinoli P, Ceri S, Masseroli M. Matrix factorization-based technique for drug repurposing predictions. IEEE Journal of Biomedical and Health Informatics 2020; 24(11): 3162-3172. DOI: 10.1109/JBHI.2020.2991763

76. Ceol A, Montanari P, Bartolini I, Ceri S, Ciaccia P, Patella M, Masseroli M. Search and comparison of (epi)genomic feature patterns in multiple genome browser tracks. BMC Bioinformatics 2020; 21(1): 464, p. 1-13. DOI: 10.1186/s12859-020-03781-2

75. Cascianelli S, Molineris I, Isella C, Masseroli M, Medico E. Machine learning for RNA sequencing-based intrinsic subtyping of Breast Cancer. Scientific Reports 2020; 10(1): 14071, p. 1-13. DOI: 10.1038/s41598-020-70832-2

74. Cappelli E, Cumbo F, Bernasconi A, Canakoglu A, Ceri S, Masseroli M, Weitschek E. OpenGDC: unifying, modeling, and integrating cancer genomic data and clinical metadata. Applied Sciences 2020; 10: 6367. DOI: 0.3390/app10186367

73. Ceddia G, Martino LN, Parodi A, Secchi P, Campaner S, Masseroli M. Association rule mining to identify transcription factor interactions in genomic regions. Bioinformatics 2020; 36(4): 1007-1013. DOI: 10.1093/bioinformatics/btz687

72. Canakoglu A, Bernasconi A, Colombo A, Masseroli M, Ceri S. GenoSurf: Meta-data driven semantic search server for integrated genomic datasets. Database 2019; pii: baz132, p. 1-21. DOI: 10.1093/database/baz132

71. Masseroli M, Canakoglu A, Pinoli P, Kaitoua A, Gulino A, Horlova O, Nanni L, Bernasconi L, Perna S, Stamoulakatou E, Ceri S. Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data. Bioinformatics 2019; 35(5): 729-736. DOI: 10.1093/bioinformatics/bty688

70. Chicco D, Fernando Palluzzi, Masseroli M. Novelty indicator for enhanced prioritization of predicted Gene Ontology annotations. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2018; 15(3), 594-565. DOI: 10.1109/TCBB.2017.2695459

69. Jalili V, Matteucci M, Masseroli M, Ceri S. Explorative visual analytics on interval-based genomic data and their metadata. BMC Bioinformatics 2017; 18(1): 536. DOI: 10.1186/s12859-017-1945-9

68. Cumbo F, Fiscon G, Ceri S, Masseroli M, Weitschek E. TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas. BMC Bioinformatics 2017; 18(1): 6, p. 1-9. DOI: 10.1186/s12859-016-1419-5

67. Jalili V, Matteucci M, Masseroli M, Ceri S. Indexing Next Generation Sequencing data. Information Sciences 2017; 384: 90-109. DOI: 10.1016/j.ins.2016.08.085

66. Ceri S, Kaitoua A, Masseroli M, Pinoli P, Venco F. Data management for heterogeneous genomic datasets. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2017; 14(6):1251-1264. DOI: 10.1109/TCBB.2016.2576447

65. Cambiaghi A, Ferrario M, Masseroli M. Analysis of metabolomic data: tools, current strategies and future challenges for ‘omics’ data integration. Briefings in Bioinformatics 2017; 18(3):498-510. DOI: 10.1093/bib/bbw031

64. Jalili V, Matteucci M, Morelli MJ, Masseroli M. MuSERA: Multiple Sample Enriched Region Assessment. Briefings in Bioinformatics 2017; 18(3):367-381. DOI: 10.1093/bib/bbw029

63. Milanesi L, Guffanti A, Mauri G, Masseroli M. BITS 2015: the annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 2016; 17(Suppl 12): 396, p. 73-76.

62. Masseroli M, Kaitoua A, Pinoli P, Ceri S. Modeling and interoperability of heterogeneous genomic big data for integrative processing and querying. Methods 2016; 111: 3-11. DOI: 10.1016/j.ymeth.2016.09.002

61. Montanari P, Bartolini I, Ciaccia P, Patella M, Ceri S, Masseroli M. Searching patterns in genomic sequences. IEEE Transactions on Knowledge and Data Engineering 2016; 28(11): 3053-3067. DOI: 10.1109/TKDE.2016.2595582

60. Domeniconi G, Masseroli M, Moro G, Pinoli P. Cross-organism learning method to discover new gene functionalities. Computer Methods and Programs in Biomedicine 2016; 126:20-34. DOI: 10.1016/j.cmpb.2015.12.002

59. Fernandez JD, Lenzerini M, Masseroli M, Venco F, Ceri S. Ontology-based search of genomic metadata. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2016; 13(2):233-247. DOI: 10.1109/TCBB.2015.2495179

58. Chicco D, Masseroli M. Ontology-based prediction and prioritization of gene functional annotations. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2016; 13(2):248-260. DOI: 10.1109/TCBB.2015.2459694

57. Masseroli M, Canakoglu A, Ceri S. Integration and querying of genomic and proteomic semantic annotations for biomedical knowledge extraction. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2016; 13(2):209-219. DOI: 10.1109/TCBB.2015.2453944

56. Jalili V, Matteucci M, Masseroli M, Morelli MJ. Using combined evidence from replicates to evaluate ChIP-seq peaks. Bioinformatics 2015; 31(17): 2761-2769. DOI: 10.1093/bioinformatics/btv293

55. Chicco D, Masseroli M. Software suite for gene and protein annotation prediction and similarity search. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2015; 12(4):837-843. DOI: 10.1109/TCBB.2014.2382127

54. Masseroli M, Canakoglu A, Quigliatti M. Detection of gene annotations and protein-protein interaction associated disorders through transitive relationships between integrated annotations. BMC Genomics 2015; 16(Suppl 6):S5, p. 1-16. DOI: 10.1186/1471-2164-16-S6-S5

53. Masseroli M, Pinoli P, Venco F, Kaitoua A, Jalili V, Paluzzi F, Muller H, Ceri S. GenoMetric Query Language: A novel approach to large-scale genomic data management. Bioinformatics 2015; 31(12): 1881-1888.DOI: 10.1093/bioinformatics/btv048

52. Pinoli P, Chicco D, Masseroli M. Computational algorithms to predict Gene Ontology annotations. BMC Bioinformatics 2015; 16(Suppl 6): S4, p. 1-15. DOI: 10.1186/1471-2105-16-S6-S4

51. Masseroli M, Picozzi M, Ghisalberti G, Ceri S. Explorative search of distributed bio-data to answer complex biomedical questions. BMC Bioinformatics 2014; 15(Suppl 1): S3, p. 1-14.

50. Masseroli M, Mons B, Bongcam-Rudloff E, Ceri S, Kel A, Lisacek F, Rechenmann F, Romano P. Integrated Bio-Search: Challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics 2014; 15(Suppl 1): S2, p. 1-15.

49. Romano P, Lisacek F, Masseroli M. NETTAB 2012 on “Integrated Bio-Search”. BMC Bioinformatics 2014; 15(Suppl 1): S1, p. 1-5.

48. Pessina F, Masseroli M, Canakoglu A. Visual composition of complex queries on an integrative genomic and proteomic data warehouse. Engineering 2013 Oct 25; 5(10B): 94-98.

47. Bellazzi R, Masseroli M, Murphy S, Shabo A, Romano P. Clinical Bioinformatics: challenges and opportunities. BMC Bioinformatics 2012; 13(Suppl 14): S1, p. 1-8.

46. Pattini L, Bertacco R, Candiani G, Masseroli M, Servi S. Trends in biomedical engineering: focus on Genomics and Proteomics. Journal of Applied Biomaterials & Biomechanics 2011 May-Aug; 9(2): 98-108.

45. Masseroli M, Ghisalberti G, Ceri S. Bio-Search Computing: Integration and global ranking of bioinformatics search results. Journal of Integrative Bioinformatics 2011; 8(2): 166, p. 1-9.

44. Pinciroli F, Corso M, Fuggetta A, Masseroli M, Bonacina S, Marceglia S. Telemedicine and E-Health. IEEE Pulse 2011 May-Jun; 2(3): 62-70.

43. Ghisalberti G, Masseroli M, Tettamanti L. Quality controls in integrative approaches to detect errors and inconsistencies in biological databases. Journal of Integrative Bioinformatics 2010 Mar; 7(3): 119, p. 1-13.

42. D’Antonio M, Masseroli M. Extraction, integration and analysis of alternative splicing and protein structure distributed information. BMC Bioinformatics 2009 Oct 15;10 (Suppl 12):S15, p. 1-8.

41. Masseroli M, Bachi A, Boschetti E, Righetti PG. Searching for specific motifs in affinity capture in proteome analysis. Journal of Proteomics 2009 Jul 21;72(5):791-802.

40. Holst MI, Maercker C, Pintea B, Masseroli M, Liebig C, Jankowski J, Miething A, Martini J, Schwaller B, Oberdick J, Schilling K, Baader SL. Engrailed-2 regulates genes related to vesicle formation and transport in cerebellar Purkinje cells. Molecular and Cellular Neuroscience 2008 Aug;38(4):495-504.

39. Masseroli M, Marchente M. X-PAT: a multiplatform patient referral data management system for small healthcare institution requirements. IEEE Transactions on Information Technology in Biomedicine 2008 Jul;12(4):424-432.

38. Bachi A, Simó C, Restuccia U, Guerrier L, Fortis F, Boschetti E, Masseroli M, Righetti PG. Performance of combinatorial peptide libraries in capturing the low-abundance proteome of reb blood cells. II: behaviour of resins containing individual amino acids. Analytical Chemistry 2008 May 15;80(10):3557-3565.

37. Ceri S, Bolchini C, Braga D, Brambilla M, Campi A, Comai S, Fraternali P, Lanzi PL, Masseroli M, Matera M, Negri M, Pelagatti G, Pozzi G, Quintarelli E, Schreiber FA, Tanca L. Data and web management research at Politecnico di Milano. ACM SIGMOD Record 2007 Dec;36(4):43-48.

36. Masseroli M. Management and analysis of genomic functional and phenotypic controlled annotations to support biomedical investigation and practice. IEEE Transactions on Information Technology in Biomedicine 2007 Jul;11(4):376-385.

35. Del Moral FG, O’Valle F, Masseroli M, Del Moral RG. Image analysis application for automatic quantiﬁcation of intramuscular connective tissue in meat. Journal of Food Engineering 2007 Jul;81(1):33–41.

34. Masseroli M, Bellistri E, Franceschini A, Pinciroli F. Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists. BMC Bioinformatics 2007 March 8;8(Suppl 1):S14, p. 1-10.

33. Masseroli M, Pinciroli F. BioInformatics application service providers of Politecnico di Milano. Healthcare IT Management, the official Journal of the European Association of Healthcare IT Managers 2006 Summer;1(2):42-44.

32. Masseroli M, Kilicoglu H, Lang F-M, Rindflesch TC. Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. BMC Bioinformatic 2006 Jun 8;7(1):291, p. 1-12.

31. Masseroli M, Pinciroli F. Using Gene Ontology and genomic controlled vocabularies to analyze high-throughput gene lists: three tool comparison. Computers in Biology and Medicine 2006 Jul-Aug;36(7-8):731-747.

30. Masseroli M, Visconti A, Bano SG, Pinciroli F. He@lthCo-op: a web-based system to support distributed healthcare co-operative work. Computers in Biology and Medicine 2006 Feb;36(2):109-127.

29. Masseroli M, Galati O, Manzotti M, Gibert K, Pinciroli F. Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists. BMC Bioinformatics 2005;6(Suppl 4):S18, p. 1-8.

28. Burgarella S, Cattaneo D, Pinciroli F, Masseroli M. MicroGen: a MIAME compliant web system for microarray experiment information and workflow management. BMC Bioinformatics 2005;6(Suppl 4):S6, p. 1-6.

27. Masseroli M, Stella A, Alcalay M, Pinciroli F. GeneWebEx: Gene annotation Web Extraction, aggregation, and updating from web-interfaced biomolecular databanks. International Journal of Software Engineering and Knowledge Engineering 2005;15(3):511-526.

26. Masseroli M, Galati O, Pinciroli F. GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Research 2005;33:W717-W723.

25. Masseroli M, Stella A, Meani N, Alcalay M, Pinciroli F. MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks. Bioinformatics 2004;20(18):3326-3335.

24. Masseroli M, Martucci D, Pinciroli F. GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining. Nucleic Acids Research 2004;32:W293-W300.

23. Masseroli M, Cerveri P, Pelicci PG, Pinciroli F, Alcalay M. Gene Array Analyzer Software: a multi-user platform for management, analysis and visualization of gene expression data from replicate experiments. Minerva Biotecnologica 2003;15(4):207-216.

22. Pinciroli F, Masseroli M, Tognola G. The educational offer in Medical Informatics and Telemedicine at the Engineering Faculty of the Politecnico di Milano. IEEE Transactions on Education 2003;46(3):394-398.

21. Masseroli M, Cerveri P, Pelicci PG, Alcalay M. GAAS: Gene Array Analyzer Software for management, analysis and visualization of gene expression data. Bioinformatics 2003;19(6):774-775.

20. Caballero T, Pérez-Milena A, Masseroli M, O'Valle F, Salmerón FJ, Del Moral RMG, Sánchez-Salgado G. Liver fibrosis assessment with semiquantitative indexes and image analysis quantification in sustained-responder and non-responder interferon-treated patients with chronic hepatitis C. Journal Hepatology 2001;34(5):740-747.

19. Arrebola Vargas F, Masseroli M, Reguero Callejas ME, Mesa Aguado FL, Olmo Sevilla A, Aguilar Peña M, Espigares Fuentes B, Del Moral Garrido RG, O'Valle Ravassa F. Procedimiento de análisis de imagen para cuantificar bandas fluorescentes de ácidos nucleicos sobre electroforesis en geles en dos dimensiones. Investigación Clínica 2001;4:1-5.

18. Ramírez C, Olmo A, O'Valle F, Masseroli M, Aguilar M, Gómez-Morales M, Revelles F, García-Chicano MJ, Arrebola F, Reguero ME, Del Moral RG. Role of intrarenal endothelin 1, endothelin 3, and angiotensin II expression in chronic cyclosporin A nephrotoxicity in rats. Experimental Nephrology 2000;8(3):161-172.

17. Bergeron C, Masseroli M, Ghezi A, Lemarie A, Mango L, Koss LG. Quality control of cervical cytology in high-risk women. PAPNET system compared with manual rescreening. Acta Cytologica 2000;44(2):151-157.

16. Masseroli M, Caballero T, O'Valle F, Del Moral RM, Pérez-Milena A, Del Moral RG. Automatic quantification of liver fibrosis: design and validation of a new image analysis method. Comparison with semiquantitative indexes of fibrosis. Journal Hepatology 2000;32(3):453-464.

15. Bergeron C, Nogales FF, Masseroli M, Abeler V, Duvillard P, Muller-Holzner E, Pickartz H, Wells M. A multicentric European study testing the reproducibility of WHO classification of endometrial hyperplasia with a proposal of a simplified working classification for biopsy and curettage specimens. The American Journal Surgical Pathology 1999;23(9):1102-1108.

14. Masson S, Masseroli M, Fiordaliso F, Calvillo L, D'Aquila S, Bernasconi R, Garrido G, Torri M, Razzetti R, Bongrani S, Latini R. Effects of a DA₂/a₂ agonist and a ß₁-blocker in combination with an ACE inhibitor on adrenergic activity and left ventricular remodeling in an experimental model of left ventricular dysfunction after coronary artery occlusion. Journal Cardiovascular Pharmacology 1999;34(3):321-326.

13. Vergara E, Gómez-Morales M, Osuna A, O'Valle F, Aguilar D, Masseroli M, Martínez T, Asensio C, Del Moral RG. Immunohistochemical quantification of leukocyte subsets in the long-term prognosis of kidney transplants. Transplantation Proceedings 1998;30(5):2380-2383.

12. Masseroli M, O'Valle F, Andújar M, Ramírez C, Gómez-Morales M, Luna JD, Aguilar M, Aguilar D, Rodríguez-Puyol M, Del Moral RG. Design and validation of a new image analysis method for automatic quantification of interstitial fibrosis and glomerular morphometry. Laboratory Investigation 1998;78(5):511-522.

11. Ruiz-Torres MP, Bosch RJ, O'Valle F, Del Moral RG, Ramírez C, Masseroli M, Pérez-Caballero C, Iglesias MC, Rodríguez Puyol M, Rodríguez Puyol D. Age-related increased expression of TGF-ß1 in the rat kidney. Relationship to morphological changes. Journal of the American Society of Nephrology 1998;9(5):782-791.

10. Masseroli M, Cothren RM, Meier DS, Tuzcu EM, Vince DG, Nissen SE, Thomas JD, Cornhill JF. Quantification of intramural calcification in coronary intravascular ultrasound images with automated image analysis. American Heart Journal 1998;136(1):78-86.

9. Mesa F, Masseroli M, López C, Revelles F, O'Valle F. Valoración morfométrica del epitelio gingival. Cuantificación de los cambios morfológicos mediante análisis digital de imagen. Archivos de Odontoestomatología 1997;13(11):652-660.

8. Del Moral RG, Andújar M, Ramírez C, Gómez-Morales M, Masseroli M, Aguilar M, Olmo A, Arrebola F, Guillén M, García-Chicano MJ, Nogales F, O'Valle F. Chronic cyclosporin A nephrotoxicity, P-glycoprotein overexpression, and relationships with intrarenal angiotensin II deposits. The American Journal of Pathology 1997;151(6):1705-1714.

7. Pérez-Caballero C, Torres MPR, Masseroli M, O'Valle F, García Del Moral R, Rodríguez Puyol M, Rodríguez Puyol D. Papel de los inhibidores de la enzima de conversión de la angiotensina en la prevención de las alteraciones renales asociadas al envejecimiento. Nefrología 1996;16(4):319-326.

6. O'Valle F, Mesa F, Aneiros J, Gómez-Morales M, Lucena MA, Ramírez C, Revelles F, Moreno E, Navarro N, Caballero T, Masseroli M, García Del Moral R. Gingival overgrowth induced by nifedipine and cyclosporin A. Clinical and morphometric study with image analysis. Journal of Clinical Periodontology 1995;22(8):591-597.

5. Bollea A, Masseroli M, Nicotra A, Beccaglia P, Sen S, Erba E, Balconi G. Automatic quantitation of cell colonies on Petri dishes by computerized image analysis. Cytotechnology 1995;17:185-191.

4. Porzio S, Masseroli M, Messori A, Forloni G, Olivetti G, Jeremic G, Riva E, Luvarà G, Latini R. A simple, automatic method for morphometric analysis of the left ventricle in rats with myocardial infarction. Journal of Pharmacological and Toxicological Methods 1995;33(4):221-229.

3. Masseroli M, Bollea A, Forloni G. Quantitative morphology and shape classification of neurons by computerized image analysis. Computer Methods and Programs in Biomedicine 1993;41(2):89-99.

2. Masseroli M, Messori A, Bendotti C, Ponti M, Forloni G. Automatic quantitative evaluation of autoradiographic band films by computerized image analysis. Life Sciences 1993;53(20):PL331-PL336.

1. Masseroli M, Bollea A, Bendotti C, Forloni G. In situ hybridization histochemistry quantification: automatic count on single cell in digital image. Journal of Neuroscience Methods 1993;47(1-2):93-103.

B. BOOKS (Top)

3. Elementi di Informatica BioMedica. Pinciroli F. Masseroli M, editors. ISBN 88-7398-0171. Milano, IT: Polipress, 2005. (Scienze e Tecnologie per la Salute).

2. Masseroli M. Diseño y valoración de programas de análisis digital de imagen y sus aplicaciones a la cuantificación automática de patologías renales. PhD Thesis. University of Granada, Granada, Spain; 1996.

1. Masseroli M. Elaborazione di bioimmagini: sviluppo di metodi e di programmi su personal computer. Tesi di laurea. Politecnico di Milano, Milano, Italia; 1990.

C. CHAPTERS IN BOOKS (Top)

41. Masseroli M. Genomic Computing and CINECA for genomic research and precision medicine. In: Bassini S, Scipione G, Guidazzoli A, Liguori MC, editors. CINECA HPC Annual Report 2022/23. ISBN 9788886037464. Bologna, IT: CINECA; 2023. p. 39-40.

40. Cascianelli S, Cristovao F, Canakoglu A, Carman M, Nanni L, Pinoli P, Masseroli M. Evaluating deep semi-supervised learning for whole-transcriptome breast cancer subtyping. In: Cazzaniga P, Besozzi D, Merelli I, Manzoni L, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-030-63060-7. Heidelberg, D: Springer; 2020. p. 232-244. LNBI (Lecture Notes in Bioinformatics; vol 12313). DOI: 10.1007/978-3-030-63061-4_21.

39. Ceddia G, Pidò S, Masseroli M. Network modeling and analysis of normal and cancer gene expression data. In: Cazzaniga P, Besozzi D, Merelli I, Manzoni L, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-030-63060-7. Heidelberg, D: Springer; 2020. p. 257-270. LNBI (Lecture Notes in Bioinformatics; vol 12313). DOI: 10.1007/978-3-030-63061-4_23.

38. Frasca F, Matteucci M, Morelli MJ, Masseroli M. Exposing and characterizing subpopulations of distinctly regulated genes by k-plane regression. In: Raposo M, Ribeiro P, Susana S, Staiano A, Ciaramella A, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-030-34584-6. Heidelberg, D: Springer; 2020. p. 227-238. LNCS (Lecture Notes in Bioinformatics; vol 11925). DOI: 10.1007/978-3-030-34585-3_20.

37. Stamoulakatou E, Piccardi C, Masseroli M. Analysis of gene regulatory networks inferred from ChIP-seq data. In: Rojas I, Valenzuela O, Rojas F, Ortuño F, editors. Bioinformatics and Biomedical Engineering. ISBN 978-3-030-17937-3. Heidelberg, D: Springer; 2019. p. 319-331. LNBI (Lecture Notes in Bioinformatics; vol 11465). DOI: 10.1007/978-3-030-17938-0.

36. Masseroli M. Biological and Medical Ontologies: Introduction. In: Ranganathan S, Nakai K, Schönbach C, Gribskov M, editors. Encyclopedia of Bioinformatics and Computational Biology - volume 1: Methods. Oxford, UK: Elsevier; 2019. p. 813-822. ISBN 978-0-12-811432-2 DOI: 10.1016/B978-0-12-809633-8.20395-6

35. Masseroli M. Biological and Medical Ontologies: GO and GOA. In: Ranganathan S, Nakai K, Schönbach C, Gribskov M, editors. Encyclopedia of Bioinformatics and Computational Biology - volume 1: Methods. Oxford, UK: Elsevier; 2019. p. 823-831. ISBN 978-0-12-811432-2 DOI: 10.1016/B978-0-12-809633-8.20491-3

34. Chicco D, Masseroli M. Biological and Medical Ontologies: PRotein Ontology (PRO). In: Ranganathan S, Nakai K, Schönbach C, Gribskov M, editors. Encyclopedia of Bioinformatics and Computational Biology - volume 1: Methods. Oxford, UK: Elsevier; 2019. p. 832-837. ISBN 978-0-12-811432-2 DOI: 10.1016/B978-0-12-809633-8.20396-8

33. Bernasconi A, Masseroli M. Biological and Medical Ontologies: Disease Ontology (DO). In: Ranganathan S, Nakai K, Schönbach C, Gribskov M, editors. Encyclopedia of Bioinformatics and Computational Biology - volume 1: Methods. Oxford, UK: Elsevier; 2019. p. 838-847. ISBN 978-0-12-811432-2 DOI: 10.1016/B978-0-12-809633-8.20397-X

32. Bernasconi A, Masseroli M. Biological and Medical Ontologies: Human Phenotype Ontology (HPO). In: Ranganathan S, Nakai K, Schönbach C, Gribskov M, editors. Encyclopedia of Bioinformatics and Computational Biology - volume 1: Methods. Oxford, UK: Elsevier; 2019. p. 848-857. ISBN 978-0-12-811432-2 DOI: 10.1016/B978-0-12-809633-8.20398-1

31. Bernasconi A, Masseroli M. Biological and Medical Ontologies: Systems Biology Ontology (SBO). In: Ranganathan S, Nakai K, Schönbach C, Gribskov M, editors. Encyclopedia of Bioinformatics and Computational Biology - volume 1: Methods. Oxford, UK: Elsevier; 2019. p. 858-866. ISBN 978-0-12-811432-2 DOI: 10.1016/B978-0-12-809633-8.20399-3

30. Masseroli M. Biological and Medical Ontologies: Integrative Bioinformatics. In: Ranganathan S, Nakai K, Schönbach C, Gribskov M, editors. Encyclopedia of Bioinformatics and Computational Biology - volume 1: Methods. Oxford, UK: Elsevier; 2019. p. 1092-1098. ISBN 978-0-12-811432-2 DOI: 10.1016/B978-0-12-809633-8.20388-9

29. Ceri S, Bernasconi A, Canakoglu A, Gulino A, Kaitoua A, Masseroli M, Nanni L, Pinoli P. Overview of GeCo: a project for exploring and integrating signals from the genome. In: Kalinichenko L, Manolopoulos Y, Skvortsov N, Stupnikov S, Sukhomlin V, editors. Data Analytics and Management in Data Intensive Domains. Revised selected papers XIX International Conference, DAMDID/RCDL 2017. Moscow, Russia, October 9-13, 2017. ISBN 978-3-319-96552-9. Cham, Switzerland: Springer; 2018. p. 46-57. CCIS (Communications in Computer and Information Science; vol 822). DOI: 10.1007/978-3-319-96553-6_4.

28. Ceri S, Canakoglu A, Kaitoua A, Masseroli M, Pinoli P. Experiences in the development of a data management system for genomics. In: Filipe J, Bernardino J, Quix C, editors. Data Management Technologies and Applications. Revised selected papers 6th International Conference, DATA 2017. Madrid, Spain, July 24-26, 2017. ISBN 978-3-319-94808-9. Cham, Switzerland: Springer; 2018. p. 197-212. CCIS (Communications in Computer and Information Science; vol 814). DOI: 10.1007/978-3-319-94809-6_10.

27. Chicco D, Masseroli M. Validation pipeline for computational prediction of genomics annotations. In: Angelini C, Rancoita PMV, Rovetta S, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-319-44331-7. Heidelberg, D: Springer; 2016. p. 233-240. LNCS (Lecture Notes in Bioinformatics; vol 9874). DOI: 10.1007/978-3-319-44332-4.

26. Canakoglu A, Ceri S, Masseroli M. Biomolecular annotation integration and querying to help unveiling new biomedical knowledge. In: Ortuño F, Rojas I, editors. Bioinformatics and Biomedical Engineering. ISBN 978-3-319-31743-4. Heidelberg, D: Springer; 2016. p. 802-813. LNCS (Lecture Notes in Bioinformatics; vol 9656). DOI: 10.1007/978-3-319-31744-1.

25. Domeniconi G, Masseroli M, Moro G, Pinoli P. Random perturbations of term weighted Gene Ontology annotations for discovering gene unknown functionalities. In: Fred A, Dietz JLG, Aveiro D, Liu K, Filipe J, editors. Knowledge Discovery, Knowledge Engineering and Knowledge Management. ISBN 978-3-319-25839-3. Heidelberg, D: Springer; 2015. p. 181-197. CCIS (Communications in Computer and Information Science; vol 553).

24. Chicco D, Ciceri E, Masseroli M. Extended Spearman and Kendall coefficients for gene annotation list correlation. In: Di Serio C, Liò P, Nonis A, Tagliaferri R, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-319-09041-2. Heidelberg, D: Springer; 2015. p. 1-14. LNCS (Lecture Notes in Bioinformatics; vol 8623).

23. Pinoli P, Chicco D, Masseroli M. Weighting scheme methods for enhanced genomic annotation prediction. In: Formenti E, Tagliaferri R, Wit E, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-319-09041-2. Heidelberg, D: Springer; 2014. p. 76-89. LNCS (Lecture Notes in Bioinformatics; vol 8452).

22. Chicco D, Tagliasacchi M, Masseroli M. Genomic annotation prediction based on integrated information. In: Biganzoli E, Vellido A, Ambrogi F, Tagliaferri R, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-642-35685-8. Heidelberg, D: Springer; 2012. p. 238-252. LNCS (Lecture Notes in Bioinformatics; vol 7548).

21. Canakoglu A, Ghisalberti G, Masseroli M. Integration of biomolecular interaction data in a genomic and proteomic data warehouse to support biomedical knowledge discovery. In: Biganzoli E, Vellido A, Ambrogi F, Tagliaferri R, editors. Computational Intelligence Methods for Bioinformatics and Biostatistics. ISBN 978-3-642-35685-8. Heidelberg, D: Springer; 2012. p. 112-126. LNCS (Lecture Notes in Bioinformatics; vol 7548).

20. Masseroli M. Banche dati biomediche e risorse on-line. In: Bernasconi C, editor. Medicina genomica e terapia personalizzata in ematologia/oncologia. Pavia, IT: Edizioni internazionali srl, 2012. p. 47-54. (Corsi di formazione avanzata; vol 11/2012).

19. Masseroli M, Ghisalbert G. Bio-SeCo: Integration and global ranking of biomedical search results. In: Ceri S, Brambilla M, editors. New Trends in Search Computing. ISBN 978-3-642-19667-6. Heidelberg, D: Springer; 2011. p. 203-214. LNCS (Lecture Notes in Computer Science; vol 6585).

18. Masseroli M, Paton NW, Ghisalberti G. Search Computing: Integrating ranked data in the Life Sciences. In: Lambrix P, Kemp G, editors. Data Integration in the Life Sciences. Proceedings 7th International Workshop, DILS 2010, 2010 Aug 25-27; Gothenburg, SE. ISBN 978-3-642-15119-4. Heidelberg, D: Springer; 2010. p. 207-214. LNCS (Lecture Notes in Bioinformatics; vol 6254).

17. Masseroli M, Paton NW, Spasić I. Chapter 15: Search Computing and the Life Sciences. In: Ceri S, Brambilla M, editors. Search Computing - Challenges and Directions. ISBN 978-3-642-12309-2. Heidelberg, D: Springer; 2010. p. 291-306. LNCS (Lecture Notes in Computer Science; vol 5950).

16. Masseroli M, Tagliasacchi M. Chapter 8: Web resources for gene list analysis in biomedicine. In: Lazakidou A, editor. Web-based Applications in Health Care and Biomedicine. ISBN 978-1-4419-1273-2. Heidelberg, D: Springer, 2010. p. 117-141. (Annals of Information Systems Series; vol 7).

15. Masseroli M, Ceri S, Campi A. Integration and mining of genomic annotations: Experiences and perspectives in GFINDer data warehousing. In: Paton NW, Missier P, Hedeler C, editors. Data Integration in the Life Sciences. Proceedings 6th International Workshop, DILS 2009, 2009 Jul 20-22; Manchester, UK. ISBN 978-3-642-02878-6. Berlin, D: Springer-Verlag; 2009. p. 88-95. LNCS (Lecture Notes in Bioinformatics; vol 5647).

14. Bonacina S, Privitera YA, Marsilio S, Montin E, Passarelli F, Masseroli M, Pinciroli F. A web-based tool for cooperating behaviors in eating and physical activity control. In: Wiederhold BK, Riva G, editors. Annual Review of Cybertherapy and Telemedicine 2009 - Advanced Technologies in the Behavioral, Social and Neurosciences. ISBN 978-1-60750-017-9. Amsterdam, NL: IOS Press; 2009. p. 155-159. (Studies in Health Technology and Informatics; vol 144).

13 Masseroli M, Ceri S. Bioinformatics for genomics and proteomics. In: A. Cigada, editor. Nanomedicine. Milano, IT: Politecnico di Milano, 2008. p. 15-18.

12. Ceresa M, Masseroli M. Chapter XI: Clinical and biomolecular ontologies for e-health. In: Lazakidou AA, Siassiakos KM, editors. Handbook of Research on Distributed Medical Informatics and E-Health. ISBN 978-1-60566-002-8. Hershey, PA: IGI Global, 2008. p. 165-179. (Medical Information Science Reference).

11. Masseroli M. Mining ed efficace utilizzo di informazioni in banche dati biomolecolari. In: Bellazzi R, Bicciato S, Cavalcanti S, Cobelli C, Toffolo GM, editors. Genomica e proteomica computazionale. ISBN: 978-88-555-2944-0. Bologna, IT: Pàtron editore, 2007. p. 379-415. (Gruppo Nazionale di Bioingegneria; vol. 26).

10. Masseroli M. Capitolo 33: Banche dati e recupero delle informazioni. In: Bernasconi C, editor. Predizione molecolare e bioinformatica in ematologia/oncologia. Pavia, IT: Edizioni internazionali srl, 2007. p. 223-231. (Corsi di formazione avanzata; vol 6/2007).

9. Maffezzoli A, Masseroli M. Chapter XLV: Genomic databanks for biomedical informatics. In: Lazakidou AA, editor. Handbook of Research on Informatics in Healthcare and Biomedicine. ISBN 1-59140-982-9. Hershey, PA: Idea Group Inc., 2006. p. 357-366. (Medical Information Science Reference).

8. Maffezzoli A, Masseroli M. Banche genomiche. In: Pinciroli F. Masseroli M, editors. Elementi di Informatica BioMedica. ISBN 88-7398-017-1. Milano, IT: Polipress, 2005. p. 165-213. (Scienze e Tecnologie per la Salute).

7. Pinciroli F, Masseroli M, Bonacina S. New e-health tracks in engineering education of the Politecnico di Milano. In: Haux R, Kulikowski C, editors. Ubiquitous Health Care Systems. Yearbook of Medical Informatics. ISBN 3-7945-2397-0. Stuttgart, D: Schattauer Verlagsgesellschaft GmbH; 2005. p. 204-210.

6. Pinciroli F, Corbetta E, Tamburini MF, Mattasoglio A, Bonacina S, Masseroli M, Meloni G, Spaggiari P. Speak-ER: an audible web-based medical record for emergency patients. In: Demiris G, editor. e-health: current status and future trends. ISBN 1 58603 442 1. Amsterdam, The Netherlands: IOS Press; 2004. p. 93-106. (Studies in Health Technology and Informatics; vol 106).

5. Martucci D, Masseroli M, ,Pinciroli F. Gene Ontology application to genomic functional annotation, statistical analysis and knowledge mining. In: Pisanelli DM, editor. Ontologies in Medicine. ISBN 1-58603-418-9. Amsterdam, The Netherlands: IOS Press; 2004. p. 108-131. (Studies in Health Technology and Informatics; vol 102).

4. Pinciroli F, Masseroli M, Acerbo LA, Bonacina S, FerrariR, Marchente M. BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy. In: Phillips R, Hoffman HM, Haluck RS, Mogel GT, Robb RA, Westwood JD, editors. Medicine Meets Virtual Reality 12. Building a better you: the next tools for medical education, diagnosis, and care. ISBN 978-1-58603-404-7. Amsterdam, NL: IOS Press; 2004. p. 301-303. (Studies in Health Technology and Informatics; vol 98).

3. Bonacina S, Menegoni F, Pinciroli F, Masseroli M. A 3D interactive multimodal viewer as data mining tool for the Visible Human Dataset color image histograms. In: Phillips R, Hoffman HM, Haluck RS, Mogel GT, Robb RA, Westwood JD, editors. Medicine Meets Virtual Reality 12. Building a better you: the next tools for medical education, diagnosis, and care. ISBN 978-1-58603-404-7. Amsterdam, NL: IOS Press; 2004. p. 28-30. (Studies in Health Technology and Informatics; vol 98).

2. Masseroli M, Andújar M, Ramírez C, O'Valle F. Citometría digital y análisis de imagen. In: Viguer JM, García Del Moral R, editors. Laboratorio y Atlas de Citología. ISBN 84-486-0122-X. McGraw-Hill/Interamericana. Madrid, Spain; 1995:264-280.

1. García Del Moral R, O'Valle F, Masseroli M. Técnicas de análisis de imágenes en morfología microscópica. In: García Del Moral R, editor. Laboratorio de Anatomía Patológica. ISBN 84-481-0229-0. McGraw-Hill/Interamericana. Madrid, Spain; 1993:405-425.

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