Simone MARINI, PhD

(.) Research Investigator, Li LabUniversity of Michigan (since Aug 2017)

(.) Scientific Advisor, enGenome (since Dec 2016)

smarini (_at) med (_dot_) umich (dot_) edu (Linkedin) (Twitter) (Publons)

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Postdoc fellow, Laboratory for Biomedical Informatics, University of Pavia (2016 - 2017)

Postdoc fellow, Akutsu LaboratoryUniversity of Kyoto, Japan (2015 - 2016)

Postdoc fellowLaboratory for Biomedical Informatics, University of Pavia (2013 - 2015)

Last update: Aug 2018

This is a picture of me

In a nutshell

As a scientist, I design prediction models for Molecular Biology and Medicine with Machine Learning. I am particularly interested in data integration, i.e. in developing modeling harvesting heterogeneous data such as imaging, genomics, proteomics, ontologies and knowledgebases. 

The application range of my models is broad, from DSCAM Drosophila protein affinity prediction, to simulation of clinical trajectories in diabetic patients.

My research teams span over Italy, China, Japan, and USA, involving people working for:

I am (proudly) from Voghera, Italy. I lived in Pavia (Italy), Madrid (Spain), Hong Kong (PRC), Beijing (PRC), and Kyoto (Japan). I currently live in Ann Arbor, USA.

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AWARDS AND FELLOWSHIPS

2015-2016       Japanese Society for the Promotion of Science Postdoctoral Fellowship.

2015                Outstanding contribution in reviewing, Journal of Biomedical Informatics (Elsevier).

2011                Bioengineering Division Graduate Student Research Award, 1st ranked.

2010                HKUST Overseas Research Award for PhD Students.

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INVITED TALKS (extramural)

2017                June 6. Data exploration of single-cell landscapes. Centre for Health Technologies, University of Pavia, Pavia, Italy.

2017                Oct 11. Joint data integration for precision oncology. UFHCC Topics in Cancer seminar series, University of Florida, Gainsville, FL, USA.

                        Jul 18. miRNA Bioinformatics, sequence analysis and statistical processes. Training school "Omics technologies and bioinfor matics application in ME/CFS research, University                            of Pavia, Pavia, Italy. EU Cost ACTION  CA15111 (European Network on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome COST action CA15111, EUROMENE)

                        June 17. Exploring wound-healing genomic machinery with a network-based approach, 1st International Conference on Wound Healing and Monitoring, Pavia, Italy.

                        January 12. Investigating epileptogenesis with data fusion. University of Michigan, Ann Arbor, MI, USA.                        

2016                September 8. Mining heterogeneous data sources to enhance association studies. University of Arizona, Tucson, USA.

                        June 10. Leveraging on public databases for novel peptidase target discovery. CHT - Centre for Health Technologies, University of Pavia, Pavia, Italy.

2011                May 13. Motif search, sequence alignment and Support Vector Regression for Dscam protein self- and hetero-binding affinity prediction. Institute of Biophysics, the Chinese                                  Academy of Science, Beijing, China.

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TEACHING AND MENTORING EXPERIENCES

University of Michigan, USA

Supervising 1 postdoc, 2 postgraduate and 1 undergraduate students (2017-present)

Kyoto University, Japan

Supervision of summer internships (2016)

 University of Pavia, Italy.

Medical Informatics (2013-2015), Instructor of record, undergraduate

Automatic Learning in Medicine (2013-2015), Instructor of record, postgraduate.

Supervision of seven postgraduate and three undergraduate students (2013-2017)

Supervision of summer internships (2014)

The Hong Kong University of Technology, China

Introduction to Bioengineering (2010), Teaching assistant, postgraduate     

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SERVICE TO PROFESSION

Journal Reviewer                   Journal of Biomedical Informatics (2014-present)

     Bioinformatics (2018-present)

     Briefings in Bioinformatics (2015)

     Computers in Biology and Medicine (2016)

     Molecules (2108-present)

 

Conference Reviewer            Artificial Intelligence in Medicine, AIME (2016-2017)

                                               American Medical Informatics Association joint Summits on Translational Science (2016-2017)

                                               IEEE International Conference on Healthcare Informatics, ICHC (2017)

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LANGUAGES                         (Reading)                                (Speaking)        

Italian                                       Native speaker                        Native speaker

English                                    Fluent                                      Fluent

Spanish                                   Fluent                                      Fluent

Chinese                                   -                                              Survival

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PEER REVIEWED PUBLICATIONS

[*] denotes equal contribution.

[§] denotes corresponding author.

JOURNALS

 2018               Protease target prediction via matrix factorization

                       Marini S*§, Vitali F*, Rampazzi S, Demartini A, Akutsu T. Bioinformatics, in press.

                       A comprehensive roadmap of murine spermatogenesis defined by single-cell RNA-seq

                       Green CD, Ma Q, Manske GL, Shami AN, Zheng X, Marini S, Moritiz L, Sultan C, Gurczynski SJ, Moore BB, Tallquist MD, Li JZ, Hammoud SS. Developmental Cell, in press

                       MTGO: PPI network analysis via topological and functional module identification

                       Vella D, Marini S§, Vitali F, Di Silvestre D, Mauri G, and Bellazzi R. Scientific Reports, in press.

                       Patient similarity by joint matrix tri-factorization to identify subgroups in precision oncology

                       Marini S*, Vitali F*, Pala D, Demartini A, Montoli S, Zambelli A, Bellazzi R. Jamia Open, in press.

                       Towards more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.

                       Bao Y., Marini S, Tamura T, Kamada M, Maegawa S, Hosokawa H, Song J Akutsu T. Briefings in Bioinformatics, in press.

                       Risk Factors for the Development of Micro-vascular Complications of Type 2 Diabetes in a Single-Center Cohort of Patients

                       Chiovato L, Teliti M, Cogni G, Sacchi L, Dagliati A, Marini S, Tibollo V, De Cata P, Bellazzi R. Diabetes and Vascular Disease Research, in press.

2017               Exploring Wound-Healing Genomic Machinery with a Network-Based Approach

                       Vitali F, Marini S§, Balli M, Grosemans H, Sampaolesi M, Lussier YA, Cusella De Angelis MG, Bellazzi R. Pharmaceuticals 2017, 10:2

                       Dscam1 Web Server: online prediction of Dscam1 self- and hetero-affinity

                       Marini S*§, Nazzicari N*, Biscarini F, Wang GZ. Bioinformatics 2017, 33:12

                       Machine learning methods to predict Diabetes complications

                       Dagliati A, Marini S,  Sacchi  L, Cogni G, Teliti M, Decata P, Chiovato L, Bellazzi R. Journal of Diabetes Science and Technology 2017, 1932296817706375

2016               A data fusion approach to enhance association study in epilepsy

                       Marini S§, Limongelli I, Rizzo E, Errichiello E, Vetro A, Tan D, Zuffardi O, Bellazzi R. Plos One 2016, 11:12

                       "Noisy beets": impact of phenotyping errors on genomic predictions for binary traits in Beta vulgaris

                       Biscarini F, Nazzicari N, Broccanello C; Stevanato P, Marini S. Plant Methods 2016, 12:36

2015               A Dynamic Bayesian Network model for long-term simulation of clinical complications in type 1 diabetes                

                       Marini S*, Trifoglio E*, Barbarini N, Sambo F, Di Camillo B, Malovini A , Manfrini M, Cobelli C , Bellazzi R. Journal of Biomedical Informatics 2015, 57

                       PaPI: pseudo amino acid composition to score human coding variants                        

                       Limongelli I, Marini S, Bellazzi R. BMC Bioinformatics 2015, 16:123

                       Developing a parsimonius predictor for binary traits in sugar beet (Beta vulgaris)

                       Biscarini F, Marini S, Stevanato P, Broccanello C, Bellazzi R, Nazzicari N. Molecular Breeding 2015, 35:10

2014               Improvement of Dscam homophilic binding affinity throughout Drosophila evolution

                       Marini S*, Wang GZ*, Ma X, Yang Q, Zhang X, Zhu Y. BMC Evolutionary Biology 2014, 14:186

2013               The role of SwrA, DegU and P(D3) in fla/che expression in B. subtilis.

                       Mordini S, Osera C, Marini S, Scavone F, Bellazzi R, Galizzi A, Calvio C. PLoS One 2013, 8:12::e85065.

2011               In silico Protein-Protein Interaction prediction with sequence alignment and classifier stacking.

                       Marini S, Xu Q, Yang Q. Curr Protein Pept Sci. 2011, 12:7

 

CONFERENCE PAPERS

2017               MTopGO: a tool for module identification in PPI Networks.

                       Vella D, Marini S, Vitali F, Bellazzi R. 17th Network Tools and Applications for Biology., NETTAB 2017

2016               Learning T2D evolving complexity from EMR and administrative data using Continuous Time Bayesian Networks

                       Marini S, Dagliati A, Sacchi L, Bellazzi R. 9th International Joint Conference on Biomedical Engineering System and Technolgy, HEALTHINF 2016

                       A genomic data fusion framework to exploit rare and common variants for association discovery.2015

                       Marini S, Limongelli I, Rizzo E, Da T, Bellazzi R. 15th Conference of Artificial Intelligence in Medicine 2015

                       Matrix tri-factorization for miRNA-gene association discovery in acute myeloid leukemia

                       Marini S, De Martini A, Vitali F, Bellazzi R. 15th Conference of Artificial Intelligence in Medicine [Workshop] 2015

 

CONFERENCE ABSTRACTS

2018             Gene interaction discovery in myelodysplastic syndromes

                     Demartini A, Vitali F, Sauta E, Bellazzi R, Marini S§. European Conference of Human Genetics, ESHG 2018

2016             Data Fusion for cleavage target prediction

Marini S, Demartini A, Vitali F, Bellazzi R, Akutsu T. Bioinformatics Italian Society National Congress, BITS 2016

                     A continuous time, multivariate model to simulate Type 2 Diabetes patients trajectories 2015                

Marini S, Dagliati A, Bellazzi R. American Medical Informatics Association (AMIA) joint Summits on Translational Science 2015

                     Predicting Microvascular Complications from Type 2 Diabetes Retrospective Data

Sacchi L, Colombo C, Dagliati D, Marini S, Cerra C, Chiovato L, Bellazzi R. 15th Annual Diabetes Technology Meetings

2014             A multivariate data-driven model to investigate the arising of complications in T2D patients

Marini S, Malavolti M, Dagliati A, Bellazzi R. 14th Annual Diabetes Technology Meeting

                     PaPI: the Pseudo Amino acid variant Predictor

Marini S, Limongelli I, Bellazzi R.  Bioinformatics Italian Society National Congress 

A novel algorithm to predict the deleteriousness of genomic coding variants                        

                     Limongelli I, Marini S, Bellazzi R. NGS (ISCB)

                     Dynamic Bayesian Networks to simulate type I diabetes patients cohorts

Barbarini N, Bellazzi R, Cobelli C, Di Camillo B, Manfrini F, Malovini A, Marini S, Sambo F, Trifoglio E. Economics, Modelling and Diabetes: Mount Hood Challenge

PaPI: using pseudo amino acid composition to predict deleterious coding variants

                     Limongelli I, Marini S, Bellazzi R. Italian Bioengineering Group National Congress

BOOK CHAPTERS

2017               Precision oncology: a data similarity challenge

                       Zambelli A, Demartini A, Pala D, Vitali F, Marini S, Bellazzi R. In: E-Health e Medicina Digitale, S. Quaglini, M. Cesarelli, M. Giacomini, F. Pinciroli eds, Patron ed.

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VOLUNTEERING EXPERIENCES AND COMMUNITY OUTREACH

Introducing machine learning to high school students

                         Lectures. Galilei high school, Voghera, Italy. (2017, 2015, 2014, 2013)

                         Lectures and workshops. Settore Istruzione e Politiche Giovanili, Pavia. Italy. (2007)                        

Software developer volunteer

                         DCPUK, Bangladesh. VSO Poverty Alleviation, remote services. Development of a software to help managing dairy cooperatives. (2014)

Front desk volunteer

                         City social services of Pavia, Italy. Helping immigrants interact with local bureaucracy.  (2006 – 2008)

Miscellanea

Among things I like to do in my spare time, I mention here (1) traveling; (2) playing old-school, pen-and-paper role playing games; (3) enjoying learning languages, history, and philosophy.

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TL;DR

I apply machine learning to bioinformatics. I make prediction models and simulations by extracting knowledge from very diverse data.