Simone MARINI, PhD.

Postdoctoral fellow at Akutsu Laboratory,

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan.


Prev: Postdoctoral fellow, Laboratory for Biomedical Informatics, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy.


CONTACTS

at Kyoto University:

-email: smarini (_at) sunflower (_dot) kuicr (dot_) kyoto-u (_dot) ac (dot_) jp

-office phone: +81-0774-38-3017

at University of Pavia:

-email: simone (dot_) marini (at_) unipv (_dot) it

Linkedin


PROJECTS AND RESEARCH INTERESTS

Medical and biological data fusion for knowledge discovery and enhanced prediction models
Keywords: Matrix tri-factorization, Big Data, Matlab, knowledge discovery, gene espression, genomic variant

Diabetic cohort simulation
Keywords: EDIC, DCCT, Dynamic Bayesian Networks, Continuous Time Bayesian Networks, Tabu Search, Matlab, Simulation

Genomic variant deleteriousness prediction
Keywords: HGMD, 1KGP, Random Forest, Perl, Weka, feature encoding, Genetics, classification, Markov Chain Monte Carlo, feature selection, noisy data, Big Data, Human, webserver, genomic variant

SNP selection
Keywords: Markov Chain Monte Carlo, feature selection, root beet, genomic variant

DSCAM self-affinity prediction
Keywords: Drosophila, Perl, Weka, Perl, feature encoding, Support Vector Machines, protein, Genetics, regression

DNA- and RNA- and protein-protein prediction of interaction and affinity
Keywords: Weka, Perl, classification, feature encoding, Stacking, Support Vector Machines, Aptamer, Weka, Perl, feature encoding, Random Forest, short peptide, Human


EDUCATION AND QUALIFICATIONS

PhD in Bioengineering (2008 – 2012)
Hong Kong University of Science and Technology, Hong Kong, PRC, Bioengineering Division
Thesis: Qualitative and quantitative protein interaction prediction with machine learning.

MSc in Biomedical Engineering (2004 – 2007)
University of Pavia, Pavia, Italy.
Thesis: Design of a classifier by coevolution of genetic algorithms and genetic programming.

BSc In Biomedical Engineering (2000 - 2004)
University of Pavia, Pavia, Italy.
Thesis: Bone tissue engineering, effects of mechanical shear stress on human osteoblast SAOS2.


TEACHING AND RESEARCH EXPERIENCES

JSPS Postdoc fellow (Dec 2015 – Present)
Kyoto (Japan). University of Kyoto, Akutsu Laboratory, Bioinformatics Center, Institute for Chemical Research.

Postdoctoral fellow (Jan, 2013 – Dec 2015)
Pavia (Italy). University of Pavia, “Mario Stefanelli” Bioengineering Laboratory, Dept. of Industrial and Information Engineering

Instructor of record (TA) (Sep, 2013 – Sep 2015)
Pavia (Italy). University of Pavia.
Undergraduate course: Medical Informatics
Postgraduate course: Automatic Learning in Medicine

Math Teacher (Sep, 2012 – Jun, 2014)
Pavia (Italy). Centro Servizi Formazione. European project against early school leaving, high school students.

Adjunct postdoc fellow (Sep, 2012 – Jan, 2013)
Pavia (Italy). University of Pavia, CCPS Laboratory Dept. of Industrial and Information Engineering.

Teaching assistant (Jan, 2010 – Jun, 2010)
Hong Kong (PRC). The Hong Kong University of Science and Technology.  Postgraduate course: Application of Engineering in Life Science.


AWARDS
Outstanding Contribution in Reviewing (June 2015)
Journal of Biomedical Informatics, Elsevier.

BIEN Graduate Student Research Award (Sep, 2011)
1st ranked. Provided by The Hong Kong University of Science and Technology and the Hong Kong Medical and Healthcare Device Industries Association (HKMHDIA).

Overseas Research Award for PhD Students (Nov, 2010)
Provided by The Hong Kong University of Science and Technology.

VOLUNTEERING EXPERIENCES

Software Developer (Jun 2014)
Bangladesh. Debi Chowdhurani Palli Unnayan Kendra NGO, VSO Poverty Alleviation, remote services. Developement of a software to help managing dairy cooperatives in Afzalpur and Mominpur.

Front desk volunteer (Jan 2006 - Aug 2008)
Italy. Municipal social services, Pavia. Supporting immigrants, foreigners and students in job search.


PUBLICATIONS

peer-reviewed journals

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 57 (2015): 369-376.


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)

Improvement of Dscam homophilic binding affinity throughout Drosophila evolution
Wang G Z, Marini S, Ma X, Yang Q, Zhang X, Zhu Y. BMC Evolutionary Biology 2014, 14:186

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.

In silico Protein-Protein Interaction prediction with sequence alignment and classifier stacking.
Marini S, Xu Q, Yang Q. Curr Protein Pept Sci. 2011 Nov;12(7):614-20.


peer-reviewed conference papers

A genomic data fusion framework to exploit rare and common variants for association discovery.
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
De Martini A, Marini S, Vitali F, Bellazzi R. 15th Conference of Artificial Intelligence in Medicine [Workshop], 2015

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, 2016

peer-reviewed conference abstracts

Predicting Microvascular Complications from Type 2 Diabetes Retrospective Data
Sacchi L, Colombo C, Dagliati D, Marini S, Cerra C, Chiovato L, Bellazzi R. American Medical Informatics Association joint Summits on Translational Science, 2016

Enhancing type 2 diabetes adverse events: risk prediction through drug purchasing behavioral patterns

The 9th International Conference on Advanced Technologies & Treatments for Diabetes, 2016

A continuous time, multivariate model to simulate Type 2 Diabetes patients trajectories
Marini S, Dagliati A, Bellazzi R. American Medical Informatics Association joint Summits on Translational Science, 2015

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, 2014

PaPI: the Pseudo Amino acid variant Predictor
Marini S, Limongelli I, Bellazzi R.  Bioinformatics Italian Society National Congress 2014

A novel algorithm to predict the deleteriousness of genomic coding variants
Limongelli I, Marini S, Bellazzi R. NGS (ISCB) 2014

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, 2014

PaPI: using pseudo amino acid composition to predict deleterious coding variants
Limongelli I, Marini S, Bellazzi R. Italian Bioengineering Group National Congress 2014

Predicting Microvascular Complications from Type 2 Diabetes Retrospective Data
Sacchi L,  Colombo C, Dagliati A, Marini S, Cerra C, Chiovato L, Bellazzi R. 15th Annual Diabetes Technology Meeting, 201
4


PEER REVIEW
for Journal of Biomedical Informatics and Briefings in Bioinformatics. My profile on Publons.


Miscellanea
I worked odd jobs (including barman and high-school tutor) in 2007-2008.
Among the stuff that I like to do there is traveling alone and very cheaply all over the world, playing nerdy pen-and-paper role playing games, and (try to) learn languages, history and phylosophy.


TL;DR
I make prediction models and simulations applying several Machine Learning techniques.
I work on a wide variety of data (including Big Data), in both Health Informatics and Bioinformatics.


(Last update: 2016 Feb 2)