Simone MARINI, PhD


Postdoc fellow, Akutsu LaboratoryUniversity of Kyoto, Japan (Since Dec 2015)

Prev: Postdoc Fellow, Laboratory for Biomedical Informatics, University of Pavia  (Jan 2013 - Dec 2015)

2016/07/01

Room CB320 Akutsu Laboratory,

Bioinformatics Center, Institute for Chemical Research, Kyoto University,

Uji, Kyoto 611-0011, Japan.

 +81-774-38-3017

smarini (_at) sunflower (_dot) kuicr (dot__) kyoto-u (_dot_) ac (dot_) jp

simone (_dot_) marini (at_) unipv (_dot) it

Who I am

As a scientist, I work in Bioinformatics, mainly applying Machine Learning to infer prediction models and simulations.

I worked on a wide variety of data, such as electronic health records, genomic variants, ontologies, protein sequences; and techniques, e.g. support vector machines, random forest, bayesian networks, data fusion.

My research projects span over Italy, China and Japan, and involve people working for

I lived in Pavia, Madrid, Hong Kong and Beijing. I currently live in Kyoto.

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MAJOR RESEARCH PROJECTS

Technique > Matrix tri-factorization
Technology > Octave
Data > KEGG, MEROPS, Domine, Negatome, BIOGrid, Interpro, STRING

Technique > Random Forest, Burden Methods
Technology > Perl, Weka
Data > KEGG, Interpro, NGS data

Technique > Matrix tri-factorization
Technology > Octave
Data > TCGA, KEGG, GO, DO, BIOGrid, STRING, genomic variants

Technique > Dynamic Bayesian Networks, Continuous Time Bayesian Networks
Technology > MATLAB, R
Data > EDIC, DCCT, Electronic Health Records

Technique > Ensemble Learning, Cost-sensitive Learning
Technology > Perl, Weka, AJAX, Glassfish
Data > NGS, HGMD, 1TGP,  NHLBI GO Exome Sequencing Project
Web > http://papi.unipv.it/

Technique > Markov Chain Monte Carlo, Logistic Regression
Technology > Weka, MATLAB
Data > Genotyping

Technique > Ensemble Learning, Support Vector Machines
Technology > Weka, Perl
Data > Negatome, Dscam1, Protein-interactions, Aptamers
Web > http://bioinformatics.tecnoparco.org/fruitbreedomics/Dscam1-binding/webinterface/index.php
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EDUCATION

2012

PhD in Bioengineering

Hong Kong University of Science and Technology, China.

Thesis: Qualitative and quantitative protein interaction prediction with machine learning.

2007

MSc in Biomedical Engineering

University of Pavia, Italy.

Thesis: Design of a classifier by coevolution of genetic algorithms and genetic programming.

2004

BSc in Biomedical Engineering

University of Pavia, Italy.

Thesis: Bone tissue engineering, effects of mechanical shear stress on human osteoblast SAOS2.

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PEER REVIEWED PUBLICATIONS

2016

Biscarini F, Nazzicari N, Broccanello C; Stevanato P, Marini S. Plant Methods, in press.

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

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

2015

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.

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

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

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

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

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

Sacchi L, Colombo C, Dagliati D, Marini S, Cerra C, Chiovato L, Bellazzi R. 15th Annual Diabetes Technology Meetings, 2015

2014

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

*equally contributed

Marini S, Malavolti M, Dagliati A, Bellazzi R. 14th Annual Diabetes Technology Meeting 2014

Marini S, Limongelli I, Bellazzi R. Bioinformatics Italian Society National Congress 2014, podium presentation

Limongelli I, Marini S, Bellazzi R. NGS (ISCB) 2014

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, podium presentation

Limongelli I, Marini S, Bellazzi R. Italian Bioengineering Group National Congress 2014

2013

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

2011

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

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AWARDS

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

2016

June 10. Leveraging on publicly available databases for novel peptidase target discovery. Center for Health Technologies, University of Pavia.

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).

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TEACHING EXPERIENCES

2013 Sep, 2015 Sep

Instructor of record, University of Pavia.

Medical Informatics, 2nd year bachelor degree in Bioengineering.

Automatic Learning in Medicine,1st year master degree in Bioengineering.

2013 Sep, 2014 Jun

High school math teacher, Pavia.

2010 Jan, 2010 Jun

Teaching assistant, The Hong Kong University of Science and Technology.

Introduction to Bioengineering, 1st year graduate school in Bioengineering.

2007 Nov, 2008 Jun

         University tutor, CESD, Italy. Private one-to-one tutoring to undergraduate and graduate students.

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SUPERVISED STUDENTS

 2016

Alexandra Vinchent, MSc lab internship; Akutsu Laboratory, Kyoto University.

2015

Da Tan, MSc research thesis in Molecular Biology. Bioinformatics tools and methods for sequencing data: from preprocessing to forecasting; Laboratory for Biomedical Informatics, University of Pavia.

2014

Silvia Lorenzi, MSc research thesis in Molecular Biology. Identification and site-directed mutagenesis of a putative conserved domain in the SwrA protein of Bacillus subtilis; Laboratory for Biomedical Informatics, University of Pavia.

Imane Lahmiri, BSc lab internship; Laboratory for Biomedical Informatics, University of Pavia.

2013

Milad Malavolti, BSc research thesis in Bioengineering. Continuous Time Bayesian Network for patient trajectory simulation; Laboratory for Biomedical Informatics, University of Pavia.

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REVIEWER for

1. Journal of Biomedical Informatics (since 2015)

2. Briefings in Bioinformatics (since 2015)

3. Artificial Intelligence in Medicine (conferences) (since 2016)

4. American Medical Informatics Association joint Summits on Translational Science (since 2016)

5. Computers in Biology and Medicine (since 2016)

(My profile on Publons.)

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LANGUAGES

Italian (Native speaker), English (Fluent), Spanish (Fluent).

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VOLUNTEERING

2014 Jun

Software developer, DCPUK, Bangladesh. VSO Poverty Alleviation, remote services. Developement of a software to help managing dairy cooperatives.

2006 Jan, 2008 Aug

Front desk volunteer, Informagiovani, Italy. Municipal social services of Pavia.

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Miscellanea

Among the stuff that I like to do in my spare time, I mention (1) traveling; (2) playing nerdy pen-and-paper role playing games; (3) (try to) learn languages, history and philosophy.

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TL;DR

I make prediction models and simulations applying several Machine Learning techniques. I work on a wide variety of data, in both Health Informatics and Bioinformatics.