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Other IDs

Scopus Author ID: 55154974000
Loop profile: 153577
SciProfiles: 970308

Keywords

Systems Biology, Synthetic Biology, High Performance Computing, GPGPU Computing, Soft Computing, Fuzzy Logic, Evolutionary Computation, Swarm Intelligence

Biography

BSc, Msc and Ph.D. in Computer Science, received from the University of Milano-Bicocca (Italy). Associate Professor in the Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University, Venice, Italy

Activities

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Employment (3)

Università Ca' Foscari: Venezia, Veneto, IT

2021-10-15 to present | Associate Professor (Department of Environmental Sciences, Informatics and Statistics)
Employment
Source: Self-asserted source
Marco S. Nobile

Eindhoven University of Technology: Eindhoven, Noord-Brabant, NL

2019-01-08 to 2021-10-31 | Assistant Professor (Industrial Engineering and Innovation Sciences)
Employment
Source: Self-asserted source
Marco S. Nobile

Università degli Studi di Milano-Bicocca: Milano, IT

2015-01-01 to 2019-08-01 | Research Fellow (Dipartimento di Informatica, Sistemistica e Comunicazione)
Employment
Source: Self-asserted source
Marco S. Nobile

Education and qualifications (3)

Università degli Studi di Milano-Bicocca: Milano, Lombardia, IT

2012-01 to 2014-12-31 | PhD in Computer Science (Department of Informatics, Systems and Communication)
Education
Source: Self-asserted source
Marco S. Nobile

Università degli Studi di Milano-Bicocca : Milano, Lombardia, IT

2009-11 to 2011-11 | Master degree in Computer Science (Department of Informatics, Systems and Communication)
Education
Source: Self-asserted source
Marco S. Nobile

Università degli Studi di Milano-Bicocca: Milano, IT

2004-10 to 2009-04 | Bachelor degree in Computer Science (Department of Informatics, Systems and Communication)
Education
Source: Self-asserted source
Marco S. Nobile

Professional activities (3)

IEEE: New York, NY, US

Junior member
Membership
Source: Self-asserted source
Marco S. Nobile

Research Center for Advanced Science and Technolog (RCAST) - The University of Tokyo: Tokyo, JP

2018-02 to 2020-01 | Cooperative research fellow
Invited position
Source: Self-asserted source
Marco S. Nobile

IEEE: New York, NY, US

2019-07-11 | Best paper award at IEEE CIBCB 2019
Distinction
Source: Self-asserted source
Marco S. Nobile

Works (37)

Small energy benefits of in-wake flying in long-duration migratory flights

Proceedings of the Royal Society B: Biological Sciences
2024-09 | Journal article
DOI: 10.1098/rspb.2024.1173
Contributors: Elisa Perinot; Ortal Mizrahy Rewald; Johannes Fritz; Marco Salvatore Nobile; Alexei Vyssotski; Thomas Ruf; Leonida Fusani; Bernhard Voelkl
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Ten quick tips for fuzzy logic modeling of biomedical systems

PLOS Computational Biology
2023-12-21 | Journal article
DOI: 10.1371/journal.pcbi.1011700
Contributors: Davide Chicco; B. F. Francis Ouellette; Simone Spolaor; Marco S. Nobile
Source: check_circle
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Characterization of bird formations using fuzzy modelling

Journal of The Royal Society Interface
2023-02 | Journal article
DOI: 10.1098/rsif.2022.0798
Contributors: Elisa Perinot; Johannes Fritz; Leonida Fusani; Bernhard Voelkl; Marco S. Nobile
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Shaping and Dilating the Fitness Landscape for Parameter Estimation in Stochastic Biochemical Models

Applied Sciences
2022-07-01 | Journal article
DOI: 10.3390/app12136671
Contributors: Marco S. Nobile; Daniele M. Papetti; Simone Spolaor; Paolo Cazzaniga; Luca Manzoni
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SMGen: A Generator of Synthetic Models of Biochemical Reaction Networks

Symmetry
2022-01-10 | Journal article
DOI: 10.3390/sym14010119
Contributors: Simone G. Riva; Paolo Cazzaniga; Marco S. Nobile; Simone Spolaor; Leonardo Rundo; Daniela Besozzi; Andrea Tangherloni
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FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks

PLOS Computational Biology
2021-09-09 | Journal article
DOI: 10.1371/journal.pcbi.1009410
Contributors: Andrea Tangherloni; Dina Schneidman-Duhovny; Marco S. Nobile; Paolo Cazzaniga; Giulia Capitoli; Simone Spolaor; Leonardo Rundo; Giancarlo Mauri; Daniela Besozzi
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A CUDA-powered method for the feature extraction and unsupervised analysis of medical images

The Journal of Supercomputing
2021-08-21 | Journal article
DOI: 10.1007/s11227-020-03565-8
Contributors: Leonardo Rundo; Andrea Tangherloni; Paolo Cazzaniga; Matteo Mistri; Simone Galimberti; Ramona Woitek; Evis Sala; Giancarlo Mauri; Marco S. Nobile
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A Graph Theory Approach to Fuzzy Rule Base Simplification

2020 | Book chapter
DOI: 10.1007/978-3-030-50146-4_29
Contributors: Caro Fuchs; Simone Spolaor; Marco S. Nobile; Uzay Kaymak
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Crossref

Efficient and Settings-Free Calibration of Detailed Kinetic Metabolic Models with Enzyme Isoforms Characterization

2020 | Book chapter
DOI: 10.1007/978-3-030-34585-3_17
Contributors: Niccolò Totis; Andrea Tangherloni; Marco Beccuti; Paolo Cazzaniga; Marco S. Nobile; Daniela Besozzi; Marzio Pennisi; Francesco Pappalardo
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Crossref

Global Sensitivity Analysis of Constraint-Based Metabolic Models

2020 | Book chapter
DOI: 10.1007/978-3-030-34585-3_16
Contributors: Chiara Damiani; Dario Pescini; Marco S. Nobile
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cuProCell: GPU-Accelerated Analysis of Cell Proliferation With Flow Cytometry Data

IEEE Journal of Biomedical and Health Informatics
2020-11 | Journal article
DOI: 10.1109/JBHI.2020.3005423
Contributors: Marco S. Nobile; Eric Nisoli; Thalia Vlachou; Simone Spolaor; Paolo Cazzaniga; Giancarlo Mauri; Pier Giuseppe Pelicci; Daniela Besozzi
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ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy

Applied Sciences
2020-09-06 | Journal article
DOI: 10.3390/app10186187
Contributors: Leonardo Rundo; Andrea Tangherloni; Darren R. Tyson; Riccardo Betta; Carmelo Militello; Simone Spolaor; Marco S. Nobile; Daniela Besozzi; Alexander L. R. Lubbock; Vito Quaranta et al.
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Coupling Mechanistic Approaches and Fuzzy Logic to Model and Simulate Complex Systems

IEEE Transactions on Fuzzy Systems
2020-08 | Journal article
DOI: 10.1109/TFUZZ.2019.2921517
Contributors: Simone Spolaor; Marco S. Nobile; Giancarlo Mauri; Paolo Cazzaniga; Daniela Besozzi
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Crossref

ACDC: Automated Cell Detection and Counting for Time-lapse Fluorescence Microscopy

2020-07-16 | Preprint
DOI: 10.1101/2020.07.14.202804
Contributors: Leonardo Rundo; Andrea Tangherloni; Darren R. Tyson; Riccardo Betta; Carmelo Militello; Simone Spolaor; Marco S. Nobile; Daniela Besozzi; Alexander L. R. Lubbock; Vito Quaranta et al.
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Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells

Bioinformatics
2020-04-01 | Journal article
DOI: 10.1093/bioinformatics/btz868
Contributors: Marco S Nobile; Giuseppina Votta; Roberta Palorini; Simone Spolaor; Humberto De Vitto; Paolo Cazzaniga; Francesca Ricciardiello; Giancarlo Mauri; Lilia Alberghina; Ferdinando Chiaradonna et al.
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Surfing on Fitness Landscapes: A Boost on Optimization by Fourier Surrogate Modeling

Entropy
2020-02-29 | Journal article
DOI: 10.3390/e22030285
Contributors: Luca Manzoni; Daniele M. Papetti; Paolo Cazzaniga; Simone Spolaor; Giancarlo Mauri; Daniela Besozzi; Marco S. Nobile
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Estimation of Kinetic Reaction Constants: Exploiting Reboot Strategies to Improve PSO’s Performance

2019 | Book chapter
DOI: 10.1007/978-3-030-14160-8_10
Contributors: Simone Spolaor; Andrea Tangherloni; Leonardo Rundo; Paolo Cazzaniga; Marco S. Nobile
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USE-Net: Incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets

Neurocomputing
2019-11 | Journal article
DOI: 10.1016/j.neucom.2019.07.006
Contributors: Leonardo Rundo; Changhee Han; Yudai Nagano; Jin Zhang; Ryuichiro Hataya; Carmelo Militello; Andrea Tangherloni; Marco S. Nobile; Claudio Ferretti; Daniela Besozzi et al.
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Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design

Applied Soft Computing
2019-08 | Journal article
DOI: 10.1016/j.asoc.2019.105494
Contributors: Andrea Tangherloni; Simone Spolaor; Paolo Cazzaniga; Daniela Besozzi; Leonardo Rundo; Giancarlo Mauri; Marco S. Nobile
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A novel framework for MR image segmentation and quantification by using MedGA

Computer Methods and Programs in Biomedicine
2019-07 | Journal article
DOI: 10.1016/j.cmpb.2019.04.016
Contributors: Leonardo Rundo; Andrea Tangherloni; Paolo Cazzaniga; Marco S. Nobile; Giorgio Russo; Maria Carla Gilardi; Salvatore Vitabile; Giancarlo Mauri; Daniela Besozzi; Carmelo Militello
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Parallel implementation of efficient search schemes for the inference of cancer progression models

2016-07 | Conference paper
DOI: 10.1109/CIBCB.2016.7758109
Source: Self-asserted source
Marco S. Nobile

Graphics processing units in bioinformatics, computational biology and systems biology

Brief Bioinform
2016-07-08 | Journal article
DOI: 10.1093/bib/bbw058
Contributors: Marco S. Nobile; Paolo Cazzaniga; Andrea Tangherloni; Daniela Besozzi
Source: Self-asserted source
Marco S. Nobile via Crossref Metadata Search

Gillespie’s Stochastic Simulation Algorithm on MIC coprocessors

J Supercomput
2016-06 | Journal article
DOI: 10.1007/s11227-016-1778-8
Contributors: Andrea Tangherloni; Marco S. Nobile; Paolo Cazzaniga; Daniela Besozzi; Giancarlo Mauri
Source: Self-asserted source
Marco S. Nobile via Crossref Metadata Search

Parallelizing biochemical stochastic simulations: A comparison of GPUs and Intel Xeon Phi processors

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2015 | Book
DOI: 10.1007/978-3-319-21909-7_36
EID:

2-s2.0-84944233926
Contributors: Cazzaniga, P.; Ferrara, F.; Nobile, M.S.; Besozzi, D.; Mauri, G.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

A memetic hybrid method for the Molecular Distance Geometry Problem with incomplete information

Proceedings of the 2014 IEEE Congress on Evolutionary Computation, CEC 2014
2014 | Conference paper
DOI: 10.1109/CEC.2014.6900386
EID:

2-s2.0-84908577886
Contributors: Nobile, M.S.; Citrolo, A.G.; Cazzaniga, P.; Besozzi, D.; Mauri, G.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

Computational strategies for a system-level understanding of metabolism.

2014 | Journal article
DOI: 10.3390/metabo4041034
PMID: 25427076
PMC: PMC4279158
Contributors: Cazzaniga P; Damiani C; Besozzi D; Colombo R; Nobile MS; Gaglio D; Pescini D; Molinari S; Mauri G; Alberghina L et al.
Source: Self-asserted source
Marco S. Nobile via Europe PubMed Central

cuTauLeaping: a GPU-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems.

2014 | Journal article
DOI: 10.1371/journal.pone.0091963
PMID: 24663957
PMC: PMC3963881
Contributors: Nobile MS; Cazzaniga P; Besozzi D; Pescini D; Mauri G
Source: Self-asserted source
Marco S. Nobile via Europe PubMed Central
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GPU-accelerated simulations of mass-action kinetics models with cupSODA

Journal of Supercomputing
2014 | Journal article
DOI: 10.1007/s11227-014-1208-8
EID:

2-s2.0-84905581213
Contributors: Nobile, M.S.; Cazzaniga, P.; Besozzi, D.; Mauri, G.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization.

2014 | Journal article
DOI: 10.1155/2014/863298
PMID: 25025072
PMC: PMC4082904
Contributors: Cazzaniga P; Nobile MS; Besozzi D; Bellini M; Mauri G
Source: Self-asserted source
Marco S. Nobile via Europe PubMed Central
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Simulation and analysis of the blood coagulation cascade accelerated on GPU

Proceedings - 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, PDP 2014
2014 | Conference paper
DOI: 10.1109/PDP.2014.52
EID:

2-s2.0-84899447058
Contributors: Bellini, M.; Besozzi, D.; Cazzaniga, P.; Mauri, G.; Nobile, M.S.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

CupSODA: A cuda-powered simulator of mass-action kinetics

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2013 | Journal article
DOI: 10.1007/978-3-642-39958-9-32
Contributors: Nobile, M.S.; Besozzi, D.; Cazzaniga, P.; Mauri, G.; Pescini, D.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

Evolutionary inference of biochemical reaction networks accelerated on graphics processing units

Proceedings of the 2013 International Conference on High Performance Computing and Simulation, HPCS 2013
2013 | Journal article
DOI: 10.1109/HPCSim.2013.6641490
Contributors: Nobile, M.S.; Mauri, G.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

Reverse engineering of kinetic reaction networks by means of Cartesian Genetic Programming and Particle Swarm Optimization

2013 IEEE Congress on Evolutionary Computation, CEC 2013
2013 | Journal article
DOI: 10.1109/CEC.2013.6557752
Contributors: Nobile, M.S.; Besozzi, D.; Cazzaniga, P.; Pescini, D.; Mauri, G.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

The foundation of Evolutionary Petri nets

CEUR Workshop Proceedings
2013 | Conference paper
EID:

2-s2.0-84922644049
Contributors: Nobile, M.S.; Besozzi, D.; Cazzaniga, P.; Mauri, G.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

GPU-powered Simulation Methodologies for Biological Systems

EPTCS
2013-09 | Journal article
DOI: 10.4204/eptcs.130.14
Contributors: Daniela Besozzi; Giulio Caravagna; Paolo Cazzaniga; Marco Nobile; Dario Pescini; Alessandro Re
Source: Self-asserted source
Marco S. Nobile via Crossref Metadata Search

A GPU-based multi-swarm PSO method for parameter estimation in stochastic biological systems exploiting discrete-time target series

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2012 | Journal article
DOI: 10.1007/978-3-642-29066-4_7
Contributors: Nobile, M.S.; Besozzi, D.; Cazzaniga, P.; Mauri, G.; Pescini, D.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

Estimating reaction constants in stochastic biological systems with a multi-swarm PSO running on GPUs

GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion
2012 | Journal article
DOI: 10.1145/2330784.2330964
Contributors: Nobile, M.S.; Besozzi, D.; Cazzaniga, P.; Mauri, G.; Pescini, D.
Source: Self-asserted source
Marco S. Nobile via Scopus - Elsevier

Peer review (7 reviews for 2 publications/grants)

Review activity for Applied soft computing. (4)
Review activity for International journal of machine learning and cybernetics. (3)
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