Phylogenetic analysis of TET2 gene variants in Pakistani acute myeloid Leukemia patients.

Marco Antoniotti

Mawada Elmagboul Abdalla Abakar Mehad Almagboul Abdalla Abaker Marco Antoniotti Alex Graudenzi Phylogenetic analysis of TET2 gene variants in Pakistani acute myeloid Leukemia patients. 2026 4- 27 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbag058 db/journals/bib/bib27.html#AbakarAAG26 streams/journals/bib

Valentina Giansanti Francesca Giannese Oronza A. Botrugno Giorgia Gandolfi Chiara Balestrieri Marco Antoniotti Giovanni Tonon Davide Cittaro Scalable integration of multiomic single-cell data using generative adversarial networks. 2024 40 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btae300 db/journals/bioinformatics/bioinformatics40.html#GiansantiGBGBAT24

Gianluca Ascolani Fabrizio Angaroni Davide Maspero Francesco Craighero Narra Lakshmi Sai Bhavesh Rocco Piazza Chiara Damiani Daniele Ramazzotti Marco Antoniotti Alex Graudenzi LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. 99 2023 December 24 BMC Bioinform. 1 https://doi.org/10.1186/s12859-023-05221-3 db/journals/bmcbi/bmcbi24.html#AscolaniAMCBPDRAG23

Francesco Craighero Fabrizio Angaroni Fabio Stella Chiara Damiani Marco Antoniotti Alex Graudenzi Unity is strength: Improving the detection of adversarial examples with ensemble approaches. 126576 2023 October 554 Neurocomputing https://doi.org/10.1016/j.neucom.2023.126576 db/journals/ijon/ijon554.html#CraigheroASDAG23

Lucrezia Patruno Salvatore Milite Riccardo Bergamin Nicola Calonaci Alberto d'Onofrio Fabio Anselmi Marco Antoniotti Alex Graudenzi Giulio Caravagna A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. 2023 November 19 PLoS Comput. Biol. 11 https://doi.org/10.1371/journal.pcbi.1011557 db/journals/ploscb/ploscb19.html#PatrunoMBCdAAGC23

Fabrizio Angaroni Alessandro Guidi Gianluca Ascolani Alberto d'Onofrio Marco Antoniotti Alex Graudenzi J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. 269 2022 23 BMC Bioinform. 1 https://doi.org/10.1186/s12859-022-04779-8 https://www.wikidata.org/entity/Q114062815 db/journals/bmcbi/bmcbi23.html#AngaroniGAdAG22

Daniele Ramazzotti Fabrizio Angaroni Davide Maspero Gianluca Ascolani Isabella Castiglioni Rocco Piazza Marco Antoniotti Alex Graudenzi LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. 101523 2022 58 J. Comput. Sci. https://doi.org/10.1016/j.jocs.2021.101523 db/journals/jocs/jocs58.html#RamazzottiAMACP22

Daniele Ramazzotti Fabrizio Angaroni Davide Maspero Carlo Gambacorti Passerini Marco Antoniotti Alex Graudenzi Rocco Piazza VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. 100212 2021 2 Patterns 3 https://doi.org/10.1016/j.patter.2021.100212 https://www.wikidata.org/entity/Q112725875 db/journals/patterns/patterns2.html#RamazzottiAMPAG21

Fabrizio Angaroni Chiara Damiani Giulia Ramunni Marco Antoniotti Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. 1-12 2021 ANNSIM https://doi.org/10.23919/ANNSIM52504.2021.9552097 conf/annsim/2021 db/conf/annsim/annsim2021.html#AngaroniDRA21

Francesco Craighero Fabrizio Angaroni Fabio Stella Chiara Damiani Marco Antoniotti Alex Graudenzi EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. 2021 abs/2111.12631 CoRR https://arxiv.org/abs/2111.12631 db/journals/corr/corr2111.html#abs-2111-12631

Davide Maspero Chiara Damiani Marco Antoniotti Alex Graudenzi Marzia Di Filippo Marco Vanoni Giulio Caravagna Riccardo Colombo Daniele Ramazzotti Dario Pescini The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. 279-295 2020 171 Fundam. Informaticae 1-4 https://doi.org/10.3233/FI-2020-1883 db/journals/fuin/fuin171.html#MasperoDAGFVCCR20

Francesco Craighero Alex Graudenzi Fabrizio Angaroni Fabio Stella Marco Antoniotti Understanding Deep Learning with Activation Pattern Diagrams. 119-126 2020 XAI.it@AI*IA https://ceur-ws.org/Vol-2742/short6.pdf conf/aiia/2020xaiit db/conf/aiia/xaiit2020.html#CraigheroGASA20 Fabrizio Angaroni Mattia Pennati Lucrezia Patruno Davide Maspero Marco Antoniotti Alex Graudenzi A closed-loop optimization framework for personalized cancer therapy design. 1-9 2020 CIBCB https://doi.org/10.1109/CIBCB48159.2020.9277647 conf/cibcb/2020 db/conf/cibcb/cibcb2020.html#AngaroniPPMAG20 Marco Antoniotti Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp ... or: Hammering Some Sense into : ieee-floating-point. 76-83 2020 ELS https://doi.org/10.5281/zenodo.3748956 conf/els/2020 db/conf/els/els2020.html#Antoniotti20 Daniele M. Papetti Simone Spolaor Daniela Besozzi Paolo Cazzaniga Marco Antoniotti Marco S. Nobile On the automatic calibration of fully analogical spiking neuromorphic chips. 1-8 2020 IJCNN https://doi.org/10.1109/IJCNN48605.2020.9206654 conf/ijcnn/2020 db/conf/ijcnn/ijcnn2020.html#PapettiSBCAN20 Francesco Craighero Fabrizio Angaroni Alex Graudenzi Fabio Stella Marco Antoniotti Investigating the Compositional Structure of Deep Neural Networks. 322-334 2020 LOD (1) https://doi.org/10.1007/978-3-030-64583-0_30 conf/mod/2020-1 db/conf/mod/lod2020-1.html#CraigheroAGSA20

Francesco Craighero Fabrizio Angaroni Alex Graudenzi Fabio Stella Marco Antoniotti Investigating the Compositional Structure Of Deep Neural Networks. 2020 abs/2002.06967 CoRR https://arxiv.org/abs/2002.06967 db/journals/corr/corr2002.html#abs-2002-06967

Marco Antoniotti Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp. 2020 abs/2003.03831 CoRR https://arxiv.org/abs/2003.03831 db/journals/corr/corr2003.html#abs-2003-03831

Daniele Ramazzotti Alex Graudenzi Luca De Sano Marco Antoniotti Giulio Caravagna Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. 210:1-210:13 2019 20 BMC Bioinform. 1 https://doi.org/10.1186/s12859-019-2795-4 https://www.wikidata.org/entity/Q64087270 db/journals/bmcbi/bmcbi20.html#RamazzottiGSAC19

Daniele Ramazzotti Marco S. Nobile Marco Antoniotti Alex Graudenzi Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena. 1-10 2019 30 J. Comput. Sci. https://doi.org/10.1016/j.jocs.2018.10.009 db/journals/jocs/jocs30.html#RamazzottiNAG19

Lucrezia Patruno Edoardo Galimberti Daniele Ramazzotti Giulio Caravagna Luca De Sano Marco Antoniotti Alex Graudenzi cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. 13-18 2019 CIBB https://doi.org/10.1007/978-3-030-63061-4_2 conf/cibb/2019 db/conf/cibb/cibb2019.html#PatrunoGRCSAG19

Alex Graudenzi Davide Maspero Marzia Di Filippo Marco Gnugnoli Claudio Isella Giancarlo Mauri Enzo Medico Marco Antoniotti Chiara Damiani Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. 37-49 2018 87 J. Biomed. Informatics https://doi.org/10.1016/j.jbi.2018.09.010 https://www.wikidata.org/entity/Q62678513 db/journals/jbi/jbi87.html#GraudenziMFGIMM18

Daniele Ramazzotti Marco S. Nobile Marco Antoniotti Alex Graudenzi Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. 678-693 2018 ICCS (1) https://doi.org/10.1007/978-3-319-93698-7_52 conf/iccS/2018-1 db/conf/iccS/iccS2018-1.html#RamazzottiNAG18 Davide Maspero Alex Graudenzi Satwinder Singh Dario Pescini Giancarlo Mauri Marco Antoniotti Chiara Damiani Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. 115-126 2018 WIVACE https://doi.org/10.1007/978-3-030-21733-4_9 conf/wivace/2018 db/conf/wivace/wivace2018.html#MasperoGSPMAD18

Daniele Ramazzotti Marco S. Nobile Paolo Cazzaniga Giancarlo Mauri Marco Antoniotti Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models. 2017 abs/1703.03038 CoRR http://arxiv.org/abs/1703.03038 db/journals/corr/corr1703.html#RamazzottiNCMA17

Daniele Ramazzotti Marco S. Nobile Marco Antoniotti Alex Graudenzi Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. 2017 abs/1703.03074 CoRR http://arxiv.org/abs/1703.03074 db/journals/corr/corr1703.html#RamazzottiNAG17

Lucrezia Patruno Edoardo Galimberti Daniele Ramazzotti Giulio Caravagna Luca De Sano Marco Antoniotti Alex Graudenzi cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models. 2017 abs/1705.03067 CoRR http://arxiv.org/abs/1705.03067 db/journals/corr/corr1705.html#RamazzottiSSPP17

Daniele Ramazzotti Alex Graudenzi Luca De Sano Marco Antoniotti Giulio Caravagna Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. 2017 abs/1709.01076 CoRR http://arxiv.org/abs/1709.01076 db/journals/corr/corr1709.html#abs-1709-01076

Luca De Sano Giulio Caravagna Daniele Ramazzotti Alex Graudenzi Giancarlo Mauri Bud Mishra Marco Antoniotti TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. 1911-1913 2016 32 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btw035 https://www.wikidata.org/entity/Q31043962 db/journals/bioinformatics/bioinformatics32.html#SanoCRGMMA16

Andrea Paroni Alex Graudenzi Giulio Caravagna Chiara Damiani Giancarlo Mauri Marco Antoniotti CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. 64 2016 17 BMC Bioinform. https://doi.org/10.1186/s12859-016-0914-z https://www.wikidata.org/entity/Q35914932 db/journals/bmcbi/bmcbi17.html#ParoniGCDMA16

Alex Graudenzi Giulio Caravagna Iuliana M. Bocicor Claudia Cava Marco Antoniotti Giancarlo Mauri Ordering cancer mutational profiles of cross-sectional copy number alterations. 59-83 2016 15 Int. J. Data Min. Bioinform. 1 https://doi.org/10.1504/IJDMB.2016.076017 https://www.wikidata.org/entity/Q57518251 db/journals/ijdmb/ijdmb15.html#GraudenziCBCAM16

Marco Antoniotti Giulio Caravagna Luca De Sano Alex Graudenzi Giancarlo Mauri Bud Mishra Daniele Ramazzotti Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. 39 2016 8 R J. 2 https://doi.org/10.32614/rj-2016-032 db/journals/rjour/rjour8.html#AntoniottiCSGMM16

Daniele Ramazzotti Marco S. Nobile Paolo Cazzaniga Giancarlo Mauri Marco Antoniotti Parallel implementation of efficient search schemes for the inference of cancer progression models. 1-6 2016 CIBCB https://doi.org/10.1109/CIBCB.2016.7758109 https://www.wikidata.org/entity/Q57518256 conf/cibcb/2016 db/conf/cibcb/cibcb2016.html#RamazzottiNCMA16

Daniele Ramazzotti Alex Graudenzi Marco Antoniotti Modeling cumulative biological phenomena with Suppes-Bayes causal networks. 2016 abs/1602.07857 CoRR http://arxiv.org/abs/1602.07857 db/journals/corr/corr1602.html#RamazzottiGA16

Daniele Ramazzotti Giulio Caravagna Loes Olde Loohuis Alex Graudenzi Ilya Korsunsky Giancarlo Mauri Marco Antoniotti Bud Mishra CAPRI: efficient inference of cancer progression models from cross-sectional data. 3016-3026 2015 31 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btv296 https://www.wikidata.org/entity/Q30951310 db/journals/bioinformatics/bioinformatics31.html#RamazzottiCLGKM15

Giulio Caravagna Luca De Sano Marco Antoniotti Automatising the analysis of stochastic biochemical time-series. S8 2015 16 BMC Bioinform. S-9 https://doi.org/10.1186/1471-2105-16-S9-S8 https://www.wikidata.org/entity/Q35655835 db/journals/bmcbi/bmcbi16S.html#CaravagnaSA15

Giulio Caravagna Alberto d'Onofrio Marco Antoniotti Giancarlo Mauri Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. 19-34 2014 236 Inf. Comput. https://doi.org/10.1016/j.ic.2014.01.010 https://www.wikidata.org/entity/Q57518399 db/journals/iandc/iandc236.html#CaravagnadAM14

Claudia Cava Italo Zoppis Manuela Gariboldi Isabella Castiglioni Giancarlo Mauri Marco Antoniotti Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference. 2 2014 4 J. Clin. Bioinform. https://doi.org/10.1186/2043-9113-4-2 https://www.wikidata.org/entity/Q37597565 db/journals/jclinbioinf/jclinbioinf4.html#CavaZGCMA14

Alex Graudenzi Chiara Damiani Andrea Paroni Alessandro Filisetti Marco Villani 0001 Roberto Serra Marco Antoniotti Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. 151-168 2014 WIVACE https://doi.org/10.1007/978-3-319-12745-3_13 https://www.wikidata.org/entity/Q57499614 conf/wivace/2014 db/conf/wivace/wivace2014.html#GraudenziDPFVSA14

Marco Antoniotti CLAZY: Lazy Calling for Common Lisp. 2014 abs/1412.1393 CoRR http://arxiv.org/abs/1412.1393 db/journals/corr/corr1412.html#Antoniotti14

Marco Antoniotti Gary D. Bader Giulio Caravagna Silvia Crippa Alex Graudenzi Giancarlo Mauri GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. 513-514 2013 29 Bioinform. 4 https://doi.org/10.1093/bioinformatics/bts726 https://www.wikidata.org/entity/Q41854744 db/journals/bioinformatics/bioinformatics29.html#AntoniottiBCCGM13

Artiom Alhazov Marco Antoniotti Alberto Leporati Characterizing the computational power of energy-based P systems. 789-800 2013 90 Int. J. Comput. Math. 4 https://doi.org/10.1080/00207160.2012.741781 db/journals/ijcm/ijcm90.html#AlhazovAL13

Claudia Cava Italo Zoppis Manuela Gariboldi Isabella Castiglioni Giancarlo Mauri Marco Antoniotti Copy-Number Alterations for Tumor Progression Inference. 104-109 2013 AIME https://doi.org/10.1007/978-3-642-38326-7_16 https://www.wikidata.org/entity/Q57518423 conf/aime/2013 db/conf/aime/aime2013.html#CavaZGCMA13 Daniele Ramazzotti Carlo Maj Marco Antoniotti A Model of Colonic Crypts using SBML Spatial. WIVACE 2013 74-78 https://doi.org/10.4204/EPTCS.130.11 http://arxiv.org/abs/1309.7692 journals/corr/GraudenziCMA13 db/series/eptcs/eptcs130.html#RamazzottiMA13 Giulio Caravagna Alex Graudenzi Marco Antoniotti Giovanni De Matteis Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. WIVACE 2013 79-82 https://doi.org/10.4204/EPTCS.130.12 http://arxiv.org/abs/1309.7693 journals/corr/GraudenziCMA13 db/series/eptcs/eptcs130.html#CaravagnaGAM13 Alex Graudenzi Giulio Caravagna Giancarlo Mauri Marco Antoniotti Proceedings Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation, Milan, Italy, July 1-2, 2013. WIVACE 2013 EPTCS https://doi.org/10.4204/EPTCS.130 http://arxiv.org/abs/1309.7122 130 db/series/eptcs/eptcs130.html

Marco Antoniotti Rudolf Freund Alberto Leporati Giancarlo Mauri Self-Stabilization in Membrane Systems. 133-146 2012 20 Comput. Sci. J. Moldova 2 http://www.math.md/publications/csjm/issues/v20-n2/11081/ db/journals/csjm/csjm20.html#AntoniottiFLM12

Italo Zoppis Erica Gianazza Massimiliano Borsani Clizia Chinello Veronica Mainini Carmen Galbusera Carlo Ferrarese Gloria Galimberti Alessandro Sorbi Barbara Borroni Fulvio Magni Marco Antoniotti Giancarlo Mauri Mutual Information Optimization for Mass Spectra Data Alignment. 934-939 2012 9 IEEE ACM Trans. Comput. Biol. Bioinform. 3 https://doi.org/10.1109/TCBB.2011.80 https://doi.ieeecomputersociety.org/10.1109/TCBB.2011.80 https://dl.acm.org/doi/10.1109/TCBB.2011.80 https://www.wikidata.org/entity/Q33881800 db/journals/tcbb/tcbb9.html#ZoppisGBCMGFGSBMAM12

Italo Zoppis Massimiliano Borsani Erica Gianazza Clizia Chinello Francesco Rocco Giancarlo Albo André M. Deelder Yuri E. M. van der Burgt Fulvio Magni Marco Antoniotti Giancarlo Mauri Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data. 251-256 2012 BIOINFORMATICS conf/biostec/2012bi db/conf/biostec/bioinformatics2012.html#ZoppisBGCRADBMAM12 Italo Zoppis Massimiliano Borsani Erica Gianazza Clizia Chinello Giancarlo Albo Francesco Rocco André M. Deelder Yuri E. M. van der Burgt Marco Antoniotti Fulvio Magni Giancarlo Mauri Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discrimination. 1 2012 ICCABS https://doi.org/10.1109/ICCABS.2012.6182664 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2012.6182664 https://www.wikidata.org/entity/Q57518477 conf/iccabs/2012 db/conf/iccabs/iccabs2012.html#ZoppisBGCARDBAMM12 Giulio Caravagna Alex Graudenzi Marco Antoniotti Giancarlo Mauri Alberto d'Onofrio Effects of delayed immune-response in tumor immune-system interplay HSB 2012 106-121 https://doi.org/10.4204/EPTCS.92.8 http://arxiv.org/abs/1208.3855 journals/corr/abs-1208-3151 db/series/eptcs/eptcs92.html#abs-1208-3855 Marco Antoniotti Proceedings of ELS 2012 - 5th European Lisp Symposium, Zadar, Croatia, April 30 - May 1, 2012. ELS ELSAA 2012 db/conf/els/els2012.html https://european-lisp-symposium.org/static/proceedings/2012.pdf

Leonardo Vanneschi Antonella Farinaccio Giancarlo Mauri Marco Antoniotti Paolo Provero Mario Giacobini A comparison of machine learning techniques for survival prediction in breast cancer. 12 2011 4 BioData Min. https://doi.org/10.1186/1756-0381-4-12 https://www.wikidata.org/entity/Q42034959 db/journals/biodatamining/biodatamining4.html#VanneschiFMAPG11

Marco Antoniotti Marco Carreras Antonella Farinaccio Giancarlo Mauri Daniele Merico Italo Zoppis An application of kernel methods to gene cluster temporal meta-analysis. 1361-1368 2010 37 Comput. Oper. Res. 8 https://doi.org/10.1016/j.cor.2009.03.011 https://www.wikidata.org/entity/Q57518511 db/journals/cor/cor37.html#AntoniottiCFMMZ10

Gianluca Colombo Daniele Merico Giorgio Boncoraglio Flavio De Paoli John Ellul Giuseppe Frisoni Zoltán Nagy 0004 Aad van der Lugt István Vassányi Marco Antoniotti An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case. 469-484 2010 43 J. Biomed. Informatics 4 https://doi.org/10.1016/j.jbi.2009.12.005 https://www.wikidata.org/entity/Q38507693 db/journals/jbi/jbi43.html#ColomboMBPEFNLVA10

Leonardo Vanneschi Antonella Farinaccio Mario Giacobini Giancarlo Mauri Marco Antoniotti Paolo Provero Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques. 110-121 2010 EvoBIO https://doi.org/10.1007/978-3-642-12211-8_10 conf/evoW/2010bio db/conf/evoW/evobio2010.html#VanneschiFGMAP10

Gianluca Colombo Daniele Merico Zoltán Nagy 0004 Flavio De Paoli Marco Antoniotti Giancarlo Mauri Ontological modeling at a domain interface: bridging clinical and biomolecular knowledge. 205-224 2009 24 Knowl. Eng. Rev. 3 https://doi.org/10.1017/S0269888909990026 https://www.wikidata.org/entity/Q57518544 db/journals/ker/ker24.html#ColomboMNPAM09

Marco Antoniotti CLAZY: Lazy Calling for Common Lisp. 125-132 2008 ELS https://european-lisp-symposium.org/static/proceedings/2008.pdf#page=133 conf/els/2008 db/conf/els/els2008.html#Antoniotti08

Jomol P. Mathew Barry S. Taylor Gary D. Bader Saiju Pyarajan Marco Antoniotti Arul M. Chinnaiyan Chris Sander Steven J. Burakoff Bud Mishra From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. 2007 3 PLoS Comput. Biol. 2 https://doi.org/10.1371/journal.pcbi.0030012 https://www.wikidata.org/entity/Q21145672 db/journals/ploscb/ploscb3.html#MathewTBPACSBM07

Gianluca Colombo Daniele Merico Marco Antoniotti Flavio De Paoli Giancarlo Mauri Ontological Modelling for Neurovascular Disease Study: Issues in the Adoption of Description Logic. 2007 Description Logics https://ceur-ws.org/Vol-250/paper_68.pdf conf/dlog/2007 db/conf/dlog/dlog2007.html#ColomboMAPM07 Italo Zoppis Daniele Merico Marco Antoniotti Bud Mishra Giancarlo Mauri Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods. 158-169 2007 conf/isbra/2007 ISBRA https://doi.org/10.1007/978-3-540-72031-7_15 db/conf/isbra/isbra2007.html#ZoppisMAMM07 Daniele Merico Italo Zoppis Marco Antoniotti Giancarlo Mauri Evaluating Graph Kernel Methods for Relation Discovery in GO-Annotated Clusters. 892-900 2007 conf/kes/2007-3 KES (3) https://doi.org/10.1007/978-3-540-74829-8_109 db/conf/kes/kes2007-3.html#MericoZAM07 Carla Piazza Marco Antoniotti Venkatesh Mysore Alberto Policriti Franz Winkler 0001 Bud Mishra Algorithmic Algebraic Model Checking I: Challenges from Systems Biology. 5-19 2005 conf/cav/2005 CAV https://doi.org/10.1007/11513988_3 db/conf/cav/cav2005.html#PiazzaAMPWM05

Marco Antoniotti Carla Piazza Alberto Policriti Marta Simeoni Bud Mishra Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice. 45-67 2004 325 Theor. Comput. Sci. 1 https://doi.org/10.1016/j.tcs.2004.03.064 db/journals/tcs/tcs325.html#AntoniottiPPSM04

Marco Antoniotti Bhubaneswar Mishra Carla Piazza Alberto Policriti Marta Simeoni Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing. 57-74 2003 conf/cmsb/2003 CMSB https://doi.org/10.1007/3-540-36481-1_6 db/conf/cmsb/cmsb2003.html#AntoniottiMPPS03 Marco Antoniotti F. Park Alberto Policriti Nadia Ugel Bud Mishra Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. 116-127 2003 conf/psb/2003 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb03/antoniotti.pdf db/conf/psb/psb2003.html#AntoniottiPPUM03 Marco Antoniotti Alberto Policriti Nadia Ugel Bud Mishra XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior. 431-442 2002 conf/hipc/2002 HiPC https://doi.org/10.1007/3-540-36265-7_41 db/conf/hipc/hipc2002.html#AntoniottiPUM02 Marco Antoniotti Alberto Ferrari Luciano Lavagno Alberto L. Sangiovanni-Vincentelli Ellen Sentovich Embedded system design specification: merging reactive control and data computation. 3302-3307 2001 CDC https://doi.org/10.1109/.2001.980331 conf/cdc/2001 db/conf/cdc/cdc2001.html#AntoniottiFLSS01 Marco Antoniotti Aleks Göllü SHIFT and SMART-AHS: A Language for Hybrid System Engineering Modeling and Simulation. 171-182 1997 conf/dsl/1997 DSL http://www.usenix.org/publications/library/proceedings/dsl97/antoniotti.html db/conf/dsl/dsl1997.html#AntoniottiG97 Marco Antoniotti Synthesis and Verification of Controllers for Robotics and Manufacturing Devices with Temporal Logic and the "Control-D" System. New York University, USA 1995 https://cs.nyu.edu/media/publications/antoniotti_marco.pdf Marco Antoniotti Bud Mishra Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers. 1441-1446 1995 conf/icra/1995 ICRA db/conf/icra/icra1995-1.html#AntoniottiM95 https://doi.org/10.1109/ROBOT.1995.525480 Mawada Elmagboul Abdalla Abakar Mehad Almagboul Abdalla Abaker Giancarlo Albo Artiom Alhazov Fabrizio Angaroni Fabio Anselmi Gianluca Ascolani Gary D. Bader Chiara Balestrieri Riccardo Bergamin Daniela Besozzi Narra Lakshmi Sai Bhavesh Maria-Iuliana BocicorIuliana M. Bocicor Giorgio Boncoraglio Barbara Borroni Massimiliano Borsani Oronza A. Botrugno Steven J. Burakoff Yuri E. M. van der Burgt Nicola Calonaci Giulio Caravagna Marco Carreras Isabella Castiglioni Claudia Cava Paolo Cazzaniga Clizia Chinello Arul M. Chinnaiyan Davide Cittaro Gianluca Colombo Riccardo Colombo Francesco Craighero Silvia Crippa Chiara Damiani André M. Deelder Alberto d'Onofrio John Ellul Antonella Farinaccio Carlo Ferrarese Alberto Ferrari Marzia Di Filippo Alessandro Filisetti Rudolf Freund Giuseppe Frisoni Carmen Galbusera Edoardo Galimberti Gloria Galimberti Giorgia Gandolfi Manuela Gariboldi Mario Giacobini Erica Gianazza Francesca Giannese Valentina Giansanti Marco Gnugnoli Aleks Göllü Alex Graudenzi Alessandro Guidi Claudio Isella Ilya Korsunsky Luciano Lavagno Alberto Leporati Loes Olde Loohuis Aad van der Lugt Fulvio Magni Veronica Mainini Carlo Maj Davide Maspero Jomol P. Mathew Giovanni De Matteis Giancarlo Mauri Enzo Medico Daniele Merico Salvatore Milite Bud MishraBhubaneswar Mishra Venkatesh Mysore Zoltán Nagy 0004 Marco S. Nobile Flavio De Paoli Daniele M. Papetti F. Park Andrea Paroni Carlo Gambacorti Passerini Lucrezia Patruno Mattia Pennati Dario Pescini Carla Piazza Rocco Piazza Alberto Policriti Paolo Provero Saiju Pyarajan Daniele Ramazzotti Giulia Ramunni Francesco Rocco Chris Sander Alberto L. Sangiovanni-Vincentelli Luca De Sano Ellen Sentovich Roberto Serra Marta Simeoni Satwinder Singh Alessandro Sorbi Simone Spolaor Fabio Stella Barry S. Taylor Giovanni Tonon Nadia Ugel Leonardo Vanneschi Marco Vanoni István Vassányi Marco Villani 0001 Franz Winkler 0001 Italo Zoppis