Standardizing the Presentation Layer. Why and What? - Fausto Caneschi; Emanuela Merelli (ICDCS, 1987)

An Architecture for an ASN.1 Encoder/Decoder. - Fausto Caneschi; Emanuela Merelli (Comput. Networks, 1987)

A successive overrelaxation backpropagation algorithm for neural-network training. - Renato De Leone; Rosario Capparuccia; Emanuela Merelli (IEEE Trans. Neural Networks, 1998)

Agent-Oriented and Constraint Technologies for Distributed Transaction Management. - Viviana Mascardi; Emanuela Merelli (IIA/SOCO, 1999)

A tabu search method guided by shifting bottleneck for the job shop scheduling problem. - Ferdinando Pezzella; Emanuela Merelli (Eur. J. Oper. Res., 2000)

Patterns for web applications. - Diego Bonura; Rosario Culmone; Emanuela Merelli (SEKE, 2002)

An XML View of the "World". - Ezio Bartocci; Emanuela Merelli; Leonardo Mariani (ICEIS (1), 2003)

A Programming Environment for Global Activity-based Applications. - Flavio Corradini; Leonardo Mariani; Emanuela Merelli (WOA, 2003)

FarMAS: A MAS for Extended Quality Workflow. - Diego Bonura; Flavio Corradini; Emanuela Merelli; Gino Romiti (WETICE, 2004)

An agent-based matchmaker. - Flavio Corradini; Chiara Ercoli; Emanuela Merelli; Barbara Re 001 (WOA, 2004)

An agent-based approach to tool integration. - Flavio Corradini; Leonardo Mariani; Emanuela Merelli (Int. J. Softw. Tools Technol. Transf., 2004)

A Multi-agent System for Modelling Carbohydrate Oxidation in Cell. - Flavio Corradini; Emanuela Merelli; Marco Vita (ICCSA (2), 2005)

Hermes: Agent-Based Middleware for Mobile Computing. - Flavio Corradini; Emanuela Merelli (SFM, 2005)

Integrating Ontologies in Mobile Agents. - Flavio Corradini; Rosario Culmone; Maria Rita Di Berardini; Emanuela Merelli (WOA, 2005)

Agents in bioinformatics. - Michael Luck; Emanuela Merelli (Knowl. Eng. Rev., 2005)

Time to Organize the Bioinformatics Resourceome. - Nicola Cannata; Emanuela Merelli; Russ B. Altman (PLoS Comput. Biol., 2005)

An Agent-Oriented Conceptual Framework for Systems Biology. - Nicola Cannata; Flavio Corradini; Emanuela Merelli; Andrea Omicini; Alessandro Ricci (Trans. Comp. Sys. Biology, 2005)

Enacting Proactive Workflows Engine in e-Science. - Ezio Bartocci; Flavio Corradini; Emanuela Merelli (International Conference on Computational Science (3), 2006)

Building a MultiAgent System from a User Workflow Specification. - Ezio Bartocci; Flavio Corradini; Emanuela Merelli (WOA, 2006)

Model driven design and implementation of activity-based applications in Hermes. - Ezio Bartocci; Flavio Corradini; Emanuela Merelli; Leonardo Vito (WOA, 2006)

Network integration of data and analysis of oncology interest. - Paolo Romano 001; Guglielmo Bertolini; Flavio De Paoli; M. Fattore; Domenico Marra; Giancarlo Mauri; Emanuela Merelli; Ivan Porro; Silvia Scaglione; Luciano Milanesi (J. Integr. Bioinform., 2006)

Correction: Time to Organize the Bioinformatics Resourceome. - Nicola Cannata; Emanuela Merelli; Russ B. Altman (PLoS Comput. Biol., 2006)

Semantic Resource Management in MAS. - Nicola Cannata; Flavio Corradini; Francesca Piersigilli; Emanuela Merelli; Leonardo Vito (WOA, 2007)

Agents in bioinformatics, computational and systems biology. - Emanuela Merelli; Giuliano Armano; Nicola Cannata; Flavio Corradini; Mark d'Inverno; Andreas Doms; Phillip W. Lord; Andrew C. R. Martin; Luciano Milanesi; Steffen Möller; Michael Schroeder 001; Michael Luck (Briefings Bioinform., 2007)

BioWMS: a web-based Workflow Management System for bioinformatics. - Ezio Bartocci; Flavio Corradini; Emanuela Merelli; Lorenzo Scortichini (BMC Bioinform., 2007)

Biowep: a workflow enactment portal for bioinformatics applications. - Paolo Romano 001; Ezio Bartocci; Guglielmo Bertolini; Flavio De Paoli; Domenico Marra; Giancarlo Mauri; Emanuela Merelli; Luciano Milanesi (BMC Bioinform., 2007)

A Resourceomic Grid for bioinformatics. - Nicola Cannata; Flavio Corradini; Emanuela Merelli (Future Gener. Comput. Syst., 2007)

Validating MAS simulation models with mutation. - Emanuela Merelli; Michal Young (Multiagent Grid Syst., 2007)

StonyCam: A Formal Framework for Modeling, Analyzing and Regulating Cardiac Myocytes. - Ezio Bartocci; Flavio Corradini; Radu Grosu; Emanuela Merelli; Oliviero Riganelli; Scott A. Smolka (Concurrency, Graphs and Models, 2008)

Model Checking Biological Oscillators. - Ezio Bartocci; Flavio Corradini; Emanuela Merelli; Luca Tesei (FBTC@ICALP, 2008)

Preface. - Nicola Cannata; Emanuela Merelli; Irek Ulidowski (FBTC@ICALP, 2008)

Multiagent modelling and simulation of carbohydrate oxidation in cell. - Nicola Cannata; Flavio Corradini; Emanuela Merelli (Int. J. Model. Identif. Control., 2008)

Resourceome for e-Government: Semantic Web Tool for Managing PA Resources. - Flavio Corradini; Emanuela Merelli; Alberto Polzonetti; Barbara Re 001; Leonardo Vito (CSREA EE, 2009)

A Shape Calculus for Biological Processes. - Ezio Bartocci; Flavio Corradini; Maria Rita Di Berardini; Emanuela Merelli; Luca Tesei (ICTCS, 2009)

Preface. - Nicola Cannata; Emanuela Merelli (Theor. Comput. Sci., 2009)

Towards Bioinformatics Resourceomes. - Nicola Cannata; Flavio Corradini; Emanuela Merelli; Francesca Piersigilli; Leonardo Vito (Biomedical Data and Applications, 2009)

Bone Remodelling: A Complex Automata-Based Model Running in BioShape. - Diletta Cacciagrano; Flavio Corradini; Emanuela Merelli (ACRI, 2010)

An Individual-based Probabilistic Model for Fish Stock Simulation - Federico Buti; Flavio Corradini; Emanuela Merelli; Elio Paschini; Pierluigi Penna; Luca Tesei (AMCA-POP, 2010)

Multiscale Bone Remodelling with Spatial P Systems - Diletta Cacciagrano; Flavio Corradini; Emanuela Merelli; Luca Tesei (MeCBIC, 2010)

Shape Calculus: Timed Operational Semantics and Well-formedness - Ezio Bartocci; Diletta Romana Cacciagrano; Maria Rita Di Berardini; Emanuela Merelli; Luca Tesei (CoRR, 2010)

Shape Calculus. A Spatial Mobile Calculus for 3D Shapes. - Ezio Bartocci; Flavio Corradini; Maria Rita Di Berardini; Emanuela Merelli; Luca Tesei (Sci. Ann. Comput. Sci., 2010)

Timed Operational Semantics and Well-Formedness of Shape Calculus. - Ezio Bartocci; Diletta Romana Cacciagrano; Maria Rita Di Berardini; Emanuela Merelli; Luca Tesei (Sci. Ann. Comput. Sci., 2010)

Bone Remodelling in BioShape. - Federico Buti; Diletta Cacciagrano; Flavio Corradini; Emanuela Merelli; Luca Tesei; M. Pani (CS2Bio, 2010)

BioShape: a spatial shape-based scale-independent simulation environment for biological systems. - Federico Buti; Diletta Cacciagrano; Flavio Corradini; Emanuela Merelli; Luca Tesei (ICCS, 2010)

Detecting synchronisation of biological oscillators by model checking. - Ezio Bartocci; Flavio Corradini; Emanuela Merelli; Luca Tesei (Theor. Comput. Sci., 2010)

Preface: Hybrid automata and oscillatory behaviour in biological systems. - Nicola Cannata; Emanuela Merelli; Irek Ulidowski (Theor. Comput. Sci., 2010)

Osteoporosis: a multiscale modeling viewpoint. - Nicola Paoletti; Pietro Liò; Emanuela Merelli; Marco Viceconti (CMSB, 2011)

BIOSHAPE textsc{BioShape}: End-User Development for Simulating Biological Systems. - Federico Buti; Diletta Cacciagrano; Massimo Callisto De Donato; Flavio Corradini; Emanuela Merelli; Luca Tesei (IS-EUD, 2011)

Modeling the cell cycle: From deterministic models to hybrid systems. - Roberta Alfieri; Ezio Bartocci; Emanuela Merelli; Luciano Milanesi (Biosyst., 2011)

Multiscale Modelling: A Mobile Membrane Approach - Federico Buti; Massimo Callisto De Donato; Flavio Corradini; Emanuela Merelli; Luca Tesei (CoRR, 2011)

Multiple verification in computational modeling of bone pathologies - Pietro Liò; Emanuela Merelli; Nicola Paoletti (CompMod, 2011)

A Uniform Multiscale Meta-model of BioShape. - Federico Buti; Diletta Cacciagrano; Flavio Corradini; Emanuela Merelli; Luca Tesei (CS2Bio@DisCoTec, 2011)

Towards Abstraction-Based Verification of Shape Calculus. - Federico Buti; Massimo Callisto De Donato; Flavio Corradini; Maria Rita Di Berardini; Emanuela Merelli; Luca Tesei (SASB, 2011)

A Combined Process Algebraic and Stochastic Approach to Bone Remodeling. - Pietro Liò; Emanuela Merelli; Nicola Paoletti; Marco Viceconti (CS2Bio@DisCoTec, 2011)

ACTIVAge: proACTIVe and Self-Adaptive Social Sensor Network for Ageing People. - Flavio Corradini; Emanuela Merelli; Diletta Romana Cacciagrano; Rosario Culmone; Luca Tesei; Leonardo Vito (ERCIM News, 2011)

Methodological Bridges for Multi-Level Systems. - Emanuela Merelli; Nicola Paoletti; Pietro Liò (FET, 2011)

The Immune System as a Metaphor for Topology Driven Patterns Formation in Complex Systems. - Emanuela Merelli; Mario Rasetti (ICARIS, 2012)

A Geometrical Refinement of Shape Calculus Enabling Direct Simulation. - Federico Buti; Flavio Corradini; Emanuela Merelli; Luca Tesei (SIMULTECH, 2012)

Modelling osteomyelitis. - Pietro Liò; Nicola Paoletti; Mohammad Ali Moni; Kathryn Atwell; Emanuela Merelli; Marco Viceconti (BMC Bioinform., 2012)

Disease processes as hybrid dynamical systems - Pietro Liò; Emanuela Merelli; Nicola Paoletti (HSB, 2012)

A multi-level model for self-adaptive systems - Emanuela Merelli; Nicola Paoletti; Luca Tesei (FOCLASA, 2012)

UBioLab: a web-LABoratory for Ubiquitous in-silico experiments. - Ezio Bartocci; Diletta Cacciagrano; Maria Rita Di Berardini; Emanuela Merelli; Leonardo Vito (J. Integr. Bioinform., 2012)

Multilevel Computational Modeling and Quantitative Analysis of Bone Remodeling. - Nicola Paoletti; Pietro Liò; Emanuela Merelli; Marco Viceconti (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Multiple Verification in Complex Biological Systems: The Bone Remodelling Case Study. - Ezio Bartocci; Pietro Liò; Emanuela Merelli; Nicola Paoletti (Trans. Comp. Sys. Biology, 2012)

Non locality, Topology, Formal languages: New Global Tools to Handle Large Data Sets. - Emanuela Merelli; Mario Rasetti (ICCS, 2013)

DISPAS: An Agent-Based Tool for the Management of Fishing Effort. - Pierluigi Penna; Nicola Paoletti; Giuseppe Scarcella; Luca Tesei; Mauro Marini; Emanuela Merelli (SEFM Workshops, 2013)

Preface. - Emanuela Merelli; Angelo Troina (CS2Bio, 2013)

Characterisation of the Idiotypic Immune Network Through Persistent Entropy. - Matteo Rucco; Filippo Castiglione; Emanuela Merelli; Marco Pettini (ECCS, 2014)

RNN-based Model for Self-adaptive Systems - The Emergence of Epilepsy in the Human Brain. - Emanuela Merelli; Marco Piangerelli (IJCCI (NCTA), 2014)

AAL domain ontology for event-based human activity recognition. - Rosario Culmone; Marco Falcioni; Paolo Giuliodori; Emanuela Merelli; Alessandro Orrù; Michela Quadrini; Paolo Ciampolini; Ferdinando Grossi; Guido Matrella (MESA, 2014)

Interoperability issues among smart home technological frameworks. - Lorena Rossi; Alberto Belli; Adelmo De Santis; Claudia Diamantini; Emanuele Frontoni; Ennio Gambi; Lorenzo Palma; Luca Pernini; Paola Pierleoni; Domenico Potena; Laura Raffaeli; Susanna Spinsante; et al. (MESA, 2014)

Sea-Scale Agent-Based Simulator of Solea solea in the Adriatic Sea. - Cesar Augusto Nieto Coria; Luca Tesei; Giuseppe Scarcella; Tommaso Russo; Emanuela Merelli (SEFM Workshops, 2014)

Adaptability Checking in Multi-Level Complex Systems. - Emanuela Merelli; Nicola Paoletti; Luca Tesei (CoRR, 2014)

Neural Hypernetwork Approach for Pulmonary Embolism diagnosis. - Matteo Rucco; David M. S. Rodrigues; Emanuela Merelli; Jeffrey H. Johnson; Lorenzo Falsetti; Cinzia Nitti; Aldo Salvi (CoRR, 2014)

jHoles: A Tool for Understanding Biological Complex Networks via Clique Weight Rank Persistent Homology. - Jacopo Binchi; Emanuela Merelli; Matteo Rucco; Giovanni Petri; Francesco Vaccarino (CS2Bio, 2014)

Preface. - Emanuela Merelli; Ion Petre (CS2Bio, 2014)

Towards a Shape Language for Interpreting RNA Folding. - Adane Letta Mamuye; Emanuela Merelli; Luca Tesei (BICT, 2015)

Topological classification of small DC motors. - Matteo Rucco; Enrico Concettoni; Cristina Cristalli; Andrea Ferrante; Emanuela Merelli (RTSI, 2015)

Probabilistic Modelling and Analysis of a Fish Population. - Chiara Cini; Luca Tesei; Giuseppe Scarcella; Cesar Augusto Nieto Coria; Emanuela Merelli (SEFM Workshops, 2015)

Topological characterization of S[B] systems: From data to models of complexity. - Emanuela Merelli; Matteo Rucco; Peter M. A. Sloot; Luca Tesei (CoRR, 2015)

Topological Characterization of Complex Systems: Using Persistent Entropy. - Emanuela Merelli; Matteo Rucco; Peter M. A. Sloot; Luca Tesei (Entropy, 2015)

Topology driven modeling: the IS metaphor. - Emanuela Merelli; Marco Pettini; Mario Rasetti (Nat. Comput., 2015)

Interactions between Computer Science and Biology. - Paola Giannini; Emanuela Merelli; Angelo Troina (Theor. Comput. Sci., 2015)

From Computer Science to Biology and Back. - Emanuela Merelli; Ion Petre (Theor. Comput. Sci., 2015)

Survey of TOPDRIM Applications of Topological Data Analysis. - Emanuela Merelli; Matteo Rucco; Luca Tesei; Marco Piangerelli; Adane Letta Mamuye; Michela Quadrini (KDWeb, 2016)

A Graph Grammar for Modelling RNA Folding. - Adane Letta Mamuye; Emanuela Merelli; Luca Tesei (GaM@ETAPS, 2016)

Topological classifier for detecting the emergence of epileptic seizures. - Marco Piangerelli; Matteo Rucco; Emanuela Merelli (CoRR, 2016)

A topological approach for multivariate time series characterization: the epileptic brain. - Emanuela Merelli; Marco Piangerelli; Matteo Rucco; Daniele Toller (EAI Endorsed Trans. Self Adapt. Syst., 2016)

Adaptability checking in complex systems. - Emanuela Merelli; Nicola Paoletti; Luca Tesei (Sci. Comput. Program., 2016)

Topological Classification of RNA Structures via Intersection Graph. - Michela Quadrini; Rosario Culmone; Emanuela Merelli (TPNC, 2017)

Uniformity in Multiscale Models: From Complex Automata to BioShape. - Diletta Cacciagrano; Flavio Corradini; Emanuela Merelli; Luca Tesei (J. Cell. Autom., 2017)

An algebraic representation for tree alignment of RNA pseudoknotted structures. - Michela Quadrini; Luca Tesei; Emanuela Merelli (PeerJ Prepr., 2017)

A new topological entropy-based approach for measuring similarities among piecewise linear functions. - Matteo Rucco; Rocío González-Díaz; Maria Jose Jimenez 001; Nieves Atienza; Cristina Cristalli; Enrico Concettoni; Andrea Ferrante; Emanuela Merelli (Signal Process., 2017)

Loop-loop Interaction Metrics on RNA Secondary Structures with Pseudoknots. - Michela Quadrini; Emanuela Merelli (BIOINFORMATICS, 2018)

Big Data: Business, Technology, Education, and Science: Big Data (Ubiquity symposium). - Jeffrey H. Johnson; Luca Tesei; Marco Piangerelli; Emanuela Merelli; Riccardo Paci; Nenad Stojanovic; Paulo Leitão; José Barbosa; Marco Amador (Ubiquity, 2018)

Loop Grammars to Identify RNA Structural Patterns. - Michela Quadrini; Emanuela Merelli; Riccardo Piergallini (BIOINFORMATICS, 2019)

X-Klaim Is Back. - Lorenzo Bettini; Emanuela Merelli; Francesco Tiezzi 001 (Models, Languages, and Tools for Concurrent and Distributed Programming, 2019)

Topological Interpretation of Interactive Computation. - Emanuela Merelli; Anita Wasilewska (From Reactive Systems to Cyber-Physical Systems, 2019)

Algebraic Characterisation of Non-coding RNA. - Stefano Maestri; Emanuela Merelli (CIBB, 2019)

Label Core for Understanding RNA Structure. - Michela Quadrini; Emanuela Merelli; Riccardo Piergallini (CIBB, 2019)

A Persistent Entropy Automaton for the Dow Jones Stock Market. - Marco Piangerelli; Luca Tesei; Emanuela Merelli (FSEN, 2019)

An algebraic language for RNA pseudoknots comparison. - Michela Quadrini; Luca Tesei; Emanuela Merelli (BMC Bioinform., 2019)

Topological Run-time Monitoring for Complex Systems. - Matteo Rucco; Luca Tesei; Emanuela Merelli (CoRR, 2019)

ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots. - Michela Quadrini; Luca Tesei; Emanuela Merelli (Bioinform., 2020)

Machine learning models predicting multidrug resistant urinary tract infections using "DsaaS". - Alessio Mancini; Leonardo Vito; Elisa Marcelli; Marco Piangerelli; Renato De Leone; Sandra Pucciarelli; Emanuela Merelli (BMC Bioinform., 2020)

Automaton of molecular perceptions in biochemical reactions. - Stefano Maestri; Emanuela Merelli (CoRR, 2021)

RNA secondary structure factorization in prime tangles. - Daniele Marchei; Emanuela Merelli (BMC Bioinform., 2022)

Automatic generation of pseudoknotted RNAs taxonomy. - Michela Quadrini; Luca Tesei; Emanuela Merelli (BMC Bioinform., 2022)

Factorizing the Brauer monoid in polynomial time. - Daniele Marchei; Emanuela Merelli; Andrew R. Francis (CoRR, 2024)

Space of Data through the Lens of Multilevel Graph. - Marco Caputo; Michele Russo; Emanuela Merelli (CoRR, 2025)