Simon J. Puglisi is a Professor in the Department of Computer Science at the University of Helsinki. His research focuses on algorithms, data structures, pattern matching, and data compression, with applications in bioinformatics and genomics. He has collaborated extensively with researchers in the field, including Travis Gagie, Juha Kärkkäinen, and Andrew Turpin. His work spans theoretical computer science and practical applications in genomic data processing and efficient indexing techniques. Key research interests include genome sequencing algorithms, efficient compression methods (e.g., Lempel-Ziv and relative Lempel-Ziv), and the development of succinct data structures for handling large genomic datasets. His contributions to suffix arrays, wavelet trees, and de Bruijn graphs have advanced computational methods in bioinformatics and information retrieval. Puglisi's articles frequently address challenges in text indexing, error correction in short-read sequencing, and optimizing algorithms for scalability. He is known for his work on self-indexing techniques and the SHREC error correction method for genomic data. His research bridges theoretical algorithm design with real-world applications in high-throughput sequencing and large-scale data management.
Violetta Lonati is an Assistant Professor at the University of Milan 's Department of Computer Science since 2005. Her research spans Formal Languages and Automata (operator precedence languages, Wang automata, tiling systems) and Computer Science Education . She co-authored over 15 publications in theoretical computer science and education, focusing on 2D language recognition, logic characterization of automata, and pattern statistics in stochastic models. Education : PhD in Computer Science (2005) and Laurea in Mathematics (2001) from University of Milan Research Groups : ALaDDIn Lab for Didactics and Dissemination of Informatics, Bebras International Initiative Her work on Wang automata established their equivalence to tiling systems while introducing deterministic variants. In education, she designed workshops for schools and contributed to Italy's national computing curriculum proposal (2019). She held leadership roles at ACM ITiCSE (WG5 leader 2022), served as Associate Program Chair (2019-2022), and reviewed for top venues like ICER and SIGCSE TS. She received Google CS[4]HS and Informatics Europe awards for her educational contributions. Key Publications (2017-2001): Input-driven locally parsable languages (TCS 2017) Operator precedence logic characterization (SICOMP 2015) Snake-deterministic tiling systems (MFCS 2009) Graph fibrations and PageRank (RAIRO 2006) Pattern statistics in rational models (STACS 2005) Scientific awards include Google CS[4]HS (2011, 2017, 2019) and the Informatics Europe Best Practices in Education (2016). As part of ALaDDIn, she developed teacher training programs and graduate courses on computing education. Her teaching experience covers Algorithms & Data Structures (2013-2023), Computer Science Teaching (2014-2023), and courses for Biotechnology and Geological Sciences programs (2005-2007).
Gabriele Fici is an Associate Professor at the Department of Mathematics and Computer Science, University of Palermo (Unipa). His research focuses on combinatorics on words, string algorithms, and algorithmic pattern matching. He teaches courses in text sequence analysis, data mining, and software development. Research Interests : Combinatorial pattern matching, Abelian repetitions, digital convexity, and theoretical foundations of string processing. Key Contributions : Pioneering work on Lyndon words, de Bruijn sequences, and jumbled pattern matching algorithms. Publications : Extensive publications in top-tier conferences like CPM and journals, with a focus on 2013-2025 trends in algorithmic complexity and computational linguistics.
Chiara Epifanio is a researcher (INFO-01/A) at the University of Palermo , based in the Department of Mathematics and Computer Science . She holds regular office hours on Tuesdays 14:30–17:00 in Room 104, first floor, Via Archirafi 34, and can be reached at chiara.epifanio@unipa.it . Over the past fifteen years she has designed and taught a diverse portfolio of courses spanning Programming , Bioinformatics , Advanced Programming , Teaching Methodologies and Techniques for Computer Science and Pattern Discovery for Life Sciences . These offerings serve degree programmes in Mathematics, Computer Science, Statistics & Data Science, and the recently launched curricula in Data, Algorithms & Machine Intelligence and Computer Science & Artificial Intelligence . Her research lies at the intersection of combinatorics on words , string algorithms , and bioinformatics . She has made sustained contributions to the design of alignment-free distances for biological data, the theory of Sturmian words and their associated graphs, suffix automata tolerant to mismatches, and compact data structures such as linear-size suffix tries. The work repeatedly draws on deep results from formal language theory, automata theory, and discrete mathematics to solve practical problems in sequence analysis. Publications trend: From 2004 onward she has produced a steady stream of peer-reviewed articles that move from foundational combinatorial results on Sturmian words and critical factorization theorems toward application-driven studies on approximate string matching and genomic data mining. A marked acceleration is visible in the 2023 publications addressing k-Hamming and k-edit distances, reflecting current demands in large-scale biological data analytics. Scientific awards: None explicitly mentioned in the provided material. Advising & grants: No PhD or Master’s students are listed in the supplied pages, and no funded project descriptions are available. Laboratories & teams: While no specific lab is named, her teaching and research are embedded within the Department of Mathematics and Computer Science, which hosts groups in algorithms, discrete mathematics, and bioinformatics, and provides access to the university’s ATeN Center and other research infrastructures.
Marinella Sciortino is a Professor at the University of Palermo , affiliated with the School of Basic and Applied Sciences and the Department of Mathematics and Computer Science . She serves as Director of the CINI Research Unit and is a member of the Academic Senate (2022-2024). Sciortino contributes to editorial and scientific committees for journals and conferences, including Theoretical Computer Science and the GRIN Committee . Research focuses on: Combinatorics on Words String Algorithms Automata Theory Symbolic Dynamics Data Compression Biological Sequence Analysis Her work includes groundbreaking studies on the Burrows-Wheeler Transform (BWT) , extending its application to multiple sequences and improving compression efficiency. She has supervised PhD student Giuseppe Romana and participated in numerous conference program committees (e.g., SPIRE , ICTCS , CiE ). Recent scientific contributions (2022-2020): BWT teaching methodologies String attractors Variant discovery in genomics Algorithmic perspectives on alternating BWT Positional clustering for SNP detection Mental rotation effects on computational learning Teaching roles include Laboratorio di Algoritmi (Computer Science) and Teoria dell'Informazione e Compressione Dati (Master's in Computer Science). Contact: marinella.sciortino@unipa.it , +39-091-238-91080.
Matthieu Rosenfeld is an Assistant Professor at the University of Montpellier, affiliated with the LIRMM laboratory and the ESCAPE team. He teaches in the Computer Science department of IUT Montpellier-Sète. His research interests include combinatorics , theoretical computer science , and discrete mathematics , focusing on combinatorics on words and graph theory . He frequently employs computer-assisted proofs for avoidability problems. Recent publications explore topics like nonrepetitive colorings in Euclidean space, undecidability in bilinear systems , Vizing's problem for triangle-free graphs, Shur's conjecture in power-free languages, and word reconstruction via subword queries . His work often intersects formal languages , graph coloring , and algebraic structures , with applications to automata theory, logic, and algorithm design.
Alessandro De Luca is an Assistant Professor of Computer Science at the Department of Electrical Engineering and Information Technology (DIETI) of the University of Naples Federico II, Italy. He has held previous positions at the University of Turku (Finland) and UQAM (Canada). PhD in Mathematical and Computer Science (2008), University of Naples Federico II MSc in Mathematics (2003), University of Naples Federico II His research focuses on combinatorics on words , with emphasis on Sturmian words, Christoffel words, pseudopalindromes, rich words, and their connections to number theory, automata theory, and discrete mathematics. Key contributions include work on well-distributed occurrences (WDO) in infinite words, aperiodic pseudorandom number generation, and the study of open/closed prefixes in Sturmian sequences. Recent publications highlight his expertise in digital segments , semi-regular continuants , and structural properties of combinatorial words . Collaborative efforts include work with Gabriele Fici (University of Palermo), Golnaz Badkobeh (Goldsmiths University of London), and Luca Zamboni (Université Lyon 1). He has participated in international conferences such as WORDS , DLT , and FLA , and is affiliated with research groups including the Centre for Combinatorics on Words and Applications (CCWA) at Murdoch University and GNSAGA (INdAM).
Florin Silviu Manea is a Professor for Theoretical Computer Science at the Institute of Computer Science, University of Göttingen, Germany. He has held this W3-Professor position since 2022, funded by the Heisenberg programme of the DFG. Prior to this, he was a W2-Professor for Fundamentals of Computer Science at the same university (2019-2022). His academic career includes research positions at Kiel University (2011-2019) and an Alexander von Humboldt fellowship at the University of Magdeburg (2009-2011). Dr. Manea received his PhD in December 2007 from the University of Bucharest with the distinction Summa cum Laude. His PhD thesis was titled "Networks of bio-processors" and was supervised by Victor Mitrana. He also earned a Master of Science (2005) and Bachelor of Science in Computer Science (2003) from the University of Bucharest, both with perfect GPA scores of 10/10. Professor Manea's research focuses on the theoretical foundations of computer science, with particular emphasis on string algorithms and combinatorics. His work explores the intricate relationships between formal language theory, automata theory, and practical applications in string solving. He has made significant contributions to understanding pattern matching with variables, combinatorial properties of strings, and the computational aspects of word equations. His research bridges theoretical concepts with practical applications in areas like bioinformatics and programming language theory. Analysis of Professor Manea's recent publications reveals a strong focus on string algorithms, particularly in the areas of pattern matching, word equations, and combinatorics on words. His work often explores the computational complexity of string problems while developing efficient algorithms to solve them. A recurring theme is the investigation of repetitions, palindromes, and gapped structures in strings, with applications ranging from DNA sequence analysis to programming language design. His research demonstrates a consistent pattern of advancing both the theoretical understanding and practical applications of string algorithms. Professor Manea has received several prestigious awards for his contributions to computer science: Lehrpreis 2020 (Teaching Award) by CS-students from Göttingen The "Tudor Tanasescu" Prize of the Romanian Academy (2009) Honorable Mention at ACM International Collegiate Programming Contest World Finals (2004, 2007) As an advisor, Professor Manea has successfully supervised multiple PhD students to completion with highest honors, including Maria Kosche (2023), Stefan Siemer (2024), and Tore Koß (2024), all achieving Summa cum Laude distinctions. He currently leads a research group focused on theoretical computer science at the University of Göttingen. His research is supported by significant funding, including a DFG grant for "String Constraint Solving: Combinatorial, Algorithmic, and Language-Theoretic Approaches" and continued Heisenberg-programme funding until 2027 for his project "Combinatorial String Solving." Professor Manea leads the Theoretical Computer Science research group at the University of Göttingen, which focuses on string algorithms, combinatorics, and computational models. His group actively collaborates with researchers worldwide and has organized several major conferences including DLT 2024, NCMA 2024, and CSL 2022. The group offers supervision for BSc and MSc theses on both theoretical and applied topics related to their research areas.
Simone Rinaldi is a full Professor at the Department of Information Engineering and Mathematical Sciences, University of Siena. His research spans combinatorics, formal languages, and discrete tomography, with a focus on enumeration and algorithmic generation of combinatorial structures. Research Interests: Enumerative and bijective combinatorics Pattern avoiding permutations and lattice paths Discrete tomography for hypergraphs and polyominoes Formal languages and tiling systems Applications to computer science and mathematical biology Publication Trends : His recent work emphasizes hypergraph reconstruction, discrete geometry, and combinatorial optimization for game theory problems, alongside advancements in tiling systems and Burrows-Wheeler transform properties.
Giuseppa Castiglione is a Researcher (INFO-01/A) in the Department of Mathematics and Computer Science at the University of Palermo's School of Basic and Applied Sciences. She maintains regular office hours on Tuesdays and Thursdays from 2:00 PM to 3:00 PM in Room 209, second floor, and teaches Theoretical Computer Science for both Computer Science and Mathematics degree programs. Her primary research interests span several interconnected areas within theoretical computer science and discrete mathematics. These include automata theory, formal language theory, combinatorics on words, enumerative combinatorics, and discrete two-dimensional structures. Her work demonstrates a consistent focus on the mathematical foundations of computer science, particularly in the analysis of string algorithms, word combinatorics, and discrete geometric structures. Analysis of her publication record from 2017-2025 reveals a strong concentration on combinatorial aspects of words and automata, with recent work expanding into isometric words, Fibonacci cubes, and Wheeler automata. Her research shows a progression from foundational work on polyominoes and automata minimization toward more complex combinatorial structures and their applications in string processing. Castiglione has participated in numerous significant research projects including the Prin 2010-11 project on mathematical aspects of automata and formal languages, the PO FESR 2007/2013 Neverlost project, PON Research and Competitiveness 2007/2013 SMART HEALTH initiative, and GNCS 2016 on combinatorial methods for handling large data sets. These projects demonstrate her ability to secure competitive research funding across multiple domains. She collaborates with researchers including Marinella Sciortino, Gabriele Fici, Chiara Epifanio, Sabrina Mantaci, and Antonio Restivio, forming a productive research network focused on theoretical computer science and combinatorics. Her extensive publication record in high-quality venues demonstrates her sustained contribution to the field over more than two decades.
Roberto Grossi is a Professor of Algorithms and Data Structures at the University of Pisa's Dipartimento di Informatica. He is actively involved in editorial roles for journals like Theory of Computing Systems and RAIRO-Theoretical Informatics, and has served on program committees for conferences such as SWAT, IWOCA, ESA, FOCS, and SPIRE. His research focuses on algorithms, data structures, graph theory, and bioinformatics, with contributions to string processing, compressed data structures, and algorithm engineering. He advises Ph.D. students and collaborates on projects involving large-scale networks and community detection. Grossi has authored numerous publications, including works on clique enumeration, graphlet algorithms, and phylogenetic reconstruction. His teaching includes courses on Algorithm Design and Data Structures, and he maintains an active presence in academic networks through his research and editorial activities. Education: Not explicitly stated, but inferred from his role as a professor at a top Italian university. Research Interests: Dynamic algorithms, external memory methods, experimental algorithmics, pattern matching in strings and graphs. Grants/Awards: While no specific prizes are listed, his extensive publication record and editorial roles reflect sustained recognition in the field. Lab/Teams: Leads research groups focused on algorithmic foundations and applications, collaborating with international teams on projects like Zuckerli (compressed graph representations) and motif trie indexing. His work bridges theoretical computer science with practical applications in bioinformatics and network analysis.
Giovanna Rosone is an Associate Professor at the University of Pisa (Università di Pisa) within the Department of Computer Science (Dipartimento di Informatica) . Her research focuses on Sequence Analysis , Combinatorics on Words , Bioinformatics , and Algorithms and Data Structures , with a strong emphasis on applications leveraging the Burrows-Wheeler Transform . She leads the CMACBioSeq project funded by the Italian MIUR-SIR grant, developing combinatorial methods for biological sequence analysis and compression. Her work includes tools like BCR_LCP_GSA and ebwt2InDel for efficient genome analysis, SNPs/indel detection, and alignment-free variation discovery. These tools are used in metagenomics, rare-variant identification, and genotyping.
France Gheeraert is an Associate Professor in Mathematics at the University of Picardie Jules Verne, France, since September 2024. They are affiliated with the SymPA research team at the Laboratoire Amiénois de Mathématique Fondamentale et Appliquée (LAMFA) and organize the dyna-proba seminar. Previously, they were a Postdoctoral Researcher at Radboud University (Netherlands) and an FNRS Research Fellow at the University of Liege (Belgium), focusing on combinatorics on words and symbolic dynamics. Education Bachelor and Master in Mathematics with Computer Science focus from the University of Liege Research Interests Combinatorics on Words (core work on dendric words, generalizing Sturmian words) String Attractors in data compression Symbolic Dynamics and numeration systems Applications of morphisms in word structures Connections to group theory and algorithmic complexity Recent Publications 2024: String attractor-based complexities for infinite words 2024: String attractors in bi-infinite sequences 2023-2022: Studies on dendric words, S-adic systems, and morphic fixed points Scientific Awards FNRS Research Fellow (Belgium, 2020-2024) Labs & Teams SymPA team, LAMFA (University of Picardie) Discrete Mathematics team, University of Liege (2020-2024)
Zsuzsanna Lipták is an Associate Professor in the Department of Computer Science at the University of Verona, Italy, where she has been a faculty member since November 2011. Her research is centered on string algorithms, combinatorics on words, and algorithmic bioinformatics, with a particular focus on the Burrows-Wheeler Transform (BWT) and its applications in data compression and biological sequence analysis. She is an active member of the Algorithmic Bioinformatics and Natural Computing Group and the Algorithms Group at the university. She leads research within the PRIN-funded project 'PINC – Pangenome Informatics: From Theory to Practice' and collaborates internationally with institutions in South Africa, Finland, Chile, and the USA. Her research interests include string indexing, suffix trees, suffix arrays, data compression, computational biology, and combinatorial properties of permutations and BWT. She has made significant contributions to the theory and application of BWT variants, matching statistics, and de Bruijn sequence construction. Her recent publications reflect a consistent focus on improving the efficiency and understanding of text indexing and compression methods, particularly in the context of genomic data. These works often involve both theoretical analysis and experimental validation, bridging the gap between pure theory and practical implementation. Lipták actively supervises PhD and master’s students, including Davide Cenzato, Sara Giuliani, Francesco Masillo, and Martina Lucà. She teaches advanced courses such as 'Fundamental Algorithms for Bioinformatics,' 'Computational Analysis of Genome-Scale Sequences,' and 'Advanced Data Structures for Textual Data.' She has also supervised numerous bachelor’s theses and student projects. She has secured research funding through national projects like PRIN and has collaborated on international initiatives, including a Marie Curie IEF fellowship during her postdoctoral work. She is deeply involved in the academic community, having served as PC chair for SPIRE 2024, PC co-chair for CPM 2023, and a member of the Steering Committee of SPIRE since 2024. She has served on the program committees of major conferences such as ESA, DLT, WABI, and IWOCA. She co-organizes the weekly 'Monday Meetings' seminar series for the Algorithms Group and has co-edited special issues and conference proceedings in journals like Theory of Computing Systems , Discrete Applied Mathematics , and European Journal of Combinatorics . She earned her Diplom in Mathematics from Freie Universität Berlin and her PhD in Computer Science from Bielefeld University, Germany, where her thesis addressed algorithmic problems in mass spectrometry. She has held research positions at ETH Zurich, Bielefeld University, and Salerno University, and has been a visiting researcher at the Rényi Institute (Hungary), University of the Witwatersrand, and SANBI (South Africa). She is the scientific coordinator for Erasmus+ exchanges with Bielefeld and Jena Universities.
