Zsuzsanna Lipták Associate Professor Department of Computer Science University of Verona, Italy email: zsuzsanna DOT liptak AT univr DOT it address: University of Verona Department of Computer Science Strada le Grazie, 15 I-37134 Verona, Italy office: Ca' Vignal 2, room 1.79 (1st floor) tel: +39 045 802-7032 Student hours: Wednesdays, 10-12 (during term-time). Here is my institutional page.

This page is always under construction...

• I gave a keynote talk with the title "How to use the BWT for constructing random de Bruijn sequences" at SeqBIM 2024 ("Séquences en Bioinformatique, Informatique et Mathématiques") in Rennes, France, on 29 Nov. 2024: slides, paper, and code.
• Prof. Scott Hazelhurst (University of the Witwatersrand, Johannesburg, South Africa), who visited my group in June/July 2024, gave a little interview which you can view here: video.
• Together with Ricardo Baeza-Yates, I am guest editing a Topical Collection of the journal Theory of Computing Systems, with the title "Advances on String Processing and Information Retrieval". It will contain extended version of selected papers from SPIRE 2024, as well as other high-quality papers that fit in the conference's scope. See here for the call: Call for Papers. Submission deadline is 1 February 2025.
• I was PC co-chair of SPIRE 2024 (31st International Symposium on String Processing and Information Retrieval), which took place from Sept. 23-25, 2024, in Puerto Vallarta, Jalisco, Mexico. See here for the proceedings.
• The Monday Meetings have started again. Webpages of previous years: Monday meetings. New page for this semester will be up soon.
• I gave a keynote with the title "BWT everywhere" at CPM 2024 on 26 June 2024 in Fukuoka, Japan: slides.
• We organized a PINC workshop in Verona on May 23-24, 2024, within the PRIN project PINC - Pangenome Informatics: From Theory to Practice.

Brief Vita

I am associate professor at the University of Verona, and have been working here since November 2011. I got my first degree (Diplom Mathematik) from Freie Universität in Berlin, Germany, and my PhD (in Computer Science) from Bielefeld University, Germany. My PhD thesis treated algorithmic problems in Mass Spectrometry, and was supervised by Sebastian Böcker (now in Jena, Germany). I have worked as a research assistant at ETH Zurich, Switzerland; as a research assistant and later postdoc at Bielefeld University, Germany; and as a postdoc at Salerno University, Italy, where I had a Marie Curie IEF fellowship. In addition, I spent time as a visiting researcher at the following scientific institutions: Rényi Institute, Budapest (Hungary); the University of the Witwatersrand, Johannesburg (South Africa); and at the South African National Bioinformatics Institute (SANBI), Cape Town (South Africa).

I am member of the Algorithmic Bioinformatics and Natural Computing Group and the Algorithms Group of the Department of Computer Science of Verona University.

There is a (usually somewhat outdated) CV on my institutional page.

Our weekly group seminar, the Monday meetings, take place every Monday at 5 p.m. during termtime. If you are interested in participating, write me an email!

Research Interests

I work on text indexes, mostly on different aspects of the Burrows-Wheeler Transform (BWT), but also on suffix trees and suffix arrays. For some recent results on the BWT, see my keynote talk at CPM 2024 in Fukuoka, Japan: "BWT everywhere" (June 2024), my keynote at SeqBIM 2024 in Rennes, France: "How to use the BWT for constructing random de Bruijn sequences" (Nov. 2024), my invited talk at Primavera dell'Informatica Teorica "On the Burrows-Wheeler Transform of string collections" (Jan. 2024), or my keynote at Journées Montoises 2022 in Prague: "Dollar or no dollar, that is the question (New combinatorial results on the Burrows-Wheeler-Transform)" (Sept. 2022).

I am generally interested in string algorithms and other algorithmic and combinatorial problems, mostly as arising in computational biology applications. In algorithmic bioinformatics, my current focus is on problems relating to textual data compression and data processing. I am member of the PRIN project 'PINC', financed by the Ministry for University and Research (MUR): PRIN project PINC - Pangenome Informatics: From Theory to Practice, led by the University of Milano-Bicocca (Paola Bonizzoni). In a related project, I am currently collaborating with Scott Hazelhurst of the University of the Witwatersrand (Johannesburg, South Africa) on different algorithmic aspects of structural variation problems. In the past, I also worked on mass spectrometry data interpretation (genomics, proteomics, metabolomics) and on string distance measures for expression clustering (transcriptomics).

On the theory side, apart from algorithms and data structures, I am also interested in combinatorics on words, in particular to do with the combinatorics of permutations and the Burrows-Wheeler Transform. Further, Gabriele Fici and I introduced prefix normal words in our paper at DLT 2011; here is a short writeup on open problems on prefix normal words (updated May 2021).

Recent Talks

• How to use the BWT for constructing random de Bruijn sequences, keynote talk at SeqBIM 2024 ("Séquences en Bioinformatique, Informatique et Mathématiques") in Rennes, France, on 29 Nov. 2024: slides.
• BWT everywhere, keynote talk at CPM 2024 on 26 June 2024: slides.
• A BWT-based algorithm for construction of random de Bruijn sequences. Talk given at the Dept of Computer Science (DCC), University of Chile, Santiago, on March 27, 2024: slides.
• On the Burrows-Wheeler Transform of string collections. Invited talk given at the seminar series of the Italian Chapter of the EATCS, "Primavera dell'Informatica Teorica", 11 Jan. 2024: slides.
• On the combinatorics of the BWT of string collections. Talk given at the workshop 'Sequences in London', 11-12 May 2023: slides.
• Dollar or no dollar, that is the question (New combinatorial results on the Burrows-Wheeler-Transform), Pontificia Universidad Católica de Chile (PUC Chile), Santiago, Chile, on Nov. 4, 2022: slides.
• Dollar or no dollar, that is the question (New combinatorial results on the Burrows-Wheeler-Transform), keynote talk at the international conference 18th Mons Days on Theoretical Informatics, 5-9 Sept. 2022, Prague (Journées Montoises): slides.

Recent Publications

• Elena Biagi, Davide Cenzato, Zsuzsanna Lipták, Giuseppe Romana: On the number of equal-letter runs of the Bijective Burrows-Wheeler Transform. Accepted for publication in Theoretical Computer Science (2024). See here: paper.
• Zsuzsanna Lipták, Edleno Silva de Moura, Karina Figueroa, Ricardo Baeza-Yates (editors): Proceedings of the 31st International Symposium on String Processing and Information Retrieval (SPIRE 2024), Puerto Vallarta, Mexico, September 23-25, 2024. Lecture Notes in Computer Science 14899, Springer 2025, ISBN 978-3-031-72199-1: Proceedings.
• Zsuzsanna Lipták, Francesco Masillo, Gonzalo Navarro: A Textbook Solution for Dynamic Strings. Proc. of the European Symposium on Algorithms (ESA 2024), LIPIcs 308, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2024, 86:1-86:16. Paper.
• Zsuzsanna Lipták, Martina Lucà, Francesco Masillo, and Simon J. Puglisi: Fast matching statistics for set of long similar strings. Prague Stringology Conference (PSC 2024), Prague, Czech Republic, Aug. 26-27, 2024.
• Davide Cenzato and Zsuzsanna Lipták: A survey of BWT variants for string collections. Bioinformatics, doi: 10.1093/bioinformatics/btae333, (2024). Paper.
• Zsuzsanna Lipták, Francesco Masillo, Gonzalo Navarro: BAT-LZ Out of Hell. Proc. of the 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024), LIPIcs 296, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2024, 21:1-21:17. Paper.
• Christina Boucher, Davide Cenzato, Zsuzsanna Lipták, Massimiliano Rossi, Marinella Sciortino: r-Indexing the eBWT. Information and Computation, vol. 298: 105155 (2024): Paper.
• Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi: Suffix Sorting via Matching Statistics. Algorithms for Molecular Biology 19(1): 11 (2024): paper.
• Zsuzsanna Lipták and Luca Parmigiani: A BWT-based algorithm for random de Bruijn sequence construction. Proc. of 16th Latin American Symposium on Theoretical Informatics (LATIN 2024), LNCS 14578: 130-145 (2024).
• Zsuzsanna Lipták, Francesco Masillo, Gonzalo Navarro, Aaron Williams: Constant time and space updates for the sigma-tau problem. Proc. of the 30th International Symposium on String Processing and Information Retrieval (SPIRE 2023), Sept. 26-28, 2023, Pisa, Italy.
• Elena Biagi, Davide Cenzato, Zsuzsanna Lipták, Giuseppe Romana: On the number of equal-letter runs of the Bijective Burrows-Wheeler Transform. Proc. of the 24th Italian Conference on Theoretical Computer Science (ICTCS 2023), 13-15 Sept. 2023, Palermo, Italy (2023).
• Sara Giuliani, Shunsuke Inenaga, Zsuzsanna Lipták, Giuseppe Romana, Marinella Sciortino, Cristian Urbina: Bit catastrophes for the Burrows-Wheeler Transform. Proc. of the 26th Int. Conf. on Developments in Language Theory (DLT 2023), 12-16 June 2023, Umeå, Sweden (2023).
• Davide Cenzato, Veronica Guerrini, Zsuzsanna Lipták, Giovanna Rosone: Computing the optimal BWT of very large string collections, Proc. of the 2023 Data Compression Conference (DCC 2023), March 21-24, 2023, Snowbird, UT, USA. See here for Arxiv version (2022).
• Davide Cenzato and Zsuzsanna Lipták: Computing the optimal BWT using SAIS. Presented at the 17th Workshop on Compression, Text, and Algorithms (WCTA 2022), Concepción, Chile, Nov. 11, 2022.
• Zsuzsanna Lipták and Francesco Masillo: Maintaining the cycle structure of permutations efficiently. Presented at the 17th Workshop on Compression, Text, and Algorithms (WCTA 2022), Concepción, Chile, Nov. 11, 2022.
• Sara Giuliani, Zsuzsanna Lipták, Francesco Masillo: When a Dollar in a Fully Clustered Word Makes a BWT. Proc. of the 23rd Italian Conference on Theoretical Computer Science (ICTCS 2022), CEUR vol. 3284, pp. 122-135: Paper.
• Golnaz Badkobeh, Sara Giuliani, Zsuzsanna Lipták, Simon J. Puglisi: On Compressing Collections of Substring Samples. Proc. of the 23rd Italian Conference on Theoretical Computer Science (ICTCS 2022), CEUR vol. 3284, pp. 136-147: Paper.
• Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi: Suffix Sorting via Matching Statistics. Proc. of the 22nd Workshop on Algorithms in Bioinformatics (WABI 2022), LIPIcs vol. 242, pp. 20:1-20:15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2022, ISBN 978-3-95977-243-3. Arxiv version.
• Davide Cenzato and Zsuzsanna Lipták: A theoretical and experimental analysis of BWT variants for string collections. Proc. of Combinatorial Pattern Matching (CPM 2022), LIPIcs 223, pp. 25:1-25:18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2022, ISBN 978-3-95977-234-1. Published paper and Arxiv version (with a large appendix containing details of the experiments).
• Marco Oliva, Davide Cenzato, Massimiliano Rossi, Zsuzsanna Lipták, Travis Gagie and Christina Boucher: CSTs for Terabyte-Sized Data. Proc. of the IEEE Data Compression Conference (DCC 2022), pp. 93-102 (2022).
• Davide Cenzato and Zsuzsanna Lipták: On different variants of the BWT for string collections (poster). Proc. of the IEEE Data Compression Conference (DCC 2022), p. 448 (2022).

Teaching (in Verona)

Here is an introductory talk on Bioinformatics for high school students (in Italian):
Una presentazione per studenti di liceo: "Che cos'è la bioinformatica?" (7/3/2018).


I currently teach the following courses:

• "Fundamental Algorithms for Bioinformatics" (module 1, together with F. Cicalese, 1st semester), and module 2 (2nd semester), an obligatory course in the first year of the masters program Medical Bioinformatics (1st and 2nd semester, 12 credits).
  The second module (Bioinformatics Algorithms, 2nd semester) is also one of the optional courses for students of Molecular and Medical Biotechnology under the name "Algorithms for Computational Biology" (6 credits, "mutuato").
  The second module can also be taken by students Computer Science and Engineering (LM 18-32) or students of Computer Engineering for Robotics and Smart Industry (LM 32), as an optional course; we study specialized algorithms for bioinformatics, our syllabus does not overlap with any other course.
  
  
• "Computational Analysis of Genome-Scale Sequences", an optional course in the second year of the masters program Medical Bioinformatics (1st semester, 6 credits). See here for the syllabus, which varies a bit each year.
  This course can also be taken by students of Computer Science and Engineering (LM 18-32) or students of Computer Engineering for Robotics and Smart Industry (LM 32), in their first or second year. No prerequisite knowledge in biology is necessary. For these students, the exam can be in Italian on request.
  
  
• "Modelli biologici discreti" (together with Giuditta Franco, in Italian), an optional course in the third year of the bachelor program Bioinformatics (2nd semester).
  
  
• PhD course "Advanced data structures for textual data" (12 hours): flyer 2024. The most recent edition took place from 16-19 Sept. 2024.
  

• I have been teaching a course on Bioinformatics Algorithms, master level, with varying contents and in different master programs, since 2011: "Fundamental Algorithms in Bioinformatics": 2023/2024, 2022/2023, 2021/2022, 2020/2021 (modulo 1, "Algorithm Design", with F. Cicalese; entire modulo 2, "Bioinformatics Algorithms"); previously only modulo 2: 2019/2020, 2018/2019, 2017/2018, 2016/2017; "Algorithms for Computational Biology" (2015/2016), fall semester of 2015/2016, Masters in Molecular and Medical Biotechnology (new LM9); "Algoritmi e Linguaggi per Bionformatica: Algoritmi", Laurea magistrale in Bioinformatica e biotecnologie mediche (LM9), masters: 2014/2015, 2013/2014, 2012/2013, 2011/2012.
  
  
• Computational analysis of genome-scale sequences is my specialized master course on algorithms and data structures for textual data (strings, sequences), which I have been teaching since 2016/2017, within the Masters Program Medical Bioinformatics (LM18).
  
  
• Bachelor course "Modelli Biologici Discreti" (2014/2015) (in Italian), within the Laurea Triennale "Bioinformatica" (bachelor).
  
  
• PhD course "Advanced data structures for textual data": edition 2024 (12 hours), ; edition 2023 (12 hours), on four Tuesdays in January 2023; edition 2020 (20 hours) from 21 to 25 September 2020.
  
  
• PhD course "Computational methods for handling textual data" (flyer): PhD course, jointly with Ferdinando Cicalese and Giuditta Franco (March 2016).

Theses/Tesi

Progetti nell'ambito di sequenze/stringhe (genomiche e no), bioinformatica algoritmica, algoritmi su stringhe. Ho disponibile diversi argomenti sia per tesi (magistrali o triennali), che per stage/tirocinio/progetto. (E naturalmente parlo anche italiano...)

If you are a student who likes algorithms and strings (sequences), or in general topics in algorithmic bioinformatics, come and see me. I have topics both for small student projects ("internship"/"stage") or for bachelor or master theses.

Short Term Mobility (STM) projects are available for several destinations, depending on the subject.

You can also opt to do your thesis in Erasmus, in collaboration with one of the groups I collaborate with, e.g. in Bielefeld, Jena, Dortmund, or Budapest.

Students

• Martina Lucà: PhD student, since Oct. 2024, University of Verona.
• Francesco Masillo: PhD student, since Oct. 2021, University of Verona.
• Davide Cenzato: PhD student, Oct. 2019 - Sept. 2023, University of Verona. Defended his PhD thesis entitled Processing and indexing large biological datasets using the Burrows-Wheeler Transform of string collections on 22 Sept. 2023. Now postdoc in Nicola Prezza's group at University of Venice Ca' Foscari.
• Sara Giuliani: PhD student, Oct. 2019 - Sept. 2023, University of Verona. Defended her PhD thesis entitled Sensitivity of the Burrows-Wheeler Transform to Small Modifications, and Other Problems on String Compressors in Bioinformatics on 18 Sept. 2023.
• Massimiliano Rossi: PhD student Oct. 2016 - Sept. 2019, University of Verona, co-supervised with Ferdinando Cicalese. Thesis entitled Algorithms and Data Structures for Coding, Indexing, and Mining of Sequential Data, defended in Feb. 2020. Went on to do a post-doc in Christina Boucher's group, University of Florida, Gainesville (FL), USA. Now at Illumina, San Diego, California, USA.

• Thomas Tosoni: ongoing. Master thesis in Medical Bioinformatics.
• Vincenzo Minolfi: ongoing. Master thesis in Computer Science and Engineering.
• Martina Lucà: Parameters for Prefix-Free Parsing: Analysis and Experimentation. Master thesis in Molecular and Medical Biotechnology. Graduated in March 2024 with grade 110/110 e lode (top grade with distinction).
• Simona Busiol: On Powers of BWT Images. Master thesis in Medical Bioinformatics. Graduated in March 2023 with grade 110/110 e lode (top grade with distinction).
• Elena Biagi: On comparing the Bijective Burrows-Wheeler-Transform of a word and its reverse. Master thesis in Medical Bioinformatics. Graduated in July 2022 with grade 110/110 e lode (top grade with distinction). Now PhD student at University of Helsinki, supervised by Simon Puglisi.
• Sonia Morasso: From multisets to phylogenetic trees. Master thesis in Medical Bioinformatics. Graduated in March 2022 with grade 110/110 e lode (top grade with distinction).
• Francesco Masillo: On data structures and algorithms for permutations and the Burrows-Wheeler-Transform. Master thesis in Medical Bioinformatics. Graduated in July 2021 with grade 110/110 e lode (top grade with distinction). Since Oct. 2021 PhD student at the Dept. of Computer Science, Verona.
• Anna Toffanello: Experiments on the Runs-Ratio of the Burrows-Wheeler-Transform, Master thesis in Medical Bioinformatics. Graduated March 2021 with grade 110/110.
• Giulia Pegoraro: Characterization of Leaderless Transcripts, Master thesis in Molecular and Medical Biotechnology, in co-supervision with Jörn Kalinowski and Andreas Albersmeier, Univ. of Bielefeld, Germany (two Erasmus-semesters fall 2018- summer 2019). Graduated in March 2020 with grade 110/110 e lode (top grade with distinction). Currently trainee at EMBL (European Molecular Biology Laboratory) in Rome, Italy.
• Imane Ait Taleb: Promoter Prediction in Corynebacterium Glutamicum, Master thesis in Molecular and Medical Biotechnology, in co-supervision with Jörn Kalinowski and Andreas Albersmeier, Univ. of Bielefeld, Germany (Erasmus-semester Sept. 2018-March 2019). Graduated in March 2020 with grade 109/110.
• Elena Peretti: An experimental analysis of the threshold q-gram distance. Master thesis in Medical Bioinformatics. Graduated March 2019, with grade 104/110.
• Sara Giuliani: When a Dollar makes a BWT. Master thesis in Medical Bioinformatics. Graduated in March 2019, with grade 110/110 e lode (top grade with distinction). Now PhD student at the Dept. of Computer Science, Verona.
• Ana Damatar: On computing the DCJ distance with duplications, insertions, and deletions, master thesis (Master in Medical Bioinformatics) supervised by Jens Stoye and Daniel Dörr at Bielefeld University, Germany, during an Erasmus-semester Sept 2017-Feb. 2018. Graduated March 2018 with grade 105/110. Now PhD student at the University of Ulm, Germany.
• Giovanni Pasquini: ONT MinION sequencing technology: Statistical and algorithmic approaches to detect sequence related errors, master thesis (Master in Bioinformatics and Medical Biotechnology), in collaboration with Massimo Delledonne's lab (Dept. of Biotechnology, University of Verona). Graduated in March 2017 with grade 110/110 e lode (top grade with distinction). Now PhD student at the Dresden International Graduate School for Biomedicine and Bioengineering (DIGS-BB) (Germany) and a member of Volker Busskamp's lab.
• Alessio Milanese: On a new distance measure for genomic repeat discovery. Master thesis (Master in Bioinformatics and Medical Biotechnology), graduated in March 2015 with grade 110/110 e lode (top grade with distinction). Got his PhD at EMBL (European Molecular Biology Laboratory) in Heidelberg, Germany, in Georg Zeller's group. Now postdoc at ETH Zurich, in Shinichi Sunagawa's lab.

• Alice Saleri: ongoing, co-supervised with Prof. Scott Hazelhurst, University of the Witwatersrand, Johannesburg, South Africa.
• Alessandra Sabato: ongoing, co-supervised with Prof. Scott Hazelhurst, University of the Witwatersrand, Johannesburg, South Africa.
• Chiara Dani: Experiments on the Suffix Array (2023).
• Martina Lucà: Implementing an alternative suffix comparison within the tool CMS-BWT of Masillo, ESA 2023 (2023).
• Elena Soriato: Experiments on the number of runs of the BWT (2023).
• Vincenzo Minolfi: experiments on de Bruijn sequences (2023).
• Elena Biagi: experiments on the BBWT (2022).
• Alberto Azzari: experiments on the BBWT (2022).
• Davide Canevazzi: experiments on BWT and LZ (2021).
• Lorenzo Mendo: development of a command-line tool in python to generate examples for different alignment algorithms (2021).
• Francesco Masillo: implementation of the dollar-BWT algorithm by Giuliani et al. 2019 (2021).
• Luca Parmigiani: study of de Bruijn sequences and the BWT: theory and experiments (2020).
• Margherita De Riu: study of power-BWTs: theory and experiments (2020).
• Anna Toffanello: study and analysis of a specific python implementation of the SAIS suffix array construction algorithm (2020).
• Francesco Gualdi: internship with Aptuit, Verona: evaluation of some tools for in silico protein target prediction (2020).
• Imane Ait Taleb: Application of various software for motif finding for promoter prediction to a data set of Corynebacterium glutamicum, in collaboration with the group of Prof. Kalinowski, University of Bielefeld, Germany (2019).
• Davide Cenzato: study and implementation of several non-alignment based string similarity measures, based on the eBWT and on LZ77 (2019).

• Pietro Mosele: ongoing. Bachelor thesis (bioinformatics).
• Caterina Ambrosi: ongoing. Bachelor thesis (bioinformatics), co-supervised with Scott Hazelhurst (University of the Witwatersrand, Johannesburg, South Africa).
• Muhamed Refati: ongoing. Bachelor thesis (bioinformatics), co-supervised with Roberto Posenato (Verona).
• Andrea Toffaletti: NYM protocol: A framework for enhancing anonymity on the web. Bachelor thesis (informatica). Thesis done in Erasmus at ELTE Budapest, co-supervised by Prof. Péter Burcsi and Dr. István Seres. Graduated March 2023 with grade 96/110.
• Paolo Pulcini: Experiments on abelian complexity. Bachelor thesis (bioinformatica). Graduated July 2019 with grade 108/110. Now master student at Univ. of Trieste, in the program "Data Science and Scientific Computing".

Scientific events I am or have been involved in:

• PC-chair:
  • SPIRE 2024 (31st International Symposium on String Processing and Information Retrieval), Sept. 23-25, 2024, Puerto Vallarta, Jalisco, Mexico. PC co-chair (with Edleno Silva de Moura).
  • CPM 2023 (34th Annual Symposium on Combinatorial Pattern Matching), June 26-28, 2023, Marne-la-Vallée, France: PC co-chair (with Laurent Bulteau).
  • IWOCA 2015 (26th International Workshop on Combinatorial Algorithms), Oct. 5-7, 2015, Verona, Italy: PC co-chair (with Bill Smyth) and OC chair.
• Member of the Steering Committee:
  • International Symposium on String Processing and Information Retrieval (SPIRE), since 2024.
• PC-member:
  • CiE 2025 (21st International Conference on Computability in Europe), July 14-18, 2025, Lisbon, Portugal: PC-member.
  • ESA 2024 (32nd Annual European Symposium on Algorithms), Track B, Sept. 2-4, 2024, Royal Holloway, UK: PC-member.
  • DLT 2024 (28th International Conference on Developments in Language Theory), Aug. 12-16, 2024, Göttingen, Germany: PC-member.
  • SPIRE 2023 (30th International Symposium on String Processing and Information Retrieval), Sept. 26-28, 2023, Pisa, Italy: PC member.
  • ICTCS 2023 (24th Italian Conference on Theoretical Computer Science), September 13-15, 2023, Palermo, Italy: PC member.
  • SPIRE 2022 (29th International Symposium on String Processing and Information Retrieval), Nov. 8-10, 2022, Conceptión, Chile: PC member.
  • ICTCS 2022 (23rd Italian Conference on Theoretical Computer Science), September 7-9, 2022, Rome, Italy: PC member.
  • SPIRE 2021 (28th International Symposium on String Processing and Information Retrieval), Oct. 4-6, 2021, Lille, France: PC member.
  • FCT 2021 (23rd International Symposium on Fundamentals of Computation Theory), Sept. 12-15, 2021, Athens, Greece: PC member.
  • IWOCA 2021 (32nd International Workshop on Combinatorial Algorithms), July 5-8, 2021, Ottawa, Canada: PC member.
  • SOFSEM 2021 (47th International Conference on Current Trends in Theory and Practice of Computer Science), Jan. 25-18, 2021, Bolzano, Italy: PC member.
  • SPIRE 2020 (27th International Symposium on String Processing and Information Retrieval), 13-15 Oct. 2020, Orlando, FL, USA: PC member.
  • ICTCS 2020 (21st Italian Conference on Theoretical Computer Science), September 14-16, 2020, Ischia, Italy: PC member.
  • CPM 2020 (31st Annual Symposium on Combinatorial Pattern Matching), June 17-19, 2020, Copenhagen, Denmark: PC member.
  • SOFSEM 2020 (46th International Conference on Current Trends in Theory & Practice of Computer Science), Jan. 20-24, 2020, Limassol, Cyprus: PC member.
  • SPIRE 2019 (26th International Symposium on String Processing and Information Retrieval), Oct. 7 - Oct 9, 2019, Segovia, Spain: PC member.
  • WABI 2019 (19th Workshop on Algorithms in Bioinformatics), September 8-10, 2019, Niagara Falls, NY: PC member.
  • WABI 2018 (18th Workshop on Algorithms in Bioinformatics), August 20-24, 2018, Helsinki, Finland: PC member.
  • IWOCA 2018 (29th International Workshop on Combinatorial Algorithms), July 16-19, 2018, Singapore: PC member.
  • WABI 2017 (17th Workshop on Algorithms in Bioinformatics), August 21-23, 2017, Boston, USA: PC member.
  • SPIRE 2017 (24th International Symposium on String Processing and Information Retrieval), Sept. 26-29, 2017, Palermo, Italy: PC member.
  • IWOCA 2017 (28th International Workshop on Combinatorial Algorithms), July 17-21, 2017, Newcastle, Australia: PC member.
  • WABI 2016 (16th Workshop on Algorithms in Bioinformatics), August 22-24, 2016, Aarhus, Denmark: PC member.
  • IWOCA 2016 (27th International Workshop on Combinatorial Algorithms), 17-19 Aug. 2016, Helsinki, Finland: PC member.
  • CPM 2016 (27th Annual Symposium on Combinatorial Pattern Matching), June 27-29, 2016, Tel Aviv, Israel: PC member.
  • RECOMB-CG 2015 (6th RECOMB Satellite Workshop on Comparative Genomics 2015), 5-7 Oct. 2015, Frankfurt, Germany: PC member.
  • SPIRE 2015 (22nd International Symposium on String Processing and Information Retrieval), Aug. 31-Sept. 4, 2015, London, UK: PC member.
  • IWOCA 2014 (25th International Workshop on Combinatorial Algorithms), 15-17 Oct. 2014, Duluth, Minnesota, USA: PC member.
  • WABI 2014 (14th Workshop on Algorithms in Bioinformatics), 8-10 Sept. 2014, Wroclaw, Poland: PC member.
  • IWOCA 2013 (24th International Workshop on Combinatorial Algorithms), 10-12 July 2013, Rouen, France: PC member.
  • WABI 2013 (13th Workshop on Algorithms in Bioinformatics), 2-4 Sept. 2013, Sophia Antipolis, France: PC member.
• OC-member:
  • StringMasters, International Workshop on Open Problems on Strings, June 16 and 20, 2025, Milano, Italy. Co-organizer (with Golnaz Badkobeh).
  • SPIRE 2024 (31st International Symposium on String Processing and Information Retrieval), Sept. 23-25, 2024, Puerto Vallarta, Jalisco, Mexico. OC member.
  • CPM 2015 (26th Annual Symposium on Combinatorial Pattern Matching), June 28-July 1st, 2015, Ischia, Italy: OC member.
  • 11th StringMasters, workshop on open problems in string algorithms, 20-23 Feb. 2013, Verona, Italy: Co-organizer (with Giuditta Franco).
    Here is a report on the workshop, which appeared in the June 2013 issue of the Bulletin of the European Association of Theoretical Computer Science (BEATCS).
• I took care of the Open Problems Section of IWOCA (International Workshop on Combinatorial Algorithms, which takes place annually) from Jan. 2011 until early 2015.

Recent scientific guests

• Martin Milanič (University of Primorska, Slovenia) visited Prof. Cicalese and me during the week of 25 Nov. 2024. He gave a mini-course on bioinformatics algorithms, within the course "Fundamental Algorithms in Bioinformatics". See here: announcement.
• Simon J. Puglisi (University of Helsinki, Finland) visited during the week of Nov. 11, 2024. On Monday, Nov. 11, he gave a mini-course on suffix arrays and related data structures, within my course "Computational Analysis of Genome-Scale Sequences". See here: announcement.
• Scott Hazelhurst visited from 21 May until 29 June 2024, from the University of the Witwatersrand, Johannesburg, South Africa. He gave a departmental seminar on Monday, June 10, 2024, see here.
• During the PINC workshop in Verona (May 23-24, 2024): Marinella Sciortino and Giuseppe Romana from the University of Palermo, Scott Hazelhurst from the University of the Witwatersrand, Luca Denti and Simone Ciccolella from the University of Milano-Bicocca, Giovanna Rosone and Moses Njagi Mwaniki from the University of Pisa.
• Gonzalo Navarro (University of Chile) visited from 20 to 27 January 2024 and gave a mini-course on compressed text indexes (6 hours within my course "Computational Analysis of Genome-Scale Sequences").
• Travis Gagie (University of Dalhousie, Canada) visited on 23 and 24 Jan. 2023. He taught part of my PhD course on text data structures, and gave a talk in the departmental seminar on Tuesday 24 Jan. at 16.30.
• Johannes Fischer (University of Dortmund, Germany) gave a mini-course on Suffix Arrays 21-23 Nov. 2022, as part of my course ''Computational Analysis of Genomic Sequences'' within the Masters Program Medical Bioinformatics.
• Marília Braga (Bielefeld University, Germany) taught a mini-course on Genome Rearrangements from 25-27 Oct. 2022 in our course "Fundamental Algorithms in Bioinformatics" within the Masters Program Medical Bioinformatics.
• During the week Sept. 12-16, 2022, I had a wonderful group of researchers here in Verona: Christina Boucher (University of Florida, Gainesville, US), Scott Hazelhurst (University of the Witwatersrand, Johannesburg, South Africa), Simon Puglisi (University of Helsinki, Finland), and Marinella Sciortino (University of Palermo, Italy).
  Christina gave two talks during her visit here: one on Computational Problems in Metagenomic Amplification, and another one on Questions and Solutions Related to Broadening Participation in Computer Science.
• Simon Puglisi (University of Helsinki) came to Verona in early November 2021 and gave a mini-course on suffix arrays and wavelet trees, as part of my course "Computational Analysis of Genome-Scale Sequences", the slides are available on request.
• Marinella Sciortino (University of Palermo) visited 12-18 Feb. 2020. The slides of her talk are available on request (just send me an email).
• Péter Burcsi (Eötvös Loránd University, Budapest), visited from 15-23 Jan. 2020, and taught a course on SageMath.
• Johannes Fischer (University of Dortmund, Germany) gave a mini-course on Suffix Arrays 27-29 Nov. 2019, as part of my course Computational Analysis of Genomic Sequences within the Master Program Medical Bioinformatics. You can get his notes by writing to me.
• Joe Sawada from the University of Guelph, Canada, gave a talk on de Bruijn sequences on June 18, 2019, see here: abstract and slides.
• Péter Burcsi (Eötvös Loránd University, Budapest) visited in May 2019, for research.
• László Szabó from ELTE Budapest visited March 25-29, 2019, to teach a PhD course on the Stable Marriage Problem within the Erasmus teaching exchange program.
• Simon Puglisi (University of Helsinki, Finland) visited at the end of November 2018 and taught in my course Computational Analysis of Genomic Sequences within the Master Program Medical Bioinformatics. If you would like to have the slides of his mini-course on Suffix Arrays, send me an email.
• Jens Stoye (Bielefeld University, Germany), May 2018, is giving a Lectio Magistralis on Monday, 14/5/2018, on "Genome Rearrangement by Double Cut and Join" for the Scuola di Dottorato Scienze Naturali ed Ingegneristiche, and a minicourse on Phylogenetic Reconstruction Algorithms within my course "Bioinformatics Algorithms".
• Marília Braga (Bielefeld University, Germany), May 2018, is giving a talk on "Computing the Family-Free DCJ Similarity" on Tuesday, 16/5/2018.
• Péter Burcsi (Eötvös Loránd University, Budapest), February 2018, for research and to teach a course on SageMath.
• Katalin Lázár from ELTE Budapest gave a PhD course between 1 and 15 Oct. 2017 with the title "Bio-inspired models of computation" within the Erasmus teaching exchange program.
• Travis Gagie (Diego Portales University, Santiago de Chile) came to Verona to teach as part of the course "Algorithm Design" during the week 5-9 June, 2017. This course is within the Masters Program Medical Bioinformatics (LM18) (II sem. 2016/2017).
• Stéphane Vialette (CNRS and Université Paris-Est Marne-la-Valleé, France) came to Verona to teach in my course "Bioinformatics Algorithms" during the week 22-26 May, 2017. This course is within the Masters Program Medical Bioinformatics (LM18) (II sem. 2016/2017).
• Johannes Fischer (Univ. Dortmund, Germany) came to Verona to teach in my course "Computational analysis of genomic sequences" during the week 10-14 April, 2017. This course is within the Masters Program Medical Bioinformatics (LM18) (II sem. 2016/2017).
• Elena Konstatinova (Sobolev Institute of Mathematics and Novosibirsk State University, Novosibirsk, Russia), visited in May 2016.

Editorial Work

• Special issue of Discrete Applied Mathematics on "The Combinatorics of Graphs and Strings", guest editor (with William F. Smyth), vol. 246, pp. 1-154, Sept. 2018.
• Special issue of European Journal of Combinatorics on "Combinatorial Algorithms, Dedicated to the Memory of Mirka Miller." guest editor (with Jan Kratochvíl and Mirka Miller), vol. 68, pp. 1-266, Febr. 2018.
• Proceedings of the 26th International Workshop on Combinatorial Algorithms (IWOCA 2015), co-editor (with William F. Smyth), Lecture Notes in Computer Science (LNCS vol. 9538, see here for the online version).
• Special issue of the Journal of Discrete Algorithms on "StringMasters 2012 & 2013," guest editor (with Maxime Crochemore and Jacqueline Daykin): Volume 1 (vol. 28, pp. 1-84, Sept. 2014) and Volume 2 (vol. 32, pp. 1-86, May 2015)

Erasmus

I am still scientific coordinator for the Erasmus+ exchange with Bielefeld University (Technical Faculty), Germany (only computer science and bioinformatics; for mathematics contact Prof. Di Persio, for biotechnology, Prof. Dall'Osto).

And starting 2024/2025, I am again scientific coordinator for the Erasmus+ exchange with Jena (Friedrich-Schiller University), Germany.

My other partner universities have passed to the following scientific coordinators: Please contact them if you are interested in doing an Erasmus semester in one of these universities (unless you want to write a thesis in collaboration with one of these universities, then you should speak to me).

• ELTE Budapest (Computer Science), Hungary: Prof. Matteo Cristani
  (for Mathematics, the coordinator is Prof. Mazzuoccolo)
• University of Dortmund, Germany: Prof. Matteo Cristani
• University of Primorska, Koper (FAMNIT), Slovenia: Prof. Ferdinando Cicalese.
• University of Helsinki, Finland: agreement has been closed by Helsinki.
• (for PhD students only:) King's College, London (Dept. of Computer Science): Prof. Alessandra Di Pierro

More info coming soon.

In the meanwhile, you can read this poem by Roald Dahl which expresses wonderfully what I think about television.