Zsuzsanna Lipták

Associate Professor Department of Computer Science University of Verona, Italy email: 1. zsuzsanna DOT liptak AT univr DOT it   2. zsuzsa AT cebitec DOT uni-bielefeld DOT de (In case of problems, please resend to both email addresses.) 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 fax: +39 045 802-7068 Student hours: Wed 10.00-12.00; currently only by appointment (pandemic regulations): Please send me an email if you would like to talk to me. Here is my institutional page.

This page is always under construction...

• The Monday meetings of the Algorithms Group are taking place this term on Tuesdays and online. If you would like to participate, write me an email, so I can send you an invitation.
  
• My student hours take place every Wed 10.00-12.00, either in person or via zoom, currently only by appointment (due to the coronavirus emergency). Please send me an email if you would like to talk to me.
  
• If you are interested in prefix normal words, there have been recent advances, see our latest paper accepted at Theoretical Computer Science (preprint see here). Here is a short (updated!) writeup on open problems on prefix normal words.

Research Interests

I work on string algorithms and other discrete and algorithmic problems, mostly arising in bioinformatics applications. In algorithmic bioinformatics, I have mostly worked on mass spectrometry data interpretation (genomics, proteomics, metabolomics) and on string distance measures for expression clustering (transcriptomics), but am interested in all algorithmic and combinatorial problems on discrete structures (strings, sequences, trees, graphs) arising in the context of biological applications.

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 have 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 SANBI, Cape Town (South Africa).

I am member of the Bioinformatics and Natural Computing Group at the Department of Computer Science of Verona University. We organized the international conference IWOCA 2015 (26th International Workshop on Combinatorial Algorithms), of which I was PC co-chair (with Bill Smyth) and OC chair; as well as the 11th StringMasters, an international workshop on string algorithms (with Giuditta Franco). I am also member of the Center for Biomedical Computing (CBMC) in Verona, and of the Centre for Combinatorics on Words and Applications (CCWA) at Murdoch University, Perth, Australia.

There is a (usually somewhat outdated) CV on my institutional page.

Publications

Teaching (in Verona)

• PhD course on Advanced data structures for textual data, from 21 to 25 September 2020.
• "Fundamental Algorithms for Bioinformatics - module Bioinformatics Algorithms" (in English), within the Masters Program Medical Bioinformatics (LM18), 1st year (II sem. 2019/2020).
• "Computational analysis of genomic sequences" (in English): Elective course in the Masters Program Medical Bioinformatics (LM18), 2nd year (I sem. 2019/2020).
• "Fundamental Algorithms for Bioinformatics - module Bioinformatics Algorithms" (in English), within the Masters Program Medical Bioinformatics (LM18), 1st year (II sem. 2018/2019).
• "Computational analysis of genomic sequences" (in English): Elective course in the Masters Program Medical Bioinformatics (LM18), 2nd year (I sem. 2018/2019).
• "Fundamental Algorithms for Bioinformatics - module Bioinformatics Algorithms" (in English), within the Masters Program Medical Bioinformatics (LM18), 1st year (II sem. 2017/2018).
• "Computational analysis of genomic sequences" (in English): Elective course in the Masters Program Medical Bioinformatics (LM18), 2nd year (I sem. 2017/2018).
• "Fundamental Algorithms for Bioinformatics - module Bioinformatics Algorithms" (in English), within the Masters Program Medical Bioinformatics (LM18), 1st year (II sem. 2016/2017).
• "Computational analysis of genomic sequences" (in English): Elective course in the Masters Program Medical Bioinformatics (LM18), 2nd year (II sem. 2016/2017).
• "Computational methods for handling textual data" (flyer): PhD course, jointly with Ferdinando Cicalese and Giuditta Franco (March 2016).
• "Algorithms for Computational Biology" (2015/2016) (in English), fall semester of 2015/2016, Masters in Molecular and Medical Biotechnology (new LM9).
• "Algoritmi e Linguaggi per Bionformatica: Algoritmi" (2014/2015) (in English), Laurea magistrale in Bioinformatica e biotecnologie mediche (LM9), masters.
• "Modelli Biologici Discreti" (2014/2015) (in Italian), within the Laurea Triennale "Bioinformatica" (bachelor).
• "Algoritmi e Linguaggi per Bionformatica: Algoritmi" (2013/2014) (in English), Laurea magistrale in Bioinformatica e biotecnologie mediche (LM9), masters.
• "Algoritmi e Linguaggi per Bionformatica: Algoritmi" (2012/2013) (in English), Laurea magistrale in Bioinformatica e biotecnologie mediche (LM9), masters.
• "Algoritmi e Linguaggi per Bionformatica: Algoritmi" (2011/2012) (in English), Laurea magistrale in Bioinformatica e biotecnologie mediche (LM9), masters.

Theses/Tesi

Progetti nell'ambito di sequenze/stringhe (genomiche e no), bioinformatica algoritmica, algoritmi su stringhe. Ho vari 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 ("stage") or for bachelor or master theses.

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

Students

PhD

• Sara Giuliani: PhD student, since Oct. 2019, University of Verona.
• Davide Cenzato: PhD student, since Oct. 2019, University of Verona.
• Massimiliano Rossi: PhD student Oct. 2016 - Sept. 2019, University of Verona, co-supervised with Ferdinando Cicalese. Defended in Feb. 2020. Now post-doc in Christina Boucher's group, University of Florida, USA.

Master

• Sonia Morasso: Master thesis in Medical Bioinformatics. Ongoing.
• Simona Busiol: Master thesis in Medical Bioinformatics. Ongoing.
• Anna Toffanello: Master thesis in Medical Bioinformatics. Ongoing.
• 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.
• 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.

Bachelor

• Paolo Pulcini: Experiments on abelian complexity. Bachelor thesis. Graduated July 2019 with grade 108/110. Now master student at Univ. of Trieste, in the program "Data Science and Scientific Computing".

Recent Talks

• Presentazione "Che cos'è la bioinformatica?" per studenti del liceo, 7/3/2018.
  (Introductory talk for high school students on Bioinformatics, given on 7 March 2018.)
• On the Parikh-de-Bruijn grid.
  Workshop on Words and Complexity, Lyon, France, 19-23 Feb. 2018;
  
• Reconstruction of Trees from Jumbled and Weighted Subtrees.
  27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), Tel Aviv, Israel, June 27 - 29, 2016;
  I gave a shorter version of the same talk at the AxA Workshop (Workshop on Advanced Algorithms on Strings,
  in memoriam Alberto Apostolico), Venice, Italy, June 21-24, 2016; talk pdf, paper at CPM2016.
• More on prefix normal words.
  London Stringology Day/London Algorithmic Workshop 2015 (LSD/LAW 2015),
  King's College, London, UK, 5-6 Feb. 2015; abstract, talk pdf.
• Jumbled Pattern Matching: Online, offline, binary, or not.
  (This talk includes the connection of binary JPM to prefix normal words.)
  McMaster University, Hamilton, ON, Canada, 10 Oct. 2014. talk pdf.
  
• Normal, Abby Normal, Prefix Normal.
  Seventh International Conference on Fun with Algorithms (FUN 2014),
  Lipari Island, Italy, 1-3 July, 2014. talk pdf, paper in proceedings.
• Prefix normal words, binary jumbled pattern matching, and bubble languages.
  London Stringology Day/London Algorithmic Workshop 2014 (LSD/LAW 2014),
  King's College, London, UK, 6-7 Feb. 2014; abstract, talk pdf.
  This paper was also presented at CPM 2014 in Moscow in June, by my co-author Gabriele Fici.
  See paper in CPM proceedings.
• Jumbled String Matching: Motivations, Variants, Algorithms.
  Workshop Combinatorial structures for sequence analysis in bioinformatics,
  University of Milano-Bicocca, Milano, Italy, 27 Nov. 2013; abstract, talk pdf.
  
• Algorithms on strings and other discrete problems in bioinformatics.
  Center for Biomedical Computing (CBMC),
  Verona, Italy, 30 Oct. 2013; talk pdf.
• See here for more talks.

Scientific events I am or have been involved in:

• 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.
• IWOCA 2015 (26th International Workshop on Combinatorial Algorithms), 5-7 Oct. 2015, Verona, Italy: PC co-chair (with Bill Smyth) and OC chair.
• 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.
• CPM 2015 (26th Annual Symposium on Combinatorial Pattern Matching), June 28-July 1st, 2015, Ischia, Italy: OC 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.
• 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. The open problem section was taken over by Gabriele Fici (Univ. of Palermo, Italy) and Oliver Schaudt (Univ. of Köln, Germany). Please contact one of them if you are interested in contributing an open problem. This is independent of attending the conferences.

Recent scientific guests

• Marinella Sciortino from the 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.
• 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.
• 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, 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 also scientific coordinator for Erasmus+ exchanges with

• ELTE Budapest (Computer Science), Hungary
  (for Mathematics, the coordinator is now Prof. Mazzuoccolo)
• Bielefeld University (Technical Faculty), Germany (only copmuter science and bioinformatics; for mathematics contact Prof. Di Persio, for biotechnology, Prof. Dall'Osto)
• University of Dortmund, Germany
• University of Jena, Germany
• University of Helsinki, Finland (in the past together with Prof. Solitro)
• for PhD students only: King's College, London (Dept. of Computer Science)

Note that the agreement with the University of Primorska, Koper (FAMNIT), Slovenia, is now coordinated by Prof. Cicalese.

The universities of Bielefeld, Jena, and Helsinki are of particular interest for Bioinformatics students (both bachelor and master).

Come and see me if you are an interested student and have questions, I have lots of material. I have so far sent 32 students from Verona to one of these places for one or two semesters.

More info coming soon.

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