Department of Computer Science
University of Verona, Italy
zsuzsanna DOT liptak AT univr DOT it
University of Verona
Department of Computer Science
Strada le Grazie, 15
I-37134 Verona, Italy
Ca' Vignal, 2, room 1.79 (1st floor)
tel: +39 045 802-7032
fax: +39 045 802-7068
Thu 11:00-13:00 and by appointment
Here is my institutional page.
This page is always under construction...
- My master thesis student Giovanni Pasquini just graduated with a final grade of 110/110 e lode (top grade with distincition). His thesis treated error profiles in DNA samples sequenced with MinION technology (nanopore sequencing).
- Prof. Johannes Fischer (Univ. Dortmund, Germany) is coming to Verona to teach in my course
"Computational analysis of genomic sequences" during the week 10-13 April, 2017. This course is within the Masters Program Medical Bioinformatics (LM18) (II sem. 2016/2017), which is fully taught in English.
- If you are interested in prefix normal words, see our paper and the following 3 integer sequences in the
The Online Encyclopedia of Integer Sequences (OEIS): A194850, A238109, and A238110.
- My former masters thesis student Alessio Milanese started as a PhD student at EMBL (European Molecular Biology Laboratory) in Heidelberg, Germany, in the group of Georg Zeller.
I am assistant professor (with tenure) in Verona. I 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). In addition to Bielefeld, where I was research assistant and later postdoc, I have also worked as research assistant at ETH Zurich, Switzerland; and as visiting researcher at the Rényi Institute, Budapest (Hungary), at the University of the Witwatersrand, Johannesburg (South Africa), at SANBI, Cape Town (South Africa); and as postdoc at Salerno University (Italy), where I had a Marie Curie IEF fellowship.
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, workshop on open problems in 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 slightly outdated CV on my institutional page.
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.
You can find my publications at my
DBLP entry or my
Google Scholar page. If you can't access a paper, please write to me and I'll send you a copy.
- 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)
- 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 Discrete Applied Mathematics on "Combinatorial Algorithms," guest editor (with William F. Smyth).
- Special issue of European Journal of Combinatorics on "Combinatorial Algorithms," guest editor (with Jan Kratochvíl and Mirka Miller).
Teaching in Verona:
- "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) (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.
Past teaching activities: coming soon...
Se sei uno studente interessato agli algoritmi e stringhe, sopratutto con delle applicazioni alla bioinformatica, sei benvenuto/a; io ho vari argomenti per tesi (magistrali o triennali) oppure per le stage. (Sì, parlo 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.
- 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.
- 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.
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.
- Recent Advances on Prefix Normal Words.
Seminars of the Words and Automata Research Group,
Dept. of Mathematics and Computer Science of the University of Palermo, Italy, 24 Oct. 2013; abstract.
- See here for more talks.
Events I am or have been involved in:
(PC = Program Committee, OC = Organizing Committee)
- WABI 2017 (17th Workshop on Algorithms in Bioinformatics),
August 21-23, 2017, Boston, USA: PC member.
- SPIRE 2017 (24nth 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, Isreal: 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 has recently been 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.
I am scientific coordinator for Erasmus exchange with
- ELTE Budapest (Computer Science, Mathematics), Hungary;
- Bielefeld University (Technical Faculty), Germany;
- University of Primorska, Koper (FAMNIT), Slovenia;
- King's College, London (Dept. of Computer Science; for PhD students only!),
- University of Dortmund, Germany (new!)
- and the University of Jena, Germany (new!)
The universities of Bielefeld, Jena, and Helsinki (scientific coordinator: Prof. Ugo Solitro) are of particular interest for Bioinformatics students.
Come and see me if you are an interested student and have questions, I have lots of material.
More info coming soon.
In the meanwhile, you can read a poem by Roald Dahl which expresses wonderfully what I think about television.