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Publications of Nadia Pisanti
If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple.
But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas. G.B.Shaw
Journal papers
P.Charalampopoulos, H.Chen, P.Christen, G.Loukides, N.Pisanti, S.P.Pissis, J.Radoszewski:
Pattern Masking for Dictionary Matching: Theory and Practice,
Algorithmica, 2023. In press.
G.Bernardini, A.Conte, G.Gourdel, R.Grossi, G.Loukides, N.Pisanti, S.P.Pissis, G.Punzi, L.Stougie, Michelle Sweering:
Hide and Mine in Strings: Hardness, Algorithms, and Experiments,
IEEE Transaction on Knowledge and Data Engineering,35(6), 5948-5963, 2023.
A.Teramo, A.Binatti, E.Ciabatti, G.Schiavoni, G.Tarrini, G.Barilà, G.Calabretto, C.Vicenzetto, V.Gasparini, M.Facco, I.Petrini, R.Grossi, N.Pisanti, S.Bortoluzzi, B.Falini, E.Tiacci, S.Galimberti, G.Semenzato, R.Zambello:
Defining TCRγδ lymphoproliferative disorders by combined immunophenotypic and molecular evaluation,
Nature Communications, 13(3298), 1-11, 2022.
G.Bernardini, P.Gawrychowski, N.Pisanti, S.P.Pissis, G.Rosone:
Elastic-Degenerate String Matching via Fast Matrix Multiplicationn,
SIAM Journal of Computing, 51(3), 549-576, 2022.
G.Bernardini, H.Chen, A.Conte, R.Grossi, G.Loukides, N.Pisanti, S.P.Pissis, G.Rosone, Michelle Sweering:
Combinatorial Algorithms for String Sanitization,
ACM Transaction on Knowledge Discovery from Data, 15(1), 8:1-8:34, 2021.
N.Prezza, N.Pisanti, M.Sciortino, G.Rosone:
Variable-Order Reference-Free Variant Discovery with the Burrows-Wheeler Transform,
BMC Bioinformatics, 21(8), 2020.
M.Alzamel, L.A.K.Ayad, G.Bernardini, R.Grossi, C.S.Iliopoulos, N.Pisanti, S.P.Pissis, G.Rosone:
Comparing Degenerate Strings,
Fundamenta Informaticae 175(1-4), 41-58, 2020.
G.Bernardini, N.Pisanti, S.Pissis, G.Rosone:
Approximate Pattern Matching on Elastic-Degenerate Text,
Theoretical Computer Science, 812, 109-122, 2020.
L.A.K.Ayad, G.Bernardini, R.Grossi, Costas.S.Iliopoulos, N.Pisanti, S.Pissis, G.Rosone:
Longest property-preservied common factor: a new string-processing framework,
Theoretical Computer Science, 812, 244-251, 2020.
T.Marschall et al. ("The Computational Pan-Genomics Consortium"):
Computational Pan-Genomics: Status, Promises and Challenges,
Briefings in Bioinformatics, 19(1), 118-135, 2018.
R.Grossi, G.Menconi, N.Pisanti, R.Trani, S.Vind:
Motif Trie: An Efficient Text Index for Pattern Discovery with Don't Cares,
Theoretical Computer Science, 710, 74-87, 2018.
R.Grossi, C.S.Iliopulos, R.Mercas, N.Pisanti, S.P.Pissis, A.Retha, F.Vayani:
Circular Sequence Comparison: Algorithms and Applications,
Algorithms for Molecular Biology, 11(1), 12, 2016.
M.Aldinucci, A.Bracciali, M.Patterson, T.Marschall, N.Pisanti, I.Merelli, M.Torquati:
pWhatsHap: efficient haplotyping for future generation sequencing,
BMC Bioinformatics, 17(11):342, 27-41, 2016.
P.Bonizzoni, R.Dondi, G.W.Klau, Y.Pirola, N.Pisanti, S.Zaccaria:
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes,
Journal of Computational Biology, 23(9), 718-736, 2016.
Y.Pirola, S.Zaccaria, R.Dondi, G.W.Klau, N.Pisanti, P.Bonizzoni:
HapCol: Accurate and Memory-efficient Haplotype Assembly from Long Reads,
Bioinformatics, 32(11), 1610-1617, 2016.
M.Patterson, T.Marschall, N.Pisanti, L.van Iersel, L.Stougie, G.W.Klau, A.Schonhuth:
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads,
Journal
of Computational Biology, 22(6), 498-509, 2015.
G.Menconi, G.Battaglia, R.Grossi, N.Pisanti, R.Marangoni:
Mobilomics in Saccharomyces cerevisiae Strains,
BMC Bioinformatics, 14(1), 1-17, 2013.
R.Grossi, A.Pietracaprina, N.Pisanti, G.Pucci, E.Upfal, F.Vandin:
MADMX: A Strategy for Maximal Dense Motif Extraction,
Journal
of Computational Biology, 18(4), 535-545, 2011.
G.Battaglia, R.Grossi, D.Cangelosi, N.Pisanti:
Masking Patterns in Sequences: A New Class of Motif Discovery with Don't Cares,
Theoretical Computer Science 410(43), 4327-4340, 2009.
N.Pisanti, H.Soldano, M.Carpentier, J.Pothier::
A Relational Extension of the Notion of Motifs: Application to the Protein Common 3D Substructures Searching Problem,
Journal
of Computational Biology, 16(12) 1635-1660, 2009.
P.Peterlongo, G.A.T.Sacamoto, A.Pereira do Lago, N.Pisanti, M.-F.Sagot:
Lossless Filter for Multiple Repeats with Bounded Edit Distancee,
BMC Algorithms for Molecular Biology, 4(3), 1-20, 2009.
M.Federico, N.Pisanti:
Suffix Tree Characterization of Maximal Motifs in Biological Sequences,
Theoretical Computer Science, 410(43), 4391-4401, 2009.
P.Peterlongo, N.Pisanti, F.Boyer, A.Pereira do Lago, M.-F.Sagot:
Lossless filter for multiple repetitions with Hamming Distance,
Journal of Discrete Algorithms, 6(3), 497--509, 2008.
V.Ciriani, N.Pisanti, A.Bernasconi:
Room Allocation: a Polynomial subcase of the Quadratic Assignment Problem,
Discrete Applied Mathematics
144(3), 263--269, 2004.
N.Pisanti, R.Marangoni, P.Ferragina, A.Frangioni,
A.Savona, C.Pisanelli, F.Luccio:
PaTre: a method for Paralogy Trees Construction,
Journal
of Computational Biology 10(5), 791--802, 2003.
N. Pisanti, M.-F. Sagot:
Further thoughts on the syntenic distance between genomes,
Algorithmica 34(2), 157--180, 2002.
N. Pisanti:
DNA Computing: a survey,
Bulletin of EATCS 64, 188--216, 1998.
Edited Books and Journal Issues
F.M.Nardini, N. Pisanti, R.Venturini:
Proceedings of 30th International Symposium on String processing and Information Retrieval (SPIRE 2023),
Springer Lecture Notes in Computer Science 14240, 2023.
C.Colbourn, R.Grossi, N. Pisanti:
Special Issue dedicated to selected papers from IWOCA 2019,
Theory of Computing Systems, 64(7), 2020.
Carl Kingsford, Nadia Pisanti:
Proceedings of 20th Conference on Algorithms for BioInformatics (WABI 2020),
LIPIcs 172, 2020.
Charles J. Colbourn, R. Grossi, N. Pisanti:
Proceedings of 30th International Workshop On Combinatorial Algorithms (IWOCA 2019),
Springer Lecture Notes in Computer Science 11638, 2019.
N. Pisanti, S. Pissis:
Proceedings of 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019),
LIPIcs 128, 2019.
C. Bohm, S. Khuri, L. Lhotska, N. Pisanti:
Proceedings of Information Technology in Bio- and Medical Informatics (ITBAM 2011),
Springer Lecture Notes in Computer Science 6865, 2011.
S. Khuri, L. Lhotska, N. Pisanti:
Proceedings of Information Technology in Bio- and Medical Informatics (ITBAM 2010),
Springer Lecture Notes in Computer Science 6266, 2010.
Books
J.-P.Allouche, V.Berthe, M.Crochemore, P.Jacquet, R.Kolpakov, G.Koucherov, E.Laporte, M.Mohri, N.Pisanti, D.Poulalhon, G.Reinert, M\
.-F.Sagot, G.Schaeffer, S.Schbath, W.Szpankowski, M.Waterman:
Applied combinatorics on words by M. Lothaire,
Cambridge University Press, 2005.
A.Liccardo, S.Borelli, C.Canali, M.D'Onghia, M.Damiani, C.Di Letizia, M.Gianecchini, C.Oppi, N.Pisanti, A.Rosselli, B.Siboni, P.Tomio:
Linee guida per il Bilancio di Genere negli Atenei italiani,
Fondazione CRUI, 2019.
Chapters in Books and Papers in Volumes
N. Pisanti:
Algorithms Foundations,
In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics,
Elsevier, 1-4, 2018.
N. Pisanti, M.Giraud, P.Peterlongo:
Filters and Seeds Approaches for Fast Homology Searches in Large Datasets,
Chapter 15 in ALGORITHMS IN COMPUTATIONAL MOLECULAR BIOLOGY Techniques, Approaches and Applications,
A.Y.Zomaya and M.Elloumi editors,
John Wiley & sons inc. publication, 299-320, 2010.
N. Pisanti, H. Soldano, M. Carpentier, J. Pothier:
Implicit and Explicit Representation of Approximated Motifs,
in Algorithms for Bioinformatics,
C. Iliopoulos and K. Park and K. Steinhofel editors,
King's College London Press, 2006.
N. Pisanti, M. Crochemore, R. Grossi, M.-F. Sagot:
A Comparative Study of Bases for Motif Inference,
in String Algorithmics,
C. Iliopoulos and T. Lecroq editors,
pages 195--226, KCL publications, 2004. [For a presentation of the volume see here]
Theses
N. Pisanti:
Segment-based distances and similarities in genomic sequences,
PhD thesis, Dipartimento di Informatica, University of Pisa, 2002.
N. Pisanti:
Recent duplications in genomes: a graph theory approach,
DEA memoire, Institut Garpard Monge,
University of Marne-la-Vallee (France), 1998.
GZIPPED PS FILE
Conference papers
G.Bernardini, H.Chen, A.Conte, R.Grossi, V.Guerrini, G.Loukides, N.Pisanti, S.P.Pissis
Utility-Oriented String Mining,
proceedings of SIAM International Conference on Data Mining (SDM 2024), 2024. In press.
E.Gabory, N.M.Mwaniki, N.Pisanti, S.P.Pissis, J.Radoszweski, W.Zuba:
Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications
proceedings of 34th International Symposium on Combinatorial Pattern Matching (CPM), LIPIcs 259, 11:1-11:20, 2023.
N.M.Mwaniki, E.Garrison, N.Pisanti:
Inferring Mobile Elements in S.Cerevisiae strains,
proceedings of 14th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS), SciTePress, pages 170-79, 2023.
Njagi Moses Mwaniki, Nadia Pisanti
Optimal sequence alignment to ED-strings
proceedings of the 18th International Symposium on Bioinformatics Research and Applications (ISBRA), Springer LNCS, 2022. In press.
Panagiotis Charalampopoulos, Huiping Chen, Peter Christen, Grigorios Loukides, Nadia Pisanti, Solon Pissis and Jakub Radoszweski:
Pattern Masking for Dictionary Matching
proceedings of 32nd International Symposium on Algorithms and Computation (ISAAC), LIPIcs 212, 2021.
Nadia Pisanti:
On-Line Pattern Matching on D-Texts (Invited Talk)
proceedings of 32nd Annual Symposium on Combinatorial Pattern Matching (CPM), LIPIcs 191, 2021.
Alessio Conte, Roberto Grossi, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis, Giulia Punzi
Beyond the BEST Theorem: Fast Assessment of Eulerian Trails
proceedings of the 23rd International Symposium on Fundamentals of Computation Theory (FCT), Springer LNCS 12867, 162--175, 2021.
Giulia Bernardini, Alessio Conte, Garance Gourdel, Roberto Grossi, Grigorios Loukides, Nadia Pisanti, Solon Pissis, Giulia Punzi, Leen Stougie, Michelle Sweering:
Hide and Mine in Strings: Hardness and Algorithms
proceedings of IEEE International Conference on Data Mining (ICDM), 2020.
Giulia Bernardini, Huiping Chen, Grigorios Loukides, Nadia Pisanti, Solon Pissis, Leen Stougie, Michelle Sweering:
String Sanitization under Edit Distance
proceedings of 31st Annual Symposium on Combinatorial Pattern Matching (CPM), 2020.
G.Bernardini, H.Chen, A.Conte, R.Grossi, G.Loukides, N.Pisanti, S.P.Pissis, G.Rosone:
String sanitization: a combinatorial approach
proceedings of European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD 2019), LNAI 11906, 627-644, 2020.
F. Geraci, R. Massidda, N. Pisanti:
Technology and Species independent Simulation of Sequencing data and Genomic Variants
proceedings of 19th IEEE International Conference on BioInformatics and BioEngineering (BIBE), 2019.
M. Alzamel, A. Conte, D. Greco, V. Guerrini, C. Iliopoulos, N. Pisanti, N. Prezza, G. Punzi, G. Rosone:
Online Algorithms on Antipowers and Antiperiods
proceedings of 26th International Symposium on String Processing and Information Retrieval (SPIRE), 2019.
G.Bernardini, P.Gawrychowski, N.Pisanti, S.P.Pissis, G.Rosone:
Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication
proceedings of 46th International Colloquium on Automata, Languages and Programming (ICALP), 2019.
L.Ayad, G.Bernardini, R.Grossi, C.S.Iliopoulos, N.Pisanti, S.P.Pissis, G.Rosone:
Longest Property-Preserved Common Factor
proceedings of 25th International Symposium on String Processing and Information Retrieval (SPIRE), 2018.
N.Prezza, N.Pisanti, M.Sciortino, G.Rosone:
Detecting Mutations by eBWT
proceedings of 18th Conference on Algorithms in Bioinformatics (WABI), 2018.
M.Alzamel, L.Ayad, G.Bernardini, R.Grossi, C.S.Iliopoulos, N.Pisanti, S.P.Pissis, G.Rosone:
Degenerate String Comparison and Applications
proceedings of 18th Conference on Algorithms in Bioinformatics (WABI), 2018.
G.Bernardini, N.Pisanti, S.P.Pissis, G.Rosone:
Pattern matching on Elastic-Degenerate Text with Errors
proceedings of 24th International Symposium on String Processing and Information Retrieval (SPIRE), 2017.
R.Grossi, C.S.Iliopoulos, C.Liu, N.Pisanti, S.P.Pissis, A.Retha, G.Rosone, F.Vayani, L.Versari:
On-line pattern matching on similar texts,
proceedings of 28th Annual Symposium on Combinatorial Pattern Matching (CPM), 2017.
M.Martin, M.Patterson, S.Garg, N.Pisanti, G.W.Klau, A.Schönhuth, T.Marschall
Read-Based Phasing Using WhatsHap,
Technical Track at Intelligent Systems for Molecular Biology Conference (ISMB), 2016.
M.F.Zini, S.Bonaretti, N.Pisanti, E.Biasci, A.Podda, V.Mey, F.Piras, G.L.L'Abbate, S.Marini, D.Fratta, S.Trasciatti
Preclinical Tests for Cerebral Stroke,
proceedings of 7th IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) and Network Enabled Health Informatics, Biomedicine and Bioinformatics (Hi-Bi-Bi), 1063-1067, 2015.
R.Grossi, C.S.Iliopoulos, R.Mercas, N.Pisanti, S.P.Pissis, A.Retha, F.Vayiani
Circular Sequence Comparison with q-grams,
proceedings of 15th International Conference on Algorithms in BioInformatics (WABI), Springer LNCS 9289, 203-216, 2015.
P.Bonizzoni, R.Dondi, G.W.Klau, Y.Pirola, N.Pisanti and S.Zaccaria:
On the Tractability and Approximability of the Minimum Error Correction problem for Haplotype Assembly,
proceedings of 26th Annual Symposium on Combinatorial Pattern Matching (CPM), Springer LNCS 9133, 100-113, 2015.
M. Aldinucci, A. Bracciali, T. Marschall, M. Patterson, N. Pisanti, M. Torquati:
High-Performance Haplotype Assembly,
Selected papers from the 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), LNCS 8623, 245-258, 2015.
R.Grossi, G.Menconi, N.Pisanti, R.Trani, S.Vind:
Output-Sensitive Pattern Extraction in Sequences,
Proceedings of 34th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS), 303-314, 2014.
M. Aldinucci, A. Bracciali, N. Pisanti, M. Torquati:
Towards High-Performance Haplotype Assembly for Future Generation Sequencing,
Proceedings of 11th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), 1-6, 2014.
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau and Alexander Schoenhuth
WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads,
proceedings of 18th ACM Annual International Conference on Research in Computational Molecular Biology (RECOMB), 237-249, 2014.
E.Birmele, R.Ferreira, R.Grossi, A.Marino, N.Pisanti, R.Rizzi, G.Sacomoto
Optimal Listing of Cycles and st-Paths in Undirected Graphs,
proceedings of 24th ACM/SIAM Symposium On Discrete Algorithms (SODA), ACM Press, pages 1884-1896, 2013.
E.Birmele, P.Crescenzi, R.Ferreira, R.Grossi, V.Lacroix, A.Marino, N.Pisanti, G.Sacomoto and M.-F.Sagot
Efficient bubble enumeration in directed graphs,
proceedings of 19th Conference on String Processing and Information Retrieval (SPIRE) 2012, Springer LNCS 7608, pages 118-129, 2012.
G.Menconi, G.Battaglia, R.Grossi, N.Pisanti, R.Marangoni:
A Taste of Yeast Mobilomics,
proceedings of 3rd International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS). SciTePress, pages 271-274, 2012.
M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot:
Finding Long and Multiple repetitions with Edit Distance
Proceedings of the 15th Prague Stringology Conference (PSC 2011), Prague, Czech Republic, 2011.
M. Federico, N. Pisanti:
Removing artifacts of approximated motifs
Proceedings of 2nd Conference on Information Technology in Bio- and Medical Informatics (ITBAM 2011).
Springer Lecture Notes in Computer Science 6865, pages 153-167, 2011.
G.Battaglia, R.Grossi, N.Pisanti, R.Marangoni, G.Menconi:
Inferring Mobile Elements in S.Cerevisiae strains,
proceedings of 2nd International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS), SciTePress, pages 131-136, 2011.
P.Peterlongo, N.Schnel, N.Pisanti, M.-F. Sagot, V.Lacroix:
Identifying SNPs without a reference genome by comparing raw reads,
proceedings of 17th Conference on String Processing and Information Retrieval (SPIRE) 2010, Springer LNCS 6393, pages 147-158, 2010.
M.Federico, N.Pisanti, P.Peterlongo:
An optimized filter for finding multiple repeats in DNA sequences,
Proceedings of 8th ACS/IEEE International Conference on Computer Systems and
Applications (AICCSA), IEEE Computer Society Press, 2010.
R.Grossi, A.Pietracaprina, N. Pisanti, G.Pucci, E.Upfal, F.Vandin:
MADMX: A Novel Strategy for Maximal Dense Motif Extraction,
Proceedings of the 9th Workshop on Algorithms in BioInformatics (WABI), Springer LNCS 5724, pages 362-374, 2009.
G.Battaglia, R.Grossi, R.Marangoni, N.Pisanti:
Mining Biological Sequences with Masks,
Proceedings of BIOlogical Knowledge Discovery from Databases (BIOKDD), IEEE Computer Society Press, pages 193-197, 2009.
M. Federico, N. Pisanti:
Suffix Tree Characterization of Maximal Motifs in Biological Sequences,
Proceedings of BIoinformatics Research and Development (BIRD), Springer Communications in Computer and Information Science 13, pages 456-465, 2008.
N. Pisanti, A. Carvalho, L. Marsan, M.-F. Sagot:
RISOTTO: Fast extraction of motifs with mismatches,
Proceedings of 7th Latin American Theoretical INformatics conference (LATIN), Springer LNCS 3887, pages 757-768, 2006.
P. Peterlongo, N. Pisanti, F. Boyer, M.-F. Sagot:
Filtre exact de sélection de longues répétitions approchées utilisant le tableau des bi-facteurs,
Journée MATHStic Algorithmique Génomique, Orsay (France), pages 22-23, 2005.
P. Peterlongo, N. Pisanti, F. Boyer, M.-F. Sagot:
Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-Factor Array,
proceedings of the 12th Conference on String Processing and Information Retrieval (SPIRE), Springer LNCS 3772, pages 179-190, 2005.
N. Pisanti, H. Soldano, M. Carpentier:
Incremental Inference of Relational Motifs with a Degenerate Alphabet,
proceedings of 16th Combinatorial Pattern Matching conference (CPM), Springer LNCS 3537, pages 229-240, 2005.
C. Iliopoulos, J. McHugh, P. Peterlongo, N. Pisanti, W. Rytter, M.-F. Sagot:
A First Approach to Finding Common Motifs with Gaps,
proceedings of 9th Prague Stringology Conference (PSC), pages 88-97, 2004.
F. Luccio, S. Brunetti, V. Ciriani, E. Lodi, N. Pisanti, :
Locally free substitutions are not so free: an open problem
in sequence alignment,
proceedings of 3rd Fun with Algorithms conference (FUN), Edizioni Plus,
pages 5-6, 2004.
N. Pisanti, M. Crochemore, R. Grossi, M.-F. Sagot:
A Basis of Tiling Motifs for Generating Repeated Patterns and its
Complexity for Higher Quorum,
proceedings of the 28th Mathematical Foundations of Computer Science (MFCS), Springer LNCS 2747, pages 622-632, 2003.
R. Marangoni, C. Pisanelli, N. Pisanti, P. Ferragina, A. Frangioni,
F. Luccio:
Genomic information and biological evolution: some
results on genes families,
16th Conference of the Italian Society of Pure and Applied Biophysics (SIBPA), 2002.
Outreach
A. Magi, N. Pisanti, L. Tattini:
The Source of the Data Flood: Sequencing Technologies,
In ERCIM News 104, pages 25-26, January 2016.
N. Pisanti:
From Discrete to Continuous: Turing's Morphogenesis,
In ERCIM News 91, pages 15-16, October 2012.
N. Pisanti and G. Longo:
(in italian) Le equazioni della natura,
In Sapere 4, pages 28-32, July 2012.
This article is part of a dossier (edited by F.Gadducci and N.Pisanti) on Alan Turing in occasion of the centenary of his birth.
N. Pisanti:
Bioinformatica,
in Lo Stato Vivente della Materia,
M. Buiatti,
pages 195--216, UTET, 2000.
Technical Reports and Posters
P.Bonizzoni, R.Dondi, G.W.Klau, Y.Pirola, N.Pisanti, S.Zaccaria:
HAPCOL: Accurate and Memory-efficient Haplotype Assembly from Long Reads
Poster at the High Throughput Sequencing SIG of ISMB/ECCB (HitSeq), 2015.
[BECAME THE PAPER IN BIOINFORMATICS]
M.F. Zini, S. Bonaretti, N. Pisanti, E. Biasci, A. Podda, V.Mey, F. Piras, GL. Labbate, S. Marini, D. Fratta, S. Trasciatti:
Preclinical data for cerebral stroke: A Knowledge Base for collecting, processing and analysing biological data derived from animal models of cerebral stroke.
Poster al meeting Regionale della Bioinformatics Italian Society Conference (BIOINFORMATIHA), 2013.
[BECAME THE PAPER AT Hi-Bi-Bi 2015]
G.Menconi, G.Battaglia, R.Grossi, R.Marangoni, N.Pisanti:
Towards Mobilome Inference in Yeast Genomes
Poster al meeting della Bioinformatics Italian Society Conference (BITS), 2010.
[BECAME THE PAPER IN BMC BIOINFORMATICS]
R. Grossi, A. Pietracaprina, N.Pisanti, G. Pucci, E. Upfal, F. Vandin:
MADMX: A Novel Strategy for Maximal Dense Motif Extraction
CoRR abs/1002.0874, 2010.
[BECAME THE PAPER IN JOURNAL OF COMPUTATIONAL BIOLOGY]
G. Battaglia, D. Cangelosi, R. Grossi, N. Pisanti:
Masking Patterns in Sequences: a New Class of Motif Discovery with Don't Cares.
TR-08-18, Department of Computer Science, University of Pisa, 2008.
[BECAME THE PAPER IN THEORETICAL COMPUTER SCIENCE]
N. Pisanti, H. Soldano, M. Carpentier, J. Pothier:
Inference of Approximated Motifs with Conserved Relations
TR-06-17, Department of Computer Science, University of Pisa, 2006.
[BECAME THE PAPER IN JOURNAL OF COMPUTATIONAL BIOLOGY]
P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot:
Lossless Filter for Long Multiple Repetitions with Edit Distance
TR-06-11, Department of Computer Science, University of Pisa, 2006.
[BECAME THE PAPER IN ALGORITHMS FOR MOLECULAR BIOLOGY]
M. Carpentier, N. Pisanti, J. Pothier, H. Soldano:
Application of relational motifs to multiple structural alignment
Poster at the 7th Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), 2006.
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P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot:
Ed'Nimbus: a Lossless Filter for Long Multiple Repetitions with Edit Distance
Poster at the 7th Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), 2006.
PNG FILE
N. Pisanti, H. Soldano, M. Carpentier, J. Pothier:
Implicit and Explicit Representation of Approximated Motifs
Technical
Report TR-05-19, Department of Computer Science, University of Pisa, 2005.
[BECAME THE PAPER IN ALGORITHMS FOR BIOINFORMATICS KCL BOOK]
R. Marangoni, A. La Terza, N. Pisanti, S. Barchetta, C. Miceli:
Searching for structured motifs in the upstream regions of hsp70 genes
in Tetrahymena termophila
Poster at the 2nd Bioinformatics ITalian Society (BITS) meeting, 2005.
PPT FILE
A. La Terza, R. Marangoni, N. Pisanti, S. Barchetta, C. Miceli:
Bioinformatics tools to identify structured motifs in the upstream regions
of stress-response-involved genes in Tetrahymena thermophila
Poster at the 4th International Workshop on NETwork Tools and Applications in Biology (NETTAB) 2004. PPT FILE
N. Pisanti, M.Crochemore, R. Grossi, M.-F. Sagot:
Bases of Motifs for Generating Repeated Patterns with Don't Cares
Technical Report TR-03-02, Department of Computer Science,
University of Pisa, 2003.
[BECAME THE PAPER IN IEEE/ACM TRANSACTION ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS]
R. Marangoni, N. Pisanti, P. Ferragina, A. Frangioni, F. Luccio:
Trying to recontruct the history of genes families,
Poster at the First European Conference on Computational Biology (ECCB), 2002.
PPT FILE
N. Pisanti, M.Crochemore, R. Grossi, M.-F. Sagot:
A basis for repeated motifs in pattern discovery and text mining,
Technical Report Institut Gaspard Monge IGM-02-10,
University of Marne-la-Valleée, France, 2002.
[BECAME THE PAPER OF MFCS 2003]
N. Pisanti, R. Marangoni, P. Ferragina, A. Frangioni,
F. Luccio, A. Savona:
PaTre: a method for Paralogy Trees Construction,
Technical Report TR-01-20, Department of Computer Science,
University of Pisa, 2001.
[BECAME THE PAPER IN JOURNAL OF COMPUTATIONAL BIOLOGY]
N. Pisanti, M.-F. Sagot:
Further thoughts on syntenic distances among genomes,
Technical Report Institut Gaspard Monge IGM-00-14,
University of Marne-la-Valleée, France, 2001.
[BECAME THE PAPER IN ALGORITHMICA]
R. Marangoni, A. Savona, P. Ferragina, N. Pisanti, L. Pagli, F. Luccio,
A method for paralogy trees construction,
Poster at the German Conference on Bioinformatics (GCB), 2000.
ABSTRACT
N. Pisanti and A. Viari:
On studying duplications in
genomes by using random graphs
Poster at the Third Annual ACM Conference
on Research in Computational Molecular Biology (RECOMB), 1999.
ABSTRACT
N.Pisanti, M.Crochemore, R.Grossi, M.-F.Sagot:
C.S.Iliopoulos, J.McHugh, P.Peterlongo, N.Pisanti, W.Rytter, M.Sagot:
N. Pisanti:
