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Publications of Nadia Pisanti

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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


R. Mercas, N. Pisanti:
Preface,
Journal of Discrete Algorithms, 42, 1-2, 2017.

T.Marschall et al. ("The Computational Pan-Genomics Consortium"):
Computational Pan-Genomics: Status, Promises and Challenges,
Briefings in Bioinformatics. In press, 2016.

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.

M.Federico, P.Peterlongo, N.Pisanti, M.-F.Sagot:
RIME: Repeat Identification,
Discrete Applied Mathematics, 163(3), 275-286, 2014.

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.

N.Pisanti, M.Crochemore, R.Grossi, M.-F.Sagot:
Bases of Motifs for Generating Repeated Patterns with Wild Cards,
IEEE/ACM Transaction on Computational Biology and Bioinformatics, 2(1), 40--50, 2005.

C.S.Iliopoulos, J.McHugh, P.Peterlongo, N.Pisanti, W.Rytter, M.Sagot:
A first approach to finding common motifs with gaps,
International Journal of Foundation of Computer Science, 16(6), 1145--1155, 2005.

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


R. Mercas, N. Pisanti:
Special Issue dedicated to LSD&LAW 2016,
Journal of Discrete Algorithms, 42, 2017.

C. Bohm, S. Khuri, L. Lhotska, N. Pisanti:
Proceedings of Information Technology in Bio- and Medical Informatics,
Springer Lecture Notes in Computer Science 6865, 2011.

S. Khuri, L. Lhotska, N. Pisanti:
Proceedings of Information Technology in Bio- and Medical Informatics,
Springer Lecture Notes in Computer Science 6266, 2010.


Chapters in Books and Papers in Volumes


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.-F. Sagot:
Inference of Network Expressions,
Chapter 5 in Applied combinatorics on words by M. Lothaire, J. Berstel and D. Perrin editors,
pages 241--267, Cambridge University Press, 2005. [For a presentation of the volume see here]

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

R.Grossi, C.S.Iliopoulos, C.Liu, N.Pisanti, S.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.



Divulgation


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:
(in italian) Intelligenza artificiale Pisa ne celebra il "padre",
In the national daily newspaper La Repubblica, 2012.

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. PDF FILE

  • 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

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