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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.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 the EATCS 64, 188--216, 1998.



Edited Books


Christian 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, 2011.



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]



N. Pisanti:
Bioinformatica,
in Lo stato vivente della materia by M. Buiatti,
pages 195--216, UTET, 2000.


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.Menconi, G.Battaglia, R.Grossi, N.Pisanti, R.Marangoni:
A Taste of Yeast Mobilomics,
proceedings of International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS), SciTePress, 2012. In press.




M. Federico, P. Peterlongo, N. Pisanti, M.-F. Sagot:
Finding Long and Multiple repetitions with Edit Distance
Proceedings of the Prague Stringology Conference (PSC 2011), Prague, Czech Republic, in press.
Springer Lecture Notes in Computer Science, 2011.



M. Federico, N. Pisanti:
Removing artifacts of approximated motifs
Proceedings of Information Technology in Bio- and Medical Informatics (ITBAM 2011). In press.
Springer Lecture Notes in Computer Science 6865, 2011.




G.Battaglia, R.Grossi, N.Pisanti, R.Marangoni, G.Menconi:
Inferring Mobile Elements in S.Cerevisiae strains,
proceedings of 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 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. In press.





R.Grossi, A.Pietracaprina, N. Pisanti, G.Pucci, E.Upfal, F.Vandin:
MADMX: A Novel Strategy for Maximal Dense Motif Extraction,
Proceedings of 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 Latin American Theoretical INformatics (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 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 Combinatorial Pattern Matching (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 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 Fun with Algorithms 3 (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 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.



V. Ciriani, N. Pisanti, A. Bernasconi:
Efficient Optimal Greedy Algorithms for Room Allocation,
proceedings of Fun with Algorithms 2 (FUN), Carleton Scientific, pages 43-60, 2001.




N. Pisanti:
DNA computing: a new computational paradigm using molecules,
invited talk at the conference of the Italian Society of Logic and Phylosophy of Science (SILFS), 1999.
In Grounding Effective Processes in Empirical Laws: reflections on the notion of algorithm, pages 101-116, 2000. GZIPPED PS FILE




Technical Reports and Posters


  • 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.
    [AN EXTENDED VERSION IS SUBMITTED TO A JOURNAL]

  • 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

  • N. Pisanti:
    A Survey on DNA computing
    Technical Report TR-97-07, Department of Computer Science, University of Pisa, 1997. ABSTRACT and PS FILE
    [PART OF IT BECAME THE PAPER IN BULLETIN OF EATCS]

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