DNA Computing: A Survey. - Nadia Pisanti (Bull. EATCS, 1998)

Segment-based distances and similarities in genomic sequences. - Nadia Pisanti (2001)

Further Thoughts on the Syntenic Distance between Genomes. - Nadia Pisanti; Marie-France Sagot (Algorithmica, 2002)

A Basis of Tiling Motifs for Generating Repeated Patterns and Its Complexity for Higher Quorum. - Nadia Pisanti; Maxime Crochemore; Roberto Grossi; Marie-France Sagot (MFCS, 2003)

PaTre: A Method for Paralogy Trees Construction. - Nadia Pisanti; Roberto Marangoni; Paolo Ferragina; Antonio Frangioni; A. Savona; C. Pisanelli; Fabrizio Luccio (J. Comput. Biol., 2003)

Room allocation: a polynomial subcase of the quadratic assignment problem. - Valentina Ciriani; Nadia Pisanti; Anna Bernasconi 001 (Discret. Appl. Math., 2004)

Incremental Inference of Relational Motifs with a Degenerate Alphabet. - Nadia Pisanti; Henry Soldano; Mathilde Carpentier (CPM, 2005)

Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array. - Pierre Peterlongo; Nadia Pisanti; Frédéric Boyer; Marie-France Sagot (SPIRE, 2005)

A first approach to finding common motifs with gaps. - Costas S. Iliopoulos; James A. M. McHugh; Pierre Peterlongo; Nadia Pisanti; Wojciech Rytter; Marie-France Sagot (Int. J. Found. Comput. Sci., 2005)

Bases of Motifs for Generating Repeated Patterns with Wild Cards. - Nadia Pisanti; Maxime Crochemore; Roberto Grossi; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

RISOTTO: Fast Extraction of Motifs with Mismatches. - Nadia Pisanti; Alexandra M. Carvalho; Laurent Marsan; Marie-France Sagot (LATIN, 2006)

Lossless filter for multiple repetitions with Hamming distance. - Pierre Peterlongo; Nadia Pisanti; Frédéric Boyer; Alair Pereira do Lago; Marie-France Sagot (J. Discrete Algorithms, 2008)

Mining Biological Sequences with Masks. - Giovanni Battaglia; Roberto Grossi; Roberto Marangoni; Nadia Pisanti (DEXA Workshops, 2009)

MADMX: A Novel Strategy for Maximal Dense Motif Extraction. - Roberto Grossi; Andrea Pietracaprina; Nadia Pisanti; Geppino Pucci; Eli Upfal; Fabio Vandin (WABI, 2009)

Lossless filter for multiple repeats with bounded edit distance. - Pierre Peterlongo; Gustavo Akio Tominaga Sacomoto; Alair Pereira do Lago; Nadia Pisanti; Marie-France Sagot (Algorithms Mol. Biol., 2009)

A Relational Extension of the Notion of Motifs: Application to the Common 3D Protein Substructures Searching Problem. - Nadia Pisanti; Henry Soldano; Mathilde Carpentier; Joël Pothier (J. Comput. Biol., 2009)

Masking patterns in sequences: A new class of motif discovery with don't cares. - Giovanni Battaglia; Davide Cangelosi; Roberto Grossi; Nadia Pisanti (Theor. Comput. Sci., 2009)

Suffix tree characterization of maximal motifs in biological sequences. - Maria Federico; Nadia Pisanti (Theor. Comput. Sci., 2009)

An optimized filter for finding multiple repeats in DNA sequences. - Maria Federico; Pierre Peterlongo; Nadia Pisanti (AICCSA, 2010)

Identifying SNPs without a Reference Genome by Comparing Raw Reads. - Pierre Peterlongo; Nicolas Schnel; Nadia Pisanti; Marie-France Sagot; Vincent Lacroix (SPIRE, 2010)

Inferring Mobile Elements in S. Cerevisiae Strains. - Giulia Menconi; Giovanni Battaglia; Roberto Grossi; Nadia Pisanti; Roberto Marangoni (BIOINFORMATICS, 2011)

Removing Artifacts of Approximated Motifs. - Maria Federico; Nadia Pisanti (ITBAM, 2011)

Finding Long and Multiple Repeats with Edit Distance. - Maria Federico; Pierre Peterlongo; Nadia Pisanti; Marie-France Sagot (Stringology, 2011)

MADMX: A Strategy for Maximal Dense Motif Extraction. - Roberto Grossi; Andrea Pietracaprina; Nadia Pisanti; Geppino Pucci; Eli Upfal; Fabio Vandin (J. Comput. Biol., 2011)

A Taste of Yeast Mobilomics. - Giulia Menconi; Giovanni Battaglia; Roberto Grossi; Nadia Pisanti; Roberto Marangoni (BIOINFORMATICS, 2012)

Efficient Bubble Enumeration in Directed Graphs. - Etienne Birmelé; Pierluigi Crescenzi; Rui A. Ferreira; Roberto Grossi; Vincent Lacroix; Andrea Marino 001; Nadia Pisanti; Gustavo Akio Tominaga Sacomoto; Marie-France Sagot (SPIRE, 2012)

Optimal Listing of Cycles and st-Paths in Undirected Graphs - Etienne Birmelé; Rui A. Ferreira; Roberto Grossi; Andrea Marino 001; Nadia Pisanti; Romeo Rizzi; Gustavo Akio Tominaga Sacomoto; Marie-France Sagot (CoRR, 2012)

From Discrete to Continuous: Turing's Morphogenesis. - Nadia Pisanti (ERCIM News, 2012)

Optimal Listing of Cycles and st-Paths in Undirected Graphs. - Etienne Birmelé; Rui A. Ferreira; Roberto Grossi; Andrea Marino 001; Nadia Pisanti; Romeo Rizzi; Gustavo Sacomoto (SODA, 2013)

Mobilomics in Saccharomyces cerevisiae strains. - Giulia Menconi; Giovanni Battaglia; Roberto Grossi; Nadia Pisanti; Roberto Marangoni (BMC Bioinform., 2013)

High-Performance Haplotype Assembly. - Marco Aldinucci; Andrea Bracciali; Tobias Marschall; Murray Patterson; Nadia Pisanti; Massimo Torquati (CIBB, 2014)

Output-Sensitive Pattern Extraction in Sequences. - Roberto Grossi; Giulia Menconi; Nadia Pisanti; Roberto Trani; Søren Vind (FSTTCS, 2014)

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. - Murray Patterson; Tobias Marschall; Nadia Pisanti; Leo van Iersel; Leen Stougie; Gunnar W. Klau; Alexander Schönhuth (RECOMB, 2014)

Rime: Repeat identification. - Maria Federico; Pierre Peterlongo; Nadia Pisanti; Marie-France Sagot (Discret. Appl. Math., 2014)

Preclinical Tests for Cerebral Stroke. - Maria Francesca Zini; Nadia Pisanti; E. Biasci; A. Podda; V. Mey; F. Piras; G. L. L'Abbate; Simone Marini; D. Fratta; S. Bonaretti; S. Trasciatti (ASONAM, 2015)

On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem. - Paola Bonizzoni; Riccardo Dondi; Gunnar W. Klau; Yuri Pirola; Nadia Pisanti; Simone Zaccaria (CPM, 2015)

Circular Sequence Comparison with q-grams. - Roberto Grossi; Costas S. Iliopoulos; Robert Mercas; Nadia Pisanti; Solon P. Pissis; Ahmad Retha; Fatima Vayani (WABI, 2015)

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. - Murray Patterson; Tobias Marschall; Nadia Pisanti; Leo van Iersel; Leen Stougie; Gunnar W. Klau; Alexander Schönhuth (J. Comput. Biol., 2015)

Circular sequence comparison: algorithms and applications. - Roberto Grossi; Costas S. Iliopoulos; Robert Mercas; Nadia Pisanti; Solon P. Pissis; Ahmad Retha; Fatima Vayani (Algorithms Mol. Biol., 2016)

Erratum to: Circular sequence comparison: algorithms and applications. - Roberto Grossi; Costas S. Iliopoulos; Robert Mercas; Nadia Pisanti; Solon P. Pissis; Ahmad Retha; Fatima Vayani (Algorithms Mol. Biol., 2016)

HapCol: accurate and memory-efficient haplotype assembly from long reads. - Yuri Pirola; Simone Zaccaria; Riccardo Dondi; Gunnar W. Klau; Nadia Pisanti; Paola Bonizzoni (Bioinform., 2016)

PWHATSHAP: efficient haplotyping for future generation sequencing. - Andrea Bracciali; Marco Aldinucci; Murray Patterson; Tobias Marschall; Nadia Pisanti; Ivan Merelli; Massimo Torquati (BMC Bioinform., 2016)

The Source of the Data Flood: Sequencing Technologies. - Alberto Magi; Nadia Pisanti; Lorenzo Tattini (ERCIM News, 2016)

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. - Paola Bonizzoni; Riccardo Dondi; Gunnar W. Klau; Yuri Pirola; Nadia Pisanti; Simone Zaccaria (J. Comput. Biol., 2016)

On-Line Pattern Matching on Similar Texts. - Roberto Grossi; Costas S. Iliopoulos; Chang Liu 035; Nadia Pisanti; Solon P. Pissis; Ahmad Retha; Giovanna Rosone; Fatima Vayani; Luca Versari (CPM, 2017)

Pattern Matching on Elastic-Degenerate Text with Errors. - Giulia Bernardini 001; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (SPIRE, 2017)

Preface. - Robert Mercas; Nadia Pisanti (J. Discrete Algorithms, 2017)

Longest Property-Preserved Common Factor. - Lorraine A. K. Ayad; Giulia Bernardini 001; Roberto Grossi; Costas S. Iliopoulos; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (SPIRE, 2018)

Degenerate String Comparison and Applications. - Mai Alzamel; Lorraine A. K. Ayad; Giulia Bernardini 001; Roberto Grossi; Costas S. Iliopoulos; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (WABI, 2018)

Detecting Mutations by eBWT. - Nicola Prezza; Nadia Pisanti; Marinella Sciortino; Giovanna Rosone (WABI, 2018)

Motif trie: An efficient text index for pattern discovery with don't cares. - Roberto Grossi; Giulia Menconi; Nadia Pisanti; Roberto Trani; Søren Vind (Theor. Comput. Sci., 2018)

Technology and Species Independent Simulation of Sequencing Data and Genomic Variants. - Filippo Geraci; Riccardo Massidda; Nadia Pisanti (BIBE, 2019)

Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication. - Giulia Bernardini 001; Pawel Gawrychowski; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (ICALP, 2019)

String Sanitization: A Combinatorial Approach. - Giulia Bernardini 001; Huiping Chen; Alessio Conte; Roberto Grossi; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (ECML/PKDD (1), 2019)

Online Algorithms on Antipowers and Antiperiods. - Mai Alzamel; Alessio Conte; Daniele Greco; Veronica Guerrini; Costas S. Iliopoulos; Nadia Pisanti; Nicola Prezza; Giulia Punzi; Giovanna Rosone (SPIRE, 2019)

SNPs detection by eBWT positional clustering. - Nicola Prezza; Nadia Pisanti; Marinella Sciortino; Giovanna Rosone (Algorithms Mol. Biol., 2019)

Algorithms Foundations. - Nadia Pisanti (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

String Sanitization Under Edit Distance. - Giulia Bernardini 001; Huiping Chen; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Leen Stougie; Michelle Sweering (CPM, 2020)

Hide and Mine in Strings: Hardness and Algorithms. - Giulia Bernardini 001; Alessio Conte; Garance Gourdel; Roberto Grossi; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Giulia Punzi; Leen Stougie; Michelle Sweering (ICDM, 2020)

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform. - Nicola Prezza; Nadia Pisanti; Marinella Sciortino; Giovanna Rosone (BMC Bioinform., 2020)

Comparing Degenerate Strings. - Mai Alzamel; Lorraine A. K. Ayad; Giulia Bernardini 001; Roberto Grossi; Costas S. Iliopoulos; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (Fundam. Informaticae, 2020)

Editorial: Special Issue on International Workshop on Combinatorial Algorithms (IWOCA 2019). - Nadia Pisanti; Charles J. Colbourn; Roberto Grossi (Theory Comput. Syst., 2020)

Longest property-preserved common factor: A new string-processing framework. - Lorraine A. K. Ayad; Giulia Bernardini 001; Roberto Grossi; Costas S. Iliopoulos; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (Theor. Comput. Sci., 2020)

Approximate pattern matching on elastic-degenerate text. - Giulia Bernardini 001; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (Theor. Comput. Sci., 2020)

On-Line Pattern Matching on D-Texts (Invited Talk). - Nadia Pisanti (CPM, 2021)

Beyond the BEST Theorem: Fast Assessment of Eulerian Trails. - Alessio Conte; Roberto Grossi; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Giulia Punzi (FCT, 2021)

Pattern Masking for Dictionary Matching. - Panagiotis Charalampopoulos; Huiping Chen; Peter Christen; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Jakub Radoszewski (ISAAC, 2021)

Combinatorial Algorithms for String Sanitization. - Giulia Bernardini 001; Huiping Chen; Alessio Conte; Roberto Grossi; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone; Michelle Sweering (ACM Trans. Knowl. Discov. Data, 2021)

Optimal Sequence Alignment to ED-Strings. - Njagi Moses Mwaniki; Nadia Pisanti (ISBRA, 2022)

Report on CPM 2022. - Nadia Pisanti (Bull. EATCS, 2022)

Elastic-Degenerate String Matching via Fast Matrix Multiplication. - Giulia Bernardini 001; Pawel Gawrychowski; Nadia Pisanti; Solon P. Pissis; Giovanna Rosone (SIAM J. Comput., 2022)

Fast Exact String to D-Texts Alignments. - Njagi Moses Mwaniki; Erik Garrison; Nadia Pisanti (BIOINFORMATICS, 2023)

Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications. - Estéban Gabory; Njagi Moses Mwaniki; Nadia Pisanti; Solon P. Pissis; Jakub Radoszewski; Michelle Sweering; Wiktor Zuba (CPM, 2023)

Hide and Mine in Strings: Hardness, Algorithms, and Experiments. - Giulia Bernardini 001; Alessio Conte; Garance Gourdel; Roberto Grossi; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Giulia Punzi; Leen Stougie; Michelle Sweering (IEEE Trans. Knowl. Data Eng., 2023)

Utility-Oriented String Mining. - Giulia Bernardini 001; Huiping Chen; Alessio Conte; Roberto Grossi; Veronica Guerrini; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis (SDM, 2024)

A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs. - Rocco Ascone; Giulia Bernardini 001; Alessio Conte; Massimo Equi; Estéban Gabory; Roberto Grossi; Nadia Pisanti (WABI, 2024)

Popping Bubbles in Pangenome Graphs. - Njagi Moses Mwaniki; Erik Garrison; Nadia Pisanti (CoRR, 2024)

Pangenome comparison via ED strings. - Estéban Gabory; Njagi Moses Mwaniki; Nadia Pisanti; Solon P. Pissis; Jakub Radoszewski; Michelle Sweering; Wiktor Zuba (Frontiers Bioinform., 2024)

RettDb: the Rett syndrome omics database to navigate the Rett syndrome genomic landscape. - Nico Cillari; Giuseppe Neri; Nadia Pisanti; Paolo Milazzo; Ugo Borello (Database J. Biol. Databases Curation, 2024)

Pattern Masking for Dictionary Matching: Theory and Practice. - Panagiotis Charalampopoulos; Huiping Chen; Peter Christen; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis; Jakub Radoszewski (Algorithmica, 2024)

On the Construction of Elastic Degenerate Strings. - Nicola Rizzo 001; Veli Mäkinen; Nadia Pisanti (From Strings to Graphs, and Back Again, 2025)

BWT for String Collections. - Davide Cenzato; Zsuzsanna Lipták; Nadia Pisanti; Giovanna Rosone; Marinella Sciortino (The Expanding World of Compressed Data, 2025)

Indexing Strings with Utilities. - Giulia Bernardini 001; Huiping Chen; Alessio Conte; Roberto Grossi; Veronica Guerrini; Grigorios Loukides; Nadia Pisanti; Solon P. Pissis (ICDE, 2025)

Elastic-degenerate string comparison. - Estéban Gabory; Njagi Moses Mwaniki; Nadia Pisanti; Solon P. Pissis; Jakub Radoszewski; Michelle Sweering; Wiktor Zuba (Inf. Comput., 2025)