Raffaele Giancarlo

According to our database1, Raffaele Giancarlo authored at least 91 papers between 1984 and 2020.

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Bibliography

2020
The Alternating BWT: An algorithmic perspective.
Theor. Comput. Sci., 2020

2019
DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes.
Theor. Comput. Sci., 2019

Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics.
BMC Bioinformatics, 2019

A New Class of Searchable and Provably Highly Compressible String Transformations.
Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, 2019

2018
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms.
Bioinformatics, 2018

In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes.
Bioinformatics, 2018

Block Sorting-Based Transformations on Words: Beyond the Magic BWT.
Proceedings of the Developments in Language Theory - 22nd International Conference, 2018

2017
An effective extension of the applicability of alignment-free biological sequence comparison algorithms with Hadoop.
The Journal of Supercomputing, 2017

FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications.
Bioinformatics, 2017

2016
Indexed Two-Dimensional String Matching.
Encyclopedia of Algorithms, 2016

Table Compression.
Encyclopedia of Algorithms, 2016

The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes.
Bioinformatics, 2016

MapReduce in Computational Biology - A Synopsis.
Proceedings of the Advances in Artificial Life, Evolutionary Computation, and Systems Chemistry, 2016

2015
Bayesian versus data driven model selection for microarray data.
Natural Computing, 2015

ValWorkBench: An open source Java library for cluster validation, with applications to microarray data analysis.
Comput. Methods Programs Biomed., 2015

Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning.
Bioinformatics, 2015

Alignment-Free Sequence Comparison over Hadoop for Computational Biology.
Proceedings of the 44th International Conference on Parallel Processing Workshops, 2015

2014
Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies.
Briefings in Bioinformatics, 2014

GIMT: A Tool for Ontology and Goal Modeling in BDI Multi-Agent Design.
Proceedings of the XV Workshop "Dagli Oggetti agli Agenti", 2014

2013
Foreword.
Theor. Comput. Sci., 2013

A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis.
BMC Bioinformatics, 2013

Algorithmics for the Life Sciences.
Proceedings of the Power of Algorithms - Inspiration and Examples in Everyday Life, 2013

2012
Algorithmic paradigms for stability-based cluster validity and model selection statistical methods, with applications to microarray data analysis.
Theor. Comput. Sci., 2012

Textual data compression in computational biology: Algorithmic techniques.
Comput. Sci. Rev., 2012

The Chromatin Organization of an Eukaryotic Genome : Sequence Specific+ Statistical=Combinatorial (Extended Abstract)
CoRR, 2012

Stability-Based Model Selection for High Throughput Genomic Data: An Algorithmic Paradigm.
Proceedings of the Artificial Immune Systems - 11th International Conference, 2012

2011
Speeding up the Consensus Clustering methodology for microarray data analysis.
Algorithms for Molecular Biology, 2011

2010
Distance Functions, Clustering Algorithms and Microarray Data Analysis.
Proceedings of the Learning and Intelligent Optimization, 4th International Conference, 2010

Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures.
Proceedings of the Structure Discovery in Biology: Motifs, Networks & Phylogenies, 06.06., 2010

The Three Steps of Clustering in the Post-Genomic Era: A Synopsis.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2010

2009
The myriad virtues of Wavelet Trees.
Inf. Comput., 2009

Textual data compression in computational biology: a synopsis.
Bioinformatics, 2009

2008
Two-Dimensional Pattern Indexing.
Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Table Compression.
Proceedings of the Encyclopedia of Algorithms - 2008 Edition, 2008

Foreword: Special issue in honor of the 60th Birthday of Professor Alberto Apostolico: Work is for people who do not know how to: SAIL - String Algorithms, Information and Learning.
Theor. Comput. Sci., 2008

New results for finding common neighborhoods in massive graphs in the data stream model.
Theor. Comput. Sci., 2008

Guest Editors' Introduction to the Special Section on Algorithms in Bioinformatics.
IEEE/ACM Trans. Comput. Biology Bioinform., 2008

A Tutorial on Computational Cluster Analysis with Applications to Pattern Discovery in Microarray Data.
Mathematics in Computer Science, 2008

Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistics and Model Explorer.
BMC Bioinformatics, 2008

2007
From first principles to the Burrows and Wheeler transform and beyond, via combinatorial optimization.
Theor. Comput. Sci., 2007

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
BMC Bioinformatics, 2007

Articles selected from posters presented at the Tenth Annual International Conference on Research in Computational Biology - Preface.
BMC Bioinformatics, 2007

A basic analysis toolkit for biological sequences.
Algorithms for Molecular Biology, 2007

On-Line Construction of Two-Dimensional Suffix Trees in O(n2 log n) Time.
Algorithmica, 2007

2006
The Engineering of a Compression Boosting Library: Theory vs Practice in BWT Compression.
Proceedings of the Algorithms, 2006

2005
Foreword: Pattern Discovery in the Post Genome.
Theor. Comput. Sci., 2005

Boosting textual compression in optimal linear time.
J. ACM, 2005

Periodicity and Repetitions in Parameterized Strings.
Electron. Notes Discret. Math., 2005

GenClust: A genetic algorithm for clustering gene expression data.
BMC Bioinformatics, 2005

O(n2log n) Time On-Line Construction of Two-Dimensional Suffix Trees.
Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

2004
Editorial: Combinatiorial Pattern Matching.
J. Discrete Algorithms, 2004

Longest Motifs with a Functionally Equivalent Central Block.
Proceedings of the String Processing and Information Retrieval, 2004

2003
On finding common neighborhoods in massive graphs.
Theor. Comput. Sci., 2003

Improving table compression with combinatorial optimization.
J. ACM, 2003

Optimal Partitions of Strings: A New Class of Burrows-Wheeler Compression Algorithms.
Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003

2002
Sparse Dynamic Programming for Longest Common Subsequence from Fragments.
J. Algorithms, 2002

2001
An Approximate Determinization Algorithm for Weighted Finite-State Automata.
Algorithmica, 2001

2000
On the Determinization of Weighted Finite Automata.
SIAM J. Comput., 2000

Algorithmic Aspects of Speech Recognition: A Synopsis.
Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1999
On-line Construction of Two-Dimensional Suffix Trees.
J. Complex., 1999

Parallel Construction and Query of Index Data Structures for Pattern Matching on Square Matrices.
J. Complex., 1999

1998
Seqeunce Alignment in Molecular Biology.
Journal of Computational Biology, 1998

Shrinking language models by robust approximation.
Proceedings of the 1998 IEEE International Conference on Acoustics, 1998

Longest Common Subsequence from Fragments via Sparse Dynamic Programming.
Proceedings of the Algorithms, 1998

Sequence alignment in molecular biology.
Proceedings of the Mathematical Support for Molecular Biology, 1998

1997
Algorithmic Aspects in Speech Recognition: An Introduction.
ACM Journal of Experimental Algorithmics, 1997

Multi-Dimensional Pattern Matching with Dimensional Wildcards: Data Structures and Optimal On-Line Search Algorithms.
J. Algorithms, 1997

Suffix tree data structures for matrices.
Proceedings of the Pattern Matching Algorithms, 1997

Dynamic programming: special cases.
Proceedings of the Pattern Matching Algorithms, 1997

1996
On the Construction of Classes of Suffix Trees for Square Matrices: Algorithms and Applications.
Inf. Comput., 1996

1995
A Generalization of the Suffix Tree to Square Matrices, with Applications.
SIAM J. Comput., 1995

Multi-Dimensional Pattern Matching with Dimensional Wildcards.
Proceedings of the Combinatorial Pattern Matching, 6th Annual Symposium, 1995

1994
Dynamic Dictionary Matching.
J. Comput. Syst. Sci., 1994

Generalizations of the Periodicity Theorem of Fine and Wilf.
Proceedings of the Trees in Algebra and Programming, 1994

1993
An Index Data Structure For Matrices, with Applications to Fast Two-Dimensional Pattern Matching.
Proceedings of the Algorithms and Data Structures, Third Workshop, 1993

Parallel Construction and Query of Suffix Trees for Two-Dimensional Matrices.
Proceedings of the 5th Annual ACM Symposium on Parallel Algorithms and Architectures, 1993

The Suffix of a Square Matrix, with Applications.
Proceedings of the Fourth Annual ACM/SIGACT-SIAM Symposium on Discrete Algorithms, 1993

1992
On the Exact Complexity of String Matching: Upper Bounds.
SIAM J. Comput., 1992

Sparse Dynamic Programming II: Convex and Concave Cost Functions.
J. ACM, 1992

Sparse Dynamic Programming I: Linear Cost Functions.
J. ACM, 1992

1991
On the Exact Complexity of String Matching: Lower Bounds.
SIAM J. Comput., 1991

1990
Sparse Dynamic Programming.
Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms, 1990

On the Exact Complexity of String Matching (Extended Abstract)
Proceedings of the 31st Annual Symposium on Foundations of Computer Science, 1990

1989
Speeding up Dynamic Programming with Applications to Molecular Biology.
Theor. Comput. Sci., 1989

1988
Data structures and algorithms for approximate string matching.
J. Complex., 1988

Speeding up Dynamic Programming
Proceedings of the 29th Annual Symposium on Foundations of Computer Science, 1988

1987
Optimal Parallel Parsing of Bracket Languages.
Theor. Comput. Sci., 1987

Parallel String Matching with k Mismatches.
Theor. Comput. Sci., 1987

1986
Bounds on the redundancy of Huffman codes.
IEEE Trans. Information Theory, 1986

The Boyer-Moore-Galil String Searching Strategies Revisited.
SIAM J. Comput., 1986

1984
Pattern Matching Machine Implementation of a Fast Test for Unique Decipherability.
Inf. Process. Lett., 1984


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