Alberto Apostolico

Encyclopedia of Algorithms, 2016

Sequence similarity measures based on bounded hamming distance.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2016

Algorithms for Jumbled Indexing, Jumbled Border and Jumbled Square on run-length encoded strings.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2016

ALFRED: A Practical Method for Alignment-Free Distance Computation.

[BibT_eX]

[DOI]

Sharma V. Thankachan

Sriram P. Chockalingam

Yongchao Liu

Srinivas Aluru

J. Comput. Biol., 2016

A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.

[BibT_eX]

[DOI]

Sharma V. Thankachan

Srinivas Aluru

J. Comput. Biol., 2016

40 years of suffix trees.

[BibT_eX]

[DOI]

Commun. ACM, 2016

2015

A PTAS for the Square Tiling Problem.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2015

Efficient Alignment Free Sequence Comparison with Bounded Mismatches.

[BibT_eX]

[DOI]

Srinivas Aluru

Sharma V. Thankachan

Proceedings of the Research in Computational Molecular Biology, 2015

2014

Modulated string searching.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2014

Detecting approximate periodic patterns.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2014

Range LCP.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 2014

Alignment Free Sequence Similarity with Bounded Hamming Distance.

[BibT_eX]

[DOI]

Concettina Guerra

Proceedings of the Data Compression Conference, 2014

2013

Ultrametric networks: a new tool for phylogenetic analysis.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

Forty Years of Text Indexing.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 24th Annual Symposium, 2013

2012

Parameterized searching with mismatches for run-length encoded strings.

[BibT_eX]

[DOI]

Péter L. Erdös

Alpár Jüttner

Theor. Comput. Sci., 2012

Efficient algorithms for the periodic subgraphs mining problem.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2012

Phylogeny Construction with Rigid Gapped Motifs.

[BibT_eX]

[DOI]

J. Comput. Biol., 2012

Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291).

[BibT_eX]

[DOI]

Andreas W. M. Dress

Dagstuhl Reports, 2012

2011

Speedup for a periodic subgraph miner.

[BibT_eX]

[DOI]

Manuel Barbares

Inf. Process. Lett., 2011

Efficient algorithms for the discovery of gapped factors.

[BibT_eX]

[DOI]

Esko Ukkonen

Algorithms Mol. Biol., 2011

Sequence Similarity by Gapped LZW.

[BibT_eX]

[DOI]

Proceedings of the 2011 Data Compression Conference (DCC 2011), 2011

Image Compression by 2D Motif Basis.

[BibT_eX]

[DOI]

Alessia Amelio

Simona E. Rombo

Proceedings of the 2011 Data Compression Conference (DCC 2011), 2011

2010

VARUN: Discovering Extensible Motifs under Saturation Constraints.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

The Subsequence Composition of Polypeptides.

[BibT_eX]

[DOI]

J. Comput. Biol., 2010

Optimal Extraction of Irredundant Motif Bases.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2010

Parameterized Searching with Mismatches for Run-Length Encoded Strings - (Extended Abstract).

[BibT_eX]

[DOI]

Péter L. Erdös

Alpár Jüttner

Proceedings of the String Processing and Information Retrieval, 2010

A PTAS for the Square Tiling Problem.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2010

10231 Abstracts Collection - Structure Discovery in Biology: Motifs, Networks & Phylogenies.

[BibT_eX]

[DOI]

Andreas W. M. Dress

Proceedings of the Structure Discovery in Biology: Motifs, Networks & Phylogenies, 06.06., 2010

Maximal Words in Sequence Comparisons Based on Subword Composition.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Applications, 2010

2009

The subsequence composition of a string.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2009

Discovering subword associations in strings in time linear in the output size.

[BibT_eX]

[DOI]

Giorgio Satta

J. Discrete Algorithms, 2009

Alignment of biological sequences with quality scores.

[BibT_eX]

[DOI]

Int. J. Bioinform. Res. Appl., 2009

Ask Not What Stringology Can Do for You: Advances in Pattern Matching Driven by Computational Biology.

[BibT_eX]

[DOI]

Commun. Inf. Syst., 2009

Graph Compression by BFS.

[BibT_eX]

[DOI]

Guido Drovandi

Algorithms, 2009

Probing the Randomness of Proteins by Their Subsequence Composition.

[BibT_eX]

[DOI]

Proceedings of the 2009 Data Compression Conference (DCC 2009), 2009

2008

Incremental discovery of the irredundant motif bases for all suffixes of a string in O(n2logn) time.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2008

Motif patterns in 2D.

[BibT_eX]

[DOI]

Simona E. Rombo

Theor. Comput. Sci., 2008

Scoring Unusual Words with Varying Mismatch Errors.

[BibT_eX]

[DOI]

Math. Comput. Sci., 2008

Periodicity and repetitions in parameterized strings.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2008

Fast algorithms for computing sequence distances by exhaustive substring composition.

[BibT_eX]

[DOI]

Olgert Denas

Algorithms Mol. Biol., 2008

Sequence distances based on exhaustive substring composition.

[BibT_eX]

[DOI]

Olgert Denas

Proceedings of the 2008 IEEE Information Theory Workshop, 2008

Table Compression by Record Intersections.

[BibT_eX]

[DOI]

Vineith Kaul

Proceedings of the 2008 Data Compression Conference (DCC 2008), 2008

2007

Parameterized matching with mismatches.

[BibT_eX]

[DOI]

Péter L. Erdös

Moshe Lewenstein

J. Discrete Algorithms, 2007

2004 Symposium on String Processing and Information Retrieval.

[BibT_eX]

[DOI]

Ricardo A. Baeza-Yates

Massimo Melucci

J. Discrete Algorithms, 2007

Preface.

[BibT_eX]

[DOI]

J. Comput. Biol., 2007

Fast gapped variants for Lempel-Ziv-Welch compression.

[BibT_eX]

[DOI]

Inf. Comput., 2007

Motif discovery by monotone scores.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2007

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

[BibT_eX]

[DOI]

BMC Bioinform., 2007

Incremental Discovery of Irredundant Motif Bases in Time O(|Sigma| n2 log n).

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Optimal Offline Extraction of Irredundant Motif Bases.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics, 13th Annual International Conference, 2007

2006

Advances in information retrieval: An introduction to the special issue.

[BibT_eX]

[DOI]

Ricardo A. Baeza-Yates

Massimo Melucci

Inf. Syst., 2006

Mining, compressing and classifying with extensible motifs.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2006

Compressing with Collapsible Tries.

[BibT_eX]

[DOI]

Yongwook Choi

Proceedings of the 2006 IEEE Information Theory Workshop, 2006

Textual Compression by Collapsible Tries.

[BibT_eX]

[DOI]

Yongwook Choi

Proceedings of the 2006 Data Compression Conference (DCC 2006), 2006

On the Monotonicity of the String Correction Factor for Words with Mismatches.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial and Algorithmic Foundations of Pattern and Association Discovery, 14.05., 2006

06201 Abstracts Collection -- Combinatorial and Algorithmic Foundations of Pattern and Association Discovery.

[BibT_eX]

[DOI]

Rudolf Ahlswede

Vladimir I. Levenshtein

Proceedings of the Combinatorial and Algorithmic Foundations of Pattern and Association Discovery, 14.05., 2006

06201 Executive Summary -- Combinatorial and Algorithmic Foundations of Pattern and Association Discovery.

[BibT_eX]

[DOI]

Rudolf Ahlswede

Vladimir I. Levenshtein

Proceedings of the Combinatorial and Algorithmic Foundations of Pattern and Association Discovery, 14.05., 2006

2005

Foreword: Pattern Discovery in the Post Genome.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2005

Bridging Lossy and Lossless Compression by Motif Pattern Discovery.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2005

Optimal discovery of repetitions in 2D.

[BibT_eX]

[DOI]

Valentin E. Brimkov

Discret. Appl. Math., 2005

Conservative extraction of over-represented extensible motifs.

[BibT_eX]

[DOI]

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Off-Line Compression by Extensible Motifs.

[BibT_eX]

[DOI]

Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

Of Lempel-Ziv-Welch Parses with Refillable Gaps.

[BibT_eX]

[DOI]

Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

Monotony and Surprise.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

2004

Verbumculus and the Discovery of Unusual Words.

[BibT_eX]

[DOI]

Fang-Cheng Gong

J. Comput. Sci. Technol., 2004

Incremental Paradigms of Motif Discovery.

[BibT_eX]

[DOI]

J. Comput. Biol., 2004

Monotone Scoring of Patterns with Mismatches: (Extended Abstract).

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

Optimal Discovery of Subword Associations in Strings.

[BibT_eX]

[DOI]

Giorgio Satta

Proceedings of the Discovery Science, 7th International Conference, 2004

Motifs in Ziv-Lempel-Welch Clef.

[BibT_eX]

[DOI]

Proceedings of the 2004 Data Compression Conference (DCC 2004), 2004

2003

Truncated suffix trees and their application to data compression.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2003

Efficient text fingerprinting via Parikh mapping.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2003

Monotony of Surprise and Large-Scale Quest for Unusual Words.

[BibT_eX]

[DOI]

Mary Ellen Bock

J. Comput. Biol., 2003

Compression and the Wheel of Fortune.

[BibT_eX]

[DOI]

Proceedings of the 2003 Data Compression Conference (DCC 2003), 2003

2002

A speed-up for the commute between subword trees and DAWGs.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2002

Compact Recognizers of Episode Sequences.

[BibT_eX]

[DOI]

Inf. Comput., 2002

2001

Of Maps Bigger than the Empire (Invited Paper).

[BibT_eX]

[DOI]

Proceedings of the Eighth International Symposium on String Processing and Information Retrieval, 2001

2000

Fibonacci arrays and their two-dimensional repetitions.

[BibT_eX]

[DOI]

Valentin E. Brimkov

Theor. Comput. Sci., 2000

Off-line compression by greedy textual substitution.

[BibT_eX]

[DOI]

Proc. IEEE, 2000

Efficient Detection of Unusual Words.

[BibT_eX]

[DOI]

J. Comput. Biol., 2000

Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space.

[BibT_eX]

[DOI]

Gill Bejerano

J. Comput. Biol., 2000

Compression of Biological Sequences by Greedy Off-Line Textual Substitution.

[BibT_eX]

[DOI]

Proceedings of the Data Compression Conference, 2000

Notes on Learning Probabilistic Automata.

[BibT_eX]

[DOI]

Proceedings of the Data Compression Conference, 2000

1999

Matching for Run-Length Encoded Strings.

[BibT_eX]

[DOI]

Gad M. Landau

Steven Skiena

J. Complex., 1999

Linear Global Detectors of Redundant and Rare Substrings.

[BibT_eX]

[DOI]

Mary Ellen Bock

Proceedings of the Data Compression Conference, 1999

General Pattern Matching.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Theory of Computation Handbook., 1999

1998

Seqeunce Alignment in Molecular Biology.

[BibT_eX]

[DOI]

J. Comput. Biol., 1998

Sequence alignment in molecular biology.

[BibT_eX]

[DOI]

Proceedings of the Mathematical Support for Molecular Biology, 1998

Some Theory and Practice of Greedy Off-Line Textual Substitution.

[BibT_eX]

[DOI]

Proceedings of the Data Compression Conference, 1998

1997

String Editing and Longest Common Subsequences.

[BibT_eX]

[DOI]

Proceedings of the Handbook of Formal Languages, 1997

Inverse Pattern Matching.

[BibT_eX]

[DOI]

Amihood Amir

Moshe Lewenstein

J. Algorithms, 1997

Annotated statistical indices for sequence analysis.

[BibT_eX]

[DOI]

Mary Ellen Bock

Xuyan Xu

Proceedings of the Compression and Complexity of SEQUENCES 1997, 1997

Of Periods, Quasiperiods, Repetitions and Covers.

[BibT_eX]

[DOI]

Proceedings of the Structures in Logic and Computer Science, 1997

Parallel computations of Levenshtein distances.

[BibT_eX]

Proceedings of the Pattern Matching Algorithms, 1997

On-line string searching.

[BibT_eX]

Proceedings of the Pattern Matching Algorithms, 1997

1996

An Optimal O(log log N)-Time Parallel Algorithm for Detecting All Squares in a String.

[BibT_eX]

[DOI]

SIAM J. Comput., 1996

Data Structures and Algorithms for the String Statistics Problem.

[BibT_eX]

[DOI]

Franco P. Preparata

Algorithmica, 1996

1995

Parallel Detection of all Palindromes in a String.

[BibT_eX]

[DOI]

Zvi Galil

Theor. Comput. Sci., 1995

Fast Parallel Lyndon Factorization with Applications.

[BibT_eX]

[DOI]

Maxime Crochemore

Math. Syst. Theory, 1995

An International Masters in Software Engineering: Experience and Prospects.

[BibT_eX]

[DOI]

Proceedings of the Eleventh International Conference on Data Engineering, 1995

1994

The Set Union Problem With Unlimited Backtracking.

[BibT_eX]

[DOI]

SIAM J. Comput., 1994

Guest Editor's Foreword: Special Issue on String Algorithmics and Its Applications.

[BibT_eX]

[DOI]

Algorithmica, 1994

1993

Efficient Detection of Quasiperiodicities in Strings.

[BibT_eX]

[DOI]

Andrzej Ehrenfeucht

Theor. Comput. Sci., 1993

Efficient CRCW-PRAM Algorithms for Universal Substring Searching.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1993

New Clique and Independent Set Algorithms for Circle Graphs (Discrete Applied Mathematics 36 (1992) 1-24).

[BibT_eX]

[DOI]

Susanne E. Hambrusch

Discret. Appl. Math., 1993

1992

Fast Linear-Space Computations of Longest Common Subsequences.

[BibT_eX]

[DOI]

S. Browne

Concettina Guerra

Theor. Comput. Sci., 1992

Self-Alignments in Words and Their Applications.

[BibT_eX]

[DOI]

Wojciech Szpankowski

J. Algorithms, 1992

New clique and independent set algorithms for circle graphs.

[BibT_eX]

[DOI]

Susanne E. Hambrusch

Discret. Appl. Math., 1992

Optimal Parallel Detection of Squares in Strings.

[BibT_eX]

[DOI]

Algorithmica, 1992

Optimal Parallel Algorithms for Periods, Palindromes and Squares (Extended Abstract).

[BibT_eX]

[DOI]

Zvi Galil

Proceedings of the Automata, Languages and Programming, 19th International Colloquium, 1992

1991

Optimal Canonization of All Substrings of a String

[BibT_eX]

[DOI]

Maxime Crochemore

Inf. Comput., November, 1991

Optimal Superprimitivity Testing for Strings.

[BibT_eX]

[DOI]

Martin Farach

Costas S. Iliopoulos

Inf. Process. Lett., 1991

1990

Efficient Parallel Algorithms for String Editing and Related Problems.

[BibT_eX]

[DOI]

SIAM J. Comput., 1990

1988

Parallel Construction of a Suffix Tree with Applications.

[BibT_eX]

[DOI]

Algorithmica, 1988

1987

Robust transmission of unbounded strings using Fibonacci representations.

[BibT_eX]

[DOI]

Aviezri S. Fraenkel

IEEE Trans. Inf. Theory, 1987

Finding Maximum Cliques on Circular-Arc Graphs.

[BibT_eX]

[DOI]

Susanne E. Hambrusch

Inf. Process. Lett., 1987

Remark on the Hsu-Du New Algorithm for the Longest Common Subsequence Problem.

[BibT_eX]

[DOI]

Inf. Process. Lett., 1987

The Longest Common Subsequence Problem Revisited.

[BibT_eX]

[DOI]

Concettina Guerra

Algorithmica, 1987

On O(n log n) Cost Parallel Algorithm for the Single Function Coarsest Partition Problem.

[BibT_eX]

[DOI]

Costas S. Iliopoulos

Robert Paige

Proceedings of the Parallel Algorithms and Architectures, 1987

1986

The Boyer-Moore-Galil String Searching Strategies Revisited.

[BibT_eX]

[DOI]

SIAM J. Comput., 1986

Improving the Worst-Case Performance of the Hunt-Szymanski Strategy for the Longest Common Subsequence of Two Strings.

[BibT_eX]

[DOI]

Inf. Process. Lett., 1986

1985

Structural Properties of the String Statistics Problem.

[BibT_eX]

[DOI]

Franco P. Preparata

J. Comput. Syst. Sci., 1985

1984

Systolic Algorithms for String Manipulations.

[BibT_eX]

[DOI]

Alberto Negro

IEEE Trans. Computers, 1984

On Context Constrained Squares and Repetitions in a String.

[BibT_eX]

[DOI]

RAIRO Theor. Informatics Appl., 1984

Pattern Matching Machine Implementation of a Fast Test for Unique Decipherability.

[BibT_eX]

[DOI]

Inf. Process. Lett., 1984

1983

Optimal Off-Line Detection of Repetitions in a String.

[BibT_eX]

[DOI]

Franco P. Preparata

Theor. Comput. Sci., 1983

1978

An application of C-calculus to texture analysis: C-transforms.

[BibT_eX]

[DOI]

Eduardo R. Caianiello

Enrico Fischetti

Sergio Vitulano

Pattern Recognit., 1978

C-calculus: An elementary approach to some problems in pattern recognition .

[BibT_eX]

[DOI]

Eduardo R. Caianiello

Enrico Fischetti

Sergio Vitulano

Pattern Recognit., 1978

1977

An image transform emphasizing textual features.

[BibT_eX]

[DOI]