Solon P. Pissis

Chang Liu

Proceedings of the LATIN 2018: Theoretical Informatics, 2018

Longest Unbordered Factor in Quasilinear Time.

[BibT_eX]

[DOI]

Proceedings of the 29th International Symposium on Algorithms and Computation, 2018

Linear-Time Algorithm for Long LCF with k Mismatches.

[BibT_eX]

[DOI]

Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

2017

A faster and more accurate heuristic for cyclic edit distance computation.

[BibT_eX]

[DOI]

Lorraine A. K. Ayad

Pattern Recognit. Lett., 2017

Fast circular dictionary-matching algorithm.

[BibT_eX]

[DOI]

Math. Struct. Comput. Sci., 2017

emMAW: computing minimal absent words in external memory.

[BibT_eX]

[DOI]

Alice Héliou

Simon J. Puglisi

Bioinform., 2017

On avoided words, absent words, and their application to biological sequence analysis.

[BibT_eX]

[DOI]

Yannis Almirantis

Dimitris Polychronopoulos

Algorithms Mol. Biol., 2017

Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time.

[BibT_eX]

[DOI]

Maxime Crochemore

Alexandre P. Francisco

Cátia Vaz

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Optimal Computation of Overabundant Words.

[BibT_eX]

[DOI]

Yannis Almirantis

Dimitris Polychronopoulos

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Pattern Matching on Elastic-Degenerate Text with Errors.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2017

Longest Common Factor After One Edit Operation.

[BibT_eX]

[DOI]

Amihood Amir

Jakub Radoszewski

Proceedings of the String Processing and Information Retrieval, 2017

Efficient Pattern Matching in Elastic-Degenerate Texts.

[BibT_eX]

[DOI]

Ritu Kundu

Proceedings of the Language and Automata Theory and Applications, 2017

How to Answer a Small Batch of RMQs or LCA Queries in Practice.

[BibT_eX]

[DOI]

Mai Alzamel

Proceedings of the Combinatorial Algorithms - 28th International Workshop, 2017

Minimal Absent Words in a Sliding Window and Applications to On-Line Pattern Matching.

[BibT_eX]

[DOI]

Proceedings of the Fundamentals of Computation Theory - 21st International Symposium, 2017

Efficient Computation of Palindromes in Sequences with Uncertainties.

[BibT_eX]

[DOI]

Proceedings of the Engineering Applications of Neural Networks, 2017

On-Line Pattern Matching on Similar Texts.

[BibT_eX]

[DOI]

Proceedings of the 28th Annual Symposium on Combinatorial Pattern Matching, 2017

Searching and Indexing Circular Patterns.

[BibT_eX]

[DOI]

M. Sohel Rahman

Proceedings of the Algorithms for Next-Generation Sequencing Data, Techniques, 2017

2016

Order-preserving indexing.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2016

Linear-time superbubble identification algorithm for genome assembly.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2016

Linear-time computation of prefix table for weighted strings & applications.

[BibT_eX]

[DOI]

Chang Liu

Theor. Comput. Sci., 2016

Parameterizing PWM- and Profile-Matching and Knapsack by the feasible-weight solutions count.

[BibT_eX]

[DOI]

Tomasz Kociumaka

Jakub Radoszewski

CoRR, 2016

libFLASM: a software library for fixed-length approximate string matching.

[BibT_eX]

[DOI]

Lorraine A. K. Ayad

Ahmad Retha

BMC Bioinform., 2016

Erratum to: Circular sequence comparison: algorithms and applications.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2016

Circular sequence comparison: algorithms and applications.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2016

Optimal Computation of Avoided Words.

[BibT_eX]

[DOI]

Yannis Almirantis

Dimitris Polychronopoulos

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Near-Optimal Computation of Runs over General Alphabet via Non-Crossing LCE Queries.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2016

Linear-Time Sequence Comparison Using Minimal Absent Words & Applications.

[BibT_eX]

[DOI]

Proceedings of the LATIN 2016: Theoretical Informatics, 2016

Efficient Index for Weighted Sequences.

[BibT_eX]

[DOI]

Proceedings of the 27th Annual Symposium on Combinatorial Pattern Matching, 2016

On-Line Pattern Matching on Uncertain Sequences and Applications.

[BibT_eX]

[DOI]

Chang Liu

Proceedings of the Combinatorial Optimization and Applications, 2016

2015

Global and local sequence alignment with a bounded number of gaps.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2015

Editorial.

[BibT_eX]

[DOI]

Hideo Bannai

J. Discrete Algorithms, 2015

Linear-Time Superbubble Identification Algorithm.

[BibT_eX]

[DOI]

CoRR, 2015

Fast Algorithm for Partial Covers in Words.

[BibT_eX]

[DOI]

Algorithmica, 2015

Accurate and Efficient Methods to Improve Multiple Circular Sequence Alignment.

[BibT_eX]

[DOI]

Proceedings of the Experimental Algorithms - 14th International Symposium, 2015

Circular Sequence Comparison with q-grams.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

Parallelising the Computation of Minimal Absent Words.

[BibT_eX]

[DOI]

Proceedings of the Parallel Processing and Applied Mathematics, 2015

Average-Case Optimal Approximate Circular String Matching.

[BibT_eX]

[DOI]

Proceedings of the Language and Automata Theory and Applications, 2015

Generalised Implementation for Fixed-Length Approximate String Matching under Hamming Distance and Applications.

[BibT_eX]

[DOI]

Ahmad Retha

Proceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, 2015

Linear-Time Computation of Prefix Table for Weighted Strings.

[BibT_eX]

[DOI]

Proceedings of the Combinatorics on Words - 10th International Conference, 2015

2014

Extending alignments with k-mismatches and ℓ-gaps.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2014

MoTeX-II: structured MoTif eXtraction from large-scale datasets.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

Linear-time computation of minimal absent words using suffix array.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

Optimal computation of all tandem repeats in a weighted sequence.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2014

Fast algorithms for approximate circular string matching.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2014

Fast and Simple Computations Using Prefix Tables Under Hamming and Edit Distance.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Algorithms - 25th International Workshop, 2014

Optimal Computation of all Repetitions in a Weighted String.

[BibT_eX]

[DOI]

Proceedings of the 2nd International Conference on Algorithms for Big Data , 2014

Detection of Web Spambot in the Presence of Decoy Actions.

[BibT_eX]

[DOI]

Vida Ghanaei

Proceedings of the 2014 IEEE Fourth International Conference on Big Data and Cloud Computing, 2014

2013

Enhanced string covering.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2013

Efficient seed computation revisited.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2013

Tree template matching in unranked ordered trees.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2013

Querying highly similar sequences.

[BibT_eX]

[DOI]

Int. J. Comput. Biol. Drug Des., 2013

Order-Preserving Suffix Trees and Their Algorithmic Applications

[BibT_eX]

[DOI]

CoRR, 2013

libgapmis: extending short-read alignments.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

Order-Preserving Incomplete Suffix Trees and Order-Preserving Indexes.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2013

Accelerating String Matching on MIC Architecture for Motif Extraction.

[BibT_eX]

[DOI]

Christian Goll

Pavlos Pavlidis

Proceedings of the Parallel Processing and Applied Mathematics, 2013

An Optimal Algorithm for Computing All Subtree Repeats in Trees.

[BibT_eX]

[DOI]

Tomás Flouri

Kassian Kobert

Fernando Izquierdo-Carrasco

Proceedings of the Combinatorial Algorithms - 24th International Workshop, 2013

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library.

[BibT_eX]

[DOI]

Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

MoTeX: A word-based HPC tool for MoTif eXtraction.

[BibT_eX]

[DOI]

Pavlos Pavlidis

Proceedings of the ACM Conference on Bioinformatics, 2013

GapsMis: flexible sequence alignment with a bounded number of gaps.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

An algorithm for mapping short reads to a dynamically changing genomic sequence.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2012

Tree template matching in ranked ordered trees by pushdown automata.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2012

On left and right seeds of a string.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2012

Computing all subtree repeats in ordered trees.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2012

Parallel Algorithms for Mapping Short degenerate and Weighted DNA Sequences to a Reference genome.

[BibT_eX]

[DOI]

Mirka Miller

Int. J. Found. Comput. Sci., 2012

New and Efficient Approaches to the Quasiperiodic Characterisation of a String.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference 2012, 2012

GapMis-OMP: Pairwise Short-Read Alignment on Multi-core Architectures.

[BibT_eX]

[DOI]

Proceedings of the Artificial Intelligence Applications and Innovations, 2012

Detection of fixed length web spambot using REAL (read aligner).

[BibT_eX]

[DOI]

Proceedings of the CUBE International IT Conference & Exhibition, 2012

Libgapmis: An ultrafast library for short-read single-gap alignment.

[BibT_eX]

[DOI]

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011

Construction of Antimagic Labeling for the Cartesian Product of Regular Graphs.

[BibT_eX]

[DOI]

Math. Comput. Sci., 2011

Computing All Subtree Repeats in Ordered Ranked Trees.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2011

Tree Indexing by Pushdown Automata and Repeats of Subtrees.

[BibT_eX]

[DOI]

Proceedings of the Federated Conference on Computer Science and Information Systems, 2011

Efficient Seeds Computation Revisited.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching - 22nd Annual Symposium, 2011

On the Right-Seed Array of a String.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics - 17th Annual International Conference, 2011

Approximate string-matching with a single gap for sequence alignment.

[BibT_eX]

[DOI]

Proceedings of the ACM International Conference on Bioinformatics, 2011

DynMap: mapping short reads to multiple related genomes.

[BibT_eX]

[DOI]

Tomás Flouri

Proceedings of the ACM International Conference on Bioinformatics, 2011

2010

Cover Array String Reconstruction.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 21st Annual Symposium, 2010

A Parallel Algorithm for Fixed-Length Approximate String-Matching with <i>k</i>-mismatches.

[BibT_eX]

[DOI]

Maxime Crochemore

Proceedings of the Algorithms and Applications, 2010

An algorithm for mapping short reads to a dynamically changing genomic sequence.

[BibT_eX]

[DOI]

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

REAL: an efficient REad ALigner for next generation sequencing reads.

[BibT_eX]

[DOI]

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009

Algorithms for mapping short degenerate and weighted sequences to a reference genome.

[BibT_eX]

[DOI]

Int. J. Comput. Biol. Drug Des., 2009

Parallel Algorithms for Degenerate and Weighted Sequences Derived from High Throughput Sequencing Technologies.

[BibT_eX]

[DOI]

Mirka Miller

Proceedings of the Prague Stringology Conference 2009, Prague, Czech Republic, August 31, 2009

A Parallel Algorithm for the Fixed-length Approximate String Matching Problem for High Throughput Sequencing Technologies.

[BibT_eX]

[DOI]

Laurent Mouchard