Eric Rivals

Michelle Sweering

Pengfei Wang

Proceedings of the 50th International Colloquium on Automata, Languages, and Programming, 2023

2021

Rapid screening and detection of inter-type viral recombinants using phylo-k-mers.

[BibT_eX]

[DOI]

Bioinform., 2021

PEWO: a collection of workflows to benchmark phylogenetic placement.

[BibT_eX]

[DOI]

Bioinform., 2021

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs.

[BibT_eX]

[DOI]

Proceedings of the 32nd Annual Symposium on Combinatorial Pattern Matching, 2021

2020

Hierarchical Overlap Graph.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2020

Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring.

[BibT_eX]

[DOI]

CoRR, 2020

Efficient Construction of Hierarchical Overlap Graphs.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2020

2019

Linking indexing data structures to de Bruijn graphs: Construction and update.

[BibT_eX]

[DOI]

Thierry Lecroq

J. Comput. Syst. Sci., 2019

AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees.

[BibT_eX]

[DOI]

Guillaume Castel

Bioinform., 2019

Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding.

[BibT_eX]

[DOI]

Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, 2019

2018

Relationship between superstring and compression measures: New insights on the greedy conjecture.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2018

Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding.

[BibT_eX]

[DOI]

CoRR, 2018

Practical lower and upper bounds for the Shortest Linear Superstring.

[BibT_eX]

[DOI]

Samuel Juhel

Proceedings of the 17th International Symposium on Experimental Algorithms, 2018

Superstrings with multiplicities.

[BibT_eX]

[DOI]

Proceedings of the Annual Symposium on Combinatorial Pattern Matching, 2018

Fast and Accurate Genome-Scale Identification of DNA-Binding Sites.

[BibT_eX]

[DOI]

David Martin

Vincent Maillol

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2017

The Compressed Overlap Index.

[BibT_eX]

[DOI]

Rodrigo Cánovas

CoRR, 2017

Accurate self-correction of errors in long reads using de Bruijn graphs.

[BibT_eX]

[DOI]

Bioinform., 2017

Rearrangement Scenarios Guided by Chromatin Structure.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

Full Compressed Affix Tree Representations.

[BibT_eX]

[DOI]

Rodrigo Cánovas

Proceedings of the 2017 Data Compression Conference, 2017

2016

A linear time algorithm for Shortest Cyclic Cover of Strings.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2016

The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2016

Read mapping on de Bruijn graphs.

[BibT_eX]

[DOI]

BMC Bioinform., 2016

Shortest DNA Cyclic Cover in Compressed Space.

[BibT_eX]

[DOI]

Rodrigo Cánovas

Proceedings of the 2016 Data Compression Conference, 2016

Superstring Graph: A New Approach for Genome Assembly.

[BibT_eX]

[DOI]

Gustavo Sacomoto

Proceedings of the Algorithmic Aspects in Information and Management, 2016

2015

YOC, A new strategy for pairwise alignment of collinear genomes.

[BibT_eX]

[DOI]

BMC Bioinform., 2015

Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree.

[BibT_eX]

[DOI]

Thierry Lecroq

Proceedings of the Language and Automata Theory and Applications, 2015

2014

Reverse engineering of compact suffix trees and links: A novel algorithm.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2014

LoRDEC: accurate and efficient long read error correction.

[BibT_eX]

[DOI]

Leena Salmela

Bioinform., 2014

Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings.

[BibT_eX]

[DOI]

Proceedings of the Prague Stringology Conference 2014, Prague, Czech Republic, 2014

From Indexing Data Structures to de Bruijn Graphs.

[BibT_eX]

[DOI]

Thierry Lecroq

Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014

2013

Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data.

[BibT_eX]

[DOI]

Niko Välimäki

Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

2012

A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections.

[BibT_eX]

[DOI]

ERCIM News, 2012

2011

Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps.

[BibT_eX]

[DOI]

Raluca Uricaru

Alban Mancheron

J. Comput. Biol., 2011

Querying large read collections in main memory: a versatile data structure.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

Approximate Common Intervals in Multiple Genome Comparison.

[BibT_eX]

[DOI]

Annie Chateau

Pierre Riou

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2010

Reliable Bacterial Genome Comparison Tools.

[BibT_eX]

[DOI]

Alban Mancheron

Raluca Uricaru

ERCIM News, 2010

2009

mpscan: Fast Localisation of Multiple Reads in Genomes.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

2008

Hardness of optimal spaced seed design.

[BibT_eX]

[DOI]

J. Comput. Syst. Sci., 2008

2007

Longest common subsequence problem for unoriented and cyclic strings.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2007

Detection of recombination in variable number tandem repeat sequences.

[BibT_eX]

[DOI]

Ezekiel F. Adebiyi

South Afr. Comput. J., 2007

Detecting microsatellites within genomes: significant variation among algorithms.

[BibT_eX]

[DOI]

Sébastien Leclercq

Philippe Jarne

BMC Bioinform., 2007

2006

Tiling an Interval of the Discrete Line.

[BibT_eX]

[DOI]

Olivier Bodini

Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006

2005

Hardness results for the center and median string problems under the weighted and unweighted edit distances.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2005

2004

A Survey On Algorithmic Aspects Of Tandem Repeats Evolution.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2004

STAR: an algorithm to Search for Tandem Approximate Repeats.

[BibT_eX]

[DOI]

Olivier Delgrange

Bioinform., 2004

2003

Combinatorics of periods in strings.

[BibT_eX]

[DOI]

Sven Rahmann

J. Comb. Theory, Ser. A, 2003

Comparison of Minisatellites.

[BibT_eX]

[DOI]

Sèverine Bérard

J. Comput. Biol., 2003

On The Distribution Of The Number Of Missing Words In Random Texts.

[BibT_eX]

[DOI]

Sven Rahmann

Comb. Probab. Comput., 2003

Complexities of the Centre and Median String Problems.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003

2000

Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts.

[BibT_eX]

[DOI]

Sven Rahmann

Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1999

Transformation distances: a family of dissimilarity measures based on movements of segments.

[BibT_eX]

[DOI]

Jean-Stéphane Varré

Jean-Paul Delahaye

Bioinform., 1999

q-gram based database searching using a suffix array (QUASAR).

[BibT_eX]

[DOI]

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

Location of Repetitive Regions in Sequences By Optimizing A Compression Method.

[BibT_eX]

[DOI]

Olivier Delgrange

Max Dauchet

Proceedings of the 4th Pacific Symposium on Biocomputing, 1999

1998

Optimal Representation in Average Using Kolmogorov Complexity.

[BibT_eX]

[DOI]

Jean-Paul Delahaye

Theor. Comput. Sci., 1998

The transformation distance: A dissimilarity measure based an movements of segments.

[BibT_eX]

Jean-Stéphane Varré

Jean-Paul Delahaye