A Guaranteed Compression Scheme for Repetitive DNA Sequences. - Eric Rivals; Jean-Paul Delahaye; Max Dauchet; Olivier Delgrange (Data Compression Conference, 1996)

Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences. - Eric Rivals; Olivier Delgrange; Jean-Paul Delahaye; Max Dauchet; Marie-Odile Delorme; Alain Hénaut; Emmanuelle Ollivier (Comput. Appl. Biosci., 1997)

The transformation distance: A dissimilarity measure based an movements of segments. - Jean-Stéphane Varré; Jean-Paul Delahaye; Eric Rivals (German Conference on Bioinformatics, 1998)

Optimal Representation in Average Using Kolmogorov Complexity. - Eric Rivals; Jean-Paul Delahaye (Theor. Comput. Sci., 1998)

Location of Repetitive Regions in Sequences By Optimizing A Compression Method. - Olivier Delgrange; Max Dauchet; Eric Rivals (Pacific Symposium on Biocomputing, 1999)

q-gram based database searching using a suffix array (QUASAR). - Stefan Burkhardt; Andreas Crauser; Paolo Ferragina; Hans-Peter Lenhof; Eric Rivals; Martin Vingron (RECOMB, 1999)

Transformation distances: a family of dissimilarity measures based on movements of segments. - Jean-Stéphane Varré; Jean-Paul Delahaye; Eric Rivals (Bioinform., 1999)

Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. - Sven Rahmann; Eric Rivals (CPM, 2000)

Complexities of the Centre and Median String Problems. - François Nicolas; Eric Rivals (CPM, 2003)

On The Distribution Of The Number Of Missing Words In Random Texts. - Sven Rahmann; Eric Rivals (Comb. Probab. Comput., 2003)

Comparison of Minisatellites. - Sèverine Bérard; Eric Rivals (J. Comput. Biol., 2003)

Combinatorics of periods in strings. - Eric Rivals; Sven Rahmann (J. Comb. Theory A, 2003)

STAR: an algorithm to Search for Tandem Approximate Repeats. - Olivier Delgrange; Eric Rivals (Bioinform., 2004)

A Survey On Algorithmic Aspects Of Tandem Repeats Evolution. - Eric Rivals (Int. J. Found. Comput. Sci., 2004)

Hardness results for the center and median string problems under the weighted and unweighted edit distances. - François Nicolas; Eric Rivals (J. Discrete Algorithms, 2005)

Tiling an Interval of the Discrete Line. - Olivier Bodini; Eric Rivals (CPM, 2006)

Detecting microsatellites within genomes: significant variation among algorithms. - Sébastien Leclercq; Eric Rivals; Philippe Jarne (BMC Bioinform., 2007)

Detection of recombination in variable number tandem repeat sequences. - Ezekiel F. Adebiyi; Eric Rivals (South Afr. Comput. J., 2007)

Longest common subsequence problem for unoriented and cyclic strings. - François Nicolas; Eric Rivals (Theor. Comput. Sci., 2007)

Hardness of optimal spaced seed design. - François Nicolas; Eric Rivals (J. Comput. Syst. Sci., 2008)

mpscan: Fast Localisation of Multiple Reads in Genomes. - Eric Rivals; Leena Salmela; Petteri Kiiskinen; Petri Kalsi; Jorma Tarhio (WABI, 2009)

Reliable Bacterial Genome Comparison Tools. - Eric Rivals; Alban Mancheron; Raluca Uricaru (ERCIM News, 2010)

Approximate Common Intervals in Multiple Genome Comparison. - Annie Chateau; Pierre Riou; Eric Rivals (BIBM, 2011)

Querying large read collections in main memory: a versatile data structure. - Nicolas Philippe; Mikaël Salson; Thierry Lecroq; Martine Léonard; Therese Commes; Eric Rivals (BMC Bioinform., 2011)

Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps. - Raluca Uricaru; Alban Mancheron; Eric Rivals (J. Comput. Biol., 2011)

A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections. - Eric Rivals; Nicolas Philippe; Mikaël Salson; Martine Léonard; Therese Commes; Thierry Lecroq (ERCIM News, 2012)

Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. - Niko Välimäki; Eric Rivals (ISBRA, 2013)

From Indexing Data Structures to de Bruijn Graphs. - Bastien Cazaux; Thierry Lecroq; Eric Rivals (CPM, 2014)

Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings. - Bastien Cazaux; Eric Rivals (Stringology, 2014)

LoRDEC: accurate and efficient long read error correction. - Leena Salmela; Eric Rivals (Bioinform., 2014)

Reverse engineering of compact suffix trees and links: A novel algorithm. - Bastien Cazaux; Eric Rivals (J. Discrete Algorithms, 2014)

Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree. - Bastien Cazaux; Thierry Lecroq; Eric Rivals (LATA, 2015)

YOC, A new strategy for pairwise alignment of collinear genomes. - Raluca Uricaru; Célia Michotey; Hélène Chiapello; Eric Rivals (BMC Bioinform., 2015)

Superstring Graph: A New Approach for Genome Assembly. - Bastien Cazaux; Gustavo Sacomoto; Eric Rivals (AAIM, 2016)

Shortest DNA Cyclic Cover in Compressed Space. - Bastien Cazaux; Rodrigo Cánovas; Eric Rivals (DCC, 2016)

Read mapping on de Bruijn graphs. - Antoine Limasset; Bastien Cazaux; Eric Rivals; Pierre Peterlongo (BMC Bioinform., 2016)

The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings. - Bastien Cazaux; Eric Rivals (Discret. Appl. Math., 2016)

A linear time algorithm for Shortest Cyclic Cover of Strings. - Bastien Cazaux; Eric Rivals (J. Discrete Algorithms, 2016)

Full Compressed Affix Tree Representations. - Rodrigo Cánovas; Eric Rivals (DCC, 2017)

Rearrangement Scenarios Guided by Chromatin Structure. - Sylvain Pulicani; Pijus Simonaitis; Eric Rivals; Krister M. Swenson (RECOMB-CG, 2017)

Accurate self-correction of errors in long reads using de Bruijn graphs. - Leena Salmela; Riku Walve; Eric Rivals; Esko Ukkonen (Bioinform., 2017)

The Compressed Overlap Index. - Rodrigo Cánovas; Bastien Cazaux; Eric Rivals (CoRR, 2017)

Fast and Accurate Genome-Scale Identification of DNA-Binding Sites. - David Martin; Vincent Maillol; Eric Rivals (BIBM, 2018)

Superstrings with multiplicities. - Bastien Cazaux; Eric Rivals (CPM, 2018)

Practical lower and upper bounds for the Shortest Linear Superstring. - Bastien Cazaux; Samuel Juhel; Eric Rivals (SEA, 2018)

Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding. - Bastien Cazaux; Eric Rivals (CoRR, 2018)

Relationship between superstring and compression measures: New insights on the greedy conjecture. - Bastien Cazaux; Eric Rivals (Discret. Appl. Math., 2018)

Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding. - Bastien Cazaux; Eric Rivals (CPM, 2019)

AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees. - Bastien Cazaux; Guillaume Castel; Eric Rivals (Bioinform., 2019)

Linking indexing data structures to de Bruijn graphs: Construction and update. - Bastien Cazaux; Thierry Lecroq; Eric Rivals (J. Comput. Syst. Sci., 2019)

Efficient Construction of Hierarchical Overlap Graphs. - Sung Gwan Park; Bastien Cazaux; Kunsoo Park; Eric Rivals (SPIRE, 2020)

Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring. - Bastien Cazaux; Eric Rivals (CoRR, 2020)

Hierarchical Overlap Graph. - Bastien Cazaux; Eric Rivals (Inf. Process. Lett., 2020)

A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs. - Sangsoo Park; Sung Gwan Park; Bastien Cazaux; Kunsoo Park; Eric Rivals (CPM, 2021)

PEWO: a collection of workflows to benchmark phylogenetic placement. - Benjamin Linard; Nikolai Romashchenko; Fabio Pardi; Eric Rivals (Bioinform., 2021)

Rapid screening and detection of inter-type viral recombinants using phylo-k-mers. - Guillaume E. Scholz; Benjamin Linard; Nikolai Romashchenko; Eric Rivals; Fabio Pardi (Bioinform., 2021)

Periodicity of Degenerate Strings. - Estéban Gabory; Eric Rivals; Michelle Sweering; Hilde Verbeek 001; Pengfei Wang 014 (PSC, 2023)

Computing Phylo-$k$k-Mers. - Nikolai Romashchenko; Benjamin Linard; Eric Rivals; Fabio Pardi (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

dipwmsearch: a Python package for searching di-PWM motifs. - Marie Mille; Julie Ripoll; Bastien Cazaux; Eric Rivals (Bioinform., 2023)

Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model. - Carole Chevalier; Jérôme Dorignac; Yahaya Ibrahim; Armelle Choquet; Alexandre David; Julie Ripoll; Eric Rivals; Frédéric Geniet; Nils-Ole Walliser; John Palmeri; Andrea Parmeggiani; Jean-Charles Walter (PLoS Comput. Biol., 2023)

EPIK: precise and scalable evolutionary placement with informative k-mers. - Nikolai Romashchenko; Benjamin Linard; Fabio Pardi; Eric Rivals (Bioinform., 2023)

Counting overlapping pairs of strings. - Eric Rivals; Pengfei Wang 014 (CoRR, 2024)

Counting Overlapping Pairs of Words. - Eric Rivals; Pengfei Wang 014 (COCOON (2), 2025)

Incremental Computation of the Set of Period Sets. - Eric Rivals (SOFSEM (2), 2025)

Convergence of the Number of Period sets in Strings. - Eric Rivals; Michelle Sweering; Pengfei Wang 014 (Algorithmica, 2025)