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ORCIDEric Rivals
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- affiliation: CNRS & Univ. Montpellier, France
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Journal Articles
- 2023
[j32]Marie Mille, Julie Ripoll
, Bastien Cazaux, Eric Rivals:
dipwmsearch: a Python package for searching di-PWM motifs. Bioinform. 39(4) (2023)- [j31]Nikolai Romashchenko, Benjamin Linard, Fabio Pardi, Eric Rivals:
EPIK: precise and scalable evolutionary placement with informative k-mers. Bioinform. 39(12) (2023) - [j30]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:
Physical modeling of ribosomes along messenger RNA: Estimating kinetic parameters from ribosome profiling experiments using a ballistic model. PLoS Comput. Biol. 19(10) (2023) - [j29]Nikolai Romashchenko, Benjamin Linard, Eric Rivals, Fabio Pardi:
Computing Phylo-$k$k-Mers. IEEE ACM Trans. Comput. Biol. Bioinform. 20(5): 2889-2897 (2023) - 2021
- [j28]Benjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric Rivals:
PEWO: a collection of workflows to benchmark phylogenetic placement. Bioinform. 36(21): 5264-5266 (2021) - [j27]Guillaume E. Scholz, Benjamin Linard, Nikolai Romashchenko, Eric Rivals, Fabio Pardi:
Rapid screening and detection of inter-type viral recombinants using phylo-k-mers. Bioinform. 36(22-23): 5351-5360 (2021) - 2020
- [j26]Bastien Cazaux, Eric Rivals:
Hierarchical Overlap Graph. Inf. Process. Lett. 155 (2020) - 2019
- [j25]Bastien Cazaux, Guillaume Castel, Eric Rivals:
AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees. Bioinform. 35(17): 3163-3165 (2019) - [j24]Bastien Cazaux, Thierry Lecroq, Eric Rivals:
Linking indexing data structures to de Bruijn graphs: Construction and update. J. Comput. Syst. Sci. 104: 165-183 (2019) - 2018
- [j23]Bastien Cazaux, Eric Rivals:
Relationship between superstring and compression measures: New insights on the greedy conjecture. Discret. Appl. Math. 245: 59-64 (2018) - 2017
- [j22]Leena Salmela, Riku Walve, Eric Rivals, Esko Ukkonen:
Accurate self-correction of errors in long reads using de Bruijn graphs. Bioinform. 33(6): 799-806 (2017) - 2016
- [j21]Antoine Limasset, Bastien Cazaux, Eric Rivals, Pierre Peterlongo:
Read mapping on de Bruijn graphs. BMC Bioinform. 17: 237 (2016) - [j20]Bastien Cazaux, Eric Rivals:
The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings. Discret. Appl. Math. 212: 48-60 (2016) - [j19]Bastien Cazaux, Eric Rivals:
A linear time algorithm for Shortest Cyclic Cover of Strings. J. Discrete Algorithms 37: 56-67 (2016) - 2015
- [j18]Raluca Uricaru, Célia Michotey, Hélène Chiapello, Eric Rivals:
YOC, A new strategy for pairwise alignment of collinear genomes. BMC Bioinform. 16: 111:1-111:16 (2015) - 2014
- [j17]Leena Salmela, Eric Rivals:
LoRDEC: accurate and efficient long read error correction. Bioinform. 30(24): 3506-3514 (2014) - [j16]Bastien Cazaux, Eric Rivals:
Reverse engineering of compact suffix trees and links: A novel algorithm. J. Discrete Algorithms 28: 9-22 (2014) - 2011
- [j15]Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Therese Commes, Eric Rivals:
Querying large read collections in main memory: a versatile data structure. BMC Bioinform. 12: 242 (2011) - [j14]Raluca Uricaru, Alban Mancheron, Eric Rivals:
Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps. J. Comput. Biol. 18(9): 1141-1154 (2011) - 2008
- [j13]François Nicolas, Eric Rivals:
Hardness of optimal spaced seed design. J. Comput. Syst. Sci. 74(5): 831-849 (2008) - 2007
- [j12]Sébastien Leclercq, Eric Rivals, Philippe Jarne:
Detecting microsatellites within genomes: significant variation among algorithms. BMC Bioinform. 8 (2007) - [j11]Ezekiel F. Adebiyi, Eric Rivals:
Detection of recombination in variable number tandem repeat sequences. South Afr. Comput. J. 39: 1-7 (2007) - [j10]François Nicolas, Eric Rivals:
Longest common subsequence problem for unoriented and cyclic strings. Theor. Comput. Sci. 370(1-3): 1-18 (2007) - 2005
- [j9]François Nicolas, Eric Rivals:
Hardness results for the center and median string problems under the weighted and unweighted edit distances. J. Discrete Algorithms 3(2-4): 390-415 (2005) - 2004
- [j8]Olivier Delgrange, Eric Rivals:
STAR: an algorithm to Search for Tandem Approximate Repeats. Bioinform. 20(16): 2812-2820 (2004) - [j7]Eric Rivals:
A Survey On Algorithmic Aspects Of Tandem Repeats Evolution. Int. J. Found. Comput. Sci. 15(2): 225-257 (2004) - 2003
- [j6]Sven Rahmann, Eric Rivals:
On The Distribution Of The Number Of Missing Words In Random Texts. Comb. Probab. Comput. 12(1): 73-87 (2003) - [j5]Sèverine Bérard, Eric Rivals:
Comparison of Minisatellites. J. Comput. Biol. 10(3/4): 357-372 (2003) - [j4]Eric Rivals, Sven Rahmann:
Combinatorics of periods in strings. J. Comb. Theory A 104(1): 95-113 (2003) - 1999
- [j3]Jean-Stéphane Varré, Jean-Paul Delahaye, Eric Rivals:
Transformation distances: a family of dissimilarity measures based on movements of segments. Bioinform. 15(3): 194-202 (1999) - 1998
- [j2]Eric Rivals, Jean-Paul Delahaye:
Optimal Representation in Average Using Kolmogorov Complexity. Theor. Comput. Sci. 200(1-2): 261-287 (1998) - 1997
- [j1]Eric Rivals, Olivier Delgrange, Jean-Paul Delahaye, Max Dauchet, Marie-Odile Delorme, Alain Hénaut, Emmanuelle Ollivier:
Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences. Comput. Appl. Biosci. 13(2): 131-136 (1997)
Conference and Workshop Papers
- 2023
- [c29]Eric Rivals, Michelle Sweering, Pengfei Wang:
Convergence of the Number of Period Sets in Strings. ICALP 2023: 100:1-100:14 - [c28]Estéban Gabory, Eric Rivals, Michelle Sweering, Hilde Verbeek, Pengfei Wang:
Periodicity of Degenerate Strings. PSC 2023: 42-56 - 2021
- [c27]Sangsoo Park, Sung Gwan Park, Bastien Cazaux, Kunsoo Park, Eric Rivals:
A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs. CPM 2021: 22:1-22:9 - 2020
- [c26]Sung Gwan Park, Bastien Cazaux, Kunsoo Park, Eric Rivals:
Efficient Construction of Hierarchical Overlap Graphs. SPIRE 2020: 277-290 - 2019
- [c25]Bastien Cazaux, Eric Rivals:
Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding. CPM 2019: 24:1-24:20 - 2018
- [c24]David Martin, Vincent Maillol, Eric Rivals:
Fast and Accurate Genome-Scale Identification of DNA-Binding Sites. BIBM 2018: 201-205 - [c23]Bastien Cazaux, Eric Rivals:
Superstrings with multiplicities. CPM 2018: 21:1-21:16 - [c22]Bastien Cazaux, Samuel Juhel, Eric Rivals:
Practical lower and upper bounds for the Shortest Linear Superstring. SEA 2018: 18:1-18:14 - 2017
- [c21]Rodrigo Cánovas, Eric Rivals:
Full Compressed Affix Tree Representations. DCC 2017: 102-111 - [c20]Sylvain Pulicani, Pijus Simonaitis, Eric Rivals, Krister M. Swenson:
Rearrangement Scenarios Guided by Chromatin Structure. RECOMB-CG 2017: 141-155 - 2016
- [c19]Bastien Cazaux, Gustavo Sacomoto, Eric Rivals:
Superstring Graph: A New Approach for Genome Assembly. AAIM 2016: 39-52 - [c18]Bastien Cazaux, Rodrigo Cánovas, Eric Rivals:
Shortest DNA Cyclic Cover in Compressed Space. DCC 2016: 536-545 - 2015
- [c17]Bastien Cazaux, Thierry Lecroq, Eric Rivals:
Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree. LATA 2015: 109-120 - 2014
- [c16]Bastien Cazaux, Thierry Lecroq, Eric Rivals:
From Indexing Data Structures to de Bruijn Graphs. CPM 2014: 89-99 - [c15]Bastien Cazaux, Eric Rivals:
Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings. Stringology 2014: 148-161 - 2013
- [c14]Niko Välimäki, Eric Rivals:
Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. ISBRA 2013: 237-248 - 2011
- [c13]Annie Chateau, Pierre Riou, Eric Rivals:
Approximate Common Intervals in Multiple Genome Comparison. BIBM 2011: 131-134 - 2010
- [c12]Raluca Uricaru, Alban Mancheron, Eric Rivals:
Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps. RECOMB-CG 2010: 161-172 - 2009
- [c11]Eric Rivals, Leena Salmela, Petteri Kiiskinen, Petri Kalsi, Jorma Tarhio:
mpscan: Fast Localisation of Multiple Reads in Genomes. WABI 2009: 246-260 - 2006
- [c10]Olivier Bodini, Eric Rivals:
Tiling an Interval of the Discrete Line. CPM 2006: 117-128 - 2005
- [c9]François Nicolas, Eric Rivals:
Hardness of Optimal Spaced Seed Design. CPM 2005: 144-155 - 2003
- [c8]François Nicolas, Eric Rivals:
Complexities of the Centre and Median String Problems. CPM 2003: 315-327 - 2002
- [c7]Sèverine Bérard, Eric Rivals:
Comparison of minisatellites. RECOMB 2002: 67-76 - 2001
- [c6]Eric Rivals, Sven Rahmann:
Combinatorics of Periods in Strings. ICALP 2001: 615-626 - 2000
- [c5]Sven Rahmann, Eric Rivals:
Exact and Efficient Computation of the Expected Number of Missing and Common Words in Random Texts. CPM 2000: 375-387 - 1999
- [c4]Olivier Delgrange, Max Dauchet, Eric Rivals:
Location of Repetitive Regions in Sequences By Optimizing A Compression Method. Pacific Symposium on Biocomputing 1999: 254-265 - [c3]Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-Peter Lenhof, Eric Rivals, Martin Vingron:
q-gram based database searching using a suffix array (QUASAR). RECOMB 1999: 77-83 - 1998
- [c2]Jean-Stéphane Varré, Jean-Paul Delahaye, Eric Rivals:
The transformation distance: A dissimilarity measure based an movements of segments. German Conference on Bioinformatics 1998 - 1996
- [c1]Eric Rivals, Jean-Paul Delahaye, Max Dauchet, Olivier Delgrange:
A Guaranteed Compression Scheme for Repetitive DNA Sequences. Data Compression Conference 1996: 453
Informal and Other Publications
- 2024
- [i10]Eric Rivals, Pengfei Wang:
Counting overlapping pairs of strings. CoRR abs/2405.09393 (2024) - [i9]Eric Rivals:
Incremental computation of the set of period sets. CoRR abs/2410.12077 (2024) - 2022
- [i8]Eric Rivals, Michelle Sweering, Pengfei Wang:
Convergence of the number of period sets in strings. CoRR abs/2209.08926 (2022) - 2021
- [i7]Sangsoo Park, Sung Gwan Park, Bastien Cazaux, Kunsoo Park, Eric Rivals:
A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs. CoRR abs/2102.12824 (2021) - 2020
- [i6]Bastien Cazaux, Eric Rivals:
Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring. CoRR abs/2012.08878 (2020) - 2018
- [i5]Bastien Cazaux, Eric Rivals:
Hierarchical Overlap Graph. CoRR abs/1802.04632 (2018) - [i4]Bastien Cazaux, Eric Rivals:
Strong link between BWT and XBW via Aho-Corasick automaton and applications to Run-Length Encoding. CoRR abs/1805.10070 (2018) - 2017
- [i3]Rodrigo Cánovas, Bastien Cazaux, Eric Rivals:
The Compressed Overlap Index. CoRR abs/1707.05613 (2017) - 2012
- [i2]Eric Rivals, Nicolas Philippe, Mikaël Salson, Martine Léonard, Therese Commes, Thierry Lecroq:
A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections. ERCIM News 2012(89) (2012) - 2010
- [i1]Eric Rivals, Alban Mancheron, Raluca Uricaru:
Reliable Bacterial Genome Comparison Tools. ERCIM News 2010(82): 17 (2010)
Coauthor Index
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