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1

flowLearn: Fast and precise identification and quality checking of cell populations in flow cytometry

Lux, Markus, Brinkman, Ryan Remy, Chauve, Cedric, Laing, Adam, Lorenc, Anna, Abeler-Dörner, Lucie, Hammer, Barbara, Wren, Jonathan

Journal:

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

2

ReMixT: clone-specific genomic structure estimation in cancer

McPherson, Andrew W., Roth, Andrew, Ha, Gavin, Chauve, Cedric, Steif, Adi, de Souza, Camila P. E., Eirew, Peter, Bouchard-Côté, Alexandre, Aparicio, Sam, Sahinalp, S. Cenk, Shah, Sohrab P.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.80 MB

english, 2017

3

Enumerating Alternating Trees

Cedric Chauve, Serge Dulucq, Andrew Rechnitzer

Journal:

Journal of Combinatorial Theory, Series A

Year:

2001

Language:

english

File:

PDF, 164 KB

english, 2001

4

On the Gapped Consecutive-Ones Property

Cedric Chauve, Ján Maňuch, Murray Patterson

Journal:

Electronic Notes in Discrete Mathematics

Year:

2009

Language:

english

File:

PDF, 182 KB

english, 2009

5

On maximal instances for the original syntenic distance

Cedric Chauve, Guillaume Fertin

Journal:

Theoretical Computer Science

Year:

2004

Language:

english

File:

PDF, 254 KB

english, 2004

6

A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes

Aïda Ouangraoua, Valentin Guignon, Sylvie Hamel, Cedric Chauve

Journal:

Theoretical Computer Science

Year:

2011

Language:

english

File:

PDF, 714 KB

english, 2011

7

Tree pattern matching with a more general notion of occurrence of the pattern

Journal:

Information Processing Letters

Year:

2002

Language:

english

File:

PDF, 105 KB

english, 2002

8

Two bijective proofs for the arborescent form of the Good–Lagrange formula and some applications to colored rooted trees and cacti

Michel Bousquet, Cedric Chauve, Gilbert Labelle, Pierre Leroux

Journal:

Theoretical Computer Science

Year:

2003

Language:

english

File:

PDF, 598 KB

english, 2003

9

Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes

Roland Wittler, Cedric Chauve

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 322 KB

english, 2011

10

A more efficient algorithm for perfect sorting by reversals

Sèverine Bérard, Cedric Chauve, Christophe Paul

Journal:

Information Processing Letters

Year:

2008

Language:

english

File:

PDF, 191 KB

english, 2008

11

A geometric version of the Robinson–Schensted correspondence for skew oscillating tableaux

Cedric Chauve, Serge Dulucq

Journal:

Discrete Mathematics

Year:

2002

Language:

english

File:

PDF, 145 KB

english, 2002

12

Efficient chaining of seeds in ordered trees

Julien Allali, Cedric Chauve, Pascal Ferraro, Anne-Laure Gaillard

Journal:

Journal of Discrete Algorithms

Year:

2012

Language:

english

File:

PDF, 318 KB

english, 2012

13

A tight bound on the length of odd cycles in the incompatibility graph of a non-C1P matrix

Mehrnoush Malekesmaeili, Cedric Chauve, Tamon Stephen

Journal:

Information Processing Letters

Year:

2012

Language:

english

File:

PDF, 296 KB

english, 2012

14

FragAnchor: A Large-Scale Predictor of Glycosylphosphatidylinositol Anchors in Eukaryote Protein Sequences by Qualitative Scoring

Guylaine Poisson, Cedric Chauve, Xin Chen, Anne Bergeron

Journal:

Genomics, Proteomics & Bioinformatics

Year:

2007

Language:

english

File:

PDF, 422 KB

english, 2007

15

Computing Common Intervals of K Permutations, with Applications to Modular Decomposition of Graphs

Bergeron, Anne, Chauve, Cedric, de Montgolfier, Fabien, Raffinot, Mathieu

Journal:

SIAM Journal on Discrete Mathematics

Year:

2008

Language:

english

File:

PDF, 218 KB

english, 2008

16

Hardness results on the gapped consecutive-ones property problem

Ján Maňuch, Murray Patterson, Cedric Chauve

Journal:

Discrete Applied Mathematics

Year:

2012

Language:

english

File:

PDF, 308 KB

english, 2012

17

Linearization of ancestral multichromosomal genomes

Ján Maňuch, Murray Patterson, Roland Wittler, Cedric Chauve…

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

18

[Computational Biology] Models and Algorithms for Genome Evolution Volume 19 ||

Chauve, Cedric, El-Mabrouk, Nadia, Tannier, Eric

Year:

2013

Language:

english

File:

PDF, 6.77 MB

english, 2013

19

A 2-Approximation for the Minimum Duplication Speciation Problem

Ouangraoua, Aïda, Swenson, Krister M., Chauve, Cedric

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 632 KB

english, 2011

20

Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction

Chauve, Cedric, Haus, Utz-Uwe, Stephen, Tamon, You, Vivija P.

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 370 KB

english, 2010

21

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II

Chauve, Cedric, Gavranovic, Haris, Ouangraoua, Aida, Tannier, Eric

Journal:

Journal of Computational Biology

Year:

2010

Language:

english

File:

PDF, 2.24 MB

english, 2010

22

Space of Gene/Species Trees Reconciliations and Parsimonious Models

Doyon, Jean-Philippe, Chauve, Cedric, Hamel, Sylvie

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 540 KB

english, 2009

23

Computation of Perfect DCJ Rearrangement Scenarios with Linear and Circular Chromosomes

Bérard, Sèverine, Chateau, Annie, Chauve, Cedric, Paul, Christophe, Tannier, Eric

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.03 MB

english, 2009

24

Gene Family Evolution by Duplication, Speciation, and Loss

Chauve, Cedric, Doyon, Jean-Philippe, El-Mabrouk, Nadia

Journal:

Journal of Computational Biology

Year:

2008

Language:

english

File:

PDF, 434 KB

english, 2008

25

AVERAGE-CASE ANALYSIS OF PERFECT SORTING BY REVERSALS

BOUVEL, MATHILDE, CHAUVE, CEDRIC, MISHNA, MARNI, ROSSIN, DOMINIQUE

Journal:

Discrete Mathematics Algorithms and Applications

Year:

2011

Language:

english

File:

PDF, 325 KB

english, 2011

26

[Computational Biology] Models and Algorithms for Genome Evolution Volume 19 || The Genesis of the DCJ Formula

Chauve, Cedric, El-Mabrouk, Nadia, Tannier, Eric

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

27

Chaining Sequence/Structure Seeds for Computing RNA Similarity

Bourgeade, Laetitia, Chauve, Cédric, Allali, Julien

Journal:

Journal of Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.44 MB

english, 2015

28

Algorithms and complexity results for genome mapping problems

Rajaraman, Ashok, Zanetti, Joao, Manuch, Jan, Chauve, Cedric

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 372 KB

english, 2016

29

Identification, Expression, and Evolutionary Analyses of Plant Lipocalins

Jean-Benoit Frenette Charron, François Ouellet, Mélanie Pelletier , Jean Danyluk, Cédric Chauve and Fathey Sarhan

Journal:

PLANT PHYSIOLOGY

Year:

2005

Language:

english

File:

PDF, 2.62 MB

english, 2005

30

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1.

Jacox, Edwin, Chauve, Cedric, Szöllősi, Gergely J., Ponty, Yann, Scornavacca, Celine

Journal:

Year:

2016

Language:

english

File:

PDF, 102 KB

english, 2016

31

The BRaliBase dent—a tale of benchmark design and interpretation

Löwes, Benedikt, Chauve, Cedric, Ponty, Yann, Giegerich, Robert

Journal:

Briefings in Bioinformatics

Year:

2016

Language:

english

File:

PDF, 438 KB

english, 2016

32

CoLoRMap: Correcting Long Reads by Mapping short reads

Haghshenas, Ehsan, Hach, Faraz, Sahinalp, S. Cenk, Chauve, Cedric

Journal:

Year:

2016

Language:

english

File:

PDF, 208 KB

english, 2016

33

DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies

Duchemin, Wandrille, Anselmetti, Yoann, Patterson, Murray, Ponty, Yann, Berard, Severine, Chauve, Cedric, Scornavacca, Celine, Daubin, Vincent, Tannier, Eric

Journal:

Genome Biology and Evolution

Year:

2017

Language:

english

File:

PDF, 526 KB

english, 2017

34

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies

Luhmann, Nina, Lafond, Manuel, Thevenin, Annelyse, Ouangraoua, Aida, Wittler, Roland, Chauve, Cedric

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 509 KB

english, 2017

35

Ancestral gene synteny reconstruction improves extant species scaffolding

Yoann Anselmetti,Vincent Berry,Cedric Chauve,Annie Chateau,Eric Tannier…

Journal:

Year:

2015

Language:

english

File:

PDF, 1.85 MB

english, 2015

36

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve,Yann Ponty,João Paulo Pereira Zanetti

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 994 KB

english, 2015

37

Gene Tree Construction and Correction using SuperTree and Reconciliation

Lafond, Manuel, Chauve, Cedric, El-Mabrouk, Nadia, Ouangraoua, Aida

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 1.17 MB

english, 2017

38

LRCstats, a tool for evaluating long reads correction methods

La, Sean, Haghshenas, Ehsan, Chauve, Cedric

Journal:

Year:

2017

Language:

english

File:

PDF, 142 KB

english, 2017

39

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

Luhmann, Nina, Chauve, Cedric, Stoye, Jens, Wittler, Roland

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2018

Language:

english

File:

PDF, 778 KB

english, 2018

40

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis

Tsui, Clement K.-M., Miller, Ruth, Uyaguari-Diaz, Miguel, Tang, Patrick, Chauve, Cedric, Hsiao, William, Isaac-Renton, Judith, Prystajecky, Natalie, Singh, Upinder

Journal:

Year:

2018

Language:

english

File:

PDF, 2.40 MB

english, 2018

41

Correction to: ReMixT: clone-specific genomic structure estimation in cancer

McPherson, Andrew W., Roth, Andrew, Ha, Gavin, Chauve, Cedric, Steif, Adi, de Souza, Camila P. E., Eirew, Peter, Bouchard-Côté, Alexandre, Aparicio, Sam, Sahinalp, S. Cenk, Shah, Sohrab P.

Journal:

Year:

2017

Language:

english

File:

PDF, 214 KB

english, 2017

42

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

Anselmetti, Yoann, Duchemin, Wandrille, Tannier, Eric, Chauve, Cedric, Bérard, Sèverine

Journal:

Year:

2018

Language:

english

File:

PDF, 578 KB

english, 2018

43

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Allali, Julien, Saule, Cédric, Chauve, Cédric, d’Aubenton-Carafa, Yves, Denise, Alain, Drevet, Christine, Ferraro, Pascal, Gautheret, Daniel, Herrbach, Claire, Leclerc, Fabrice, de Monte, Antoine, Oua

Journal:

Advances in Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.86 MB

english, 2012

44

Counting, Generating, Analyzing and Sampling Tree Alignments

Chauve, Cedric, Courtiel, Julien, Ponty, Yann

Journal:

International Journal of Foundations of Computer Science

Year:

2018

Language:

english

File:

PDF, 785 KB

english, 2018

45

Alignment-free Clustering of UMI Tagged DNA Molecules

Orabi, Baraa, Erhan, Emre, McConeghy, Brian, Volik, Stanislav V, Le Bihan, Stephane, Bell, Robert, Collins, Colin C, Chauve, Cedric, Hach, Faraz, Berger, Bonnie

Journal:

Year:

2018

Language:

english

File:

PDF, 436 KB

english, 2018

46

[Society for Industrial and Applied Mathematics 2017 Proceedings of the Fourteenth Workshop on Analytic Algorithmics and Combinatorics (ANALCO) - ()] 2017 Proceedings of the Fourteenth Workshop on Analytic Algorithmics and Combinatorics (ANALCO) - An Exact Enumeration of Distance-Hereditary Graphs

Chauve, Cédric, Fusy, Éric, Lumbroso, Jérémie

Language:

english

File:

PDF, 592 KB

english

47

HyAsP, a greedy tool for plasmids identification

Müller, Robert, Chauve, Cedric, Valencia, Alfonso

Journal:

Year:

2019

File:

PDF, 198 KB

2019

48

Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework

Gan, Guo Liang, Willie, Elijah, Chauve, Cedric, Chindelevitch, Leonid

Journal:

BMC Bioinformatics

Year:

2019

File:

PDF, 1.67 MB

2019

49

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

Chauve, Cedric, Ponty, Yann, Wallner, Michael

Journal:

Journal of Mathematical Biology

Year:

2020

File:

PDF, 2.00 MB

2020

50

The distance and median problems in the single-cut-or-join model with single-gene duplications

Mane, Aniket C., Lafond, Manuel, Feijao, Pedro C., Chauve, Cedric

Journal:

Algorithms for Molecular Biology

Year:

2020

File:

PDF, 2.01 MB

2020

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