cedric.chauve [at] sfu.ca
(SFU) : SC K10516
Tel: (778) 782-7091
Fax: (778) 782-4947
Dep. Mathematics, SFU
8888 University Drive
Burnaby, BC, V5A 1S6
Cedric Chauve - Publications
Note. The publications below are grouped by project. For each publication, the most complete and recent version of this publication is
listed first, followed by (selected) preliminary versions that have appeared previously (conference proceedings, posters, short or extended abstracts,
Reconstruction and assembly of ancestral and ancient genomes (See also Section "Consecutive-Ones Property and PQ-trees" in Discrete Mathematics, algorithms and computational complexity below)
Cancer genomics and NGS
Evolution of gene families and gene adjacencies.
- ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics 32(13)56-58. 2016.
- Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics 16(Suppl 10):S11 (Proceedings of RECOMB-CG). 2015.
Ancestral gene synteny reconstruction improves extant species scaffolding. bioRxiv:023085
- Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies.
LNCS/LNBI 9096:260-271, ISBRA 2015.
Preprint: HAL: hal-0104587, arXiv:1503.05292.
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics 2015, 16(Suppl 19):S6, 2015.
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BiorXiv:026310, 2015.
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.
LNCS/LNBI 8826:49-56, BSB 2014.
- Polytomy Reﬁnement for the Correction of Dubious Duplications in Gene Trees. Bioinformatics 30:i519-i526, ECCB 2014.
- Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later.
Computational Biology 19:47-62, Models and Algorithms for Genome Evolution. 2013.
- An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework. IEEE/ACM TCBB 9(1):26-39. 2012.
An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework. LIRMM technical report RR-10002. 2010.
A 2-Approximation for the Minimum Duplication Speciation Problem
J. Comp. Biol. 18:1041-1053. 2011.
An approximation algorithm for computing a parsimonious first speciation in the gene duplication model.
A 3-approximation algorithm for computing a parsimonious first speciation in the gene duplication model.
HAL: hal-00374851, version 2. 2009.
Branch-and-Bound Approach for Parsimonious Inference of a Species Tree From a Set of Gene Family Trees. Chapter 29 of Software Tools and Algorithms for Biological Systems. 2011.
Branch-and-Bound Approach for Parsimonious Inference of a Species Tree From a Set of Gene Family Trees. LIRMM technical report RR-10001. 2010.
New perspectives on gene family
evolution: losses in reconciliation and a link with supertrees. LNCS/LNBI 5541:46-58, RECOMB 2009.
Space of Gene/Species Trees Reconciliations and
Parsimonious Models, J. Comput. Biol., 16(10):1399-1418. 2009.
Algorithms for exploring the space of gene tree/species tree reconciliations.
Gene family evolution by duplication, speciation and loss.
J. Comput. Biol. 15:1043-1062. 2008.
Inferring a duplication, speciation and loss history from a
gene tree (extended abstract).
Inferring a duplication and speciation history from a gene tree.
Poster T69, SMBE 2007.
Perfect rearrangement algorithms
RNA secondary structure comparison
- Counting, generating and sampling tree alignments. LNCS/LNBI 9702:53-64. AlCoB 2016
Counting, generating and sampling tree alignments. Preprint. 2016.
- The Bralibase dent: A tale of benchmark design and interpretation. Briefings in Bioinformatics. Advance access. 2016.
- Chaining fragments in sequences: to sweep or not (Extended abstract). LNCS 9309:116-123,
Chaining fragments in sequences: to sweep or not.
An Unambiguous And Complete Dynamic Programming
Algorithm For Tree Alignment. arXiv:1505.05983, 2015.
Chaining Sequence/Structure Seeds for Computing RNA Similarity. J. Comput. Biol. 23:205-217. 2015.
Chaining Sequence/Structure Seeds for Computing RNA Similarity. CMSR 2014, pp. 1-12. 2014.
- Efficient chaining of seeds in ordered trees. JDA 14:107-118. 2012.
Efficient chaining of seeds in ordered trees. arXiv:q-bio.QM/1007.0942. 2010.
Efficient chaining of seeds in ordered trees. LNCS 6460:260-273, IWOCA 2010.
- BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms. Advances in Bioinformatics, article 893048. 2012.
secondary structure comparison algorithms. Poster 77
A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes. TCS 412:753-764. 2011.
New algorithms for aligning nested arc-annotated sequences.
LaBRI Research Report 1443-08. 2008.
RNA StrAT: RNA Structure Analysis Toolkit. Poster D31
(abstract), ISMB 2008.
RNA StrAT. Webserver. 2007.
An edit distance between RNA stem-loops.
3772:334-345, SPIRE 2005.
Conserved structures in gene orders (See also section "Common intervals of permutations" in Discrete Mathematics, algorithms and computational complexity below)
Computing gene order distances and orthologs from genomes with duplicated genes
- Virtual hybridation for gene order datasets.
- Theoretical properties of genomic distances.
Discrete Mathematics, algorithms and computational complexity.
Consecutive-Ones Property and variants, PQ-trees
Common intervals of permutations
Trees and arc-annotated sequences edit distance
See section "RNA secondary structure comparison" in Comparative bioinformatics above.
Enumerative and algebraic combinatorics.
Academic works (in french)