Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution, Journal of Computational Biology, vol.14, issue.4, pp.436-445, 2007. ,
DOI : 10.1089/cmb.2007.A005
Colored de Bruijn Graphs and the Genome Halving Problem, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.1, pp.98-107, 2007. ,
DOI : 10.1109/TCBB.2007.1002
Physical Mapping of Chromosomes Using Unique Probes, Journal of Computational Biology, vol.2, issue.2, pp.159-184, 1995. ,
DOI : 10.1089/cmb.1995.2.159
An algorithmic view of gene teams, Theoretical Computer Science, vol.320, issue.2-3, pp.395-418, 2004. ,
DOI : 10.1016/j.tcs.2004.02.036
URL : https://hal.archives-ouvertes.fr/hal-00619206
EXPLORING GENOME REARRANGEMENTS USING VIRTUAL HYBRIDIZATION, Proceedings of the 5th Asia-Pacific Bioinformatics Conference, pp.205-214, 2007. ,
DOI : 10.1142/9781860947995_0023
URL : https://hal.archives-ouvertes.fr/lirmm-00203873
Paleontological Evidence to Date the Tree of Life, Molecular Biology and Evolution, vol.24, issue.1, pp.26-53, 2007. ,
DOI : 10.1093/molbev/msl150
Perfect Sorting by Reversals Is Not Always Difficult, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.1, pp.4-16, 2007. ,
DOI : 10.1109/TCBB.2007.1011
Reconstructing Ancestral Gene Orders Using Conserved Intervals, Algorithms in Bioinformatics Lecture Notes in Computer Science, vol.3240, pp.14-25, 2004. ,
DOI : 10.1007/978-3-540-30219-3_2
Bioinformatics Algorithms: Techniques and Applications (A. Zelikovsky and I. Mandoiu, editors), chapter INRIA Formal models of gene clusters, Wiley Series on Bioinformatics: Computational Techniques and Engineering. Wiley Interscience ,
Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study, Genome Biology, vol.8, issue.11, p.236, 2007. ,
DOI : 10.1186/gb-2007-8-11-r236
Testing for the consecutive ones property, interval graphs, and graph planarity using PQ-tree algorithms, Journal of Computer and System Sciences, vol.13, issue.3, pp.335-379, 1976. ,
DOI : 10.1016/S0022-0000(76)80045-1
Genome-scale evolution: reconstructing gene orders in the ancestral species, Genome Research, vol.12, pp.26-36, 2002. ,
Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons From Human, Mouse, and Rat Genomes, Genome Research, vol.14, issue.4 ,
DOI : 10.1101/gr.1975204
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction, Genome Research, vol.16, issue.3, pp.311-313, 2006. ,
DOI : 10.1101/gr.4631806
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages, Genome Research, vol.15, issue.1, pp.98-110, 2005. ,
DOI : 10.1101/gr.3002305
On bandwidth-2 graphs, Discrete Applied Mathematics, vol.117, issue.1-3, pp.1-13, 2002. ,
DOI : 10.1016/S0166-218X(01)00196-2
A Branch-and-Cut Approach to Physical Mapping of Chromosomes by Unique End-Probes, Journal of Computational Biology, vol.4, issue.4, pp.433-447, 1997. ,
DOI : 10.1089/cmb.1997.4.433
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements, Genome Research, vol.14, issue.7, pp.1394-1403, 2004. ,
DOI : 10.1101/gr.2289704
Computational approaches to unveiling ancient genome duplications, Nature Reviews Genetics, vol.19, issue.10, pp.752-763, 2004. ,
DOI : 10.1093/molbev/msh114
Approximability and Parameterized Complexity of Consecutive Ones Submatrix Problems, Theory and Applications of Models of Computation, 4th International Conference Proceedings, volume 4484 of Lecture Notes in Computer Science, pp.680-691, 2007. ,
DOI : 10.1007/978-3-540-72504-6_62
Minimum Membership Set Covering and the Consecutive Ones Property, Algorithm Theory -SWAT 2006, pp.339-350, 2006. ,
DOI : 10.1007/11785293_32
Reversing Gene Erosion ??? Reconstructing Ancestral Bacterial Genomes from Gene-Content and Order Data ,
DOI : 10.1007/978-3-540-30219-3_1
URL : https://hal.archives-ouvertes.fr/hal-00427561
The Reconstruction of Doubled Genomes, SIAM Journal on Computing, vol.32, issue.3, pp.754-792, 2003. ,
DOI : 10.1137/S0097539700377177
Addressing chromosome evolution in the whole-genome sequence era, Chromosome Research, vol.298, issue.1, pp.5-16, 2008. ,
DOI : 10.1007/s10577-007-1208-0
Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?, Genome Research, vol.16, issue.3, pp.306-310, 2006. ,
DOI : 10.1101/gr.3955206
Towards the delineation of the ancestral eutherian genome organization: comparative genome maps of human and the African elephant (Loxodonta africana) generated by chromosome painting, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.1522, pp.1331-1340, 2003. ,
DOI : 10.1098/rspb.2003.2383
Four Strikes Against Physical Mapping of DNA, Journal of Computational Biology, vol.2, issue.1, pp.139-152, 1995. ,
DOI : 10.1089/cmb.1995.2.139
Lex-BFS and partition refinement, with applications to transitive orientation, interval graph recognition and consecutive ones testing, Theoretical Computer Science, vol.234, issue.1-2, pp.59-84, 2000. ,
DOI : 10.1016/S0304-3975(97)00241-7
A note on the Consecutive Ones Submatrix problem, Information Processing Letters, vol.83, issue.3, pp.163-166, 2002. ,
DOI : 10.1016/S0020-0190(01)00325-8
The UCSC Genome Browser Database: 2008 update, Nucleic Acids Research, vol.36, issue.Database, pp.773-779, 2007. ,
DOI : 10.1093/nar/gkm966
Reconstruction of the ancestral ferungulate karyotype by electronic chromosome painting (E-painting), Chromosome Research, vol.215, issue.8, pp.899-907, 2006. ,
DOI : 10.1007/s10577-006-1097-7
Genome sequence, comparative analysis and haplotype structure of the domestic dog, Nature, vol.426, issue.7069, pp.803-819, 2005. ,
DOI : 10.1038/nature04338
Gene teams: a new formalization of gene clusters for comparative genomics, Computational Biology and Chemistry, vol.27, issue.1, pp.59-67, 2003. ,
DOI : 10.1016/S1476-9271(02)00097-X
Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, issue.12, pp.1557-1565, 2006. ,
DOI : 10.1101/gr.5383506
A certifying algorithm for the consecutive-ones property ,
On the consecutive ones property, Discrete Applied Mathematics, vol.88, issue.1-3, pp.325-354, 1998. ,
DOI : 10.1016/S0166-218X(98)00078-X
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences, Nature, vol.22, issue.7141, pp.167-177, 2007. ,
DOI : 10.1038/nature05805
Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time, BioEssays, vol.270, issue.2, pp.122-134, 2008. ,
DOI : 10.1002/bies.20707
Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps, Science, vol.309, issue.5734, pp.613-617, 2005. ,
DOI : 10.1126/science.1111387
Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates, Genome Research, vol.17, issue.9, pp.1254-1265, 2007. ,
DOI : 10.1101/gr.6316407
Using PQ Structures for Genomic Rearrangement Phylogeny, Journal of Computational Biology, vol.13, issue.10, pp.1685-1700, 2006. ,
DOI : 10.1089/cmb.2006.13.1685
Identification of genomic features using microsyntenies of domains: Domain teams, Genome Research, vol.15, issue.6, pp.867-874, 2005. ,
DOI : 10.1101/gr.3638405
Ancestral animal genomes reconstruction, Current Opinion in Immunology, vol.19, issue.5, pp.542-546, 2007. ,
DOI : 10.1016/j.coi.2007.06.009
Genome sequence of the Brown Norway rat yields insights into mammalian evolution, Nature, vol.428, issue.6982, pp.493-521, 2004. ,
DOI : 10.1038/nature02426
Reconstruction of the ancestral karyotype of eutherian mammals, Chromosome Research, vol.11, issue.6, pp.605-618, 2003. ,
DOI : 10.1023/A:1024957002755
Ancestral genomes reconstruction: An integrated, multi-disciplinary approach is needed, Genome Research, vol.16, issue.12, pp.1441-1444, 2006. ,
DOI : 10.1101/gr.5687906
Polyploids, genome halving and phylogeny, Bioinformatics, vol.23, issue.13, pp.433-439, 2007. ,
DOI : 10.1093/bioinformatics/btm169
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms, BMC Bioinformatics, vol.8, issue.1, 2007. ,
DOI : 10.1186/1471-2105-8-82
A chromosome painting test of the basal Eutherian karyotype, Chromosome Research, vol.12, issue.1, pp.45-53, 2004. ,
DOI : 10.1023/B:CHRO.0000009294.18760.e4
The Ancestral Eutherian Karyotype Is Present in Xenarthra, PLoS Genetics, vol.11, issue.7, p.109, 2006. ,
DOI : 0140-6736(1971)011[0971:ARBTFH]2.0.CO;2
An Integrative Method for Accurate Comparative Genome Mapping, PLoS Computational Biology, vol.34, issue.8, p.75, 2006. ,
DOI : 10.1371/journal.pcbi.0020075.st005
The consecutive ones submatrix problem for sparse matrices, Algorithmica, vol.48, pp.287-299, 2007. ,
The evolution of eutherian chromosomes, Current Opinion in Genetics & Development, vol.14, issue.6, pp.657-666, 2004. ,
DOI : 10.1016/j.gde.2004.10.001
ROCI; -reconstruction of conserved intervals ,
Reciprocal chromsome painting among human, aardvark, and elephant (superorder afrotheria) reveals the likely eutherian ancestral karyotype, Proceedings of the National Academy of Science of the United States of America, pp.1062-1066, 2003. ,