, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proc. Int. Conf. Intell. Syst. Mol. Biol. ISMB Int. Conf. Intell. Syst. Mol. Biol, vol.2, pp.28-36, 1994.
, Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions, Nature Biotechnology, vol.39, issue.12, pp.1119-1125, 2013.
DOI : 10.1006/jmbi.1990.9999
, After the Duplication: Gene Loss and Adaptation in Saccharomyces Genomes, Genetics, vol.172, issue.2, pp.863-872, 2006.
DOI : 10.1534/genetics.105.048900
, Normalization of a chromosomal contact map, BMC Genomics, vol.13, issue.1, p.436, 2012.
DOI : 10.1186/gb-2009-10-3-r25
URL : https://hal.archives-ouvertes.fr/pasteur-00769663
, Capturing Chromosome Conformation, Science, vol.295, issue.5558, pp.1306-1311, 2002.
DOI : 10.1126/science.1067799
, SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes, PLoS ONE, vol.334, issue.3, 2014.
DOI : 10.1371/journal.pone.0092621.t002
URL : https://hal.archives-ouvertes.fr/hal-01358096
, A three-dimensional model of the yeast genome, Nature, vol.465, issue.7296, pp.363-367, 2010.
DOI : 10.1073/pnas.0402766101
, Genome evolution in yeasts, Nature, vol.316, issue.6995, pp.35-44, 2004.
DOI : 10.1093/nar/gkg056
URL : https://hal.archives-ouvertes.fr/hal-00104411
, Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs, Cell, vol.29, issue.1, pp.235-244, 1982.
DOI : 10.1016/0092-8674(82)90108-8
, Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser, BMC Genomics, vol.11, issue.1, p.290, 2010.
DOI : 10.1093/nar/gkm321
, Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome, PLoS Genetics, vol.55, issue.5, p.1000485, 2009.
DOI : 10.1371/journal.pgen.1000485.s003
, Mechanisms of Chromosome Number Evolution in Yeast, PLoS Genetics, vol.55, issue.4, p.1002190, 2011.
DOI : 10.1371/journal.pgen.1002190.s010
, Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-652, 2011.
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
, Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Nature Methods, vol.10, issue.10, pp.999-1003, 2012.
DOI : 10.1038/nmeth.2148
, Population Polymorphism of Nuclear Mitochondrial DNA Insertions Reveals Widespread Diploidy Associated with Loss of Heterozygosity in Debaryomyces hansenii, Eukaryotic Cell, vol.9, issue.3, pp.449-459, 2010.
DOI : 10.1128/EC.00263-09
, Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis, Nature Biotechnology, vol.32, issue.2, pp.319-326, 2007.
DOI : 10.1038/nbt1290
, High-throughput genome scaffolding from in vivo DNA interaction frequency, Nature Biotechnology, vol.12, issue.12, pp.1143-1147, 2013.
DOI : 10.1090/S0025-5718-1980-0572855-7
, Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature, vol.428, issue.6983, pp.617-624, 2004.
DOI : 10.1038/nature02424
, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322381
, Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome, Science, vol.27, issue.2, pp.289-293, 2009.
DOI : 10.1038/nbt.1523
, Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome, Science, vol.27, issue.2, pp.289-93, 2009.
DOI : 10.1038/nbt.1523
, , an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization, G3: Genes|Genomes|Genetics, vol.2, issue.2, pp.299-311, 2012.
DOI : 10.1534/g3.111.000745
, Chromosomal G + C Content Evolution in Yeasts: Systematic Interspecies Differences, and GC-Poor Troughs at Centromeres, Genome Biology and Evolution, vol.2, issue.0, pp.572-583, 2010.
DOI : 10.1093/gbe/evq042
, Localization Accuracy in Single-Molecule Microscopy, Biophysical Journal, vol.86, issue.2, pp.1185-1200, 2004.
DOI : 10.1016/S0006-3495(04)74193-4
, Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery, Genes & Development, vol.23, issue.8, pp.912-927, 2009.
DOI : 10.1101/gad.1782209
, Evolutionary Mobility of the Ribosomal DNA Array in Yeasts, Genome Biology and Evolution, vol.5, issue.3, pp.525-531, 2013.
DOI : 10.1093/gbe/evt022
, Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE, Science, vol.330, pp.1787-1797, 2010.
, Using the transcriptome to annotate the genome, Nature Biotechnology, vol.20, issue.5, pp.508-512, 2002.
DOI : 10.1038/nbt0502-508
, Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome, Cell, vol.148, issue.3, pp.458-472, 2012.
DOI : 10.1016/j.cell.2012.01.010
, Comparative genomics of protoploid Saccharomycetaceae, Genome Res, vol.19, pp.1696-1709, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00407511
, Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors, Genome Research, vol.22, issue.9, pp.1798-1812, 2012.
DOI : 10.1101/gr.139105.112
, A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus, Current Biology, vol.22, issue.20, pp.1881-90, 2012.
DOI : 10.1016/j.cub.2012.07.069
URL : https://hal.archives-ouvertes.fr/pasteur-01420017
, Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture, Nature Genetics, vol.464, issue.11, pp.1059-1065, 2011.
DOI : 10.1038/nature06008