Notes de cours

Génomes et le contexte phylogénétique
  • génomes: aperçus généraux, composition, taille
  • homologie de gènes
  • profils phylétiques
Lectures obligatoires
  • Lander, E.S. Initial impact of the sequencing of the human genome. Nature 470:187-197 (2011) paywall HTML.
  • Koonin, E. V. Darwinian evolution in the light of genomics. Nucleic Acids Research 37:1011-1034 (2009) open access HTML .
  • Affiche PDF icon PDF.
  • Note № 1: introduction PDF icon PDF.
  • Note № 2: profils phylétiques PDF icon PDF.
  • Diapos № 1: le génome PDF icon PDF.
  • Diapos № 2: profils phylétiques PDF icon PDF.
  • Date, S. V. & E. M. Marcotte. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnology 21:1055-1062 (2003) paywall HTML.
  • Glazko, G. V. & A. R. Mushegian. Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biology 5:R32 (2004) open access HTML.
  • Jothi, R., T. M. Przytycka & L. Aravind. Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 8:73 (2007) open access HTML.
  • Koonin, E. V. Comparative genomics, minimal gene-sets, and the last universal common ancestor. Nature Reviews Microbiology 1:127-136 (2003) paywall HTML.
  • Mirkin, B. G., T. I. Fenner, M. Y. Galperin & E. V. Koonin. Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evolutionary Biology 3:2 (2003) open access HTML.
  • Pellegrini, M., E. M. Marcotte, M. J. Thompson, D. Eisenberg & T. O. Yates. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proceedings of the National Academy of Sciences of the USA 96:4285-4288 (1999) open access HTML.
  • Sankoff D & P. Rousseau. Locating the vertices of a Steiner tree in an arbitrary metric space. Mathematical Programming 9:240-246 (1975) PDF.
  • Tatusov, R. L. & al. (17 auteurs) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41 (2003) open access HTML.
Alignement: substitutions et conservation
  • modèle Markovien de substitutions
  • procéssus de Poisson
  • conservation et accélération
Lectures obligatoires
  • Liò, P. & N. Goldman. Models of molecular evolution and phylogeny. Genome Research 8:1233-1244 (1998) open access HTML.
  • Graur, D. Y. Zheng, N. Price, R. B. Azevedo, R. A. Zufall & E. Elhaik. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biology and Evolution 5:578-590 (2013) open access HTML.
  • Note № 3: substitutions PDF icon PDF.
  • Note № 4: programmation dynamique avec modèles probabilistes PDF icon PDF.
  • Note № 5: procéssus de Markov à temps continu PDF icon PDF.
  • Diapos № 3: conservation PDF icon PDF.
  • Asthana, S., M.Roytberg, J. Stamatoyannopoulos & S. Sunyaev. Analysis of sequence conservation at nucleotide resolution. PLoS Computational Biology 3:e254 (2007) open access HTML. [SCONE]
  • Boffelli, D., J. McAuliffe, D. Ovcharenko, K. D. Lewis, I. Ovcharenko, L. Pachter & E. M. Rubin. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299:1391-1394 (2003) paywall HTML.
  • Davydov, E.V., D. L. Goode, M. Sirota, G. M. Cooper, A. Sidow & S. Batzoglou. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Computational Biology 6:e1001025 (2010) open access HTML.
  • Eddy, S. A model of the statistical power of comparative genome sequence analysis. PLoS Biology 3:e10 (2005) open access HTML.
  • Garber, M., M. Guttmann, M. Clamp, M. C. Zody, N. Friedman & X. Xe. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics 25:i54-i62 (2009) open access HTML. [SiPhy]
  • Miller, W., K. D. Makova, A. Nekrutenko & R. C. Hardison. Comparative genomics. Annual Review of Genomics and Human Genetics 5:15-56 (2004) paywall HTML.
  • Pollard K. S. & al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443:167-172 (2006) paywall HTML.
  • Pollard, K. S., M. J. Hubisz, K. R. Rosenbloom & A. Siepel. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Research 20:110-121 (2010) open access HTML. [PhyloP]
  • Ponting, C. P. & R. C. Hardison. What fraction of the human genome is functional? Genome Research 21:1769-1776 (2011) open access HTML.
  • Siepel, A. & al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Research 15:1034-1050 (2005) open access HTML.
  • Siepel, A., K. S. Pollard & D. Haussler. New methods for detecting lineage-specific selection. Proc. RECOMB 190-205 (2006) paywall HTML.
  • Stone, E. A., G. M. Cooper & A. Sidow. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annual Review of Genomics and Human Genetics 6:143-164 (2005) paywall HTML.
Séquençage haut débit
Lectures obligatoires
  • Shendure, J. & E. L. Arden. The expanding scope of DNA sequencing. Nature Biotechnology 30:1084-1094 (2012) paywall HTML.
  • Diapos № 4: séquençage PDF icon PDF.
  • Dressman, D., H. Yan, G. Traverso, K. W. Kinzler & B. Vogelstein. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proceedings of National Academy of Sciences of the USA 100:8817-8822 (2003) [perles / beads] open access HTML.
  • Ewing, B. & P. Green. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research 8: 186-194. (1998) [score Phred] open access HTML.
  • Green, E. D. Strategies for the systematic sequencing of complex genomes. Nature Reviews Genetics 2: 573-583 (2001). [séquençage de premiers génomes] paywall HTML.
  • IHGSC. Initial sequencing and analysis of the human genome. Nature 609: 860-921 (2001) open access HTML.
  • Mardis, E. R. Next-generation DNA sequencing methods. Annual Reviews of Genomics and Human Genetics 9:387-402 (2008) paywall HTML.
  • Mardis, E. R. A decade's perspective on DNA sequencing technology. Nature 470:198-203 (2011) paywall HTML.
  • Metzker, M. L. Sequencing technologies - the next generation. Nature Reviews Genetics 11:31-46 (2010) paywall HTML.
  • Ronaghi, M., M. Uhlén, & P. Nyrén. A sequencing method based on real-time pyrophosphate. Science 281: 363-365 (1998). [pyroséquençage] paywall HTML.
  • Ion Torrent Youtube icon
  • Illumina Youtube icon
Alignement à grande échelle
  • recherche de homologies: structures de données et algorithmes
  • seed-and-extend, graine espacée
  • Diapos № 5: hachage PDF icon PDF.
  • Diapos № 7: extension PDF icon PDF.
  • NIH/NCBI: The statistics of sequence similarity scores open access HTML
  • Ma, B., J. Tromp & M. Li. PatternHunter: faster and more sensitive homology search. Bioinformatics 18: 440-445 (2002). [implantation du tableau de k-mers, introduction des graines espacées] open access HTML
  • Lin, H., Z. Zhang, M. Q. Zhang, B. Ma & M. Li. ZOOM! Zillions of oligos mapped. Bioinformatics 24:2431-2437 (2008) open access HTML
  • placement de histones
  • modifications d'histones
  • chromatine ouverte
  • sites de liaison
  • protocoles experimentaux: Chip-seq, DNase-seq, MNase-seq, FAIRE-seq, CHIP-exo
Lectures principales
  • Hawkins, D. R., G. C. Hon & B. Ren. Next-generation genomics: an integrative approach. Nature Reviews Genetics 11:476-486 (2010) paywall HTML open access PMC.
  • Pepke, S., B. Wold & A. Mortazavi. Computation for ChIP-seq and RNA-seq studies. Nature Methods 6:S22-S32 (2009) paywall HTML.
  • Diapos № 6: séquençage haut débit et épigénomique PDF icon PDF.
  • Bhandare, R., J. Schug & al. Genome-wide analysis of histone modifications in human pancreatic islets. Genome Research 20:428-433 (2010) open access HTML.
  • Ernst, J. & M. Kellis. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature Biotechnology 28:817-825 (2010) [chromoHMM] paywall HTML.
  • Gaffney, D. J., G. McVicker & al. Controls of nucleosome positioning in the human genome. PLoS Genetics 8:e1003036 (2012) open access HTML.
  • Giresi, P. G. & al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Research 17:877-885 (2007) open access HTML.
  • Hughes, A. L., Y. Jin, O. J. Rando & K. Struhl. A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern. Molecular Cell 48:5-15 (2012) paywall HTML.
  • Kaplan, N. & al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362-366 (2009) paywall HTML.
  • Park, P. J. ChIP-seq: advantages and challenges of a maturing technology. Nature Reviews Genetics 10:669-680 (2009) paywall HTML.
  • Raj, A. & G. McVicker. The genome shows its sensitive side. Nature Methods 11:39-40 (2014) paywall HTML.
  • Rhee, H. S. & B. F. Pugh. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147:1408-1419 (2011) [ChIP-exo] paywall HTML.
  • Song, L., Z. Zhang, L. L. Grasfeder, A. P. Boyle, P. G. Giresi, B.-K. Lee, N. C. Sheffield & al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Research 21:1757-1767 (2011) open access HTML.
  • Valouev & al. Determinants of nucleosome organization in primary human cells. Nature 474:516-520 (2011) paywall HTML.
  • Wasserman, W. W. & A. Sandelin. Applied bioinformatics for the identification of regulatory elements. Nature Reviews Genetics 5:276-287 (2004) paywall HTML.
  • Wold, B. & R. M. Myers. Sequence consensus methods for functional genomics. Nature Methods 5:19-21 (2008) [survol d'applications] paywall HTML.
  • Zentner, G. E. & S. Henikoff. Surveying the epigenomic landscape, one base at a time. Genome Biology 13:250 (2012) paywall HTML.
Îlots CpG et méthylation
  • ilot CpG; régulation et la méthylation d'ADN
  • séquençage bisulfite
Lectures principales
  • Illingworth, R. S. & A. P. Bird. CpG islands - `A rough guide.' FEBS Letters 583:1713-1720 (2009) open access HTML.
  • Bock, C. Analysing and interpreting DNA methylation data. Nature Reviews Genetics 13:705-719 (2012) paywall HTML.
  • Diapos № 8: îlots CpG et méthylation PDF icon PDF.
  • Takai, D. & P. A. Jones. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proceedings of the National Academy of Sciences of the USA 99:3740-3745 (2002) [définition classique d'îlot CpG] open access HTML.
  • Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature Reviews Genetics 13:484-492 (2012) [fonctions biologiques] paywall HTML.
  • Lister, R., M. Pelizzola & al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-322 (2009) [une application pionière] paywall HTML.
  • Laird, P. W. Principles and challenges of genome-wide DNA methylation analysis. Nature Reviews Genetics 11:191-203 (2010) [survol de méthodologies] paywall HTML.
  • Xi, Y. & W. Li. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics 10:232 (2009) [logiciel BSMAP: vecteurs de bits, tableaux d'indexage] open access HTML.
  • Frith, M. C., R. Mori & K. Asai. A mostly traditional approach improves alignment of bisulfite-converted DNA. Nucleic Acids Research 40:e100 (2012) [logiciel LAST, pénalisation] open access HTML.
Read mapping
  • alignement de lectures à grande échelle
  • formats SAM et VCF; MAPQ et QUAL
  • transformation Burrows-Wheeler, FM-index
Lecture principale
  • Trapnell, C. & S. L. Salzberg. How to map billions of short reads onto genomes. Nature Biotechnology 27:455-457 (2009). paywall HTML open access PMC.
  • Diapos № 10: read mapping PDF icon PDF.
  • Li, H. Improving SNP discovery by base alignment quality. Bioinformatics 27:1157-1158 (2011). open access HTML.
  • SAM: Sequence Alignment/Map Format Specification PDF icon PDF
  • VCF Variant Call Format Specification: HTML
  • sourceforge sourceforge: samtools | vcftools
  • Wikipedia logo Wikipedia: Burrows-Wheeler FR EN | FM-index EN
  • Ferragina, P. & G. Manzini. Opportunistic data structures with applications. Proc. Symposium Foundations of Computer Science (FOCS), 390-398 (2000)
SNPs et haplotypes
  • SNP calling
  • équilibre Hardy-Weinberg
  • haplotypage
  • imputation
Lecture principale
  • Roach, J.C., G. Glusman, A. F. A. Smit, C. D. Huff, R. Hubley, P. T. Shannon, L. Rowen & al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328:636-639 (2010) paywall HTML open access PMC.
  • Diapos № 11: variant calling PDF icon PDF.
  • Schwartz, R. Theory and algorithms for the haplotype assembly problem. Communications in Information and Systems 10:23-38 (2010) open accessPDF.
  • Alkan, C., B. P. Coe & E. E. Eichler. Genome structural variation discovery and genotyping. Nature Reviews Genetics 12:363-376 (2012) paywall HTML
  • He, D., B. Han & E. Eskin. Hap-seq: An optimal algorithm for haplotype phasing with imputation using sequencing data. Journal of Computational Biology 20:80-92 (2013) paywall HTML open access PMC.
  • Li, Y. & al. MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic Epidemiology 34:816-834 (2010) open access HTML
  • Wikipedia logo Wikipedia: principe Hardy-Weinberg FR EN
  • identity by descent
  • inbreeding et coancestry
  • coefficients de Jacquard
  • segments IBD
Lectures principales
  • Browning, S. R. & B. L. Browning. Identity by descent between distant relatives: Detection and applications. Annual Reviews in Genetics 46:617-633 (2012) paywall HTML
  • Weir, B. W., A. D. Anderson & A. B. Hepler. Genetic relatedness analysis: modern data and new challenges. Nature Reviews Genetics 7:771-780 (2006) paywall HTML
  • Diapos № 12: identity by descent PDF icon PDF.
  • Lee, W.-C. Testing the genetic relation between two individuals using a panel of frequency-unknown Single Nucleotide Polymorphisms. Annals of Human Genetics 67:618-619 (2003) open access HTML
  • Stevens, E. L., G. Heckenberg, E. D. O. Roberson & al. Inference of relationships in population data using identity-by-descent and identity-by-state. PLoS Genetics 7:e1002287 (2011) open access HTML
  • Kyriazopoulou-Panagiotopoulou, S., D. K. Haghighi, S. J. Aerni & al. Reconstruction of genealogical relationships with applications to Phase III of HapMap. Bioinformatics 27:i333-i341 (2011) open access HTML
  • Gusev, A. & al. Whole population, genome-wide mapping of hidden relatedness. Genome Research 19:318-326 (2009) open access HTML
  • Browning, S. R. & B. L. Browning. High-Resolution detection of identity by descent in unrelated individuals. American Journal of Human Genetics 86:526-539 (2010) open access HTML
  • Browning, S. R. & B. L. Browning. A fast, powerful method for detecting identity by descent. American Journal of Human Genetics 88:173-182 (2011) open access HTML
  • Browning, S. R. & B. L. Browning. Efficient multilocus association testing for whole genome association studies using localized haplotype clustering. Genetic Epidemiology 31:365-375 (2007) open access HTML
  • Su, S-Y. & al. Detection of identity by descent using next-generation whole genome sequencing data. BMC Bioinformatics 13:121 (2012) open access HTML
  • Palamara, P.F., T. Lencz, A. Darvasi & I. Pe'er. American Journal of Human Genetics 91: 809-822 (2012) open access HTML
  • Gravel, S., F. Zakharia F., A. Moreno-Estrada, J. K. Byrnes & al. Reconstructing Native American migrations from whole-genome and whole-exome data. PLoS Genetics 9:e1004023 (2013) open access HTML
  • overlap-layout-consensus
  • graphe de Bruijn
Lectures principales
  • Compeau, P. E. C., P. A. Pevzner & G. Tessler How to apply de Bruijn graphs to genome assembly", Nature Biotechnology 29:987-991 (2011) paywall HTML.
  • Nagarajan N. & M. Pop. Sequence assembly demystified. Nature Reviews Genetics, 14:157-167 (2013) paywall HTML.
  • Diapos № 13: assemblage de novo PDF icon PDF.
  • Sutton G. R., O. White, M. D. Adams & A. R. Kerlavage. TIGR assembler: a new tool for assembling large shotgun sequencing projects. Genome Science and Technology, 1:9 (1995).
  • Huang, X., & A. Madan. CAP3: a DNA sequence assembly program. Genome Research, 9:868-877 (1999) open access HTML
  • Myers, E. W. Toward simplifying and accurately formulating fragment assembly. Journal of Computational Biology, 2: 275-290 (1995). [calcul de contigs, simplification du graphe de chevauchements]
  • Myers, E. W. & al. A whole-genome assembly of Drosophila. Science 287:2196-2204 (2000).
  • Pop, M. A., D. S. Kosack & S. L. Salzberg. Hierarchical scaffolding with Bambus. Genome Research 14:149-159 (2004) open access HTML
  • Wang, J. & al. RePS: A sequence assembler that masks exact repeats identified from the shotgun data. Genome Research, 12:824-831 (2004) open access HTML
  • Treangen, T. J. & S. L. Salzberg. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics, 13:36-46 (2012) paywall HTML.
  • Idury R. & M. S. Waterman. A new algorithm for DNA sequence assembly. Journal of Computational Biology, 2: 291-306 (1995).
  • Pevzner, P. A., H. Tang & M. S. Waterman. A new approach to fragment assembly in DNA sequencing. Proc. RECOMB 251-267 (2001) [première version d'EULER]
  • Pevzner, P. A. & H. Tang. Fragment assembly with double-barreled data. Bioinformatics, 17:S225-S233 (2001) [EULER-DB]
  • Zerbino, D. R. & E. Birney. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18:821-829 (2008) open access HTML
  • Simpson, T. J. & al. ABySS: a parallel assembler for short read sequence data. Genome Research, 19:1117-1123 (2009)
  • Li, R., H. Zhu, J. Ruan & al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Research, 20:265-272 (2010) [SOAPdenovo] open access HTML
  • Gnerre, S. & al. High-quality draft assemblies of mammalian genomes from massively parallel sequencing data. Proceedings of the National Academy of Sciences of the USA, 108:1513-1518 (2011) [ALLPATHS-LG] open access HTML
  • Earl, D. & al. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21:2224-2241 (2011) open access HTML
Indels et variation structurale
  • petites insertions et supressions
  • copy number variation
  • inférence par lectures appariées et couverture
Lectures principales
  • Lunter, G, A. Rocco, N. Mimouni, A. Heger, A. Caldeira & J. Hein. Uncertainty in homology inferences: Assessing and improving genomic sequence alignment. Genome Research 18:298-309 (2008) open access HTML
  • Alkan, C., B. P. Coe & E. E. Eichler. Genome structural variation discovery and genotyping. Nature Reviews Genetics 12:363-376 (2012) paywall HTML
  • Diapos № 9: alignement statistique PDF icon PDF.
  • Thorne, J. L., H. Kishino & J. Felsenstein. An evolutionary model for maximum likelihood alignment of DNA sequences. Journal of Molecular Evolution, 33: 114-124 (1991) PDF icon PDF (sur le site de Jeffrey Thorne).
  • Lunter, G., A. J. Drummond, I. Miklós & J. Hein. Statistical alignment; recent progress, new applications, and challenges. In R. Nielsen (Ed.) Statistical Methods in Molecular Evolution, Springer, 2005. paywall HTML
  • Diapos № 14: indels et variation structurale PDF icon PDF.
  • Mills, R. E. & al. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Research 21:830-839 (2011) open access HTML
  • Neuman, J. A., O. Isakov, & N. Shomron. Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in Bioinformatics, 14:46-55 (2012) paywall HTML
  • Albers, C. A. & al. Dindel: Accuate indel calls from short-read data. Genome Research 21:961-973 (2011) open access HTML
  • Chen, K. & al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods 6:677-681 (2012) paywall HTML
  • Medvedev, P. & al. Detecting copy number variation with mated short reads. Genome Research 20:1613-1622 (2010) paywall HTML
Génomique du cancer
  • petites insertions et supressions
  • copy number variation
  • inférence par lectures appariées et couverture
Lecture principale
  • Myerson, M., S. Gabriel & G. Getz. Advances in understanding cancer genomes through second-generation sequencing. Nature Reviews Genetics 11:685-696 (2010) paywall HTML
  • Diapos № 15: génomique du cancer PDF icon PDF.
  • Wheeler, D. A. & L. Wang. Fom human genome to cancer genome: The first decade. Genome Research 23:1054-1062 (2012) open access HTML
  • Frank, S. A. & M. A. Nowak. Problems of somatic mutation and cancer. BioEssays 26:291-299 (2004) paywall HTML
  • Roth, A. & al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics 28:907-913 (2012) open access HTML
  • Roberts, N. D. & al. A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics 29:2223-2230 (2013) open access HTML
  • The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487:330-337 (2012) open access HTML
  • Murnane. J. P. & L. Sabatier. Chromosome rearrangements resulting from telomere dysfunction and their role in cancer. BioEssays 26:1164-1174 (2004) paywall HTML
  • Raphael, B. J., S. Volik, C. Collins & P. A. Pevzner. Reconstructing tumor genome architectures. Bioinformatics 19:ii162-ii171 (2003) open access HTML
  • Hampton, O. A. & al. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Research 19:167-177 (2009) open access HTML
  • Yates, L. R. & P. J. Campbell. Evolution of the cancer genome. Nature Reviews Genetics 13:795-806 (2012) paywall HTML
  • Frumkin, D. & al. Cell lineage analysis of a mouse tumor. Cancer Research 68:5924-5931 (2008) open access HTML
  • Gerlinger & al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New England Journal of Medicine 366:883-892 (2012) open access HTML
  • Ding, L. & al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481:506-510 (2012) open access HTML
  • analyse taxnomique, analyse de fonctions
  • comparaisons: UniFrac
  • microbiome humain
Lecture principale
  • Cho, I. & M. J. Blaser. The human microbiome: at the interface of health and disease. Nature Reviews Genetics 13:260-270 (2011) paywall HTML
  • Diapos № 16: métagénomique PDF icon PDF.
  • Cox, M. J., W. O. C. M. Cookson & M. F. Moffatt. Sequencing the human microbiome in health and disease. Human Molecular Genetics 22:R88-R94 (2013) paywall HTML
  • Mande, S. S., M. H. Mohammed & T. S. Ghosh. Classification of metagenomic sequences: methods and challenges. Briefings in Bioinformatics 13:669-681 (2012) paywall HTML
  • Overbeek, S. & al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research 33:5691-5702 (2005) [fonctions SEED] open access HTML
  • Peng, Y., H. C. M. Leung, S. M. Yiu & F. Y. L. Chin. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420-1428 (2012) open access HTML
  • De Filippo, C., M. Ramazzotti, P. Fontana & D. Cavalieri. Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. Briefings in Bioinformatics 13:696-710 (2012) open access HTML
  • Lozupone, C. & R. Knight. UniFrac: a new phylogenetic method for comparing microbial communities Applied and Environmental Microbiology 71:8228-8235 (2005) open access HTML
  • Raes, J. & P. Bork. Molecular eco-systems biology: towards an understanding o community function. Nature Reviews Microbiology 6:1-7 (2008) paywall HTML
  • Collison, M. & al. Data mining the human gut microbiota for therapeutic targets. Briefings in Bioinformatics 13:751-768 (2012) paywall HTML
  • Qin, J., R. Li & al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464:59-65 (2010) open access HTML
  • Segata, N. & al. Computational meta'omics for microbial community studies. Molecular Systems Biology 9:666 (2013) open access HTML
  • De Filippo, C. & al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences of the USA 107:14691-14696 (2010) open access HTML
  • Dominguez-Bello, M. G., & al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences of the USA 107:11971-11975 (2010) open access HTML
  • Lozupone, C. A. & al. Meta-analyses of studies of the human microbiota. Genome Research 23:1704-1714 (2013) open access HTML


Devoir № 1 à remettre le 27 février
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Fichiers: sss5.tre (arbre de 5 espèces de levure) | yeast-geneswithintrons.txt (génes avec introns dans S. cerevisiae)
Devoir № 2 à remettre le 27 mars
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Devoir № 3 à remettre le 27 avril
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Mini-questionnaire à remettre le 27 avril
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