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)
→ HTML.
- Koonin, E. V.
Darwinian evolution in the light of genomics.
Nucleic Acids Research 37:1011-1034 (2009)
→ HTML .
- Références
- Affiche
→ PDF.
- Note № 1: introduction
→ PDF.
- Note № 2: profils phylétiques
→ PDF.
- Diapos № 1: le génome
→ PDF.
- Diapos № 2: profils phylétiques
→ 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)
→ 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)
→ 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)
→ HTML.
- Koonin, E. V.
Comparative genomics, minimal gene-sets, and the last universal common ancestor.
Nature Reviews Microbiology 1:127-136 (2003)
→ 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)
→ 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)
→ 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)
→ 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)
→ 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)
→ HTML.
- Références
- Note № 3: substitutions
→ PDF.
- Note № 4: programmation dynamique avec modèles probabilistes
→ PDF.
- Note № 5: procéssus de Markov à temps continu
→ PDF.
- Diapos № 3: conservation
→ PDF.
- Asthana, S., M.Roytberg, J. Stamatoyannopoulos & S. Sunyaev.
Analysis of sequence conservation at nucleotide resolution.
PLoS Computational Biology 3:e254 (2007)
→ 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)
→ 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)
→ HTML.
- Eddy, S.
A model of the statistical power of comparative genome sequence analysis.
PLoS Biology 3:e10 (2005)
→ 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)
→ 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)
→ HTML.
- Pollard K. S. & al.
An RNA gene expressed during cortical development evolved rapidly in humans.
Nature 443:167-172 (2006)
→ 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)
→ HTML.
[PhyloP]
- Ponting, C. P. & R. C. Hardison.
What fraction of the human genome is functional?
Genome Research 21:1769-1776 (2011)
→ HTML.
- Siepel, A. & al.
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Genome Research 15:1034-1050 (2005)
→ HTML.
- Siepel, A., K. S. Pollard & D. Haussler.
New methods for detecting lineage-specific selection.
Proc. RECOMB 190-205 (2006)
→ 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)
→ HTML.
- Séquençage haut débit
- Lectures obligatoires
- Shendure, J. & E. L. Arden.
The expanding scope of DNA sequencing.
Nature Biotechnology 30:1084-1094 (2012)
→ HTML.
- Références
- Diapos № 4: séquençage
→ 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]
→ HTML.
- Ewing, B. & P. Green. Base-calling of automated sequencer traces using
Phred. II. Error probabilities.
Genome Research 8: 186-194. (1998)
[score Phred]
→ HTML.
- Green, E. D.
Strategies for the systematic sequencing of complex genomes.
Nature Reviews Genetics 2: 573-583 (2001).
[séquençage de premiers génomes]
→ HTML.
- IHGSC.
Initial sequencing and analysis of the human genome.
Nature 609: 860-921 (2001)
→ HTML.
- Mardis, E. R.
Next-generation DNA sequencing methods.
Annual Reviews of Genomics and Human Genetics 9:387-402 (2008)
→ HTML.
- Mardis, E. R.
A decade's perspective on DNA sequencing technology.
Nature 470:198-203 (2011)
→ HTML.
- Metzker, M. L.
Sequencing technologies - the next generation.
Nature Reviews Genetics 11:31-46 (2010)
→ HTML.
- Ronaghi, M., M. Uhlén, & P. Nyrén.
A sequencing method based on real-time pyrophosphate.
Science 281: 363-365 (1998).
[pyroséquençage]
→ HTML.
- Ion Torrent
- Illumina
- Alignement à grande échelle
-
- recherche de homologies: structures de données et algorithmes
- seed-and-extend, graine espacée
- Références
- Diapos № 5: hachage
→ PDF.
- Diapos № 7: extension
→ PDF.
- NIH/NCBI: The statistics of sequence similarity scores
→ 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]
→ HTML
- Lin, H., Z. Zhang, M. Q. Zhang, B. Ma & M. Li. ZOOM! Zillions of oligos mapped.
Bioinformatics 24:2431-2437 (2008)
→ HTML
- Épigénomique
-
- 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)
→ HTML
→ PMC.
- Pepke, S., B. Wold & A. Mortazavi.
Computation for ChIP-seq and RNA-seq studies.
Nature Methods 6:S22-S32 (2009)
→ HTML.
- Références
- Diapos № 6: séquençage haut débit et épigénomique
→ PDF.
- Bhandare, R., J. Schug & al.
Genome-wide analysis of histone modifications in human pancreatic islets.
Genome Research 20:428-433 (2010)
→ 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]
→ HTML.
- Gaffney, D. J., G. McVicker & al.
Controls of nucleosome positioning in the human genome.
PLoS Genetics 8:e1003036 (2012)
→ 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)
→ 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)
→ HTML.
- Kaplan, N. & al.
The DNA-encoded nucleosome organization of a eukaryotic genome.
Nature 458:362-366 (2009)
→ HTML.
- Park, P. J.
ChIP-seq: advantages and challenges of a maturing technology.
Nature Reviews Genetics 10:669-680 (2009)
→ HTML.
- Raj, A. & G. McVicker.
The genome shows its sensitive side.
Nature Methods 11:39-40 (2014)
→ 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]
→ 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)
→ HTML.
- Valouev & al.
Determinants of nucleosome organization in primary human cells.
Nature 474:516-520 (2011)
→ HTML.
- Wasserman, W. W. & A. Sandelin.
Applied bioinformatics for the identification of regulatory elements.
Nature Reviews Genetics 5:276-287 (2004)
→ HTML.
- Wold, B. & R. M. Myers.
Sequence consensus methods for functional genomics.
Nature Methods 5:19-21 (2008)
[survol d'applications]
→ HTML.
- Zentner, G. E. & S. Henikoff.
Surveying the epigenomic landscape, one base at a time.
Genome Biology 13:250 (2012)
→ 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)
→ HTML.
- Bock, C.
Analysing and interpreting DNA methylation data.
Nature Reviews Genetics
13:705-719 (2012)
→ HTML.
- Références
- Diapos № 8: îlots CpG et méthylation
→ 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]
→ HTML.
- Jones, P. A.
Functions of DNA methylation: islands, start sites, gene bodies and beyond.
Nature Reviews Genetics 13:484-492 (2012)
[fonctions biologiques]
→ HTML.
- Lister, R., M. Pelizzola & al.
Human DNA methylomes at base resolution show widespread epigenomic differences.
Nature 462:315-322 (2009)
[une application pionière]
→ HTML.
- Laird, P. W.
Principles and challenges of genome-wide DNA methylation analysis.
Nature Reviews Genetics 11:191-203 (2010)
[survol de méthodologies]
→ 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]
→ 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]
→ 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).
→ HTML
→ PMC.
- Références
- Diapos № 10: read mapping
→ PDF.
- Li, H.
Improving SNP discovery by base alignment quality.
Bioinformatics 27:1157-1158 (2011).
→ HTML.
- SAM: Sequence Alignment/Map Format Specification → PDF
- VCF Variant Call Format Specification: →HTML
- sourceforge: samtools | vcftools
- 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)
→ HTML
→ PMC.
- Références
- Diapos № 11: variant calling
→ PDF.
- Schwartz, R. Theory and algorithms for the haplotype assembly problem.
Communications in Information and Systems 10:23-38 (2010)
→PDF.
- Alkan, C., B. P. Coe & E. E. Eichler.
Genome structural variation discovery and genotyping.
Nature Reviews Genetics
12:363-376 (2012)
→ 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)
→ HTML
→ PMC.
- Li, Y. & al.
MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes.
Genetic Epidemiology 34:816-834 (2010)
→ HTML
- Wikipedia:
principe Hardy-Weinberg FR EN
- Parenté
-
- 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)
→ 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)
→ HTML
- Références
- Diapos № 12: identity by descent
→ 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)
→ 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)
→ 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)
→ HTML
- Gusev, A. & al.
Whole population, genome-wide mapping of hidden relatedness.
Genome Research 19:318-326 (2009)
→ 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)
→ 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)
→ 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)
→ HTML
- Su, S-Y. & al.
Detection of identity by descent using next-generation whole genome sequencing data.
BMC Bioinformatics 13:121 (2012)
→ HTML
- Palamara, P.F., T. Lencz, A. Darvasi & I. Pe'er.
American Journal of Human Genetics 91: 809-822 (2012)
→ 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)
→ HTML
- Assemblage
-
- 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)
→ HTML.
- Nagarajan N. & M. Pop.
Sequence assembly demystified.
Nature Reviews Genetics, 14:157-167 (2013)
→ HTML.
- Références
- Diapos № 13: assemblage de novo
→ 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)
→ 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)
→ HTML
- Wang, J. & al.
RePS: A sequence assembler that masks exact repeats identified from the shotgun data.
Genome Research, 12:824-831 (2004)
→ HTML
- Treangen, T. J. & S. L. Salzberg.
Repetitive DNA and next-generation sequencing: computational challenges and solutions.
Nature Reviews Genetics, 13:36-46 (2012)
→ 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)
→ 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]
→ 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]
→ HTML
- Earl, D. & al.
Assemblathon 1: A competitive assessment of de novo short read assembly methods.
Genome Research, 21:2224-2241 (2011)
→ 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)
→ HTML
- Alkan, C., B. P. Coe & E. E. Eichler.
Genome structural variation discovery and genotyping.
Nature Reviews Genetics
12:363-376 (2012)
→ HTML
- Références
- Diapos № 9: alignement statistique
→ 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
(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.
→ HTML
- Diapos № 14: indels et variation structurale
→ PDF.
- Mills, R. E. & al.
Natural genetic variation caused by small insertions and deletions in the human genome.
Genome Research 21:830-839 (2011)
→ 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)
→ HTML
- Albers, C. A. & al.
Dindel: Accuate indel calls from short-read data.
Genome Research 21:961-973 (2011)
→ HTML
- Chen, K. & al.
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.
Nature Methods 6:677-681 (2012)
→ HTML
- Medvedev, P. & al.
Detecting copy number variation with mated short reads.
Genome Research 20:1613-1622 (2010)
→ 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)
→ HTML
- Références
- Diapos № 15: génomique du cancer
→ PDF.
- Wheeler, D. A. & L. Wang.
Fom human genome to cancer genome: The first decade.
Genome Research
23:1054-1062 (2012)
→ HTML
- Frank, S. A. & M. A. Nowak.
Problems of somatic mutation and cancer.
BioEssays 26:291-299 (2004)
→ 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)
→ HTML
- Roberts, N. D. & al.
A comparative analysis of algorithms for somatic SNV detection in cancer.
Bioinformatics 29:2223-2230 (2013)
→ HTML
- The Cancer Genome Atlas Network.
Comprehensive molecular characterization of human colon and rectal cancer.
Nature 487:330-337 (2012)
→ HTML
- Murnane. J. P. & L. Sabatier.
Chromosome rearrangements resulting from telomere dysfunction and their role in cancer.
BioEssays 26:1164-1174 (2004)
→ HTML
- Raphael, B. J., S. Volik, C. Collins & P. A. Pevzner.
Reconstructing tumor genome architectures.
Bioinformatics 19:ii162-ii171 (2003)
→ 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)
→ HTML
- Yates, L. R. & P. J. Campbell.
Evolution of the cancer genome.
Nature Reviews Genetics 13:795-806 (2012)
→ HTML
- Frumkin, D. & al.
Cell lineage analysis of a mouse tumor.
Cancer Research 68:5924-5931 (2008)
→ HTML
- Gerlinger & al.
Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
New England Journal of Medicine 366:883-892 (2012)
→ HTML
- Ding, L. & al.
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing.
Nature 481:506-510 (2012)
→ HTML
- Métagénomique
-
- 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)
→ HTML
- Références
- Diapos № 16: métagénomique
→ 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)
→ HTML
- Mande, S. S., M. H. Mohammed & T. S. Ghosh.
Classification of metagenomic sequences: methods and challenges.
Briefings in Bioinformatics
13:669-681 (2012)
→ 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]
→ 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)
→ 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)
→ HTML
- Lozupone, C. & R. Knight.
UniFrac: a new phylogenetic method for comparing microbial communities
Applied and Environmental Microbiology
71:8228-8235 (2005)
→ HTML
- Raes, J. & P. Bork.
Molecular eco-systems biology: towards an understanding o community function.
Nature Reviews Microbiology
6:1-7 (2008)
→ HTML
- Collison, M. & al.
Data mining the human gut microbiota for therapeutic targets.
Briefings in Bioinformatics
13:751-768 (2012)
→ HTML
- Qin, J., R. Li & al.
A human gut microbial gene catalogue established by metagenomic sequencing.
Nature,
464:59-65 (2010)
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- Segata, N. & al.
Computational meta'omics for microbial community studies.
Molecular Systems Biology
9:666 (2013)
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- 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)
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- 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)
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- Lozupone, C. A. & al.
Meta-analyses of studies of the human microbiota.
Genome Research
23:1704-1714 (2013)
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Devoirs
- Devoir № 1
à remettre le 27 février
- Énoncé
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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
- Énoncé
→ PDF
- Devoir № 3
à remettre le 27 avril
- Énoncé
→ PDF
- Mini-questionnaire
à remettre le 27 avril
- Énoncé
→ PDF