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doi.org
Andrzej Zielezinski, Susana Vinga, Jonas Almeida et Wojciech M. Karlowski, « Alignment-free sequence comparison: benefits, applications, and tools », Genome Biology, vol. 18, no 1, , p. 186 (ISSN1474-760X, DOI10.1186/s13059-017-1319-7, lire en ligne, consulté le )
Kaitlin E Samocha, Elise B Robinson, Stephan J Sanders et Christine Stevens, « A framework for the interpretation of de novo mutation in human disease », Nature Genetics, vol. 46, no 9, , p. 944–950 (ISSN1061-4036, PMID25086666, PMCID4222185, DOI10.1038/ng.3050).
Varun Aggarwala et Benjamin F Voight, « An expanded sequence context model broadly explains variability in polymorphism levels across the human genome », Nature Genetics, vol. 48, no 4, , p. 349–355 (ISSN1061-4036, PMID26878723, PMCID4811712, DOI10.1038/ng.3511).
Andrzej Zielezinski, Susana Vinga, Jonas Almeida et Wojciech M. Karlowski, « Alignment-free sequence comparison: benefits, applications, and tools », Genome Biology, vol. 18, no 1, , p. 186 (ISSN1474-760X, DOI10.1186/s13059-017-1319-7, lire en ligne, consulté le )
nih.gov
ncbi.nlm.nih.gov
P. Compeau, P. Pevzner et G. Teslar, « How to apply de Bruijn graphs to genome assembly », Nature Biotechnology, vol. 29, no 11, , p. 987–991 (PMID22068540, PMCID5531759, DOI10.1038/nbt.2023).
Kaitlin E Samocha, Elise B Robinson, Stephan J Sanders et Christine Stevens, « A framework for the interpretation of de novo mutation in human disease », Nature Genetics, vol. 46, no 9, , p. 944–950 (ISSN1061-4036, PMID25086666, PMCID4222185, DOI10.1038/ng.3050).
Varun Aggarwala et Benjamin F Voight, « An expanded sequence context model broadly explains variability in polymorphism levels across the human genome », Nature Genetics, vol. 48, no 4, , p. 349–355 (ISSN1061-4036, PMID26878723, PMCID4811712, DOI10.1038/ng.3511).
Zerbino, Daniel R. et Birney, Ewan, « Velvet: algorithms for de novo short read assembly using de Bruijn graphs », Genome Research, vol. 18, no 5, , p. 821–829 (PMID18349386, PMCID2336801, DOI10.1101/gr.074492.107)
"Rachid Ounit, Steve Wanamaker, Timothy J Close and Stefano Lonardi", « CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers », BMC Genomics, vol. 16, , p. 236 (PMID25879410, PMCID4428112, DOI10.1186/s12864-015-1419-2)
Dubinkina, Ischenko, Ulyantsev, Tyakht, Alexeev, « Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis », BMC Bioinformatics, vol. 17, , p. 38 (PMID26774270, PMCID4715287, DOI10.1186/s12859-015-0875-7)
Meher, Sahu, Rao, « Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier », Gene, vol. 592, no 2, , p. 316–324 (PMID27393648, DOI10.1016/j.gene.2016.07.010)
Li et al, « De novo assembly of human genomes with massively parallel short read sequencing », Genome Research, vol. 20, no 2, , p. 265–272 (PMID20019144, PMCID2813482, DOI10.1101/gr.097261.109)
Navarro-Gomez et al, « Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier », Bioinformatics, vol. 31, no 8, , p. 1310–1312 (PMID25505086, PMCID4393525, DOI10.1093/bioinformatics/btu825)
Newburger, Bulyk, « UniPROBE: an online database of protein binding microarray data on protein–DNA interactions », Nucleic Acids Research, vol. 37(supp 1), no Database issue, , D77–82 (PMID18842628, PMCID2686578, DOI10.1093/nar/gkn660)
Nordstrom et al, « Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers », Nature Biotechnology, vol. 31, no 4, , p. 325–330 (PMID23475072, DOI10.1038/nbt.2515)
Chae et al, « Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes », Nucleic Acids Research, vol. 41, no 9, , p. 4783–4791 (PMID23519616, PMCID3643570, DOI10.1093/nar/gkt144)
Mohamed Hashim, Abdullah, « Rare k-mer DNA: Identification of sequence motifs and prediction of CpG island and promoter », Journal of Theoretical Biology, vol. 387, , p. 88–100 (PMID26427337, DOI10.1016/j.jtbi.2015.09.014)
Jaron, Moravec, Martinkova, « SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes », Bioinformatics, vol. 30, no 8, , p. 1081–1086 (PMID24371153, DOI10.1093/bioinformatics/btt727)
Bemm et al, « Genome of a tardigrade: Horizontal gene transfer or bacterial contamination? », Proceedings of the National Academy of Sciences, vol. 113, no 22, , E3054–E3056 (PMID27173902, PMCID4896698, DOI10.1073/pnas.1525116113)
Lamichhaney et al, « Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax) », Nature Genetics, vol. 48, no 1, , p. 84–88 (PMID26569123, DOI10.1038/ng.3430)
Patro, Mount, Kingsford, « Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms », Nature Biotechnology, vol. 32, no 5, , p. 462–464 (PMID24752080, PMCID4077321, DOI10.1038/nbt.2862, arXiv1308.3700)
