MarkovBin: An Algorithm to Cluster Metagenomic Reads Using a Mixture Modeling of Hierarchical Distributions
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[1] T. Urich,et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils , 2006, Nature.
[2] Frank Oliver Glöckner,et al. Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective , 2012, Briefings Bioinform..
[3] Jonathan A Eisen,et al. Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes , 2007, PLoS biology.
[4] M. Waterman,et al. Estimating the repeat structure and length of DNA sequences using L-tuples. , 2003, Genome research.
[5] Siu-Ming Yiu,et al. MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample , 2012, Bioinform..
[6] Frank Oliver Glöckner,et al. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences , 2004, BMC Bioinformatics.
[7] Sophie Schbath,et al. Exceptional Motifs in Different Markov Chain Models for a Statistical Analysis of DNA Sequences , 1995, J. Comput. Biol..
[8] Lior Pachter,et al. Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities , 2005, PLoS Comput. Biol..
[9] J. Handelsman,et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. , 1998, Chemistry & biology.
[10] C. Deming,et al. Topographical and Temporal Diversity of the Human Skin Microbiome , 2009, Science.
[11] G J McLachlan,et al. Mixture modelling for cluster analysis , 2004, Statistical methods in medical research.
[12] Siu-Ming Yiu,et al. MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species , 2012, J. Comput. Biol..
[13] Zhaojun Bai,et al. CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads , 2007, RECOMB.
[14] N. Pace,et al. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[15] G. McLachlan,et al. The EM algorithm and extensions , 1996 .
[16] Gabriel Valiente,et al. Flexible taxonomic assignment of ambiguous sequencing reads , 2011, BMC Bioinformatics.
[17] Mihai Pop,et al. Genome assembly reborn: recent computational challenges , 2009, Briefings Bioinform..
[18] Yan Boucher,et al. Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies , 2006, Applied and Environmental Microbiology.
[19] D. Alland,et al. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. , 2007, Journal of microbiological methods.
[20] William M. Rand,et al. Objective Criteria for the Evaluation of Clustering Methods , 1971 .
[21] Alexander F. Auch,et al. MEGAN analysis of metagenomic data. , 2007, Genome research.
[22] G. McLachlan,et al. Extensions of the EM Algorithm , 2007 .
[23] Jonathan Dushoff,et al. Unsupervised statistical clustering of environmental shotgun sequences , 2009, BMC Bioinformatics.
[24] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[25] Benjamin J. Raphael,et al. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families , 2007, PLoS biology.
[26] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[27] R. Amann,et al. Application of tetranucleotide frequencies for the assignment of genomic fragments. , 2004, Environmental microbiology.
[28] John C. Wooley,et al. A Primer on Metagenomics , 2010, PLoS Comput. Biol..
[29] P. Bork,et al. A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.
[30] Daniel H. Huson,et al. MetaSim—A Sequencing Simulator for Genomics and Metagenomics , 2008, PloS one.
[31] H. Akaike. A new look at the statistical model identification , 1974 .
[32] R. Knight,et al. Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.
[33] D. Bentley,et al. Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.
[34] David Ussery,et al. Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes , 2008, PLoS Comput. Biol..
[35] S. Giovannoni,et al. The uncultured microbial majority. , 2003, Annual review of microbiology.
[36] G. Schwarz. Estimating the Dimension of a Model , 1978 .
[37] Siu-Ming Yiu,et al. A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio , 2011, Bioinform..
[38] Shigehiko Kanaya,et al. Informatics for unveiling hidden genome signatures. , 2003, Genome research.
[39] J. Banfield,et al. Community structure and metabolism through reconstruction of microbial genomes from the environment , 2004, Nature.
[40] Naryttza N. Diaz,et al. TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach , 2009, BMC Bioinformatics.
[41] James R. Cole,et al. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis , 2004, Nucleic Acids Res..
[42] BMC Bioinformatics , 2005 .
[43] Steven Salzberg,et al. Clustering metagenomic sequences with interpolated Markov models , 2010, BMC Bioinformatics.
[44] S. Salzberg,et al. Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov Models , 2009, Nature Methods.
[45] M. Cugmas,et al. On comparing partitions , 2015 .
[46] Yu-Wei Wu,et al. A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples , 2010, RECOMB.
[47] Lawrence G. Wayne,et al. International Committee on Systematic Bacteriology announcement of the report of the ad hoc Committee on Reconciliation of Approaches to Bacterial Systematics. , 1988, The Journal of applied bacteriology.
[48] J. Eisen,et al. A simple, fast, and accurate method of phylogenomic inference , 2008, Genome Biology.
[49] Huzefa Rangwala,et al. Evaluation of short read metagenomic assembly , 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
[50] I. Rigoutsos,et al. Accurate phylogenetic classification of variable-length DNA fragments , 2007, Nature Methods.