PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
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Andrzej Dziembowski | Leszek Lipinski | L. Lipiński | Pawel S Krawczyk | A. Dziembowski | P. Krawczyk
[1] Christopher M Thomas,et al. Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria , 2005, Nature Reviews Microbiology.
[2] I. Saeed,et al. Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition , 2011, Nucleic acids research.
[3] D. Ussery,et al. Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands , 2012, BMC Genomics.
[4] Eran Halperin,et al. Recycler: an algorithm for detecting plasmids from de novo assembly graphs , 2016 .
[5] Ö. Melefors,et al. Plasmidome-Analysis of ESBL-Producing Escherichia coli Using Conventional Typing and High-Throughput Sequencing , 2013, PloS one.
[6] P. Decewicz,et al. Analysis of the Genome and Mobilome of a Dissimilatory Arsenate Reducing Aeromonas sp. O23A Reveals Multiple Mechanisms for Heavy Metal Resistance and Metabolism , 2017, Front. Microbiol..
[7] Adi Doron-Faigenboim,et al. Insights into the bovine rumen plasmidome , 2012, Proceedings of the National Academy of Sciences.
[8] I. Mizrahi,et al. A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches. , 2013, Journal of microbiological methods.
[9] K. Minamisawa,et al. Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome , 2015, Proceedings of the National Academy of Sciences.
[10] Alexey A. Gurevich,et al. QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..
[11] John C. Wooley,et al. A Primer on Metagenomics , 2010, PLoS Comput. Biol..
[12] B. Dreiseikelmann,et al. A functional plasmid-borne rrn operon in soil isolates belonging to the genus Paracoccus. , 2003, Microbiology.
[13] A. Goesmann,et al. Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology. , 2008, Journal of Biotechnology.
[14] Eran Halperin,et al. Recycler: an algorithm for detecting plasmids from de novo assembly graphs , 2016, bioRxiv.
[15] Patricia Siguier,et al. Insertion sequences in prokaryotic genomes. , 2006, Current opinion in microbiology.
[16] J. Marchesi,et al. Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome , 2010, BMC Genomics.
[17] Yoseph Barash,et al. Integrative deep models for alternative splicing , 2017, bioRxiv.
[18] Sergio Arredondo-Alonso,et al. On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data , 2017, bioRxiv.
[19] John Vollmers,et al. Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters! , 2017, PloS one.
[20] A. Skłodowska,et al. Physiological and Metagenomic Analyses of Microbial Mats Involved in Self-Purification of Mine Waters Contaminated with Heavy Metals , 2016, Front. Microbiol..
[21] H. Heuer,et al. Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty. , 2008, FEMS Microbiology Ecology.
[22] J. Ramos,et al. Plasmid-Mediated Tolerance Toward Environmental Pollutants. , 2014, Microbiology spectrum.
[23] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[24] Gaël Varoquaux,et al. Scikit-learn: Machine Learning in Python , 2011, J. Mach. Learn. Res..
[25] Brian C. Thomas,et al. Community-wide analysis of microbial genome sequence signatures , 2009, Genome Biology.
[26] Anna Goldenberg,et al. TensorFlow: Biology's Gateway to Deep Learning? , 2016, Cell systems.
[27] H. Heuer,et al. Plasmids foster diversification and adaptation of bacterial populations in soil. , 2012, FEMS microbiology reviews.
[28] H. Saluz,et al. The plasmidome of a Salmonella enterica serovar Derby isolated from pork meat. , 2013, Plasmid.
[29] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[30] E. Kristiansson,et al. Pyrosequencing of Antibiotic-Contaminated River Sediments Reveals High Levels of Resistance and Gene Transfer Elements , 2011, PloS one.
[31] Eva M. Top,et al. Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes , 2008, Nucleic acids research.
[32] Derrick E. Wood,et al. Kraken: ultrafast metagenomic sequence classification using exact alignments , 2014, Genome Biology.
[33] Ying Xu,et al. Barcodes for genomes and applications , 2008, BMC Bioinformatics.
[34] J. Marchesi,et al. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome , 2007, Nature Methods.
[35] Sergey I. Nikolenko,et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..
[36] D. Willner,et al. Metagenomic signatures of 86 microbial and viral metagenomes. , 2009, Environmental microbiology.
[37] N. Leblond-Bourget,et al. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. , 2014, FEMS microbiology reviews.
[38] Masaki Shintani,et al. Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy , 2015, Front. Microbiol..
[39] S. Sørensen,et al. Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome , 2014, PloS one.
[40] J. Fry,et al. Isolation and screening of plasmids from the epilithon which mobilize recombinant plasmid pD10 , 1992, Applied and environmental microbiology.
[41] Fernando de la Cruz,et al. Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences , 2014, PLoS genetics.
[42] Seunghak Lee,et al. A network-driven approach for genome-wide association mapping , 2016, Bioinform..
[43] Shigehiko Kanaya,et al. Informatics for unveiling hidden genome signatures. , 2003, Genome research.
[44] J. Fry,et al. Novel method for studying plasmid transfer in undisturbed river epilithon , 1988, Applied and environmental microbiology.
[45] Matteo Brilli,et al. Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome , 2010, BMC Evolutionary Biology.
[46] Ryo Miyazaki,et al. Community-wide plasmid gene mobilization and selection , 2012 .
[47] T. Scheffer,et al. Taxonomic metagenome sequence assignment with structured output models , 2011, Nature Methods.
[48] Jon Bohlin,et al. Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes , 2008, BMC Genomics.
[49] I. Rigoutsos,et al. Accurate phylogenetic classification of variable-length DNA fragments , 2007, Nature Methods.
[50] Alessandra Carattoli,et al. Plasmids and the spread of resistance. , 2013, International journal of medical microbiology : IJMM.
[51] O. Stegle,et al. Deep learning for computational biology , 2016, Molecular systems biology.
[52] Tong Zhang,et al. Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge , 2011, PloS one.
[53] M. Kunnimalaiyaan,et al. Analysis of the replicon region and identification of an rRNA operon on pBM400 of Bacillus megaterium QM B1551 , 2001, Molecular microbiology.
[54] Marcel Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .
[55] Ole Lund,et al. In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing , 2014, Antimicrobial Agents and Chemotherapy.
[56] Angela C. M. Luyf,et al. Compositional discordance between prokaryotic plasmids and host chromosomes , 2006, BMC Genomics.
[57] David Ussery,et al. Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes , 2008, PLoS Comput. Biol..
[58] Fernando de la Cruz,et al. Mobility of Plasmids , 2010, Microbiology and Molecular Biology Reviews.
[59] J. Marchesi,et al. Accessing the mobile metagenome of the human gut microbiota. , 2007, Molecular bioSystems.
[60] A. Singer,et al. Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators , 2016, Front. Microbiol..
[61] J. Dib,et al. Strategies and approaches in plasmidome studies—uncovering plasmid diversity disregarding of linear elements? , 2015, Front. Microbiol..
[62] S. Djordjevic,et al. Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota , 2013, Front. Microbiol..
[63] Andreas Wilke,et al. phylogenetic and functional analysis of metagenomes , 2022 .
[64] H. Nishida. Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids , 2012, International journal of evolutionary biology.
[65] Tong Zhang,et al. Exploring antibiotic resistance genes and metal resistance genes in plasmid metagenomes from wastewater treatment plants , 2015, Front. Microbiol..
[66] Ying Xu,et al. cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data , 2010, Bioinform..
[67] Dmitry Antipov,et al. plasmidSPAdes: Assembling Plasmids from Whole Genome Sequencing Data , 2016, bioRxiv.
[68] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.