“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis
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James O. McInerney | Marco Fondi | Renato Fani | Emanuele Bosi | Marko Virta | J. McInerney | R. Fani | E. Alm | A. Karkman | M. Fondi | M. Tamminen | M. Virta | Eric Alm | Antti Karkman | Manu V. Tamminen | Emanuele Bosi
[1] Mathieu Bastian,et al. Gephi: An Open Source Software for Exploring and Manipulating Networks , 2009, ICWSM.
[2] P. Bork,et al. A Molecular Study of Microbe Transfer between Distant Environments , 2008, PloS one.
[3] Alexandros Stamatakis,et al. Metagenomic species profiling using universal phylogenetic marker genes , 2013, Nature Methods.
[4] K. Konstantinidis,et al. Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea , 2011, The ISME Journal.
[5] James H. Brown,et al. Microbial biogeography: putting microorganisms on the map , 2006, Nature Reviews Microbiology.
[6] Jianzhong Shen,et al. Occurrence of chloramphenicol-resistance genes as environmental pollutants from swine feedlots. , 2013, Environmental science & technology.
[7] D. Clewell,et al. Unconstrained bacterial promiscuity: the Tn916-Tn1545 family of conjugative transposons. , 1995, Trends in microbiology.
[8] P. Bork,et al. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data , 2011, Molecular systems biology.
[9] Stijn van Dongen,et al. Using MCL to extract clusters from networks. , 2012, Methods in molecular biology.
[10] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[11] M. Newman,et al. Mixing patterns in networks. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.
[12] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[13] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[14] J. Fuhrman. General Distributions and the 'rare Biosphere' Microbial Community Structure and Its Functional Implications Review Insight , 2022 .
[15] David Alvarez-Ponce,et al. Gene similarity networks provide tools for understanding eukaryote origins and evolution , 2013, Proceedings of the National Academy of Sciences.
[16] Mihai Pop,et al. ARDB—Antibiotic Resistance Genes Database , 2008, Nucleic Acids Res..
[17] E V Koonin,et al. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. , 1998, Trends in genetics : TIG.
[18] Gipsi Lima-Mendez,et al. Reticulate representation of evolutionary and functional relationships between phage genomes. , 2008, Molecular biology and evolution.
[19] Robert C. Edgar,et al. MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.
[20] A. Pühler,et al. Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. , 2007, FEMS microbiology reviews.
[21] F. Baquero,et al. Antibiotics and antibiotic resistance in water environments. , 2008, Current opinion in biotechnology.
[22] J. Fuhrman,et al. Beyond biogeographic patterns: processes shaping the microbial landscape , 2012, Nature Reviews Microbiology.
[23] Konstantinos Mavromatis,et al. Microbial co-habitation and lateral gene transfer: what transposases can tell us , 2009, Genome Biology.
[24] Eric Bapteste,et al. Network analyses structure genetic diversity in independent genetic worlds , 2009, Proceedings of the National Academy of Sciences.
[25] Gerard Talavera,et al. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.
[26] Michael Kohl,et al. Cytoscape: software for visualization and analysis of biological networks. , 2011, Methods in molecular biology.
[27] S. Stampi,et al. Occurrence of Listeria monocytogenes in sewage sludge. , 1998, Zentralblatt fur Hygiene und Umweltmedizin = International journal of hygiene and environmental medicine.
[28] C. Fields,et al. Biogeography of the Sulfolobus islandicus pan-genome , 2009, Proceedings of the National Academy of Sciences.
[29] G. Dunny,et al. Pheromone-inducible conjugation in Enterococcus faecalis: interbacterial and host-parasite chemical communication , 1995, Journal of bacteriology.
[30] Robert A. Edwards,et al. Identification and removal of ribosomal RNA sequences from metatranscriptomes , 2011, Bioinform..
[31] T. Sekizaki,et al. Chloramphenicol resistance transposable element TnSs1 of Streptococcus suis, a transposon flanked by IS6-family elements. , 2003, Plasmid.
[32] Ying Xu,et al. cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data , 2010, Bioinform..
[33] Stéphane Audic,et al. Testing ecological theories with sequence similarity networks: marine ciliates exhibit similar geographic dispersal patterns as multicellular organisms , 2015, BMC Biology.
[34] Tal Dagan,et al. Phylogenomic networks. , 2011, Trends in microbiology.
[35] I. Longden,et al. EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.
[36] Jing Chen,et al. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource , 2010, Nucleic Acids Res..
[37] A. Roiko,et al. Evaluation of Pathogen Removal in a Solar Sludge Drying Facility Using Microbial Indicators , 2010, International journal of environmental research and public health.
[38] P. W. Jones. Health hazards associated with the handling of animal wastes , 1980, Veterinary Record.
[39] Marco Fondi,et al. Large-scale analysis of plasmid relationships through gene-sharing networks. , 2012, Molecular biology and evolution.
[40] R. Amann,et al. Application of tetranucleotide frequencies for the assignment of genomic fragments. , 2004, Environmental microbiology.
[41] Tao Zhang,et al. The Airborne Metagenome in an Indoor Urban Environment , 2008, PloS one.
[42] G. Sermonti,et al. Chloramphenicol resistance in Streptomyces coelicolor A3(2): Possible involvement of a transposable element , 1978, Molecular and General Genetics MGG.
[43] Stephen J Chanock,et al. Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies , 2011, Investigative Genetics.
[44] Marco Fondi,et al. The mosaicism of plasmids revealed by atypical genes detection and analysis , 2011, BMC Genomics.
[45] Tal Dagan,et al. Trends and barriers to lateral gene transfer in prokaryotes. , 2011, Current opinion in microbiology.
[46] Marco Fondi,et al. The horizontal flow of the plasmid resistome: clues from inter-generic similarity networks. , 2010, Environmental microbiology.
[47] J. Gilbert,et al. The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota , 2014, PloS one.
[48] J. McInerney,et al. The public goods hypothesis for the evolution of life on Earth , 2011, Biology Direct.
[49] Tong Zhang,et al. Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge , 2011, PloS one.
[50] Robert A. Edwards,et al. Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..
[51] S. Jeffery. Evolution of Protein Molecules , 1979 .
[52] Woo Jun Sul,et al. Marine bacteria exhibit a bipolar distribution , 2013, Proceedings of the National Academy of Sciences.
[53] Otto X. Cordero,et al. Ecology drives a global network of gene exchange connecting the human microbiome , 2011, Nature.
[54] Otto X. Cordero,et al. Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations , 2011, mBio.
[55] J. T. Staley,et al. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. , 1985, Annual review of microbiology.
[56] Robert D. Finn,et al. HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..
[57] Steven H. Hinrichs,et al. RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles , 2011, BMC Bioinformatics.