Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases

PHYLIP-Phylogeny inference package (Version 3.2)

Felsenstein, J. (1989) · Cladistics · Cited by 17,682

Tree View: An application to display phylogenetic trees on personal computers

Page, R. (1996) · Computer applications in the biosciences · doi:10.1093/bioinformatics/12.4.357 · Cited by 10,223

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128

Phylogenetic structure of the prokaryotic domain: The primary kingdoms

Woese, C. R., & Fox, G. E. (1977) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.74.11.5088 · Cited by 4,131

The complete genome sequence of the gastric pathogen Helicobacter pylori

Tomb, J.-F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., et al. (1997) · Nature · doi:10.1038/41483 · Cited by 3,529

A Molecular View of Microbial Diversity and the Biosphere

Pace, N. R. (1997) · Science · doi:10.1126/science.276.5313.734 · Cited by 2,797

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7

Perna, N. T., Plunkett, G., Burland, V., Mau, B., Glasner, J. D., Rose, D. J., Mayhew, G. F., Evans, P. S., Gregor, J., Kirkpatrick, H. A., et al. (2001) · Nature · doi:10.1038/35054089 · Cited by 2,035

The RDP (Ribosomal Database Project)

Maidak, B. L., Olsen, G. J., Larsen, N. E., Overbeek, R., McCaughey, M. J., & Woese, C. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.109 · Cited by 2,018

The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

Parkhill, J., Wren, B. W., Mungall, K., Ketley, J. M., Churcher, C. M., Basham, D., Chillingworth, T., Davies, R. M., Feltwell, T., Holroyd, S. A., et al. (2000) · Nature · doi:10.1038/35001088 · Cited by 1,966

Phylogenetic Classification and the Universal Tree

Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888

Shifting the genomic gold standard for the prokaryotic species definition

Richter, M., & Rossello-Mora, R. A. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906412106 · Cited by 6,343

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) · doi:10.7717/peerj.1165 · Cited by 1,960

Phylogenomics and the reconstruction of the tree of life

Delsuc, F., Brinkmann, H., & Philippe, H. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1603 · Cited by 1,264

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

Wu, Y., Tang, Y.-H., Tringe, S. G., Simmons, B. A., & Singer, S. W. (2014) · Microbiome · doi:10.1186/2049-2618-2-26 · Cited by 725

Improved metagenome binning and assembly using deep variational autoencoders

Nissen, J. N., Johansen, J., Allesøe, R. L., Sønderby, C. K., Armenteros, J. J. A., Grønbech, C. H., Jensen, L. J., Nielsen, H. B., Petersen, T. N., Winther, O., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00777-4 · Cited by 663

Sequence modeling and design from molecular to genome scale with Evo

Nguyen, E., Poli, M., Durrant, M. G., Kang, B., Katrekar, D., Li, D. B., Bartie, L. J., Thomas, A. W., King, S. H., Brixi, G., et al. (2024) · Science · doi:10.1126/science.ado9336 · Cited by 580

Accurate phylogenetic classification of variable-length DNA fragments

McHardy, A. C., Martín, H. G., Tsirigos, A., Hugenholtz, P., & Rigoutsos, I. (2006) · Nature Methods · doi:10.1038/nmeth976 · Cited by 564

Community-wide analysis of microbial genome sequence signatures

Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., Yelton, A. P., & Banfield, J. F. (2009) · Genome biology · doi:10.1186/gb-2009-10-8-r85 · Cited by 527

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

Liu, B., Faller, L. L., Klitgord, N., Mazumdar, V., Ghodsi, M., Sommer, D. D., Gibbons, T. R., Treangen, T. J., Chang, Y.-C., Li, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037919 · Cited by 411

TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

Teeling, H., Waldmann, J., Lombardot, T., Bauer, M., & Glöckner, F. O. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-163 · Cited by 396

Application of tetranucleotide frequencies for the assignment of genomic fragments

Teeling, H., Meyerdierks, A., Bauer, M., Amann, R., & Glöckner, F. O. (2004) · Environmental Microbiology · doi:10.1111/j.1462-2920.2004.00624.x · Cited by 386

A conspicuous nickel protein in microbial mats that oxidize methane anaerobically

Krüger, M., Meyerdierks, A., Glöckner, F. O., Amann, R., Widdel, F., Kube, M., Reinhardt, R., Kahnt, J., Böcher, R., Thauer, R. K., et al. (2003) · Nature · doi:10.1038/nature02207 · Cited by 373

Phylogenomics

Philippe, H., Delsuc, F., Brinkmann, H., & Lartillot, N. (2005) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130205 · Cited by 306

En route to a genome-based classification of Archaea and Bacteria?

Klenk, H., & Göker, M. (2010) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2010.03.003 · Cited by 276

Classification of metagenomic sequences: methods and challenges

Mande, S. S., Mohammed, M. H., & Ghosh, T. S. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs054 · Cited by 257

Large-scale sequence comparisons with sourmash

Pierce‐Ward, N. T., Irber, L. C., Reiter, T. E., Brooks, P., & Brown, C. T. (2019) · F1000Research · doi:10.12688/f1000research.19675.1 · Cited by 222

Towards a prokaryotic genomic taxonomy.

Coenye, T., Gevers, D., de Peer, Y. V., Vandamme, P., & Swings, J. (2005) · FEMS Microbiology Reviews · doi:10.1016/j.femsre.2004.11.004 · Cited by 212

Lysogeny is prevalent and widely distributed in the murine gut microbiota

Kim, M., & Bae, J. (2018) · The ISME Journal · doi:10.1038/s41396-018-0061-9 · Cited by 226

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

Teeling, H., & Glöckner, F. O. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs039 · Cited by 221

Achievements and new knowledge unraveled by metagenomic approaches

Simon, C., & Daniel, R. (2009) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-009-2233-z · Cited by 220

The human gut virome: a multifaceted majority

Ogilvie, L. A., & Jones, B. V. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00918 · Cited by 212

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

Klatt, C. G., Wood, J. M., Rusch, D. B., Bateson, M. M., Hamamura, N., Heidelberg, J. F., Grossman, A. R., Bhaya, D., Cohan, F. M., Kühl, M., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.73 · Cited by 186

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

Graham, E. D., Heidelberg, J. F., & Tully, B. (2017) · PeerJ · doi:10.7717/peerj.3035 · Cited by 189

Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes

Yutin, N., Suzuki, M. T., Teeling, H., Weber, M., Venter, J. C., Rusch, D. B., & Béjà, O. (2007) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01265.x · Cited by 184

Evidence for Diversifying Selection at the Pyoverdine Locus of Pseudomonas aeruginosa

Smith, E. E., Sims, E. H., Spencer, D. H., Kaul, R., & Olson, M. V. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.6.2138-2147.2005 · Cited by 176

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution

Jun, S., Sims, G. E., Wu, G. A., & Kim, S. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0913033107 · Cited by 160

Genomic Repeat Abundances Contain Phylogenetic Signal

Dodsworth, S., Chase, M. W., Kelly, L. J., Leitch, I. J., Macas, J., Novák, P., Piednoël, M., Weiss‐Schneeweiss, H., & Leitch, A. R. (2014) · Systematic Biology · doi:10.1093/sysbio/syu080 · Cited by 155

Contribution of Horizontally Acquired Genomic Islands to the Evolution of the Tubercle Bacilli

Becq, J., Gutierrez, M. C., Rosas-Magallanes, V., Rauzier, J., Gicquel, B., Neyrolles, O., & Deschavanne, P. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm111 · Cited by 156

Metagenomic signatures of 86 microbial and viral metagenomes

Willner, D. L., Thurber, R. L. V., & Rohwer, F. L. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01901.x · Cited by 145

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

Pan, Y., Zeng, J., Li, L., Yang, J., Tang, Z., Xiong, W., Li, Y., Chen, S., & Zeng, Z. (2020) · mSystems · doi:10.1128/msystems.00821-19 · Cited by 146

Detection and characterization of horizontal transfers in prokaryotes using genomic signature

Dufraigne, C. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni004 · Cited by 140

CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads

Chatterji, S., Yamazaki, I., Bai, Z., & Eisen, J. A. (2008) · Lecture notes in computer science · doi:10.1007/978-3-540-78839-3_3 · Cited by 137

Bacteriophage and their potential roles in the human oral cavity

Edlund, A., Santiago-Rodríguez, T. M., Boehm, T. K., & Pride, D. T. (2015) · Journal of Oral Microbiology · doi:10.3402/jom.v7.27423 · Cited by 141

Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses

Pride, D. T., Wassenaar, T. M., Ghose, C., & Blaser, M. J. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-8 · Cited by 124

Towards a prokaryotic genomic taxonomy

Coenye, T., Gevers, D., de Peer, Y. V., Vandamme, P. A. R., & Swings, J. (2005) · FEMS Microbiology Reviews · doi:10.1016/j.fmrre.2004.11.004 · Cited by 122

Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov.

Lopes-Santos, L., Castro, D. B. A., Ferreira-Tonin, M., Corrêa, D. B. A., Weir, B. S., Park, D., Ottoboni, L. M. M., Neto, J. R., & Destéfano, S. A. L. (2017) · Antonie van Leeuwenhoek · doi:10.1007/s10482-017-0842-6 · Cited by 112

Comparative analysis of magnetosome gene clusters in magnetotactic bacteria provides further evidence for horizontal gene transfer

Jogler, C., Kube, M., Schübbe, S., Ullrich, S., Teeling, H., Bazylinski, D. A., Reinhardt, R., & Schüler, D. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01854.x · Cited by 111

What's in the mix: phylogenetic classification of metagenome sequence samples

McHardy, A. C., & Rigoutsos, I. (2007) · Current Opinion in Microbiology · doi:10.1016/j.mib.2007.08.004 · Cited by 112

Metagenome Fragment Classification Using N‐Mer Frequency Profiles

ROSEN, G. L., Garbarine, E., Caseiro, D., Robi Polikar, A., & Sokhansanj, B. A. (2008) · Advances in Bioinformatics · doi:10.1155/2008/205969 · Cited by 103

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

Delmont, T. O., & Eren, A. M. (2016) · PeerJ · doi:10.7717/peerj.1839 · Cited by 96

Estimating Mutation Distances from Unaligned Genomes

Haubold, B., Pfaffelhuber, P., Domazet-Lošo, M., & Wiehe, T. (2009) · Journal of Computational Biology · doi:10.1089/cmb.2009.0106 · Cited by 97

Bioinformatics for the Human Microbiome Project

Gevers, D., Pop, M., Schloss, P. D., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002779 · Cited by 91

Phylogenetic diversity and metagenomics of candidate division OP3

Glöckner, J., Kube, M., Shrestha, P. M., Weber, M., Glöckner, F. O., Reinhardt, R., & Liesack, W. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02164.x · Cited by 89

Expression of eukaryotic‐like protein in the microbiome of sponges

Díez‐Vives, C., Moitinho‐Silva, L., Nielsen, S., Reynolds, D., & Thomas, T. (2016) · Molecular Ecology · doi:10.1111/mec.14003 · Cited by 89

A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies

Criscuolo, A. (2019) · Research Ideas and Outcomes · doi:10.3897/rio.5.e36178 · Cited by 83

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes

Papudeshi, B. N., Haggerty, J. M., Doane, M. P., Morris, M. M., Walsh, K., Beattie, D. T., Pande, D., Zaeri, P., Silva, A. E. T., Thompson, F. L., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-4294-1 · Cited by 83

Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences

Ogilvie, L. A., Bowler, L. D., Caplin, J., Dedi, C., Diston, D., Cheek, E., Taylor, H. D., Ebdon, J., & Jones, B. V. (2013) · Nature Communications · doi:10.1038/ncomms3420 · Cited by 78

Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis

Dubinkina, V. B., Ischenko, D. S., Игоревич, У. В., Tyakht, A., & Alexeev, D. G. (2016) · BMC Bioinformatics · doi:10.1186/s12859-015-0875-7 · Cited by 83

Think big – giant genes in bacteria

Reva, O. N., & Tümmler, B. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01500.x · Cited by 78

High-resolution characterization of the human microbiome

Noecker, C. A., McNally, C. P., Eng, A., & Borenstein, E. (2016) · Translational research · doi:10.1016/j.trsl.2016.07.012 · Cited by 81

Targeted diversity generation by intraterrestrial archaea and archaeal viruses

Paul, B. G., Bagby, S. C., Czornyj, E., Arambula, D. G., Handa, S., Sczyrba, A., Ghosh, P., Miller, J. F., & Valentine, D. L. (2015) · Nature Communications · doi:10.1038/ncomms7585 · Cited by 77

Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy

Sant’Anna, F. H., Bach, E., Porto, R. Z., Guella, F. L., Sant’Anna, E. H., & Passaglia, L. M. P. (2019) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2019.1569587 · Cited by 82

Microbial Lifestyle and Genome Signatures

Dutta, C. (2012) · Current Genomics · doi:10.2174/138920212799860698 · Cited by 76

Comparison of metagenomic samples using sequence signatures

Jiang, B., Song, K., Ren, J., Deng, M., Sun, F., & Zhang, X. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-730 · Cited by 71

Generating viral metagenomes from the coral holobiont

Weynberg, K. D., Wood‐Charlson, E. M., Suttle, C. A., & van Oppen, M. J. H. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00206 · Cited by 76

Detecting Horizontal Gene Transfer between Closely Related Taxa

Adato, O., Ninyo, N., Gophna, U., & Snir, S. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004408 · Cited by 74

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

Mohammed, M. H., Ghosh, T. S., Singh, N. K., & Mande, S. S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq608 · Cited by 71

Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

Duhaime, M. B., Wichels, A., Waldmann, J., Teeling, H., & Glöckner, F. O. (2010) · The ISME Journal · doi:10.1038/ismej.2010.94 · Cited by 69

Phylogenomic Analysis of Oenococcus oeni Reveals Specific Domestication of Strains to Cider and Wines

Campbell-Sills, H., Khoury, M. E., Favier, M., Romano, A., Franco Biasioli, A., Spano, G., Sherman, D. J., Bouchez, O., Coton, E., Coton, M., et al. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv084 · Cited by 67

Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns

Reva, O. N., & Tümmler, B. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-90 · Cited by 65

Veillonella, Firmicutes: Microbes disguised as Gram negatives

Vesth, T., Ozen, A. I., Andersen, S. C., Kaas, R. S., Lukjančenko, O., Bohlin, J., Nookaew, I., Wassenaar, T. M., & Ussery, D. W. (2013) · Standards in Genomic Sciences · doi:10.4056/sigs.2981345 · Cited by 69

Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System

Skennerton, C. T., Angly, F. E., Breitbart, M., Bragg, L. M., He, S., McMahon, K. D., Hugenholtz, P., & Tyson, G. W. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020095 · Cited by 61

MetaDecoder: a novel method for clustering metagenomic contigs

Liu, C., Dong, S., Chen, J., Wang, C., Ning, P., Guo, Y., & Yang, T. (2022) · Microbiome · doi:10.1186/s40168-022-01237-8 · Cited by 67

Alignment-free distance measure based on return time distribution for sequence analysis: Applications to clustering, molecular phylogeny and subtyping

Kolekar, P. S., Kale, M. M., & Kulkarni‐Kale, U. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.07.003 · Cited by 60

Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

Weber, M., Teeling, H., Huang, S., Waldmann, J., Kassabgy, M., Fuchs, B. M., Klindworth, A., Klockow, C., Wichels, A., Gerdts, G., et al. (2010) · The ISME Journal · doi:10.1038/ismej.2010.180 · Cited by 57

Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

Saeed, I., Tang, S., & Halgamuge, S. K. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1204 · Cited by 57

The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components

Humbert, O., & Salama, N. R. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn718 · Cited by 55

Exploration of phylogenetic data using a global sequence analysis method

Chapus, C., Dufraigne, C., Edwards, S. V., Giron, A., Fertil, B., & Deschavanne, P. (2005) · BMC Evolutionary Biology · doi:10.1186/1471-2148-5-63 · Cited by 52

A reexamination of information theory-based methods for DNA-binding site identification

Erill, I., & O’Neill, M. C. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-57 · Cited by 45

Estimation of bacterial species phylogeny through oligonucleotide frequency distances

Ueda, M. T., Kryukov, K. A., & Saitou, N. (2009) · Genomics · doi:10.1016/j.ygeno.2009.01.009 · Cited by 44

Differentiation of regions with atypical oligonucleotide composition in bacterial genomes

Reva, O. N., & Tümmler, B. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-251 · Cited by 46

Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction

Vishnepolsky, B., Grigolava, M., Managadze, G., Gabrielian, A. E., Rosenthal, A., Hurt, D. E., Tartakovsky, M., & Pirtskhalava, M. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac233 · Cited by 45

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage

Ganesan, H., Bosman, A. S., Davenport, C., Tümmler, B., & Reva, O. N. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-333 · Cited by 45

An acquisition account of genomic islands based on genome signature comparisons

van Passel, M. W., Bart, A., Thygesen, H. H., Luyf, A. C. M., ENDE, A. V. D., & ENDE, A. V. D. (2005) · BMC Genomics · doi:10.1186/1471-2164-6-163 · Cited by 44

Exploring an alignment free approach for protein classification and structural class prediction

Deschavanne, P., & Tufféry, P. (2007) · Biochimie · doi:10.1016/j.biochi.2007.11.004 · Cited by 43

N-gram analysis of 970 microbial organisms reveals presence of biological language models

Osmanbeyoglu, H. U., & Ganapathiraju, M. K. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-12 · Cited by 43

Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled

Brbić, M., Warnecke, T., Kriško, A., & Supek, F. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv088 · Cited by 36

n -Nucleotide circular codes in graph theory

Fimmel, E., Michel, C. J., & Strüngmann, L. (2016) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2015.0058 · Cited by 42

Computational Prediction of Bacteriophage Host Ranges

Versoza, C. J., & Pfeifer, S. P. (2022) · Microorganisms · doi:10.3390/microorganisms10010149 · Cited by 39

Alignment-free supervised classification of metagenomes by recursive SVM

Cui, H., & Zhang, X. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-641 · Cited by 37

Mainstreams of Horizontal Gene Exchange in Enterobacteria: Consideration of the Outbreak of Enterohemorrhagic E. coli O104:H4 in Germany in 2011

Bezuidt, O. K. I., Pierneef, R., Mncube, K., Lima‐Mendez, G., & Reva, O. N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025702 · Cited by 35

Unexpected absence of ribosomal protein genes from metagenome-assembled genomes

Mise, K., & Iwasaki, W. (2022) · ISME Communications · doi:10.1038/s43705-022-00204-6 · Cited by 35

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

Bohlin, J., Skjerve, E., & Ussery, D. W. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-104 · Cited by 37

Signal Processing for Metagenomics: Extracting Information from the Soup

ROSEN, G. L., Sokhansanj, B. A., Robi Polikar, A., Bruns, M. A., Russell, J. A., Garbarine, E., Essinger, S., & Yok, N. (2009) · Current Genomics · doi:10.2174/138920209789208255 · Cited by 38

Bioinformatic approaches for studying the microbiome of fermented food

Walsh, L. H., Coakley, M., Walsh, A. M., O’Toole, P. W., & Cotter, P. D. (2022) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2022.2132850 · Cited by 38

Taxonomy and systematics of plant probiotic bacteria in the genomic era

Carro, L., & Nouioui, I. (2017) · AIMS Microbiology · doi:10.3934/microbiol.2017.3.383 · Cited by 37

Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies

Francois, C. M., Durand, F., Figuet, E., & Galtier, N. (2019) · G3 Genes Genomes Genetics · doi:10.1534/g3.119.400758 · Cited by 35

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

Pride, D. T., & Schoenfeld, T. W. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-420 · Cited by 33

Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil

Kielak, A. M., Rodrigues, J. L. M., Kuramae, E. E., Chain, P., van Veen, J. A., & Kowalchuk, G. A. (2009) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2009.00785.x · Cited by 33

Mapping the Space of Genomic Signatures

Lila Kari, A., Hill, K. A., Sayem, A. S. M., Karamichalis, R., Bryans, N., Davis, K., & Dattani, N. S. (2015) · PLoS ONE · doi:10.1371/journal.pone.0119815 · Cited by 33

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