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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 75 · see citing works

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 74 · see citing works

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 73 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 65 · see citing works

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 · see citing works

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 64 · see citing works

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 58 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 47 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 41 · see citing works

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 41 · see citing works

Computational Prediction of Bacteriophage Host Ranges

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

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 38 · see citing works

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 · see citing works

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 29 · see citing works

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 · see citing works

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 37 · see citing works

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 · see citing works

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 36 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Classification of COVID-19 and Other Pathogenic Sequences: A Dinucleotide Frequency and Machine Learning Approach

Dlamini, G. S., Muller, S., Meraba, R. L., Young, R. A., Mashiyane, J., Chiwewe, T. M., & Mapiye, D. S. (2020) · IEEE Access · doi:10.1109/access.2020.3031387 · Cited by 30 · see citing works

Global features of the Alcanivorax borkumensis SK2 genome

Reva, O. N., Hallin, P. F., Willenbrock, H., Sicheritz‐Pontén, T., Tümmler, B., & Ussery, D. W. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01483.x · Cited by 32 · see citing works

Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods

Bohlin, J., Snipen, L. G., Cloeckaert, A., Lagesen, K., Ussery, D. W., Kristoffersen, A. B., & Godfroid, J. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-249 · Cited by 31 · see citing works

MBBC: an efficient approach for metagenomic binning based on clustering

Wang, Y., Hu, H., & Li, X. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0473-8 · Cited by 29 · see citing works

Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

Oakley, B. B., Talundzic, E., Morales, C. A., Hiett, K. L., Siragusa, G. R., Валентинович, В. Н., & Seal, B. S. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-282 · Cited by 29 · see citing works

New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach

López‐López, A., Richter, M., Peña, A., Tamames, J., & Rossello-Mora, R. A. (2013) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2012.11.008 · Cited by 29 · see citing works

Genome Trees from Conservation Profiles

Tekaia, F., & Yeramian, E. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0010075 · Cited by 28 · see citing works

Examination of Genome Homogeneity in Prokaryotes Using Genomic Signatures

Bohlin, J., & Skjerve, E. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008113 · Cited by 29 · see citing works

The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity

Jiao, J., Zhang, B., Li, M., Zhang, Z., & Tian, C. F. (2021) · The ISME Journal · doi:10.1038/s41396-021-01118-2 · Cited by 28 · see citing works

Genomic Signatures in Microbes—Properties and Applications

Bohlin, J. (2011) · The Scientific World JOURNAL · doi:10.1100/tsw.2011.70 · Cited by 28 · see citing works

Analysis of genome similarity based on codon-pair usage

Li, H. (2011) · China Journal of Bioinformatics

Mathematical modelling of evolution of tetranucleotide usage patterns of whole bacterial genomes to improve phylogenetic inferences

Yu, X., & Reva, O. N. (2016) · Journal of Proteomics & Bioinformatics

Mathematical modeling of evolutionary changes of oligonucleotide frequency patterns of bacterial genomes for genome-scale phylogenetic inferences

Yu, X. (2018) · UpSpace Institutional Repository (University of Pretoria)

Stable tRNA-based phylogenies using only 76 nucleotides

Widmann, J. J., Harris, J. K., Lozupone, C., Wolfson, A. D., & Knight, R. D. (2010) · RNA · doi:10.1261/rna.726010 · Cited by 36 · see citing works

The reach of the genome signature in prokaryotes.

van Passel, M. W. J., Kuramae, E. E., Luyf, A. C. M., Bart, A., & Boekhout, T. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-84 · Cited by 77 · see citing works