Publications
The concept of oligonucleotide usage patterns (OUP) was described in the following two publications:
Reva,
O.N.,
Tuemmler, B. (2005).
Differentiation of regions with atypical oligonucleotide composition in
bacterial genomes. BMC Bioinformatics. 6:251. (http://www.biomedcentral.com/1471-2105/6/251)
Reva,
O.N., Tuemmler, B. (2004). Global features of sequences of bacterial
chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage
patterns. BMC Bioinformatics. 5(1):90. (http://www.biomedcentral.com/1471-2105/5/90
)
Published SeqWord tools:
Rotimi A.M., Pierneef R., Reva O.N. (2018) Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools. BMC Bioinformatics 19(1):309..
Pierneef R., Classen F.J., Reva O.N. (2018) Long Non-coding RNAs in the Human Genome Acquired by Horizontal Gene Transfer. The Open Bioinformatics Journal 11 (1).
Classen F.J., Pierneef R., Slippers B., Reva O.N. (2018) EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes. BMC Genomics 19(1):323.
Yu X., Reva O.N. (2018) SWPhylo - a novel tool for phylogenomic inferences by comparison of oligonucleotide patterns and integration of genome-based and gene-based phylogenetic trees. Evolut. Bioinf., 14, 1-12.
Pierneef R., Cronje L., Bezuidt O., Reva O (2015) Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes. Database (Oxford), 2015, 1-13..
Papers where SeqWord tools were used
Kublanov IV, Sigalova OM, Gavrilov SN, Lebedinsky AV, Rinke C, Kovaleva O, Chernyh NA, Ivanova N, Daum C, Reddy TB, Klenk HP, Spring S, Göker M, Reva ON, Miroshnichenko ML, Kyrpides NC, Woyke T, Gelfand MS, Bonch-Osmolovskaya EA. (2017) Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. Sci Rep. 7(1):3682..
Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN. (2017) Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT. Sci Rep. 7(1):3682..
Reva ON, Pierneef RE, Tümmler B. (2017) Bioinformatic, Molecular, and Genetic Tools for Exploring Genome-Wide Responses to Hydrocarbons. Cellular Ecophysiology of Microbe, pp.1-9..
Pierneef R., Bezuidt O., Reva O (2015) Optimization and Practical Use of Composition Based Approaches Towards Identification and Collection of Genomic Islands and Their Ontology in Prokaryotes. Procedia Computer Science 2015, 51, 670-679..
Reva O, Bezuidt O. (2012). Distribution of horizontally transferred heavy metal resistance operons in recent outbreak bacteria. Mobile Genetic Elements, 2(2), 96-100..
Borriss R., Rueckert C, Blom J, Bezuidt O, Reva O, Klenk H-P. (2012) Chapter 18. Whole genome sequence comparison in taxonomy. In Rainey F and Oren A (Eds) Taxonomy of Prokaryotes (Methods in Microbiology).V. 38, Waltham M.A., USA: Academic Press.
Bezuidt O, Ganesan H, Labuschange P, Emmett W, Pierneef R, Reva O. (2011) Linguistic Approaches for Annotation, Visualization and Comparison of Prokaryotic Genomes and Environmental Sequences. In N-Y Yang (Ed) Systems and Computational Biology - Molecular and Cellular Experimental Systems. Chapter 2, 27-52. InTeck, Croatia.
Bezuidt O, Pierneef R, Mncube K, Lima-Mendez G, Reva ON. (2011) Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011. PLoS ONE 6(10): e25702.
Davenport CF, Wiehlmann L, Reva ON, Tuemmler B. (2009) Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides. Environ Microbiol. 11(5): 1092-1104.
Ganesan H., Rakitianskaia A.S., Davenport C.F., Tuemmler B., Reva O. (2008) The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage. BMC Bioinformatics 9(1):333.
Reva O., Tuemmler B. (2008) Think big - giant genes in bacteria. Environ. Microbiol. 10(3), 768-777.
Reva O., Willenbrock H., Hallin P. F., Sicheritz-Ponten T., Tuemmler B., Ussary D. (2008) Global features of the Alcanivorax borkumensis SK2 genome. Environ. Microbiol. 10(3), 614-625.
Reva O. and Tuemmler B. (2008). Oligonucleotide Usage Signatures of the Pseudomonas putida KT2440 Genome. In P. Cornelis (Ed) Pseudomonas: Genomics and Molecular Biology. Chapter 3. Caister Academic Press, 2008, 43-64.
Chen X.-H., Koumoutsi A., Scholz R., Eisenreich A., Schneider K., Schneider I., Morgenstern B., Voss B., Hess W. R., Reva O., Junge H., Voigt B., Jungblut P. R., Vater J., Suessmuth R., Liesegang H., Strittmatter A., Gottschalk G., Borriss R. Comparative analysis of the complete genome sequence of the plant growth promoting Bacillus amyloliquefaciens FZB42. Nature Biotechnology. 2007, 25(9): 1007-1014.
Klockgether J, Wuerdemann D, Reva O, Wiehlmann L, Tuemmler B. (2007). Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa.J Bacteriol. 189(6): 2443-59.
Klockgether, J., Reva, O., Tuemmler, B. (2006). Spread of genomic islands between clinical and environmental isolates. In