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Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R, Redondo-Nieto M.

PLoS One. 2016 Feb 25;11(2):e0150183. doi: 10.1371/journal.pone.0150183. Erratum in: PLoS One. 2016;11(4):e0153733.


Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species.

Prior P, Ailloud F, Dalsing BL, Remenant B, Sanchez B, Allen C.

BMC Genomics. 2016 Feb 1;17:90. doi: 10.1186/s12864-016-2413-z.


Genomic insights into the taxonomic status of the Bacillus cereus group.

Liu Y, Lai Q, Göker M, Meier-Kolthoff JP, Wang M, Sun Y, Wang L, Shao Z.

Sci Rep. 2015 Sep 16;5:14082. doi: 10.1038/srep14082.


Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity.

Chapman C, Henry M, Bishop-Lilly KA, Awosika J, Briska A, Ptashkin RN, Wagner T, Rajanna C, Tsang H, Johnson SL, Mokashi VP, Chain PS, Sozhamannan S.

PLoS One. 2015 Mar 20;10(3):e0120311. doi: 10.1371/journal.pone.0120311.


Identifying strains that contribute to complex diseases through the study of microbial inheritance.

Faith JJ, Colombel JF, Gordon JI.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):633-40. doi: 10.1073/pnas.1418781112.


First genome sequences of Achromobacter phages reveal new members of the N4 family.

Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, Rohde C.

Virol J. 2014 Jan 27;11:14. doi: 10.1186/1743-422X-11-14.


Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes.

Yuan J, Zhu Q, Liu B.

PLoS One. 2014 Jan 20;9(1):e84330. doi: 10.1371/journal.pone.0084330.


Prokaryotic phylogenies inferred from whole-genome sequence and annotation data.

Du W, Cao Z, Wang Y, Sun Y, Blanzieri E, Liang Y.

Biomed Res Int. 2013;2013:409062. doi: 10.1155/2013/409062.


Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences.

Satoh S, Mimuro M, Tanaka A.

PLoS One. 2013 Jul 26;8(7):e70290. doi: 10.1371/journal.pone.0070290.


Alignment-free genome tree inference by learning group-specific distance metrics.

Patil KR, McHardy AC.

Genome Biol Evol. 2013;5(8):1470-84. doi: 10.1093/gbe/evt105.


The long-term stability of the human gut microbiota.

Faith JJ, Guruge JL, Charbonneau M, Subramanian S, Seedorf H, Goodman AL, Clemente JC, Knight R, Heath AC, Leibel RL, Rosenbaum M, Gordon JI.

Science. 2013 Jul 5;341(6141):1237439. doi: 10.1126/science.1237439.


Comparative genomics of Bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon.

Milani C, Duranti S, Lugli GA, Bottacini F, Strati F, Arioli S, Foroni E, Turroni F, van Sinderen D, Ventura M.

Appl Environ Microbiol. 2013 Jul;79(14):4304-15. doi: 10.1128/AEM.00984-13.


Genome sequence-based species delimitation with confidence intervals and improved distance functions.

Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M.

BMC Bioinformatics. 2013 Feb 21;14:60. doi: 10.1186/1471-2105-14-60.


Meta-analysis of general bacterial subclades in whole-genome phylogenies using tree topology profiling.

Meinel T, Krause A.

Evol Bioinform Online. 2012;8:489-525. doi: 10.4137/EBO.S9642.


Polytomy identification in microbial phylogenetic reconstruction.

Lin GN, Zhang C, Xu D.

BMC Syst Biol. 2011;5 Suppl 3:S2. doi: 10.1186/1752-0509-5-S3-S2.


Keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity.

Fuerst JA, Sagulenko E.

Front Microbiol. 2012 May 4;3:167. doi: 10.3389/fmicb.2012.00167.


De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology.

Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kötter P, van Ham RC, Reinders MJ, Pronk JT, de Ridder D, Daran JM.

Microb Cell Fact. 2012 Mar 26;11:36. doi: 10.1186/1475-2859-11-36.


Tracing lifestyle adaptation in prokaryotic genomes.

Altermann E.

Front Microbiol. 2012 Feb 21;3:48. doi: 10.3389/fmicb.2012.00048.


QuartetS: a fast and accurate algorithm for large-scale orthology detection.

Yu C, Zavaljevski N, Desai V, Reifman J.

Nucleic Acids Res. 2011 Jul;39(13):e88. doi: 10.1093/nar/gkr308.


Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1).

Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.

Stand Genomic Sci. 2010 Aug 20;3(1):66-75. doi: 10.4056/sigs.1072907.

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