TY - JOUR AU - Wood, A. P. AU - Kelly, D. P. PY - 1985 DA - 1985// TI - Physiological characteristics of a new thermophilic obligately chemolithotrophic Thiobacillus species, Thiobacillus tepidarius JO - Int J Syst Bact VL - 35 UR - https://doi.org/10.1099/00207713-35-4-434 DO - 10.1099/00207713-35-4-434 ID - Wood1985 ER - TY - JOUR AU - Wood, A. P. AU - Kelly, D. P. PY - 1986 DA - 1986// TI - Chemolithotrophic metabolism of the newly-isolated moderately thermophilic, obligately autotrophic Thiobacillus tepidarius JO - Arch Microbiol VL - 114 UR - https://doi.org/10.1007/BF00454959 DO - 10.1007/BF00454959 ID - Wood1986 ER - TY - JOUR AU - Kelly, D. P. AU - Wood, A. P. PY - 2000 DA - 2000// TI - Reclassification of some species of Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov JO - Int J Syst Evol Microbiol VL - 50 UR - https://doi.org/10.1099/00207713-50-2-511 DO - 10.1099/00207713-50-2-511 ID - Kelly2000 ER - TY - JOUR AU - Williams, K. P. AU - Kelly, D. P. PY - 2013 DA - 2013// TI - Proposal for a new class within the phylum Proteobacteria, Acidithiobacillia classis nov., with the type order Acidithiobacillales, and emended description of the class Gammaproteobacteria JO - Int J Syst Evol Microbiol VL - 63 UR - https://doi.org/10.1099/ijs.0.049270-0 DO - 10.1099/ijs.0.049270-0 ID - Williams2013 ER - TY - JOUR AU - Boden, R. AU - Cleland, D. AU - Green, P. N. AU - Katayama, Y. AU - Uchino, Y. AU - Murrell, J. C. AU - Kelly, D. P. PY - 2012 DA - 2012// TI - Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus JO - Arch Microbiol VL - 194 UR - https://doi.org/10.1007/s00203-011-0747-0 DO - 10.1007/s00203-011-0747-0 ID - Boden2012 ER - TY - JOUR AU - Lu, W. P. AU - Kelly, D. P. PY - 1988 DA - 1988// TI - Cellular location and partial purification of the ‘thiosulphate-oxidizing enzyme’ and ‘trithionate hydrolyase’ from Thiobacillus tepidarius JO - J Gen Microbiol VL - 134 ID - Lu1988 ER - TY - JOUR AU - Kelly, D. P. AU - Lu, W. P. AU - Poole, R. K. PY - 1993 DA - 1993// TI - Cytochromes of Thiobacillus tepidarius and the respiratory chain involved in the oxidation of thiosulfate and tetrathionate JO - Arch Microbiol VL - 160 UR - https://doi.org/10.1007/BF00288708 DO - 10.1007/BF00288708 ID - Kelly1993 ER - TY - JOUR AU - Field, D. AU - Garrity, G. AU - Gray, T. AU - Morrison, N. AU - Selengut, J. AU - Sterk, P. PY - 2008 DA - 2008// TI - The minimum information about a genome sequence (MIGS) specification JO - Nat Biotechnol VL - 26 UR - https://doi.org/10.1038/nbt1360 DO - 10.1038/nbt1360 ID - Field2008 ER - TY - JOUR AU - Fredericq, E. AU - Oth, A. AU - Fontaine, F. PY - 1961 DA - 1961// TI - The ultraviolet spectrum of deoxyribonucleic acids and their constituents JO - J Mol Biol VL - 3 UR - https://doi.org/10.1016/S0022-2836(61)80003-X DO - 10.1016/S0022-2836(61)80003-X ID - Fredericq1961 ER - TY - JOUR AU - Pagani, I. AU - Liolios, K. AU - Jansson, J. AU - Chen, I. M. AU - Smirnova, T. AU - Nosrat, B. PY - 2012 DA - 2012// TI - The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1100 DO - 10.1093/nar/gkr1100 ID - Pagani2012 ER - TY - JOUR AU - Markowitz, V. M. AU - Chen, I. -. M. A. AU - Palaniappan, K. AU - Chu, K. AU - Szeto, E. AU - Pillay, M. PY - 2014 DA - 2014// TI - IMG 4 version of the integrated microbial genomes comparative analysis system JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt963 DO - 10.1093/nar/gkt963 ID - Markowitz2014 ER - TY - JOUR AU - Mavromatis, K. AU - Land, M. L. AU - Brettin, T. S. AU - Quest, D. J. AU - Copeland, A. AU - Clum, A. PY - 2012 DA - 2012// TI - The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0048837 DO - 10.1371/journal.pone.0048837 ID - Mavromatis2012 ER - TY - JOUR AU - Bennett, S. PY - 2004 DA - 2004// TI - Solexa Ltd JO - Pharmacogenomics VL - 5 UR - https://doi.org/10.1517/14622416.5.4.433 DO - 10.1517/14622416.5.4.433 ID - Bennett2004 ER - TY - STD TI - JGI: Joint genome institute [http://www.jgi.doe.gov] UR - http://www.jgi.doe.gov ID - ref14 ER - TY - JOUR AU - Zerbino, D. AU - Birney, E. PY - 2008 DA - 2008// TI - Velvet: algorithms for de novo short read assembly using de Bruijn graphs JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.074492.107 DO - 10.1101/gr.074492.107 ID - Zerbino2008 ER - TY - STD TI - Reads simulator wgsim [https://github.com/lh3/wgsim] UR - https://github.com/lh3/wgsim ID - ref16 ER - TY - JOUR AU - Gnerre, S. AU - MacCallum, I. AU - Przybylski, D. AU - Ribeiro, F. J. AU - Burton, J. N. AU - Walker, B. J. PY - 2011 DA - 2011// TI - High-quality draft assemblies of mammalian genomes from massively parallel sequence data JO - P Natl A Sci. VL - 108 UR - https://doi.org/10.1073/pnas.1017351108 DO - 10.1073/pnas.1017351108 ID - Gnerre2011 ER - TY - JOUR AU - Hyatt, D. AU - Chen, G. L. AU - Locascio, P. F. AU - Land, M. L. AU - Larimer, F. W. AU - Hauser, L. J. PY - 2010 DA - 2010// TI - Prodigal: prokaryotic gene recognition and translation initiation site identification JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-119 DO - 10.1186/1471-2105-11-119 ID - Hyatt2010 ER - TY - JOUR AU - Huntemann, M. AU - Ivanova, N. N. AU - Mavromatis, K. AU - Tripp, H. J. AU - Paez-Espino, D. AU - Palaniappan, K. AU - Szeto, E. AU - Pillay, M. AU - Chen, I. M. -. A. AU - Pati, A. AU - Nielsen, T. AU - Markowitz, V. M. AU - Kyrpides, N. C. PY - 2015 DA - 2015// TI - The Standard Operating Procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4) JO - Stand Genom Sci VL - 10 UR - https://doi.org/10.1186/s40793-015-0077-y DO - 10.1186/s40793-015-0077-y ID - Huntemann2015 ER - TY - JOUR AU - Lowe, T. M. AU - Eddy, S. R. PY - 1997 DA - 1997// TI - tRNAscan–SE: a program for improved detection of transfer RNA genes in genomic sequence JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.5.0955 DO - 10.1093/nar/25.5.0955 ID - Lowe1997 ER - TY - JOUR AU - Pruesse, E. AU - Quast, C. AU - Knittel, F. B. AU - Ludwig, W. AU - Peplies, J. AU - Glckner, F. O. PY - 2007 DA - 2007// TI - SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB JO - Nuc Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm864 DO - 10.1093/nar/gkm864 ID - Pruesse2007 ER - TY - JOUR AU - Markowitz, V. M. AU - Mavromatis, K. AU - Ivanova, N. N. AU - Chen, I. -. M. A. AU - Chu, K. AU - Kyrpides, N. C. PY - 2009 DA - 2009// TI - IMG ER: a system for microbial genome annotation expert review and curation JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp393 DO - 10.1093/bioinformatics/btp393 ID - Markowitz2009 ER - TY - JOUR AU - Chen, I. M. A. AU - Markowitz, V. M. AU - Chu, K. AU - Anderson, I. AU - Mavromatis, K. AU - Kyrpides, N. C. AU - Ivanova, N. N. PY - 2013 DA - 2013// TI - Improving microbial genome annotations in an integrated database context JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0054859 DO - 10.1371/journal.pone.0054859 ID - Chen2013 ER - TY - JOUR AU - Wood, A. P. AU - Aurikko, J. P. AU - Kelly, D. P. PY - 2004 DA - 2004// TI - A challenge for 21st century molecular biology and biochemistry: what are the causes of obligate autotrophy and methanotrophy JO - FEMS Microbiol Rev VL - 28 UR - https://doi.org/10.1016/j.femsre.2003.12.001 DO - 10.1016/j.femsre.2003.12.001 ID - Wood2004 ER - TY - BOOK AU - Anthony, C. PY - 1982 DA - 1982// TI - The biochemistry of methylotrophs PB - Academic Press CY - London ID - Anthony1982 ER - TY - JOUR AU - Badger, M. R. AU - Bek, E. J. PY - 2008 DA - 2008// TI - Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle JO - J Exp Bot VL - 59 UR - https://doi.org/10.1093/jxb/erm297 DO - 10.1093/jxb/erm297 ID - Badger2008 ER - TY - JOUR AU - Meulenberg, R. AU - Pronk, J. T. AU - Frank, J. AU - Hazeu, W. AU - Bos, P. AU - Kuenen, J. G. PY - 1992 DA - 1992// TI - Purification and partial chracterization of a thermostable trithionate hydrolase from the acidophilic sulphur oxidizer Thiobacillus acidophilus JO - Eur J Biochem VL - 209 UR - https://doi.org/10.1111/j.1432-1033.1992.tb17298.x DO - 10.1111/j.1432-1033.1992.tb17298.x ID - Meulenberg1992 ER - TY - JOUR AU - Wood, A. P. AU - Kelly, D. P. PY - 1988 DA - 1988// TI - Isolation and characterisation of Thiobacillus aquaesulis sp. nov., a novel facultatively autotrophic moderate thermophile JO - Arch Microbiol VL - 149 UR - https://doi.org/10.1007/BF00411653 DO - 10.1007/BF00411653 ID - Wood1988 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - The Gene Ontology Consortium Nat Genet VL - 25 ID - Ashburner2000 ER - TY - STD TI - Guide to GO evidence codes [http://www.geneontology.org/GO.evidence.shtml] UR - http://www.geneontology.org/GO.evidence.shtml ID - ref30 ER - TY - JOUR AU - Tamura, K. AU - Stecher, G. AU - Peterson, D. AU - Filipski, A. AU - Sumar, S. PY - 2013 DA - 2013// TI - MEGA6: Molecular Evolutionary Generics Analysis version 6.0 JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst197 DO - 10.1093/molbev/mst197 ID - Tamura2013 ER - TY - JOUR AU - Tamura, K. AU - Nei, M. PY - 1993 DA - 1993// TI - Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees JO - Mol Biol Evol VL - 10 ID - Tamura1993 ER - TY - CHAP AU - Kelly, D. P. ED - Cole, J. A. ED - Ferguson, S. J. PY - 1988 DA - 1988// TI - Oxidation of sulphur compounds BT - The nitrogen and sulphur cycles PB - Cambridge University Press CY - Cambridge ID - Kelly1988 ER - TY - JOUR AU - Woese, C. R. AU - Kandler, O. AU - Wheelis, M. L. PY - 1990 DA - 1990// TI - Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya JO - Proc Natl Acad Sci U S A VL - 87 UR - https://doi.org/10.1073/pnas.87.12.4576 DO - 10.1073/pnas.87.12.4576 ID - Woese1990 ER - TY - CHAP AU - Garrity, G. M. AU - Bell, J. A. AU - Lilburn, T. AU - Phylum, X. I. V. ED - Garrity, G. M. ED - Brenner, D. J. ED - Krieg, N. R. ED - Staley, J. T. PY - 2005 DA - 2005// TI - Proteobacteria phyl. nov BT - Bergey’s Manual of Systematic Bacteriology PB - Springer CY - New York UR - https://doi.org/10.1007/0-387-29298-5_1 DO - 10.1007/0-387-29298-5_1 ID - Garrity2005 ER -