TY - JOUR AU - Richard, G. F. AU - Kerrest, A. AU - Dujon, B. PY - 2008 DA - 2008// TI - Comparative genomics and molecular dynamics of DNA repeats in eukaryotes JO - Microbiol Mol Biol Rev VL - 72 UR - https://doi.org/10.1128/MMBR.00011-08 DO - 10.1128/MMBR.00011-08 ID - Richard2008 ER - TY - STD TI - Garrido-Ramos MA. Repetitive DNA: Karger Medical and Scientific Publishers; 2012. ID - ref2 ER - TY - JOUR AU - Nierman, W. C. AU - DeShazer, D. AU - Kim, H. S. AU - Tettelin, H. AU - Nelson, K. E. AU - Feldblyum, T. PY - 2004 DA - 2004// TI - Structural flexibility in the Burkholderia mallei genome JO - Proc Natl Acad Sci U S A VL - 101 UR - https://doi.org/10.1073/pnas.0403306101 DO - 10.1073/pnas.0403306101 ID - Nierman2004 ER - TY - JOUR AU - Adindla, S. AU - Inampudi, K. K. AU - Guruprasad, K. AU - Guruprasad, L. PY - 2004 DA - 2004// TI - Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools JO - Comp Funct Genom VL - 5 UR - https://doi.org/10.1002/cfg.358 DO - 10.1002/cfg.358 ID - Adindla2004 ER - TY - JOUR AU - Maeder, D. L. AU - Anderson, I. AU - Brettin, T. S. AU - Bruce, D. C. AU - Gilna, P. AU - Han, C. S. PY - 2006 DA - 2006// TI - The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes JO - J Bacteriol VL - 188 UR - https://doi.org/10.1128/JB.00810-06 DO - 10.1128/JB.00810-06 ID - Maeder2006 ER - TY - JOUR AU - Mahillon, J. AU - Chandler, M. PY - 1998 DA - 1998// TI - Insertion sequences JO - Microbiol Mol Biol Rev VL - 62 ID - Mahillon1998 ER - TY - JOUR AU - Subirana, J. A. AU - Albà, M. M. AU - Messeguer, X. PY - 2015 DA - 2015// TI - High evolutionary turnover of satellite families in Caenorhabditis JO - BMC Evol Biol VL - 15 UR - https://doi.org/10.1186/s12862-015-0495-x DO - 10.1186/s12862-015-0495-x ID - Subirana2015 ER - TY - JOUR AU - Awaru, A. K. AU - Saxena, S. AU - Sowpati, D. T. AU - Mishra, R. K. PY - 2017 DA - 2017// TI - MSDB: a comprehensive database of simple sequence repeats JO - Genome Biol Evol VL - 9 UR - https://doi.org/10.1093/gbe/evx132 DO - 10.1093/gbe/evx132 ID - Awaru2017 ER - TY - JOUR AU - Leahy, S. C. AU - Kelly, W. J. AU - Altermann, E. AU - Ronimus, R. S. AU - Yeoman, C. J. AU - Pacheco, D. M. PY - 2010 DA - 2010// TI - The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0008926 DO - 10.1371/journal.pone.0008926 ID - Leahy2010 ER - TY - JOUR AU - Garushyants, S. K. AU - Kazanov, M. D. AU - Gelfand, M. S. PY - 2015 DA - 2015// TI - Horizontal gene transfer and genome evolution in Methanosarcina JO - BMC Evol Biol VL - 15 UR - https://doi.org/10.1186/s12862-015-0393-2 DO - 10.1186/s12862-015-0393-2 ID - Garushyants2015 ER - TY - JOUR AU - Deppenmeyer, U. AU - Johann, A. AU - Hartsch, T. AU - Merkl, R. AU - Schmitz, R. A. AU - Martinez-Arias, R. PY - 2002 DA - 2002// TI - The genome of Methanosarcina mazei: evidence for lateral gene transfer between Bacteria and archaea JO - J Mol Microbiol Biotechnol VL - 4 ID - Deppenmeyer2002 ER - TY - JOUR AU - Galagan, J. E. AU - Nusbaum, C. AU - Roy, A. AU - Endrizzi, M. G. AU - Macdonald, P. AU - FitzHugh, W. PY - 2002 DA - 2002// TI - The genome of M. acetivorans reveals extensive metabolic and physiological diversity JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.223902 DO - 10.1101/gr.223902 ID - Galagan2002 ER - TY - JOUR AU - Lambie, S. C. AU - Kelly, W. J. AU - Leahy, S. C. AU - Li, D. AU - Reilly, K. AU - McAllister, T. A. PY - 2015 DA - 2015// TI - The complete genome sequence of the rumen methanogen Methanosarcina barkeri CM1 JO - Stand Genomic Sci VL - 10 UR - https://doi.org/10.1186/s40793-015-0038-5 DO - 10.1186/s40793-015-0038-5 ID - Lambie2015 ER - TY - JOUR AU - Bharathi, M. AU - Chellapandi, P. PY - 2017 DA - 2017// TI - Phylogenomic proximity and metabolic discrepancy of Methanosarcina mazei Go1 across methanosarcinal genomes JO - Biosystems. VL - 155 UR - https://doi.org/10.1016/j.biosystems.2017.03.002 DO - 10.1016/j.biosystems.2017.03.002 ID - Bharathi2017 ER - TY - JOUR AU - Hildenbrand, C. AU - Stock, T. AU - Lange, C. AU - Rother, M. AU - Soppa, J. PY - 2011 DA - 2011// TI - Genome copy numbers and gene conversion in methanogenic archaea JO - J Bacteriol VL - 193 UR - https://doi.org/10.1128/JB.01016-10 DO - 10.1128/JB.01016-10 ID - Hildenbrand2011 ER - TY - JOUR AU - Jing, H. AU - Takagi, J. AU - Liu, J. AU - Lindgren, S. AU - Zhang, R. AU - Joachimiak, A. PY - 2002 DA - 2002// TI - Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins JO - Structure. VL - 10 UR - https://doi.org/10.1016/S0969-2126(02)00840-7 DO - 10.1016/S0969-2126(02)00840-7 ID - Jing2002 ER - TY - JOUR AU - Ren, S. AU - Fu, G. AU - Jiang, X. AU - Zeng, R. AU - Miao, Y. AU - Xu, H. PY - 2003 DA - 2003// TI - Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing JO - Nature. VL - 422 UR - https://doi.org/10.1038/nature01597 DO - 10.1038/nature01597 ID - Ren2003 ER - TY - JOUR AU - Losada, L. AU - Ronning, C. M. AU - DeShazer, D. AU - Woods, D. AU - Fedorova, N. AU - Kim, H. S. PY - 2010 DA - 2010// TI - Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements JO - Genome Biol Evol. VL - 2 UR - https://doi.org/10.1093/gbe/evq003 DO - 10.1093/gbe/evq003 ID - Losada2010 ER - TY - JOUR AU - Bornberg-Bauer, E. AU - Albà, M. M. PY - 2013 DA - 2013// TI - Dynamics and adaptive benefits of modular protein evolution JO - Curr Opin Struct Biol VL - 23 UR - https://doi.org/10.1016/j.sbi.2013.02.012 DO - 10.1016/j.sbi.2013.02.012 ID - Bornberg-Bauer2013 ER - TY - JOUR AU - Lees, J. G. AU - Dawson, N. L. AU - Sillitoe, I. AU - Orengo, C. A. PY - 2016 DA - 2016// TI - Functional inovation from changes in protein domains and their combinations JO - Curr Opin Struct Biol VL - 38 UR - https://doi.org/10.1016/j.sbi.2016.05.016 DO - 10.1016/j.sbi.2016.05.016 ID - Lees2016 ER - TY - JOUR AU - Klinger, C. M. AU - Spang, A. AU - Dacks, J. B. AU - Ettema, T. J. G. PY - 2016 DA - 2016// TI - Tracing the archaeal origins of eukaryotic membrane-trafficking system building blocks JO - Mol Biol Evol VL - 33 UR - https://doi.org/10.1093/molbev/msw034 DO - 10.1093/molbev/msw034 ID - Klinger2016 ER - TY - JOUR AU - Méheust, R. AU - Watson, A. K. AU - Lapointe, F. AU - Papke, R. T. AU - Lopez, P. AU - Bapteste, E. PY - 2018 DA - 2018// TI - Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution JO - Genome Biol VL - 19 UR - https://doi.org/10.1186/s13059-018-1454-9 DO - 10.1186/s13059-018-1454-9 ID - Méheust2018 ER - TY - JOUR AU - Eme, L. AU - Spang, A. AU - Lombard, J. AU - Stairs, C. W. AU - Ettema, T. J. G. PY - 2017 DA - 2017// TI - Archaea and the origin of eukaryotes JO - Nature rev microbiol VL - 15 UR - https://doi.org/10.1038/nrmicro.2017.133 DO - 10.1038/nrmicro.2017.133 ID - Eme2017 ER - TY - JOUR AU - Spang, A. AU - Eme, L. AU - Saw, J. H. AU - Caceres, E. F. AU - Zaremba-Niedzwiedzka, K. AU - Lombard, J. PY - 2018 DA - 2018// TI - Asgard archaea are the closest prokaryotic relatives of eukaryotes JO - PLoS Genet VL - 14 UR - https://doi.org/10.1371/journal.pgen.1007080 DO - 10.1371/journal.pgen.1007080 ID - Spang2018 ER - TY - JOUR AU - DaCunha, V. AU - Gaia, M. AU - Nasir, A. AU - Forterre, P. PY - 2018 DA - 2018// TI - Asgard archaea do not close the debate about the universal tree of life topology JO - PLoS Genet VL - 14 UR - https://doi.org/10.1371/journal.pgen.1007215 DO - 10.1371/journal.pgen.1007215 ID - DaCunha2018 ER - TY - JOUR AU - Fournier, G. P. AU - Poole, A. M. PY - 2018 DA - 2018// TI - A briefly argued case that Asgard archaea are part of the eukaryote tree JO - Front Microbiol VL - 9 UR - https://doi.org/10.3389/fmicb.2018.01896 DO - 10.3389/fmicb.2018.01896 ID - Fournier2018 ER - TY - STD TI - National Center for Biotechnology Information. Genome Database. https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/refseq_category:reference. UR - https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/refseq_category:reference ID - ref27 ER - TY - JOUR AU - Yoshimura, J. AU - Ichikawa, K. AU - Shoura, M. J. AU - Artiles, K. L. AU - Gabdank, I. AU - Wahba, L. PY - 2019 DA - 2019// TI - Recompleting the Caenorhabditis elegans genome JO - Genome Res VL - 29 UR - https://doi.org/10.1101/gr.244830.118 DO - 10.1101/gr.244830.118 ID - Yoshimura2019 ER - TY - STD TI - Algorithmics and Genetics Group website: http://alggen.lsi.upc.edu. . UR - http://alggen.lsi.upc.edu ID - ref29 ER - TY - STD TI - SATFIND: http://datadryad.org/review?doi=doi:10.5061/dryad.h5s2q. UR - http://datadryad.org/review?doi=doi:10.5061/dryad.h5s2q ID - ref30 ER - TY - STD TI - MALIG: http://datadryad.org/review?doi=doi:10.5061/dryad.h5s2q. UR - http://datadryad.org/review?doi=doi:10.5061/dryad.h5s2q ID - ref31 ER - TY - JOUR AU - Needleman, S. B. AU - Wunsch, C. D. PY - 1970 DA - 1970// TI - A general method applicable to the search for similarities in the amino acid sequence of two proteins JO - J Mol Biol VL - 48 UR - https://doi.org/10.1016/0022-2836(70)90057-4 DO - 10.1016/0022-2836(70)90057-4 ID - Needleman1970 ER -