TY - STD TI - Smalla K, Top EM, Jechalke S. Plasmid detection, characterization, and ecology. In: Tolmasky ME, Alonso JC, editors. Plasmids: biology and impact in biotechnology and discovery: Morgan Kaufmann, Elsevier Inc, ASM Press; 2015. https://doi.org/10.1128/microbiolspec.PLAS-0038-2014. ID - ref1 ER - TY - JOUR AU - Leplae, R. AU - Lima-Mendez, G. AU - Toussaint, A. PY - 2006 DA - 2006// TI - A first global analysis of plasmid encoded proteins in the ACLAME database JO - FEMS Microbiol Rev VL - 30 UR - https://doi.org/10.1111/j.1574-6976.2006.00044.x DO - 10.1111/j.1574-6976.2006.00044.x ID - Leplae2006 ER - TY - JOUR AU - Galperin, M. Y. AU - Makarova, K. S. AU - Wolf, Y. I. AU - Koonin, E. V. PY - 2015 DA - 2015// TI - Expanded microbial genome coverage and improved protein family annotation in the COG database JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1223 DO - 10.1093/nar/gku1223 ID - Galperin2015 ER - TY - JOUR AU - Xia, Y. AU - Franzosa, E. A. AU - Gerstein, M. B. PY - 2009 DA - 2009// TI - Integrated assessment of genomic correlates of protein evolutionary rate JO - PLoS Comput Biol VL - 5 UR - https://doi.org/10.1371/journal.pcbi.1000413 DO - 10.1371/journal.pcbi.1000413 ID - Xia2009 ER - TY - JOUR AU - Yin, Y. AU - Fischer, D. PY - 2006 DA - 2006// TI - On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer JO - BMC Evol Biol VL - 6 UR - https://doi.org/10.1186/1471-2148-6-63 DO - 10.1186/1471-2148-6-63 ID - Yin2006 ER - TY - STD TI - Diago-Navarro E, Hernandez-Arriaga AM, Diaz-Orejas R. Type II toxin-antitoxin loci encoded by plasmids. In: Gerdes K, editor. Prokaryotic Toxin-Antitoxins: Springer-Verlag Berlin Heidelberg; 2013. p. 267–94. https://doi.org/10.1007/978-3-642-33253-1_16. ID - ref6 ER - TY - JOUR AU - Loris, R. AU - Garcia-Pino, A. PY - 2014 DA - 2014// TI - Disorder-and dynamics-based regulatory mechanisms in toxin--antitoxin modules JO - Chem Rev VL - 114 UR - https://doi.org/10.1021/cr400656f DO - 10.1021/cr400656f ID - Loris2014 ER - TY - JOUR AU - Page, R. AU - Peti, W. PY - 2016 DA - 2016// TI - Toxin-antitoxin Systems in Bacterial Growth Arrest and Persistence JO - Nat Chem Biol VL - 12 UR - https://doi.org/10.1038/nchembio.2044 DO - 10.1038/nchembio.2044 ID - Page2016 ER - TY - JOUR AU - Van Melderen, L. AU - Saavedra De Bast, M. PY - 2009 DA - 2009// TI - Bacterial toxin--antitoxin systems: more than selfish entities? JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000437 DO - 10.1371/journal.pgen.1000437 ID - Van Melderen2009 ER - TY - JOUR AU - Tompa, P. PY - 2011 DA - 2011// TI - Unstructural biology coming of age JO - Curr Opin Struct Biol VL - 21 UR - https://doi.org/10.1016/j.sbi.2011.03.012 DO - 10.1016/j.sbi.2011.03.012 ID - Tompa2011 ER - TY - JOUR AU - Petrovich, A. AU - Borne, A. AU - Uversky, V. N. AU - Xue, B. PY - 2015 DA - 2015// TI - Identifying similar patterns of structural flexibility in proteins by disorder prediction and dynamic programming JO - Int J Mol Sci VL - 16 UR - https://doi.org/10.3390/ijms160613829 DO - 10.3390/ijms160613829 ID - Petrovich2015 ER - TY - JOUR AU - Uversky, V. N. PY - 2014 DA - 2014// TI - Introduction to intrinsically disordered proteins (IDPs) JO - Chem Rev VL - 114 UR - https://doi.org/10.1021/cr500288y DO - 10.1021/cr500288y ID - Uversky2014 ER - TY - STD TI - Tompa P. Structure and function of intrinsically disordered proteins: Chapman and Hall/CRC; 2009. https://doi.org/10.1201/9781420078930. ID - ref13 ER - TY - CHAP AU - Uversky, V. N. ED - Felli, I. C. ED - Pierattelli, R. PY - 2015 DA - 2015// TI - Biophysical methods to investigate intrinsically disordered proteins: avoiding an “elephant and blind men” situation BT - Intrinsically Disordered Proteins Studied by NMR Spectroscopy PB - Springer International Publishing CY - Switzerland UR - https://doi.org/10.1007/978-3-319-20164-1_7 DO - 10.1007/978-3-319-20164-1_7 ID - Uversky2015 ER - TY - CHAP AU - Punta, M. AU - Simon, I. AU - Dosztanyi, Z. ED - Owens, J. R. PY - 2015 DA - 2015// TI - Prediction and analysis of intrinsically disordered proteins BT - Structural proteomics: High-Troughput Methods, methods in molecular biology PB - SpringerScience+business media CY - New York ID - Punta2015 ER - TY - JOUR AU - Tompa, P. PY - 2005 DA - 2005// TI - The interplay between structure and function in intrinsically unstructured proteins JO - FEBS Lett VL - 579 UR - https://doi.org/10.1016/j.febslet.2005.03.072 DO - 10.1016/j.febslet.2005.03.072 ID - Tompa2005 ER - TY - JOUR AU - Pavlović-Lažetić, G. M. AU - Mitić, N. S. AU - Kovačević, J. J. AU - Obradović, Z. AU - Malkov, S. N. AU - Beljanski, V. M. PY - 2011 DA - 2011// TI - Bioinformatics analysis of disordered proteins in prokaryotes JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-66 DO - 10.1186/1471-2105-12-66 ID - Pavlović-Lažetić2011 ER - TY - JOUR AU - Habchi, J. AU - Tompa, P. AU - Longhi, S. AU - Uversky, V. N. PY - 2014 DA - 2014// TI - Introducing protein intrinsic disorder JO - Chem Rev VL - 114 UR - https://doi.org/10.1021/cr400514h DO - 10.1021/cr400514h ID - Habchi2014 ER - TY - JOUR AU - Xue, B. AU - Williams, R. W. AU - Oldfield, C. J. AU - Dunker, A. K. AU - Uversky, V. N. PY - 2010 DA - 2010// TI - Archaic chaos: intrinsically disordered proteins in Archaea JO - BMC Syst Biol VL - 4 UR - https://doi.org/10.1186/1752-0509-4-S1-S1 DO - 10.1186/1752-0509-4-S1-S1 ID - Xue2010 ER - TY - JOUR AU - Xue, B. AU - Dunker, A. K. AU - Uversky, V. N. PY - 2012 DA - 2012// TI - Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life JO - J Biomol Struct Dyn VL - 30 UR - https://doi.org/10.1080/07391102.2012.675145 DO - 10.1080/07391102.2012.675145 ID - Xue2012 ER - TY - JOUR AU - Pushker, R. AU - Mooney, C. AU - Davey, N. E. AU - Jacque, J. -. M. AU - Shields, D. C. PY - 2013 DA - 2013// TI - Marked variability in the extent of protein disorder within and between viral families JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0060724 DO - 10.1371/journal.pone.0060724 ID - Pushker2013 ER - TY - JOUR AU - Oates, M. E. AU - Romero, P. AU - Ishida, T. AU - Ghalwash, M. AU - Mizianty, M. J. AU - Xue, B. AU - Dosztányi, Z. AU - Uversky, V. N. AU - Obradovic, Z. AU - Kurgan, L. AU - Dunker, A. K. AU - Gough, J. PY - 2013 DA - 2013// TI - D2P2: database of disordered protein predictions JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1226 DO - 10.1093/nar/gks1226 ID - Oates2013 ER - TY - JOUR AU - Di Domenico, T. AU - Walsh, I. AU - Martin, A. J. AU - Tosatto, S. C. PY - 2012 DA - 2012// TI - MobiDB: a comprehensive database of intrinsic protein disorder annotations JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts327 DO - 10.1093/bioinformatics/bts327 ID - Di Domenico2012 ER - TY - JOUR AU - Peng, K. AU - Radivojac, P. AU - Vucetic, S. AU - Dunker, A. K. AU - Obradovic, Z. PY - 2006 DA - 2006// TI - Length-dependent prediction of protein intrinsic disorder JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-208 DO - 10.1186/1471-2105-7-208 ID - Peng2006 ER - TY - JOUR AU - Lobanov, M. Y. AU - Sokolovskiy, I. V. AU - Galzitskaya, O. V. PY - 2013 DA - 2013// TI - IsUnstruct: prediction of the residue status to be ordered or disordered in the protein chain by a method based on the Ising model JO - J Biomol Struct Dyn VL - 31 UR - https://doi.org/10.1080/07391102.2012.718529 DO - 10.1080/07391102.2012.718529 ID - Lobanov2013 ER - TY - JOUR AU - Dosztanyi, Z. AU - Csizmok, V. AU - Tompa, P. AU - Simon, I. PY - 2005 DA - 2005// TI - IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti541 DO - 10.1093/bioinformatics/bti541 ID - Dosztanyi2005 ER - TY - JOUR AU - Syutkin, A. S. AU - Pyatibratov, M. G. AU - Galzitskaya, O. AU - Rodríguez-Valera, F. AU - Fedorov, O. V. PY - 2014 DA - 2014// TI - Haloarcula marismortui archellin genes as ecoparalogs JO - Extremophyles VL - 18 UR - https://doi.org/10.1007/s00792-013-0619-4 DO - 10.1007/s00792-013-0619-4 ID - Syutkin2014 ER - TY - JOUR AU - Michail, L. Y. AU - Oxana, G. V. PY - 2015 DA - 2015// TI - How common is disorder? Occurrence of disordered residues in four domain of life JO - Int J Mol Sci VL - 16 UR - https://doi.org/10.3390/ijms160819490 DO - 10.3390/ijms160819490 ID - Michail2015 ER - TY - JOUR AU - Xie, H. AU - Vucetic, S. AU - Iakoucheva, L. M. AU - Oldfield, C. J. AU - Dunker, A. K. AU - Uversky, V. N. AU - Obradovic, Z. PY - 2007 DA - 2007// TI - Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions JO - J Proteome Res VL - 6 UR - https://doi.org/10.1021/pr060392u DO - 10.1021/pr060392u ID - Xie2007 ER - TY - JOUR AU - Berezovsky, I. N. PY - 2011 DA - 2011// TI - The diversity of physical forces and mechanisms in intermolecular interactions JO - Phys Biol VL - 8 UR - https://doi.org/10.1088/1478-3975/8/3/035002 DO - 10.1088/1478-3975/8/3/035002 ID - Berezovsky2011 ER - TY - JOUR AU - Tokuriki, N. AU - Oldfield, C. J. AU - Uversky, V. N. AU - Berezovsky, I. N. AU - Tawfik, D. S. PY - 2009 DA - 2009// TI - Do viral proteins possess unique biophysical features? JO - Trends Biochem Sci VL - 34 UR - https://doi.org/10.1016/j.tibs.2008.10.009 DO - 10.1016/j.tibs.2008.10.009 ID - Tokuriki2009 ER - TY - JOUR AU - Frost, L. S. AU - Leplae, R. AU - Summers, A. O. AU - Toussaint, A. PY - 2005 DA - 2005// TI - Mobile genetic elements: the agents of open source evolution JO - Nat Rev Microbiol VL - 3 UR - https://doi.org/10.1038/nrmicro1235 DO - 10.1038/nrmicro1235 ID - Frost2005 ER - TY - JOUR AU - Daubin, V. AU - Ochman, H. PY - 2004 DA - 2004// TI - Bacterial genomes as new gene homes: the genealogy of ORFans in E. Coli JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2231904 DO - 10.1101/gr.2231904 ID - Daubin2004 ER - TY - JOUR AU - Charlebois, R. L. AU - Clarke, G. D. AU - Beiko, R. G. AU - St. Jean, A. PY - 2003 DA - 2003// TI - Characterization of species-specific genes using a flexible, web-based querying system JO - FEMS Microbiol Lett VL - 225 UR - https://doi.org/10.1016/S0378-1097(03)00512-3 DO - 10.1016/S0378-1097(03)00512-3 ID - Charlebois2003 ER - TY - JOUR AU - Ochman, H. PY - 2002 DA - 2002// TI - Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes JO - Trends Genet VL - 18 UR - https://doi.org/10.1016/S0168-9525(02)02668-9 DO - 10.1016/S0168-9525(02)02668-9 ID - Ochman2002 ER - TY - JOUR AU - Mukherjee, S. AU - Panda, A. AU - Ghosh, T. C. PY - 2015 DA - 2015// TI - Elucidating evolutionary features and functional implications of orphan genes in Leishmania major JO - Infect Genet Evol VL - 32 UR - https://doi.org/10.1016/j.meegid.2015.03.031 DO - 10.1016/j.meegid.2015.03.031 ID - Mukherjee2015 ER - TY - JOUR AU - Dagan, T. AU - Artzy-Randrup, Y. AU - Martin, W. PY - 2008 DA - 2008// TI - Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution JO - Proc Natl Acad Sci U S A VL - 105 UR - https://doi.org/10.1073/pnas.0800679105 DO - 10.1073/pnas.0800679105 ID - Dagan2008 ER - TY - JOUR AU - Zhaxybayeva, O. AU - Gogarten, J. P. PY - 2004 DA - 2004// TI - Cladogenesis, coalescence and the evolution of the three domains of life JO - Trends Genet VL - 20 UR - https://doi.org/10.1016/j.tig.2004.02.004 DO - 10.1016/j.tig.2004.02.004 ID - Zhaxybayeva2004 ER - TY - JOUR AU - Halary, S. AU - Leigh, J. W. AU - Cheaib, B. AU - Lopez, P. AU - Bapteste, E. PY - 2010 DA - 2010// TI - Network analyses structure genetic diversity in independent genetic worlds JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.0908978107 DO - 10.1073/pnas.0908978107 ID - Halary2010 ER - TY - JOUR AU - Howell, M. AU - Green, R. AU - Killeen, A. AU - Wedderburn, L. AU - Picascio, V. AU - Rabionet, A. AU - Peng, Z. AU - Larina, M. AU - Xue, B. AU - Kurgan, L. AU - Uversky, V. N. PY - 2012 DA - 2012// TI - Not that rigid midgets and not so flexible giants: on the abundance and roles of intrinsic disorder in short and long proteins JO - J Biol Syst VL - 20 UR - https://doi.org/10.1142/S0218339012400086 DO - 10.1142/S0218339012400086 ID - Howell2012 ER - TY - JOUR AU - van der Lee Robin AU - Lang, B. AU - Kruse, K. AU - Gsponer, J. AU - Sánchez de Groot, N. AU - Huynen, M. A. AU - Matouschek, A. AU - Fuxreiter, M. AU - Babu, M. M. PY - 2014 DA - 2014// TI - Intrinsically disordered segments affect protein half-life in the cell and during evolution JO - Cell Rep VL - 8 UR - https://doi.org/10.1016/j.celrep.2014.07.055 DO - 10.1016/j.celrep.2014.07.055 ID - van der Lee Robin2014 ER -