TY - JOUR AU - Clarke, A. AU - Crame, J. A. AU - Stromberg, J. -. O. AU - Barker, P. PY - 1992 DA - 1992// TI - The Southern Ocean benthic fauna and climate change: a historical perspective JO - Philos Trans R Soc Lond B Biol Sci VL - 338 UR - https://doi.org/10.1098/rstb.1992.0150 DO - 10.1098/rstb.1992.0150 ID - Clarke1992 ER - TY - BOOK AU - Eastman, J. T. AU - Pratt, D. AU - Winn, W. PY - 1993 DA - 1993// TI - Antarctic Fish Biology: Evolution in a Unique Environment PB - Academic Press CY - San Diego, CA ID - Eastman1993 ER - TY - JOUR AU - Chen, L. AU - DeVries, A. L. AU - Cheng, C. H. PY - 1997 DA - 1997// TI - Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish JO - Proc Natl Acad Sci U S A VL - 94 UR - https://doi.org/10.1073/pnas.94.8.3811 DO - 10.1073/pnas.94.8.3811 ID - Chen1997 ER - TY - JOUR AU - Cheng, C. H. AU - Cziko, P. A. AU - Evans, C. W. PY - 2006 DA - 2006// TI - Nonhepatic origin of notothenioid antifreeze reveals pancreatic synthesis as common mechanism in polar fish freezing avoidance JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0603796103 DO - 10.1073/pnas.0603796103 ID - Cheng2006 ER - TY - JOUR AU - DeVries, A. L. PY - 1988 DA - 1988// TI - The role of antifreeze glycopeptides and peptides in the freezing avoidance of Antarctic fishes JO - Comp Biochem Physiol B VL - 90 UR - https://doi.org/10.1016/0300-9629(88)90675-5 DO - 10.1016/0300-9629(88)90675-5 ID - DeVries1988 ER - TY - JOUR AU - Detrich, H. W. AU - Johnson, K. A. AU - Marchese-Ragona, S. P. PY - 1989 DA - 1989// TI - Polymerization of Antarctic fish tubulins at low temperatures: energetic aspects JO - Biochemistry VL - 28 UR - https://doi.org/10.1021/bi00452a031 DO - 10.1021/bi00452a031 ID - Detrich1989 ER - TY - JOUR AU - Detrich, H. W. AU - Parker, S. K. AU - Williams, R. C. AU - Nogales, E. AU - Downing, K. H. PY - 2000 DA - 2000// TI - Cold adaptation of microtubule assembly and dynamics. Structural interpretation of primary sequence changes present in the alpha- and beta-tubulins of Antarctic fishes JO - J Biol Chem VL - 275 UR - https://doi.org/10.1074/jbc.M005699200 DO - 10.1074/jbc.M005699200 ID - Detrich2000 ER - TY - JOUR AU - Hofmann, G. E. AU - Buckley, B. A. AU - Airaksinen, S. AU - Keen, J. E. AU - Somero, G. N. PY - 2000 DA - 2000// TI - Heat-shock protein expression is absent in the Antarctic fish Trematomus bernacchii (family Nototheniidae) JO - J Exp Biol VL - 203 ID - Hofmann2000 ER - TY - JOUR AU - Place, S. P. AU - Hofmann, G. E. PY - 2005 DA - 2005// TI - Comparison of Hsc70 orthologs from polar and temperate notothenioid fishes: differences in prevention of aggregation and refolding of denatured proteins JO - Am J Physiol Regul Integr Comp Physiol VL - 288 UR - https://doi.org/10.1152/ajpregu.00660.2004 DO - 10.1152/ajpregu.00660.2004 ID - Place2005 ER - TY - JOUR AU - Place, S. P. AU - Zippay, M. L. AU - Hofmann, G. E. PY - 2004 DA - 2004// TI - Constitutive roles for inducible genes: evidence for the alteration in expression of the inducible hsp70 gene in Antarctic notothenioid fishes JO - Am J Physiol Regul Integr Comp Physiol VL - 287 UR - https://doi.org/10.1152/ajpregu.00223.2004 DO - 10.1152/ajpregu.00223.2004 ID - Place2004 ER - TY - JOUR AU - Romisch, K. AU - Collie, N. AU - Soto, N. AU - Logue, J. AU - Lindsay, M. AU - Scheper, W. AU - Cheng, C. H. PY - 2003 DA - 2003// TI - Protein translocation across the endoplasmic reticulum membrane in cold-adapted organisms JO - J Cell Sci VL - 116 UR - https://doi.org/10.1242/jcs.00597 DO - 10.1242/jcs.00597 ID - Romisch2003 ER - TY - JOUR AU - Ruud, J. T. PY - 1954 DA - 1954// TI - Vertebrates without erythrocytes and blood pigment JO - Nature VL - 173 UR - https://doi.org/10.1038/173848a0 DO - 10.1038/173848a0 ID - Ruud1954 ER - TY - JOUR AU - Sidell, B. D. AU - O’Brien, K. M. PY - 2006 DA - 2006// TI - When bad things happen to good fish: the loss of hemoglobin and myoglobin expression in Antarctic icefishes JO - J Exp Biol VL - 209 UR - https://doi.org/10.1242/jeb.02091 DO - 10.1242/jeb.02091 ID - Sidell2006 ER - TY - JOUR AU - Eastman, J. T. PY - 2005 DA - 2005// TI - The nature of the diversity of Antarctic fishes JO - Polar Biol VL - 28 UR - https://doi.org/10.1007/s00300-004-0667-4 DO - 10.1007/s00300-004-0667-4 ID - Eastman2005 ER - TY - JOUR AU - Eastman, J. T. AU - Hubold, G. PY - 1999 DA - 1999// TI - The fish fauna of the Ross Sea, Antarctica JO - Antarctic Sci VL - 11 ID - Eastman1999 ER - TY - CHAP AU - Andriashev, A. ED - Kullander, S. O. ED - Fernholm, B. PY - 1985 DA - 1985// TI - A general review of the Antarctic bottom fish fauna BT - Proceedings of the Fifth Congress of European Ichthyologists, Stockholm: 1985 PB - Swedish Museum of National History CY - Stockholm ID - Andriashev1985 ER - TY - JOUR AU - Egginton, S. PY - 1996 DA - 1996// TI - Blood rheology of Antarctic fishes: viscosity adaptations at very low temperatures JO - J Fish Biol VL - 48 UR - https://doi.org/10.1111/j.1095-8649.1996.tb01444.x DO - 10.1111/j.1095-8649.1996.tb01444.x ID - Egginton1996 ER - TY - JOUR AU - Hernandez-Blazquez, F. J. AU - Guerra, R. R. AU - Kfoury, J. R. AU - Bombonato, P. P. AU - Cogliati, B. AU - da Silva, J. R. M. C. PY - 2006 DA - 2006// TI - Fat absorptive processes in the intestine of the Antarctic fish Notothenia coriiceps(Richardson, 1844) JO - Polar Biol VL - 29 UR - https://doi.org/10.1007/s00300-006-0121-x DO - 10.1007/s00300-006-0121-x ID - Hernandez-Blazquez2006 ER - TY - JOUR AU - Johnston, I. A. AU - Fernández, D. A. AU - Calvo, J. AU - Vieira, V. L. AU - North, A. W. AU - Abercromby, M. AU - Garland, T. PY - 2003 DA - 2003// TI - Reduction in muscle fibre number during the adaptive radiation of notothenioid fishes: a phylogenetic perspective JO - J Exp Biol VL - 206 UR - https://doi.org/10.1242/jeb.00474 DO - 10.1242/jeb.00474 ID - Johnston2003 ER - TY - BOOK AU - Gon, O. AU - Heemstra, P. C. PY - 1990 DA - 1990// TI - (Eds): Fishes of the Southern Ocean PB - JLB Smith Institute of Ichthyology CY - Grahamstown ID - Gon1990 ER - TY - JOUR AU - Myers, E. W. AU - Sutton, G. G. AU - Delcher, A. L. AU - Dew, I. M. AU - Fasulo, D. P. AU - Flanigan, M. J. AU - Kravitz, S. A. AU - Mobarry, C. M. AU - Reinert, K. H. AU - Remington, K. A. AU - Anson, E. L. AU - Bolanos, R. A. AU - Chou, H. H. AU - Jordan, C. M. AU - Halpern, A. L. AU - Lonardi, S. AU - Beasley, E. M. AU - Brandon, R. C. AU - Chen, L. AU - Dunn, P. J. AU - Lai, Z. AU - Liang, Y. AU - Nusskern, D. R. AU - Zhan, M. AU - Zhang, Q. AU - Zheng, X. AU - Rubin, G. M. AU - Adams, M. D. AU - Venter, J. C. PY - 2000 DA - 2000// TI - A whole-genome assembly of Drosophila JO - Science VL - 287 UR - https://doi.org/10.1126/science.287.5461.2196 DO - 10.1126/science.287.5461.2196 ID - Myers2000 ER - TY - JOUR AU - English, A. C. AU - Richards, S. AU - Han, Y. AU - Wang, M. AU - Vee, V. AU - Qu, J. AU - Qin, X. AU - Muzny, D. M. AU - Reid, J. G. AU - Worley, K. C. PY - 2012 DA - 2012// TI - Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0047768 DO - 10.1371/journal.pone.0047768 ID - English2012 ER - TY - JOUR AU - Nadalin, F. AU - Vezzi, F. AU - Policriti, A. PY - 2012 DA - 2012// TI - GapFiller: a de novo assembly approach to fill the gap within paired reads JO - BMC Bioinform VL - 13 UR - https://doi.org/10.1186/1471-2105-13-S14-S8 DO - 10.1186/1471-2105-13-S14-S8 ID - Nadalin2012 ER - TY - JOUR AU - Cantarel, B. L. AU - Korf, I. AU - Robb, S. M. AU - Parra, G. AU - Ross, E. AU - Moore, B. AU - Holt, C. AU - Alvarado, A. S. AU - Yandell, M. PY - 2008 DA - 2008// TI - MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.6743907 DO - 10.1101/gr.6743907 ID - Cantarel2008 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2000 DA - 2000// TI - The evolutionary fate and consequences of duplicate genes JO - Science VL - 290 UR - https://doi.org/10.1126/science.290.5494.1151 DO - 10.1126/science.290.5494.1151 ID - Lynch2000 ER - TY - JOUR AU - Demuth, J. P. AU - De Bie, T. AU - Stajich, J. E. AU - Cristianini, N. AU - Hahn, M. W. PY - 2006 DA - 2006// TI - The evolution of mammalian gene families JO - PLoS One VL - 1 UR - https://doi.org/10.1371/journal.pone.0000085 DO - 10.1371/journal.pone.0000085 ID - Demuth2006 ER - TY - JOUR AU - Hahn, M. W. AU - De Bie, T. AU - Stajich, J. E. AU - Nguyen, C. AU - Cristianini, N. PY - 2005 DA - 2005// TI - Estimating the tempo and mode of gene family evolution from comparative genomic data JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3567505 DO - 10.1101/gr.3567505 ID - Hahn2005 ER - TY - JOUR AU - De Bie, T. AU - Cristianini, N. AU - Demuth, J. P. AU - Hahn, M. W. PY - 2006 DA - 2006// TI - CAFE: a computational tool for the study of gene family evolution JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl097 DO - 10.1093/bioinformatics/btl097 ID - De Bie2006 ER - TY - JOUR AU - Hahn, M. W. AU - Han, M. V. AU - Han, S. -. G. PY - 2007 DA - 2007// TI - Gene family evolution across 12 Drosophila genomes JO - PLoS Genet VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030197 DO - 10.1371/journal.pgen.0030197 ID - Hahn2007 ER - TY - JOUR AU - Castillo-Davis, C. I. AU - Kondrashov, F. A. AU - Hartl, D. L. AU - Kulathinal, R. J. PY - 2004 DA - 2004// TI - The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2195604 DO - 10.1101/gr.2195604 ID - Castillo-Davis2004 ER - TY - JOUR AU - Du, Z. AU - Zhou, X. AU - Ling, Y. AU - Zhang, Z. AU - Su, Z. PY - 2010 DA - 2010// TI - agriGO: a GO analysis toolkit for the agricultural community JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq310 DO - 10.1093/nar/gkq310 ID - Du2010 ER - TY - JOUR AU - Dunn, K. A. AU - Bielawski, J. P. AU - Yang, Z. PY - 2001 DA - 2001// TI - Substitution rates in Drosophila nuclear genes: implications for translational selection JO - Genetics VL - 157 ID - Dunn2001 ER - TY - JOUR AU - Mark, F. C. AU - Lucassen, M. AU - Strobel, A. AU - Barrera-Oro, E. AU - Koschnick, N. AU - Zane, L. AU - Patarnello, T. AU - Pörtner, H. O. AU - Papetti, C. PY - 2012 DA - 2012// TI - Mitochondrial function in Antarctic nototheniids with ND6 translocation JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0031860 DO - 10.1371/journal.pone.0031860 ID - Mark2012 ER - TY - JOUR AU - Strobel, A. AU - Graeve, M. AU - Poertner, H. O. AU - Mark, F. C. PY - 2013 DA - 2013// TI - Mitochondrial acclimation capacities to ocean warming and acidification are limited in the Antarctic Nototheniid fish, Notothenia rossii and Lepidonotothen squamifrons JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0068865 DO - 10.1371/journal.pone.0068865 ID - Strobel2013 ER - TY - JOUR AU - Weinstein, R. AU - Somero, G. PY - 1998 DA - 1998// TI - Effects of temperature on mitochondrial function in the Antarctic fish Trematomus bernacchii JO - J Comp Physiol B VL - 168 UR - https://doi.org/10.1007/s003600050136 DO - 10.1007/s003600050136 ID - Weinstein1998 ER - TY - JOUR AU - Buckley, B. A. AU - Place, S. P. AU - Hofmann, G. E. PY - 2004 DA - 2004// TI - Regulation of heat shock genes in isolated hepatocytes from an Antarctic fish, Trematomus bernacchii JO - J Exp Biol VL - 207 UR - https://doi.org/10.1242/jeb.01219 DO - 10.1242/jeb.01219 ID - Buckley2004 ER - TY - JOUR AU - Chen, Z. AU - Cheng, C. H. AU - Zhang, J. AU - Cao, L. AU - Chen, L. AU - Zhou, L. AU - Jin, Y. AU - Ye, H. AU - Deng, C. AU - Dai, Z. AU - Xu, Q. AU - Hu, P. AU - Sun, S. AU - Shen, Y. AU - Chen, L. PY - 2008 DA - 2008// TI - Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish JO - Proc Natl Acad Sci U S A VL - 105 UR - https://doi.org/10.1073/pnas.0802432105 DO - 10.1073/pnas.0802432105 ID - Chen2008 ER - TY - JOUR AU - Franks, F. PY - 1995 DA - 1995// TI - Protein destabilization at low temperatures JO - Adv Protein Chem VL - 46 UR - https://doi.org/10.1016/S0065-3233(08)60333-2 DO - 10.1016/S0065-3233(08)60333-2 ID - Franks1995 ER - TY - JOUR AU - Todgham, A. E. AU - Hoaglund, E. A. AU - Hofmann, G. E. PY - 2007 DA - 2007// TI - Is cold the new hot? Elevated ubiquitin-conjugated protein levels in tissues of Antarctic fish as evidence for cold-denaturation of proteins in vivo JO - J Comp Physiol B VL - 177 UR - https://doi.org/10.1007/s00360-007-0183-2 DO - 10.1007/s00360-007-0183-2 ID - Todgham2007 ER - TY - JOUR AU - Bettencourt, B. R. AU - Hogan, C. C. AU - Nimali, M. AU - Drohan, B. W. PY - 2008 DA - 2008// TI - Inducible and constitutive heat shock gene expression responds to modification of Hsp70 copy number in Drosophila melanogaster but does not compensate for loss of thermotolerance in Hsp70 null flies JO - BMC Biol VL - 6 UR - https://doi.org/10.1186/1741-7007-6-5 DO - 10.1186/1741-7007-6-5 ID - Bettencourt2008 ER - TY - JOUR AU - Akerfelt, M. AU - Morimoto, R. I. AU - Sistonen, L. PY - 2010 DA - 2010// TI - Heat shock factors: integrators of cell stress, development and lifespan JO - Nat Rev Mol Cell Biol VL - 11 UR - https://doi.org/10.1038/nrm2938 DO - 10.1038/nrm2938 ID - Akerfelt2010 ER - TY - JOUR AU - Hietakangas, V. AU - Ahlskog, J. K. AU - Jakobsson, A. M. AU - Hellesuo, M. AU - Sahlberg, N. M. AU - Holmberg, C. I. AU - Mikhailov, A. AU - Palvimo, J. J. AU - Pirkkala, L. AU - Sistonen, L. PY - 2003 DA - 2003// TI - Phosphorylation of serine 303 is a prerequisite for the stress-inducible SUMO modification of heat shock factor 1 JO - Mol Cell Biol VL - 23 UR - https://doi.org/10.1128/MCB.23.8.2953-2968.2003 DO - 10.1128/MCB.23.8.2953-2968.2003 ID - Hietakangas2003 ER - TY - JOUR AU - Hietakangas, V. AU - Anckar, J. AU - Blomster, H. A. AU - Fujimoto, M. AU - Palvimo, J. J. AU - Nakai, A. AU - Sistonen, L. PY - 2006 DA - 2006// TI - PDSM, a motif for phosphorylation-dependent SUMO modification JO - Proc Natl Acad Sci U S A VL - 103 UR - https://doi.org/10.1073/pnas.0503698102 DO - 10.1073/pnas.0503698102 ID - Hietakangas2006 ER - TY - JOUR AU - Kline, M. P. AU - Morimoto, R. I. PY - 1997 DA - 1997// TI - Repression of the heat shock factor 1 transcriptional activation domain is modulated by constitutive phosphorylation JO - Mol Cell Biol VL - 17 UR - https://doi.org/10.1128/MCB.17.4.2107 DO - 10.1128/MCB.17.4.2107 ID - Kline1997 ER - TY - JOUR AU - Somero, G. N. AU - DeVries, A. L. PY - 1967 DA - 1967// TI - Temperature tolerance of some Antarctic fishes JO - Science VL - 156 UR - https://doi.org/10.1126/science.156.3772.257 DO - 10.1126/science.156.3772.257 ID - Somero1967 ER - TY - JOUR AU - Gulevsky, A. K. AU - Relina, L. I. PY - 2013 DA - 2013// TI - Molecular and genetic aspects of protein cold denaturation JO - Cryo Letters VL - 34 ID - Gulevsky2013 ER - TY - JOUR AU - Bernales, S. AU - Papa, F. R. AU - Walter, P. PY - 2006 DA - 2006// TI - Intracellular signaling by the unfolded protein response JO - Annu Rev Cell Dev Biol VL - 22 UR - https://doi.org/10.1146/annurev.cellbio.21.122303.120200 DO - 10.1146/annurev.cellbio.21.122303.120200 ID - Bernales2006 ER - TY - JOUR AU - Calfon, M. AU - Zeng, H. AU - Urano, F. AU - Till, J. H. AU - Hubbard, S. R. AU - Harding, H. P. AU - Clark, S. G. AU - Ron, D. PY - 2002 DA - 2002// TI - IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA JO - Nature VL - 415 UR - https://doi.org/10.1038/415092a DO - 10.1038/415092a ID - Calfon2002 ER - TY - JOUR AU - Kaufman, R. J. PY - 1999 DA - 1999// TI - Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls JO - Genes Dev VL - 13 UR - https://doi.org/10.1101/gad.13.10.1211 DO - 10.1101/gad.13.10.1211 ID - Kaufman1999 ER - TY - JOUR AU - Bargelloni, L. AU - Marcato, S. AU - Patarnello, T. PY - 1998 DA - 1998// TI - Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperature JO - Proc Natl Acad Sci VL - 95 UR - https://doi.org/10.1073/pnas.95.15.8670 DO - 10.1073/pnas.95.15.8670 ID - Bargelloni1998 ER - TY - JOUR AU - D’avino, R. AU - di Prisco, G. PY - 1989 DA - 1989// TI - Hemoglobin from the Antarctic fish Notothenia coriicepsneglecta JO - Eur J Biochem VL - 179 UR - https://doi.org/10.1111/j.1432-1033.1989.tb14603.x DO - 10.1111/j.1432-1033.1989.tb14603.x ID - D’avino1989 ER - TY - JOUR AU - Westerheide, S. D. AU - Anckar, J. AU - Stevens, S. M. AU - Sistonen, L. AU - Morimoto, R. I. PY - 2009 DA - 2009// TI - Stress-inducible regulation of heat shock factor 1 by the deacetylase SIRT1 JO - Science VL - 323 UR - https://doi.org/10.1126/science.1165946 DO - 10.1126/science.1165946 ID - Westerheide2009 ER - TY - JOUR AU - Zukowski, S. -. S. C. PY - 1980 DA - 1980// TI - Blood of antarctic fishes : Notothenia rossi marmorata Fischer and Notothenia neglecta Nybelin JO - Pol Polar Res VL - 1 ID - Zukowski1980 ER - TY - STD TI - Gordon A, Hannon GJ: Fastx-toolkit: FASTQ/A short-reads preprocessing tools. [], [http://hannonlab.cshl.edu/fastx_toolkit] UR - http://hannonlab.cshl.edu/fastx_toolkit ID - ref54 ER - TY - JOUR AU - Rasko, D. A. AU - Webster, D. R. AU - Sahl, J. W. AU - Bashir, A. AU - Boisen, N. AU - Scheutz, F. AU - Paxinos, E. E. AU - Sebra, R. AU - Chin, C. S. AU - Iliopoulos, D. AU - Klammer, A. AU - Peluso, P. AU - Lee, L. AU - Kislyuk, A. O. AU - Bullard, J. AU - Kasarskis, A. AU - Wang, S. AU - Eid, J. AU - Rank, D. AU - Redman, J. C. AU - Steyert, S. R. AU - Frimodt-Møller, J. AU - Struve, C. AU - Petersen, A. M. AU - Krogfelt, K. A. AU - Nataro, J. P. AU - Schadt, E. E. AU - Waldor, M. K. PY - 2011 DA - 2011// TI - Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany JO - N Engl J Med VL - 365 UR - https://doi.org/10.1056/NEJMoa1106920 DO - 10.1056/NEJMoa1106920 ID - Rasko2011 ER - TY - JOUR AU - Koren, S. AU - Schatz, M. C. AU - Walenz, B. P. AU - Martin, J. AU - Howard, J. T. AU - Ganapathy, G. AU - Wang, Z. AU - Rasko, D. A. AU - McCombie, W. R. AU - Jarvis, E. D. AU - Phillippy, A. M. PY - 2012 DA - 2012// TI - Hybrid error correction and de novo assembly of single-molecule sequencing reads JO - Nat Biotechnol VL - 30 UR - https://doi.org/10.1038/nbt.2280 DO - 10.1038/nbt.2280 ID - Koren2012 ER - TY - STD TI - FastQC. [], [http://www.bioinformatics.babraham.ac.uk/projects/fastqc] UR - http://www.bioinformatics.babraham.ac.uk/projects/fastqc ID - ref57 ER - TY - JOUR AU - Boetzer, M. AU - Pirovano, W. PY - 2012 DA - 2012// TI - Toward almost closed genomes with GapFiller JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-6-r56 DO - 10.1186/gb-2012-13-6-r56 ID - Boetzer2012 ER - TY - JOUR AU - Bao, Z. AU - Eddy, S. R. PY - 2002 DA - 2002// TI - Automated de novo identification of repeat sequence families in sequenced genomes JO - Genome Res VL - 12 UR - https://doi.org/10.1101/gr.88502 DO - 10.1101/gr.88502 ID - Bao2002 ER - TY - JOUR AU - Price, A. L. AU - Jones, N. C. AU - Pevzner, P. A. PY - 2005 DA - 2005// TI - De novo identification of repeat families in large genomes JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1018 DO - 10.1093/bioinformatics/bti1018 ID - Price2005 ER - TY - JOUR AU - Benson, G. PY - 1999 DA - 1999// TI - Tandem repeats finder: a program to analyze DNA sequences JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.2.573 DO - 10.1093/nar/27.2.573 ID - Benson1999 ER - TY - JOUR AU - Delcher, A. L. AU - Salzberg, S. L. AU - Phillippy, A. M. PY - 2003 DA - 2003// TI - Using MUMmer to identify similar regions in large sequence sets JO - Curr Protoc Bioinformatics VL - Chapter 10 ID - Delcher2003 ER - TY - STD TI - Bowtie: An ultrafast memory-efficient short read aligner. [], [http://bowtie-bio.sourceforge.net/index.shtml] UR - http://bowtie-bio.sourceforge.net/index.shtml ID - ref63 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - STD TI - TopHat: A spliced read mapper for RNA-Seq. [], [http://ccb.jhu.edu/software/tophat/index.shtml] UR - http://ccb.jhu.edu/software/tophat/index.shtml ID - ref65 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - STD TI - Cufflinks: Transcript assembly, differential expression, and differential regulation for RNA-Seq. [], [http://cufflinks.cbcb.umd.edu] UR - http://cufflinks.cbcb.umd.edu ID - ref67 ER - TY - JOUR AU - Roberts, A. AU - Pimentel, H. AU - Trapnell, C. AU - Pachter, L. PY - 2011 DA - 2011// TI - Identification of novel transcripts in annotated genomes using RNA-Seq JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr355 DO - 10.1093/bioinformatics/btr355 ID - Roberts2011 ER - TY - JOUR AU - Trapnell, C. AU - Hendrickson, D. G. AU - Sauvageau, M. AU - Goff, L. AU - Rinn, J. L. AU - Pachter, L. PY - 2013 DA - 2013// TI - Differential analysis of gene regulation at transcript resolution with RNA-seq JO - Nat Biotechnol VL - 31 UR - https://doi.org/10.1038/nbt.2450 DO - 10.1038/nbt.2450 ID - Trapnell2013 ER - TY - JOUR AU - Holt, C. AU - Yandell, M. PY - 2011 DA - 2011// TI - MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects JO - BMC Bioinform VL - 12 UR - https://doi.org/10.1186/1471-2105-12-491 DO - 10.1186/1471-2105-12-491 ID - Holt2011 ER - TY - STD TI - Smit AFA HR, Green P: RepeatMasker Open-3.0. 1996-2004. [], [http://www.repeatmasker.org/] UR - http://www.repeatmasker.org/ ID - ref71 ER - TY - JOUR AU - Korf, I. PY - 2004 DA - 2004// TI - Gene finding in novel genomes JO - BMC Bioinform VL - 5 UR - https://doi.org/10.1186/1471-2105-5-59 DO - 10.1186/1471-2105-5-59 ID - Korf2004 ER - TY - JOUR AU - Conesa, A. AU - Gotz, S. AU - Garcia-Gomez, J. M. AU - Terol, J. AU - Talon, M. AU - Robles, M. PY - 2005 DA - 2005// TI - Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti610 DO - 10.1093/bioinformatics/bti610 ID - Conesa2005 ER - TY - JOUR AU - Nawrocki, E. P. AU - Kolbe, D. L. AU - Eddy, S. R. PY - 2009 DA - 2009// TI - Infernal 1.0: inference of RNA alignments JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp157 DO - 10.1093/bioinformatics/btp157 ID - Nawrocki2009 ER - TY - JOUR AU - Gardner, P. P. AU - Daub, J. AU - Tate, J. AU - Moore, B. L. AU - Osuch, I. H. AU - Griffiths-Jones, S. AU - Finn, R. D. AU - Nawrocki, E. P. AU - Kolbe, D. L. AU - Eddy, S. R. AU - Bateman, A. PY - 2011 DA - 2011// TI - Rfam: Wikipedia, clans and the “decimal” release JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1129 DO - 10.1093/nar/gkq1129 ID - Gardner2011 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 - Li, L. AU - Stoeckert, C. J. AU - Roos, D. S. PY - 2003 DA - 2003// TI - OrthoMCL: identification of ortholog groups for eukaryotic genomes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1224503 DO - 10.1101/gr.1224503 ID - Li2003 ER - TY - STD TI - CAFE: Computational analysis of (gene) family evolution. [], [www.bio.indiana.edu/~hahnlab/Software.html] UR - http://www.bio.indiana.edu/~hahnlab/Software.html ID - ref78 ER - TY - JOUR AU - Hedges, S. B. AU - Dudley, J. AU - Kumar, S. PY - 2006 DA - 2006// TI - TimeTree: a public knowledge-base of divergence times among organisms JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl505 DO - 10.1093/bioinformatics/btl505 ID - Hedges2006 ER - TY - JOUR AU - Loytynoja, A. AU - Goldman, N. PY - 2005 DA - 2005// TI - An algorithm for progressive multiple alignment of sequences with insertions JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0409137102 DO - 10.1073/pnas.0409137102 ID - Loytynoja2005 ER - TY - JOUR AU - Castresana, J. PY - 2000 DA - 2000// TI - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026334 DO - 10.1093/oxfordjournals.molbev.a026334 ID - Castresana2000 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: phylogenetic analysis by maximum likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER -