TY - JOUR AU - Storz, J. F. AU - Scott, G. R. AU - Cheviron, Z. A. PY - 2010 DA - 2010// TI - Phenotypic plasticity and genetic adaptation to high-altitude hypoxia in vertebrates JO - J Exp Biol VL - 213 UR - https://doi.org/10.1242/jeb.048181 DO - 10.1242/jeb.048181 ID - Storz2010 ER - TY - JOUR AU - Pugh, C. W. AU - Ratcliffe, P. J. PY - 2003 DA - 2003// TI - Regulation of angiogenesis by hypoxia: role of the HIF system JO - Nat Med VL - 9 UR - https://doi.org/10.1038/nm0603-677 DO - 10.1038/nm0603-677 ID - Pugh2003 ER - TY - JOUR AU - To, K. K. AU - Huang, L. E. PY - 2005 DA - 2005// TI - Suppression of hypoxia-inducible factor 1alpha (HIF-1alpha) transcriptional activity by the HIF prolyl hydroxylase EGLN1 JO - J Biol Chem VL - 280 UR - https://doi.org/10.1074/jbc.M504342200 DO - 10.1074/jbc.M504342200 ID - To2005 ER - TY - JOUR AU - Salnikow, K. AU - Kluz, T. AU - Costa, M. AU - Piquemal, D. AU - Demidenko, Z. N. AU - Xie, K. PY - 2002 DA - 2002// TI - The regulation of hypoxic genes by calcium involves c-Jun/AP-1, which cooperates with hypoxia-inducible factor 1 in response to hypoxia JO - Mol Cell Biol VL - 22 UR - https://doi.org/10.1128/MCB.22.6.1734-1741.2002 DO - 10.1128/MCB.22.6.1734-1741.2002 ID - Salnikow2002 ER - TY - JOUR AU - Stapley, J. AU - Reger, J. AU - Feulner, P. G. AU - Smadja, C. AU - Galindo, J. AU - Ekblom, R. PY - 2010 DA - 2010// TI - Adaptation genomics: the next generation JO - Trends Ecol Evol VL - 25 UR - https://doi.org/10.1016/j.tree.2010.09.002 DO - 10.1016/j.tree.2010.09.002 ID - Stapley2010 ER - TY - JOUR AU - Ekblom, R. AU - Galindo, J. PY - 2011 DA - 2011// TI - Applications of next generation sequencing in molecular ecology of non-model organisms JO - Heredity (Edinb) VL - 107 UR - https://doi.org/10.1038/hdy.2010.152 DO - 10.1038/hdy.2010.152 ID - Ekblom2011 ER - TY - JOUR AU - Qiu, Q. AU - Zhang, G. AU - Ma, T. AU - Qian, W. AU - Wang, J. AU - Ye, Z. PY - 2012 DA - 2012// TI - The yak genome and adaptation to life at high altitude JO - Nat Genet VL - 44 UR - https://doi.org/10.1038/ng.2343 DO - 10.1038/ng.2343 ID - Qiu2012 ER - TY - JOUR AU - Li, M. AU - Tian, S. AU - Jin, L. AU - Zhou, G. AU - Li, Y. AU - Zhang, Y. PY - 2013 DA - 2013// TI - Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2811 DO - 10.1038/ng.2811 ID - Li2013 ER - TY - JOUR AU - Qu, Y. AU - Zhao, H. AU - Han, N. AU - Zhou, G. AU - Song, G. AU - Gao, B. PY - 2013 DA - 2013// TI - Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau JO - Nat Commun VL - 4 ID - Qu2013 ER - TY - JOUR AU - Cho, Y. S. AU - Hu, L. AU - Hou, H. AU - Lee, H. AU - Xu, J. AU - Kwon, S. PY - 2013 DA - 2013// TI - The tiger genome and comparative analysis with lion and snow leopard genomes JO - Nat Commun VL - 4 ID - Cho2013 ER - TY - JOUR AU - Wang, G. D. AU - Fan, R. X. AU - Zhai, W. AU - Liu, F. AU - Wang, L. AU - Zhong, L. PY - 2014 DA - 2014// TI - Genetic convergence in the adaptation of dogs and humans to the high-altitude environment of the tibetan plateau JO - Genome Biol Evol VL - 6 UR - https://doi.org/10.1093/gbe/evu162 DO - 10.1093/gbe/evu162 ID - Wang2014 ER - TY - JOUR AU - Malik, A. AU - Korol, A. AU - Weber, M. AU - Hankeln, T. AU - Avivi, A. AU - Band, M. PY - 2012 DA - 2012// TI - Transcriptome analysis of the spalax hypoxia survival response includes suppression of apoptosis and tight control of angiogenesis JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-615 DO - 10.1186/1471-2164-13-615 ID - Malik2012 ER - TY - JOUR AU - Cheviron, Z. A. AU - Connaty, A. D. AU - McClelland, G. B. AU - Storz, J. F. PY - 2014 DA - 2014// TI - Functional genomics of adaptation to hypoxic cold-stress in high-altitude deer mice: transcriptomic plasticity and thermogenic performance JO - Evolution VL - 68 UR - https://doi.org/10.1111/evo.12257 DO - 10.1111/evo.12257 ID - Cheviron2014 ER - TY - JOUR AU - Cheviron, Z. A. AU - Bachman, G. C. AU - Connaty, A. D. AU - McClelland, G. B. AU - Storz, J. F. PY - 2012 DA - 2012// TI - Regulatory changes contribute to the adaptive enhancement of thermogenic capacity in high-altitude deer mice JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1120523109 DO - 10.1073/pnas.1120523109 ID - Cheviron2012 ER - TY - JOUR AU - Cheviron, Z. A. AU - Whitehead, A. AU - Brumfield, R. T. PY - 2008 DA - 2008// TI - Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient JO - Mol Ecol VL - 17 UR - https://doi.org/10.1111/j.1365-294X.2008.03942.x DO - 10.1111/j.1365-294X.2008.03942.x ID - Cheviron2008 ER - TY - JOUR AU - Jin, Y. T. AU - Brown, R. P. PY - 2013 DA - 2013// TI - Species history and divergence times of viviparous and oviparous Chinese toad-headed sand lizards (Phrynocephalus) on the Qinghai-Tibetan Plateau JO - Mol Phylogenet Evol VL - 68 UR - https://doi.org/10.1016/j.ympev.2013.03.022 DO - 10.1016/j.ympev.2013.03.022 ID - Jin2013 ER - TY - JOUR AU - Guo, X. AU - Wang, Y. PY - 2007 DA - 2007// TI - Partitioned Bayesian analyses, dispersal-vicariance analysis, and the biogeography of Chinese toad-headed lizards (Agamidae: Phrynocephalus): a re-evaluation JO - Mol Phylogenet Evol VL - 45 UR - https://doi.org/10.1016/j.ympev.2007.06.013 DO - 10.1016/j.ympev.2007.06.013 ID - Guo2007 ER - TY - STD TI - Zhu L, Liao P, Tong H, Jin Y. The complete mitochondrial genome of the subspecies, Phrynocephalus erythrurus parva (Reptilia, Squamata, Agamidae), a toad-headed lizard dwell at highest elevations of any reptile in the world. Mitochondrial DNA 2014. ID - ref18 ER - TY - STD TI - Jin Y. Evolutionary studies of Phrynocephalus (Agamidae) on the Qinghai–Xizang (Tibetan) Plateau. Ph. D. Thesis. Lanzhou University, Lanzhou (in Chinese with English abstract); 2008. ID - ref19 ER - TY - JOUR AU - Tang, X. AU - Xin, Y. AU - Wang, H. AU - Li, W. AU - Zhang, Y. AU - Liang, S. PY - 2013 DA - 2013// TI - Metabolic characteristics and response to high altitude in Phrynocephalus erythrurus (Lacertilia: Agamidae), a lizard dwell at altitudes higher than any other living lizards in the world JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0071976 DO - 10.1371/journal.pone.0071976 ID - Tang2013 ER - TY - JOUR AU - He, J. AU - Xiu, M. AU - Tang, X. AU - Wang, N. AU - Xin, Y. AU - Li, W. PY - 2013 DA - 2013// TI - Thermoregulatory and metabolic responses to hypoxia in the oviparous lizard, Phrynocephalus przewalskii JO - Comp Biochem Physiol A Mol Integr Physiol VL - 165 UR - https://doi.org/10.1016/j.cbpa.2013.03.007 DO - 10.1016/j.cbpa.2013.03.007 ID - He2013 ER - TY - JOUR AU - Yang, W. AU - Qi, Y. AU - Bi, K. AU - Fu, J. PY - 2012 DA - 2012// TI - Toward understanding the genetic basis of adaptation to high-elevation life in poikilothermic species: a comparative transcriptomic analysis of two ranid frogs JO - Rana chensinensis and R kukunoris BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-588 DO - 10.1186/1471-2164-13-588 ID - Yang2012 ER - TY - JOUR AU - Chiari, Y. AU - Cahais, V. AU - Galtier, N. AU - Delsuc, F. PY - 2012 DA - 2012// TI - Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria) JO - BMC Biol VL - 10 UR - https://doi.org/10.1186/1741-7007-10-65 DO - 10.1186/1741-7007-10-65 ID - Chiari2012 ER - TY - JOUR AU - Kumazawa, Y. PY - 2007 DA - 2007// TI - Mitochondrial genomes from major lizard families suggest their phylogenetic relationships and ancient radiations JO - Gene VL - 388 UR - https://doi.org/10.1016/j.gene.2006.09.026 DO - 10.1016/j.gene.2006.09.026 ID - Kumazawa2007 ER - TY - JOUR AU - Vidal, N. AU - Hedges, S. B. PY - 2005 DA - 2005// TI - The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes JO - C R Biol VL - 328 UR - https://doi.org/10.1016/j.crvi.2005.10.001 DO - 10.1016/j.crvi.2005.10.001 ID - Vidal2005 ER - TY - JOUR AU - Pyron, R. A. AU - Burbrink, F. T. AU - Wiens, J. J. PY - 2013 DA - 2013// TI - A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes JO - BMC Evol Biol VL - 13 UR - https://doi.org/10.1186/1471-2148-13-93 DO - 10.1186/1471-2148-13-93 ID - Pyron2013 ER - TY - JOUR AU - Hittinger, C. T. AU - Johnston, M. AU - Tossberg, J. T. AU - Rokas, A. PY - 2010 DA - 2010// TI - Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.0910449107 DO - 10.1073/pnas.0910449107 ID - Hittinger2010 ER - TY - JOUR AU - Lin, G. H. AU - Wang, K. AU - Deng, X. G. AU - Nevo, E. AU - Zhao, F. AU - Su, J. P. PY - 2014 DA - 2014// TI - Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia) JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-32 DO - 10.1186/1471-2164-15-32 ID - Lin2014 ER - TY - JOUR AU - Nabholz, B. AU - Jarvis, E. D. AU - Ellegren, H. PY - 2010 DA - 2010// TI - Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny JO - Mol Phylogenet Evol VL - 57 UR - https://doi.org/10.1016/j.ympev.2010.06.009 DO - 10.1016/j.ympev.2010.06.009 ID - Nabholz2010 ER - TY - JOUR AU - Bickler, P. E. AU - Buck, L. T. PY - 2007 DA - 2007// TI - Hypoxia tolerance in reptiles, amphibians, and fishes: life with variable oxygen availability JO - Annu Rev Physiol VL - 69 UR - https://doi.org/10.1146/annurev.physiol.69.031905.162529 DO - 10.1146/annurev.physiol.69.031905.162529 ID - Bickler2007 ER - TY - JOUR AU - Yee Koh, M. AU - Spivak-Kroizman, T. R. AU - Powis, G. PY - 2008 DA - 2008// TI - HIF-1 regulation: not so easy come, easy go JO - Trends Biochem Sci VL - 33 UR - https://doi.org/10.1016/j.tibs.2008.08.002 DO - 10.1016/j.tibs.2008.08.002 ID - Yee Koh2008 ER - TY - JOUR AU - He, J. AU - Xiu, M. AU - Tang, X. AU - Yue, F. AU - Wang, N. AU - Yang, S. PY - 2013 DA - 2013// TI - The different mechanisms of hypoxic acclimatization and adaptation in Lizard Phrynocephalus vlangalii living on Qinghai-Tibet Plateau JO - J Exp Zool A Ecol Genet Physiol VL - 319 UR - https://doi.org/10.1002/jez.1776 DO - 10.1002/jez.1776 ID - He2013 ER - TY - JOUR AU - Svobodova, A. R. AU - Galandakova, A. AU - Sianska, J. AU - Dolezal, D. AU - Lichnovska, R. AU - Ulrichova, J. PY - 2012 DA - 2012// TI - DNA damage after acute exposure of mice skin to physiological doses of UVB and UVA light JO - Arch Dermatol Res VL - 304 UR - https://doi.org/10.1007/s00403-012-1212-x DO - 10.1007/s00403-012-1212-x ID - Svobodova2012 ER - TY - JOUR AU - Huey, R. B. PY - 1982 DA - 1982// TI - Temperature, physiology, and the ecology of reptiles JO - Biology of the Reptilia VL - 12 ID - Huey1982 ER - TY - JOUR AU - Pavlidis, P. AU - Jensen, J. D. AU - Stephan, W. AU - Stamatakis, A. PY - 2012 DA - 2012// TI - A critical assessment of storytelling: gene ontology categories and the importance of validating genomic scans JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss136 DO - 10.1093/molbev/mss136 ID - Pavlidis2012 ER - TY - JOUR AU - Messier, W. AU - Stewart, C. B. PY - 1997 DA - 1997// TI - Episodic adaptive evolution of primate lysozymes JO - Nature VL - 385 UR - https://doi.org/10.1038/385151a0 DO - 10.1038/385151a0 ID - Messier1997 ER - TY - JOUR AU - Zhang, J. AU - Kumar, S. PY - 1997 DA - 1997// TI - Detection of convergent and parallel evolution at the amino acid sequence level JO - Mol Biol Evol VL - 14 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025789 DO - 10.1093/oxfordjournals.molbev.a025789 ID - Zhang1997 ER - TY - JOUR AU - Yang, Z. PY - 1998 DA - 1998// TI - Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution JO - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025957 DO - 10.1093/oxfordjournals.molbev.a025957 ID - Yang1998 ER - TY - JOUR AU - Fletcher, W. AU - Yang, Z. PY - 2010 DA - 2010// TI - The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msq115 DO - 10.1093/molbev/msq115 ID - Fletcher2010 ER - TY - JOUR AU - Zhang, J. AU - Nielsen, R. AU - Yang, Z. PY - 2005 DA - 2005// TI - Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi237 DO - 10.1093/molbev/msi237 ID - Zhang2005 ER - TY - JOUR AU - Wang, W. AU - Huang, Y. AU - Zhou, Z. AU - Tang, R. AU - Zhao, W. AU - Zeng, L. PY - 2002 DA - 2002// TI - Identification and characterization of AGTRAP, a human homolog of murine Angiotensin II Receptor-Associated Protein (Agtrap) JO - Int J Biochem Cell Biol VL - 34 UR - https://doi.org/10.1016/S1357-2725(01)00094-2 DO - 10.1016/S1357-2725(01)00094-2 ID - Wang2002 ER - TY - JOUR AU - Camelo, J. S. AU - Martins, A. R. AU - Rosa, E. AU - Ramos, S. G. AU - Hehre, D. AU - Bancalari, E. PY - 2012 DA - 2012// TI - Angiotensin II type 1 receptor blockade partially attenuates hypoxia-induced pulmonary hypertension in newborn piglets: relationship with the nitrergic system JO - Braz J Med Biol Res VL - 45 UR - https://doi.org/10.1590/S0100-879X2012007500014 DO - 10.1590/S0100-879X2012007500014 ID - Camelo2012 ER - TY - JOUR AU - Gehrke, S. G. AU - Riedel, H. D. AU - Herrmann, T. AU - Hadaschik, B. AU - Bents, K. AU - Veltkamp, C. PY - 2003 DA - 2003// TI - UbcH5A, a member of human E2 ubiquitin-conjugating enzymes, is closely related to SFT, a stimulator of iron transport, and is up-regulated in hereditary hemochromatosis JO - Blood VL - 101 UR - https://doi.org/10.1182/blood-2002-07-2192 DO - 10.1182/blood-2002-07-2192 ID - Gehrke2003 ER - TY - JOUR AU - Vanni, E. AU - Gatherer, D. AU - Tong, L. AU - Everett, R. D. AU - Boutell, C. PY - 2012 DA - 2012// TI - Functional characterization of residues required for the herpes simplex virus 1 E3 ubiquitin ligase ICP0 to interact with the cellular E2 ubiquitin-conjugating enzyme UBE2D1 (UbcH5a) JO - J Virol VL - 86 UR - https://doi.org/10.1128/JVI.07210-11 DO - 10.1128/JVI.07210-11 ID - Vanni2012 ER - TY - JOUR AU - Loublier, S. AU - Bayot, A. AU - Rak, M. AU - El-Khoury, R. AU - Benit, P. AU - Rustin, P. PY - 2011 DA - 2011// TI - The NDUFB6 subunit of the mitochondrial respiratory chain complex I is required for electron transfer activity: a proof of principle study on stable and controlled RNA interference in human cell lines JO - Biochem Biophys Res Commun VL - 414 UR - https://doi.org/10.1016/j.bbrc.2011.09.078 DO - 10.1016/j.bbrc.2011.09.078 ID - Loublier2011 ER - TY - JOUR AU - Whitfield, A. J. AU - Barrett, P. H. AU - Bockxmeer, F. M. AU - Burnett, J. R. PY - 2004 DA - 2004// TI - Lipid disorders and mutations in the APOB gene JO - Clin Chem VL - 50 UR - https://doi.org/10.1373/clinchem.2004.038026 DO - 10.1373/clinchem.2004.038026 ID - Whitfield2004 ER - TY - JOUR AU - Kadyrov, F. A. AU - Dzantiev, L. AU - Constantin, N. AU - Modrich, P. PY - 2006 DA - 2006// TI - Endonucleolytic function of MutLalpha in human mismatch repair JO - Cell VL - 126 UR - https://doi.org/10.1016/j.cell.2006.05.039 DO - 10.1016/j.cell.2006.05.039 ID - Kadyrov2006 ER - TY - JOUR AU - Merkle, C. J. AU - Karnitz, L. M. AU - Henry-Sanchez, J. T. AU - Chen, J. PY - 2003 DA - 2003// TI - Cloning and characterization of hCTF18, hCTF8, and hDCC1 JO - Human homologs of a Saccharomyces cerevisiae complex involved in sister chromatid cohesion establishment J Biol Chem VL - 278 ID - Merkle2003 ER - TY - JOUR AU - Liu, Y. AU - Zhou, K. AU - Zhang, H. AU - Shugart, Y. Y. AU - Chen, L. AU - Xu, Z. PY - 2008 DA - 2008// TI - Polymorphisms of LIG4 and XRCC4 involved in the NHEJ pathway interact to modify risk of glioma JO - Hum Mutat VL - 29 UR - https://doi.org/10.1002/humu.20645 DO - 10.1002/humu.20645 ID - Liu2008 ER - TY - JOUR AU - Chiruvella, K. K. AU - Renard, B. M. AU - Birkeland, S. R. AU - Sunder, S. AU - Liang, Z. AU - Wilson, T. E. PY - 2014 DA - 2014// TI - Yeast DNA ligase IV mutations reveal a nonhomologous end joining function of BRCT1 distinct from XRCC4/Lif1 binding JO - DNA Repair (Amst) VL - 24 UR - https://doi.org/10.1016/j.dnarep.2014.10.003 DO - 10.1016/j.dnarep.2014.10.003 ID - Chiruvella2014 ER - TY - JOUR AU - Gatei, M. AU - Young, D. AU - Cerosaletti, K. M. AU - Desai-Mehta, A. AU - Spring, K. AU - Kozlov, S. PY - 2000 DA - 2000// TI - ATM-dependent phosphorylation of nibrin in response to radiation exposure JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75508 DO - 10.1038/75508 ID - Gatei2000 ER - TY - JOUR AU - Varon, R. AU - Vissinga, C. AU - Platzer, M. AU - Cerosaletti, K. M. AU - Chrzanowska, K. H. AU - Saar, K. PY - 1998 DA - 1998// TI - Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome JO - Cell VL - 93 UR - https://doi.org/10.1016/S0092-8674(00)81174-5 DO - 10.1016/S0092-8674(00)81174-5 ID - Varon1998 ER - TY - JOUR AU - Sevcik, J. AU - Falk, M. AU - Macurek, L. AU - Kleiblova, P. AU - Lhota, F. AU - Hojny, J. PY - 2013 DA - 2013// TI - Expression of human BRCA1Delta17-19 alternative splicing variant with a truncated BRCT domain in MCF-7 cells results in impaired assembly of DNA repair complexes and aberrant DNA damage response JO - Cell Signal VL - 25 UR - https://doi.org/10.1016/j.cellsig.2013.02.008 DO - 10.1016/j.cellsig.2013.02.008 ID - Sevcik2013 ER - TY - JOUR AU - Somyajit, K. AU - Basavaraju, S. AU - Scully, R. AU - Nagaraju, G. PY - 2013 DA - 2013// TI - ATM- and ATR-mediated phosphorylation of XRCC3 regulates DNA double-strand break-induced checkpoint activation and repair JO - Mol Cell Biol VL - 33 UR - https://doi.org/10.1128/MCB.01521-12 DO - 10.1128/MCB.01521-12 ID - Somyajit2013 ER - TY - JOUR AU - Murray, J. M. AU - Carr, A. M. PY - 2008 DA - 2008// TI - Smc5/6: a link between DNA repair and unidirectional replication? JO - Nat Rev Mol Cell Biol VL - 9 UR - https://doi.org/10.1038/nrm2309 DO - 10.1038/nrm2309 ID - Murray2008 ER - TY - JOUR AU - Piwko, W. AU - Buser, R. AU - Peter, M. PY - 2011 DA - 2011// TI - Rescuing stalled replication forks: MMS22L-TONSL, a novel complex for DNA replication fork repair in human cells JO - Cell Cycle VL - 10 UR - https://doi.org/10.4161/cc.10.11.15557 DO - 10.4161/cc.10.11.15557 ID - Piwko2011 ER - TY - JOUR AU - Wu, S. AU - Shi, Y. AU - Mulligan, P. AU - Gay, F. AU - Landry, J. AU - Liu, H. PY - 2007 DA - 2007// TI - A YY1-INO80 complex regulates genomic stability through homologous recombination-based repair JO - Nat Struct Mol Biol VL - 14 UR - https://doi.org/10.1038/nsmb1332 DO - 10.1038/nsmb1332 ID - Wu2007 ER - TY - JOUR AU - Stern, D. L. PY - 2013 DA - 2013// TI - The genetic causes of convergent evolution JO - Nat Rev Genet VL - 14 UR - https://doi.org/10.1038/nrg3483 DO - 10.1038/nrg3483 ID - Stern2013 ER - TY - JOUR AU - Projecto-Garcia, J. AU - Natarajan, C. AU - Moriyama, H. AU - Weber, R. E. AU - Fago, A. AU - Cheviron, Z. A. PY - 2013 DA - 2013// TI - Repeated elevational transitions in hemoglobin function during the evolution of Andean hummingbirds JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1315456110 DO - 10.1073/pnas.1315456110 ID - Projecto-Garcia2013 ER - TY - JOUR AU - Yang, W. AU - Qi, Y. AU - Fu, J. PY - 2014 DA - 2014// TI - Exploring the genetic basis of adaptation to high elevations in reptiles: a comparative transcriptome analysis of two toad-headed agamas (genus Phrynocephalus) JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0112218 DO - 10.1371/journal.pone.0112218 ID - Yang2014 ER - TY - STD TI - Gordon A, Hannon G: FASTQ/A short-reads pre-processing tools. [http://hannonlab.cshl.edu/fastx_toolkit] UR - http://hannonlab.cshl.edu/fastx_toolkit ID - ref61 ER - TY - JOUR AU - Grabherr, M. G. AU - Haas, B. J. AU - Yassour, M. AU - Levin, J. Z. AU - Thompson, D. A. AU - Amit, I. PY - 2011 DA - 2011// TI - Full-length transcriptome assembly from RNA-Seq data without a reference genome JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1883 DO - 10.1038/nbt.1883 ID - Grabherr2011 ER - TY - JOUR AU - Fu, L. AU - Niu, B. AU - Zhu, Z. AU - Wu, S. AU - Li, W. PY - 2012 DA - 2012// TI - CD-HIT: accelerated for clustering the next-generation sequencing data JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts565 DO - 10.1093/bioinformatics/bts565 ID - Fu2012 ER - TY - JOUR AU - Li, B. AU - Dewey, C. N. PY - 2011 DA - 2011// TI - RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-323 DO - 10.1186/1471-2105-12-323 ID - Li2011 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 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 - Ye, J. AU - Fang, L. AU - Zheng, H. AU - Zhang, Y. AU - Chen, J. AU - Zhang, Z. PY - 2006 DA - 2006// TI - WEGO: a web tool for plotting GO annotations JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl031 DO - 10.1093/nar/gkl031 ID - Ye2006 ER - TY - JOUR AU - Moriya, Y. AU - Itoh, M. AU - Okuda, S. AU - Yoshizawa, A. C. AU - Kanehisa, M. PY - 2007 DA - 2007// TI - KAAS: an automatic genome annotation and pathway reconstruction server JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm321 DO - 10.1093/nar/gkm321 ID - Moriya2007 ER - TY - JOUR AU - Remm, M. AU - Storm, C. E. AU - Sonnhammer, E. L. PY - 2001 DA - 2001// TI - Automatic clustering of orthologs and in-paralogs from pairwise species comparisons JO - J Mol Biol VL - 314 UR - https://doi.org/10.1006/jmbi.2000.5197 DO - 10.1006/jmbi.2000.5197 ID - Remm2001 ER - TY - JOUR AU - Alexeyenko, A. AU - Tamas, I. AU - Liu, G. AU - Sonnhammer, E. L. PY - 2006 DA - 2006// TI - Automatic clustering of orthologs and inparalogs shared by multiple proteomes JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl213 DO - 10.1093/bioinformatics/btl213 ID - Alexeyenko2006 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 - Darriba, D. AU - Taboada, G. L. AU - Doallo, R. AU - Posada, D. PY - 2012 DA - 2012// TI - jModelTest 2: more models, new heuristics and parallel computing JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.2109 DO - 10.1038/nmeth.2109 ID - Darriba2012 ER - TY - JOUR AU - Guindon, S. AU - Dufayard, J. F. AU - Lefort, V. AU - Anisimova, M. AU - Hordijk, W. AU - Gascuel, O. PY - 2010 DA - 2010// TI - New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 JO - Syst Biol VL - 59 UR - https://doi.org/10.1093/sysbio/syq010 DO - 10.1093/sysbio/syq010 ID - Guindon2010 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 - TY - JOUR AU - Drummond, A. J. AU - Rambaut, A. PY - 2007 DA - 2007// TI - BEAST: Bayesian evolutionary analysis by sampling trees JO - BMC Evol Biol VL - 7 UR - https://doi.org/10.1186/1471-2148-7-214 DO - 10.1186/1471-2148-7-214 ID - Drummond2007 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. PY - 2002 DA - 2002// TI - Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004148 DO - 10.1093/oxfordjournals.molbev.a004148 ID - Yang2002 ER - TY - JOUR AU - Chimpanzee, S. AU - Analysis, C. PY - 2005 DA - 2005// TI - Initial sequence of the chimpanzee genome and comparison with the human genome JO - Nature VL - 437 UR - https://doi.org/10.1038/nature04072 DO - 10.1038/nature04072 ID - Chimpanzee2005 ER - TY - JOUR AU - Yang, Z. AU - Wong, W. S. AU - Nielsen, R. PY - 2005 DA - 2005// TI - Bayes empirical bayes inference of amino acid sites under positive selection JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi097 DO - 10.1093/molbev/msi097 ID - Yang2005 ER - TY - JOUR AU - Punta, M. AU - Coggill, P. C. AU - Eberhardt, R. Y. AU - Mistry, J. AU - Tate, J. AU - Boursnell, C. PY - 2012 DA - 2012// TI - The Pfam protein families database JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1065 DO - 10.1093/nar/gkr1065 ID - Punta2012 ER - TY - JOUR AU - Kelley, L. A. AU - Sternberg, M. J. PY - 2009 DA - 2009// TI - Protein structure prediction on the Web: a case study using the Phyre server JO - Nat Protoc VL - 4 UR - https://doi.org/10.1038/nprot.2009.2 DO - 10.1038/nprot.2009.2 ID - Kelley2009 ER - TY - JOUR AU - Pettersen, E. F. AU - Goddard, T. D. AU - Huang, C. C. AU - Couch, G. S. AU - Greenblatt, D. M. AU - Meng, E. C. PY - 2004 DA - 2004// TI - UCSF Chimera–a visualization system for exploratory research and analysis JO - J Comput Chem VL - 25 UR - https://doi.org/10.1002/jcc.20084 DO - 10.1002/jcc.20084 ID - Pettersen2004 ER - TY - STD TI - DeLano, WL. The PyMOL Molecular Graphics System. [www.pymol.org]. UR - http://www.pymol.org/ ID - ref82 ER - TY - JOUR AU - Unni, S. AU - Huang, Y. AU - Hanson, R. M. AU - Tobias, M. AU - Krishnan, S. AU - Li, W. W. PY - 2011 DA - 2011// TI - Web servers and services for electrostatics calculations with APBS and PDB2PQR JO - J Comput Chem VL - 32 UR - https://doi.org/10.1002/jcc.21720 DO - 10.1002/jcc.21720 ID - Unni2011 ER - TY - STD TI - Yang Y, Wang L, Han J, Tang X, Ma M, Wang K, Zhang X, Ren Q, Chen Q, Qiu Q. Data from: Comparative transcriptomic analysis revealed adaptation mechanism of Phrynocephalus erythrurus, the highest altitude Lizard living in the Qinghai-Tibet Plateau. BMC Evol Biol 2015, http://dx.doi.org/10.5061/dryad.f587b. UR - http://dx.doi.org/10.5061/dryad.f587b ID - ref84 ER -