Experts and Doctors on phylogeny in United States


Locale: United States
Topic: phylogeny

Top Publications

  1. Haynes W, Ling K, Saimi Y, Kung C. PAK paradox: Paramecium appears to have more K(+)-channel genes than humans. Eukaryot Cell. 2003;2:737-45 pubmed
  2. Evenhuis J, Bengten E, Snell C, Quiniou S, Miller N, Wilson M. Characterization of additional novel immune type receptors in channel catfish, Ictalurus punctatus. Immunogenetics. 2007;59:661-71 pubmed
    ..IpNITR12-16 are differentially expressed in various catfish immune-type cells and preferentially up regulated in peripheral blood leukocytes by allogeneic stimulation. ..
  3. Tavormina P, Ussler W, Orphan V. Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin. Appl Environ Microbiol. 2008;74:3985-95 pubmed publisher
    ..This sequence potentiates insight into the amo/pmo superfamily. Together, these findings lend perspective into the diversity and segregation of aerobic methanotrophs within different methane-rich habitats in the marine environment. ..
  4. Kanaoka M, Pillitteri L, Fujii H, Yoshida Y, Bogenschutz N, Takabayashi J, et al. SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation. Plant Cell. 2008;20:1775-85 pubmed publisher
  5. Zhou J, Lee C, Zhong R, Ye Z. MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis. Plant Cell. 2009;21:248-66 pubmed publisher
    ..Together, our results indicate that MYB58 and MYB63 are specific transcriptional activators of lignin biosynthesis in the SND1-mediated transcriptional network regulating secondary wall formation. ..
  6. Pollack Berti A, Wollenberg M, Ruby E. Natural transformation of Vibrio fischeri requires tfoX and tfoY. Environ Microbiol. 2010;12:2302-11 pubmed publisher
    ..The presence of chitin-induced competence in several vibrios highlights the potential for a conserved mechanism of genetic exchange across this family of environmentally important marine bacteria. ..
  7. Brown R, Siler C, Das I, Min Y. Testing the phylogenetic affinities of Southeast Asia's rarest geckos: Flap-legged geckos (Luperosaurus), Flying geckos (Ptychozoon) and their relationship to the pan-Asian genus Gekko. Mol Phylogenet Evol. 2012;63:915-21 pubmed publisher
    ..The Flying Gecko genus Ptychozoon is also nested within Gekko, suggesting that higher-level taxonomic revision of the generic boundaries within Southeast Asian gekkonines will be a priority for the immediate future...
  8. Rosenfeld J, Payne A, DeSalle R. Random roots and lineage sorting. Mol Phylogenet Evol. 2012;64:12-20 pubmed publisher
    ..Likelihood tends to stabilize incongruence as outgroups get further and further away from the ingroup. In one extreme case, likelihood overcompensates for sequence divergence but increases random rooting causing long branch repulsion. ..
  9. Widmer F, Shaffer B, Porteous L, Seidler R. Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon cascade mountain range. Appl Environ Microbiol. 1999;65:374-80 pubmed

More Information

Publications596 found, 100 shown here

  1. Frye R. Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun. 2000;273:793-8 pubmed
    ..The seven human sirtuin genes include all four classes: SIRT1, SIRT2, and SIRT3 are class I, SIRT4 is class II, SIRT5 is class III, and SIRT6 and SIRT7 are class IV. ..
  2. Haeseleer F, Jang G, Imanishi Y, Driessen C, Matsumura M, Nelson P, et al. Dual-substrate specificity short chain retinol dehydrogenases from the vertebrate retina. J Biol Chem. 2002;277:45537-45546 pubmed publisher
    ..These newly identified enzymes add new elements to important retinoid metabolic pathways that have not been explained by previous genetic and biochemical studies. ..
  3. Hedges S. The origin and evolution of model organisms. Nat Rev Genet. 2002;3:838-49 pubmed
    ..This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities. ..
  4. Telford S, Ernst J, Clark A, Butler J. Hepatozoon sauritus: a polytopic hemogregarine of three genera and four species of snakes in north Florida, with specific identity verified from genome analysis. J Parasitol. 2004;90:352-8 pubmed
    ..Hepatozoon sauritus, therefore, is a polytopic species in contrast to the 8 other Hepatozoon species thus far described from snakes in Florida, each of which appears to parasitize a single host species...
  5. Alkan C, Eichler E, Bailey J, Sahinalp S, Tuzun E. The role of unequal crossover in alpha-satellite DNA evolution: a computational analysis. J Comput Biol. 2004;11:933-44 pubmed
    ..It is likely that the higher order repeats developed independently in distinct regions of the genome and were carried into their current locations through an unknown mechanism of transposition. ..
  6. Damude H, Zhang H, Farrall L, Ripp K, Tomb J, Hollerbach D, et al. Identification of bifunctional delta12/omega3 fatty acid desaturases for improving the ratio of omega3 to omega6 fatty acids in microbes and plants. Proc Natl Acad Sci U S A. 2006;103:9446-51 pubmed
  7. Chojnowski J, Franklin J, Katsu Y, Iguchi T, Guillette L, Kimball R, et al. Patterns of vertebrate isochore evolution revealed by comparison of expressed mammalian, avian, and crocodilian genes. J Mol Evol. 2007;65:259-66 pubmed publisher
    ..Falsification of these models places fundamental constraints upon the plausible pathways for the evolution of isochores...
  8. Karimpour Fard A, Detweiler C, Erickson K, Hunter L, Gill R. Cross-species cluster co-conservation: a new method for generating protein interaction networks. Genome Biol. 2007;8:R185 pubmed
    ..We have extended CCC to develop protein interaction networks based on co-conservation between protein pairs across multiple species, cross-species cluster co-conservation. ..
  9. Porat I, Vishnivetskaya T, Mosher J, Brandt C, Yang Z, Brooks S, et al. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol. 2010;60:784-95 pubmed publisher
    ..The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle. ..
  10. Nyári A, Joseph L. Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae). PLoS ONE. 2012;7:e31840 pubmed publisher
    ..magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster. ..
  11. Boucias D, Garcia Maruniak A, Cherry R, Lu H, Maruniak J, Lietze V. Detection and characterization of bacterial symbionts in the Heteropteran, Blissus insularis. FEMS Microbiol Ecol. 2012;82:629-41 pubmed publisher
    ..Furthermore, these treatments resulted in retarded development and high mortality of B. insularis, indicating a beneficial impact of Burkholderia on its host...
  12. Kapczynski D, Pantin Jackwood M, Guzman S, Ricardez Y, Spackman E, Bertran K, et al. Characterization of the 2012 highly pathogenic avian influenza H7N3 virus isolated from poultry in an outbreak in Mexico: pathobiology and vaccine protection. J Virol. 2013;87:9086-96 pubmed publisher
    ..This study demonstrates the pathological consequences of the infection of chickens with the 2012 Mexican lineage H7N3 HPAI virus and provides support for effective programs of vaccination against this virus in poultry. ..
  13. Saintenac C, Zhang W, Salcedo A, Rouse M, Trick H, Akhunov E, et al. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science. 2013;341:783-786 pubmed publisher
    ..monococcum to polyploid wheat. The cloning of Sr35 opens the door to the use of biotechnological approaches to control this devastating disease and to analyses of the molecular interactions that define the wheat-rust pathosystem. ..
  14. Thekke Veetil T, Aboughanem Sabanadzovic N, Keller K, Martin R, Sabanadzovic S, Tzanetakis I. Molecular characterization and population structure of blackberry vein banding associated virus, new Ampelovirus associated with yellow vein disease. Virus Res. 2013;178:234-40 pubmed publisher
    ..Further analyses indicated that these proteins are under stringent purifying selections. High genetic variability and incongruent clustering of isolates suggested the possible involvement of recombination in the evolution of BVBaV. ..
  15. Cooper K, Sears K, Uygur A, Maier J, Baczkowski K, Brosnahan M, et al. Patterning and post-patterning modes of evolutionary digit loss in mammals. Nature. 2014;511:41-5 pubmed publisher
    ..Together these data demonstrate remarkable plasticity in the mechanisms of vertebrate limb evolution and shed light on the complexity of morphological convergence, particularly within the artiodactyl lineage. ..
  16. Li Y, Shi J, Nelson M, Chen P, Graf J, Li Y, et al. Impact of different ratios of feedstock to liquid anaerobic digestion effluent on the performance and microbiome of solid-state anaerobic digesters digesting corn stover. Bioresour Technol. 2016;200:744-52 pubmed publisher
    ..Some bacteria and methanogens were affected by non-microbial factors of the L-AD fluent. Alkalinity, the main difference between the two F/Et ratios, may be the crucial factor when SS-AD digesters were started using L-AD effluent. ..
  17. Deng D, Weidhaas J, Lin L. Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage. J Hazard Mater. 2016;305:200-208 pubmed publisher
    ..The reported COD kinetics, SRB abundances and the phylogenetic profile provide insights into the co-treatment process and help identify the parameters of concerns for such technology development. ..
  18. Gong W, Zhang L, Lu Z, Jia J, Wang M, Peng Z, et al. Complete genome sequence of a novel sub-subgenotype 2.1g isolate of classical swine fever virus from China. Arch Virol. 2016;161:2613-7 pubmed publisher
    ..This is the first report of the complete genome sequence of a 2.1g isolate, and the GD19/2011 isolate will be useful for further analysis of the evolution and virulence of CSFV isolates. ..
  19. Bigham A, Bauchet M, Pinto D, Mao X, Akey J, Mei R, et al. Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data. PLoS Genet. 2010;6:e1001116 pubmed publisher
  20. Mehra Chaudhary R, Mick J, Tanner J, Henzl M, Beamer L. Crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens. Proteins. 2011;79:1215-29 pubmed publisher
  21. Bright L, Goût J, Lynch M. Early stages of functional diversification in the Rab GTPase gene family revealed by genomic and localization studies in Paramecium species. Mol Biol Cell. 2017;28:1101-1110 pubmed publisher
  22. Chang C, da Silva S, Ideta R, Lee Y, Yeh S, Burbach J. Human and rat TR4 orphan receptors specify a subclass of the steroid receptor superfamily. Proc Natl Acad Sci U S A. 1994;91:6040-4 pubmed
    ..Unlike TR2 orphan receptors, the TR4 orphan receptor appears to be predominantly located in granule cells of the hippocampus and the cerebellum, suggesting that it may play some role(s) in transcriptional regulation in these neurons. ..
  23. Fu H, Doelling J, Arendt C, Hochstrasser M, Vierstra R. Molecular organization of the 20S proteasome gene family from Arabidopsis thaliana. Genetics. 1998;149:677-92 pubmed
  24. Gaucher E, Miyamoto M, Benner S. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc Natl Acad Sci U S A. 2001;98:548-52 pubmed
    ..We illustrate this in the elongation factor family of proteins as a paradigm for applications of this type of analysis in functional genomics generally. ..
  25. Connon S, Giovannoni S. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol. 2002;68:3878-85 pubmed
    ..This method proved successful for the cultivation of previously uncultured marine bacterioplankton that have consistently been found in marine clone libraries. ..
  26. Rikihisa Y, Zhang C, Christensen B. Molecular characterization of Aegyptianella pullorum (Rickettsiales, Anaplasmataceae). J Clin Microbiol. 2003;41:5294-7 pubmed
    ..A specific PCR test was developed to analyze A. pullorum DNA. Phylogenic analysis revealed A. pullorum is most closely related to Anaplasma spp...
  27. Hughes A, Friedman R. Poxvirus genome evolution by gene gain and loss. Mol Phylogenet Evol. 2005;35:186-95 pubmed
    ..Thus "capture" of host genes by HGT has been a recurrent feature of poxvirus evolution and has played an important role in adapting the virus to survive host antiviral defense mechanisms...
  28. Zhang N, Castlebury L, Miller A, Huhndorf S, Schoch C, Seifert K, et al. An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia. 2006;98:1076-87 pubmed
    ..In the Sordariomycetidae, the Sordariales is a strongly supported clade and occurs within a well supported clade containing the Boliniales and Chaetosphaeriales. Aspects of morphology, ecology and evolution are discussed. ..
  29. Lee J, Ji Z, Tian B. Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes. Nucleic Acids Res. 2008;36:5581-90 pubmed publisher
    ..Our results establish a conservation pattern for alternative poly(A) sites in several vertebrate species, and indicate that the 3'-end of genes can be dynamically modified by TEs through evolution. ..
  30. Gutierrez C, Matsui G, Lincoln D, Lovell C. Production of the phytohormone indole-3-acetic acid by estuarine species of the genus Vibrio. Appl Environ Microbiol. 2009;75:2253-8 pubmed publisher
    ..To our knowledge, this is the first report of IAA production by species of the genus Vibrio or by bacteria isolated from an estuarine environment. ..
  31. Lucas Lledó J, Lynch M. Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family. Mol Biol Evol. 2009;26:1143-53 pubmed publisher
    ..In contrast, the loss of photolyase genes in prokaryotes may not cause an increase in the mutation rate and be neutral in most cases. ..
  32. Parkin D, Archer L, Childress A, Wellehan J. Genotype differentiation of Agamid Adenovirus 1 in bearded dragons (Pogona vitticeps) in the USA by hexon gene sequence. Infect Genet Evol. 2009;9:501-6 pubmed publisher
    ..These findings show that this hexon region is useful for AgAdV1 genotyping, which can be used epidemiologically as well as in future investigations of AgAdV1 evolution and clinical implications of strain differences. ..
  33. Bailly M, De Crecy Lagard V. Predicting the pathway involved in post-translational modification of elongation factor P in a subset of bacterial species. Biol Direct. 2010;5:3 pubmed publisher
    ..This article was reviewed by Céline Brochier-Armanet, Igor B. Zhulin and Mikhail Gelfand. For the full reviews, please go to the Reviewers' reports section. ..
  34. Tazi L, Pérez Losada M, Gu W, Yang Y, Xue L, Crandall K, et al. Population dynamics of Neisseria gonorrhoeae in Shanghai, China: a comparative study. BMC Infect Dis. 2010;10:13 pubmed publisher
    ..Population genetic analysis of gonococcal strains in conjunction with epidemiological surveillance may provide insights into the epidemic behavior of antibiotic resistant strains and help to design control measures. ..
  35. McDonald L, Gerrelli D, Fok Y, Hurst L, Tickle C. Comparison of Iroquois gene expression in limbs/fins of vertebrate embryos. J Anat. 2010;216:683-91 pubmed publisher
    ..In zebrafish, Irx genes of all but six of the families are expressed in early stage pectoral fin buds but not at later stages, suggesting that these genes are not involved in patterning distal structures in zebrafish fins. ..
  36. Wang Z, Zhang X, Le M, Xu D, Stacey G, Cheng J. A protein domain co-occurrence network approach for predicting protein function and inferring species phylogeny. PLoS ONE. 2011;6:e17906 pubmed publisher
    ..In summary, our studies show that genome-wide DCNs contain rich information that can be effectively used to decipher protein function and reveal the evolutionary relationship among species. ..
  37. Kim H, Smith J, Ridenour J, Woloshuk C, Bluhm B. HXK1 regulates carbon catabolism, sporulation, fumonisin B? production and pathogenesis in Fusarium verticillioides. Microbiology. 2011;157:2658-69 pubmed publisher
    ..verticillioides, and thus provides a new foothold from which the genetic regulatory networks that underlie pathogenesis and mycotoxigenesis can be unravelled and defined. ..
  38. Brazee N, Ortiz Santana B, Banik M, Lindner D. Armillaria altimontana, a new species from the western interior of North America. Mycologia. 2012;104:1200-5 pubmed publisher
    ..Results indicate that isolates of A. altimontana formed a monophyletic group and clustered with A. calvescens, A. cepistipes, A. gallica and A. nabsnona, which is in agreement with recent phylogenetic studies of Armillaria. ..
  39. Weng M, Ruhlman T, Gibby M, Jansen R. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae). Mol Phylogenet Evol. 2012;64:654-70 pubmed publisher
  40. Wu Y, Doak T, Ye Y. The gain and loss of chromosomal integron systems in the Treponema species. BMC Evol Biol. 2013;13:16 pubmed publisher
    ..By characterizing integron distribution and cassette contents in the Treponema sps., we link the integrons to the speciation of the various species, especially to the pathogens T. pallidum and T. phagedenis. ..
  41. Simanshu D, Nissley D, McCormick F. RAS Proteins and Their Regulators in Human Disease. Cell. 2017;170:17-33 pubmed publisher
    ..All RAS biology occurs in membranes: a precise understanding of RAS' interaction with membranes is essential to understand RAS action and to intervene in RAS-driven diseases. ..
  42. Timoshevskiy V, Lampman R, Hess J, Porter L, Smith J. Deep ancestry of programmed genome rearrangement in lampreys. Dev Biol. 2017;429:31-34 pubmed publisher
  43. Lai E, Wilson R, Hood L. Physical maps of the mouse and human immunoglobulin-like loci. Adv Immunol. 1989;46:1-59 pubmed
  44. Shaw J, Ferl R, Baier J, St Clair D, Carson C, McCarty D, et al. Structural features of the maize sus1 gene and protein. Plant Physiol. 1994;106:1659-65 pubmed
    ..These latter observations point to an important role played by both genes in this group of plants. ..
  45. Crawford D, Segal J, Barnett J. Evolutionary analysis of TATA-less proximal promoter function. Mol Biol Evol. 1999;16:194-207 pubmed
  46. Currie C, Wong B, Stuart A, Schultz T, Rehner S, Mueller U, et al. Ancient tripartite coevolution in the attine ant-microbe symbiosis. Science. 2003;299:386-8 pubmed
    ..At recent phylogenetic levels, coevolution has been punctuated by occasional host-switching by the parasite, thus intensifying continuous coadaptation between symbionts in a tripartite arms race...
  47. Coyle I, Koh Y, Lee W, Slind J, Fergestad T, Littleton J, et al. Nervous wreck, an SH3 adaptor protein that interacts with Wsp, regulates synaptic growth in Drosophila. Neuron. 2004;41:521-34 pubmed
    ..We propose that Nwk controls synapse morphology by regulating actin dynamics downstream of growth signals in presynaptic terminals. ..
  48. Larget B, Kadane J, Simon D. A Bayesian approach to the estimation of ancestral genome arrangements. Mol Phylogenet Evol. 2005;36:214-23 pubmed
    ..We compare and contrast a Bayesian approach with a parsimony approach to infer phylogenies and ancestral arrangements from genome arrangement data by re-analyzing a number of previously published data sets...
  49. Cho M, Corea O, Yang H, Bedgar D, Laskar D, Anterola A, et al. Phenylalanine biosynthesis in Arabidopsis thaliana. Identification and characterization of arogenate dehydratases. J Biol Chem. 2007;282:30827-35 pubmed
    ..All six genes, and their corresponding proteins, are thus provisionally classified as arogenate dehydratases and designated ADT1-ADT6. ..
  50. Ithychanda S, Hsu D, Li H, Yan L, Liu D, Liu D, et al. Identification and characterization of multiple similar ligand-binding repeats in filamin: implication on filamin-mediated receptor clustering and cross-talk. J Biol Chem. 2009;284:35113-21 pubmed publisher
  51. Gross E, Leys E, Gasparovich S, Firestone N, Schwartzbaum J, Janies D, et al. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol. 2010;48:4121-8 pubmed publisher
  52. Jarvis M, Lam H, Zhang Y, Wang L, Hesse R, Hause B, et al. Genomic and evolutionary inferences between American and global strains of porcine epidemic diarrhea virus. Prev Vet Med. 2016;123:175-184 pubmed publisher
    ..These finding suggest that significant genetic events outside of the spike region have contributed to the evolution of PEDV. ..
  53. Maclean E. Unraveling the evolution of uniquely human cognition. Proc Natl Acad Sci U S A. 2016;113:6348-54 pubmed publisher
  54. Lu D, Xia J, Dunlap C, Rooney A, Du Z. Gracilimonas halophila sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol. 2017;67:3251-3255 pubmed publisher
    ..nov. is proposed. The type strain is WDS2C40T (=KCTC 52042T=MCCC 1H00135T). ..
  55. Guina T, Helfet Hilliker D, Ramamurthy V, Oliver D. Sequence and phylogenetic analysis of the Borrelia burgdorferi secA gene. Biochim Biophys Acta. 1998;1371:24-30 pubmed
  56. Jin J, Chen A, Huang Q. Three alternatively spliced mouse slow skeletal muscle troponin T isoforms: conserved primary structure and regulated expression during postnatal development. Gene. 1998;214:121-9 pubmed
    ..The highly conserved primary structure and fiber type-specific and developmentally regulated expression of sTnT indicate a physiological importance of this under-studied member of the TnT gene family. ..
  57. Knipple D, Rosenfield C, Nielsen R, You K, Jeong S. Evolution of the integral membrane desaturase gene family in moths and flies. Genetics. 2002;162:1737-52 pubmed
  58. Dupas S, Turnbull M, Webb B. Diversifying selection in a parasitoid's symbiotic virus among genes involved in inhibiting host immunity. Immunogenetics. 2003;55:351-61 pubmed
    ..The positive selection and duplication of both the gene family and the cys-motif implies either selection is driving the molecular radiation of immune suppressive genes toward novel hosts, or molecular coevolution with host targets. ..
  59. Rehfuss M, Urban J. Rhodococcus phenolicus sp. nov., a novel bioprocessor isolated actinomycete with the ability to degrade chlorobenzene, dichlorobenzene and phenol as sole carbon sources. Syst Appl Microbiol. 2005;28:695-701 pubmed
    ..The name Rhodococcus phenolicus is proposed for the isolate with the type strain G2PT (= DSM 44812) (= NRRL B-24323) [corrected] ..
  60. Diem K, Nickle D, Motoshige A, Fox A, Ross S, Mullins J, et al. Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). AIDS Res Hum Retroviruses. 2008;24:561-71 pubmed publisher
    ..As such, our study findings are important for understanding the long-term response to antiretroviral therapy, the design of vaccines, and the sexual transmission of HIV. ..
  61. Hughes A. Evolutionary conservation of amino acid composition in paralogous insect vitellogenins. Gene. 2010;467:35-40 pubmed publisher
  62. Finet C, Timme R, Delwiche C, Marlétaz F. Multigene phylogeny of the green lineage reveals the origin and diversification of land plants. Curr Biol. 2010;20:2217-22 pubmed publisher
    ..These results provide a new phylogenetic framework and represent a key step in the evolutionary interpretation of developmental and genomic characters in green plants. ..
  63. Alverson A, Beszteri B, Julius M, Theriot E. The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella. BMC Evol Biol. 2011;11:125 pubmed publisher
    ..The freshwater component of T. pseudonana's history merits careful consideration in the interpretation of experimental data collected for this important model species. ..
  64. Klatte J, Clarridge J, Bratcher D, Selvarangan R. A longitudinal case series description of meningitis due to Streptococcus gallolyticus subsp. pasteurianus in infants. J Clin Microbiol. 2012;50:57-60 pubmed publisher
    ..S. gallolyticus subsp. pasteurianus is an increasingly recognized cause of meningitis and bacteremia in the newborn period, and it merits further study with respect to etiology of infection...
  65. Pierce L, Stepien C. Evolution and biogeography of an emerging quasispecies: diversity patterns of the fish Viral Hemorrhagic Septicemia virus (VHSv). Mol Phylogenet Evol. 2012;63:327-41 pubmed publisher
    ..This study provides a baseline for future tracking of VHSv spread and interpreting its evolutionary diversification pathways. ..
  66. Tucker A, Ackerman M, Eads B, Xu S, Lynch M. Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proc Natl Acad Sci U S A. 2013;110:15740-5 pubmed publisher
    ..Our study implies that the buildup of newly introduced deleterious mutations (i.e., Muller's ratchet) may not be the dominant force imperiling nonrecombining populations of D. pulex, as previously proposed. ..
  67. Bales K, Saltzman W. Fathering in rodents: Neurobiological substrates and consequences for offspring. Horm Behav. 2016;77:249-59 pubmed publisher
  68. Chaliotis A, Vlastaridis P, Mossialos D, Ibba M, Becker H, Stathopoulos C, et al. The complex evolutionary history of aminoacyl-tRNA synthetases. Nucleic Acids Res. 2017;45:1059-1068 pubmed publisher
    ..These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code. ..
  69. Yokoyama S, Radlwimmer F. The molecular genetics of red and green color vision in mammals. Genetics. 1999;153:919-32 pubmed
    ..The additive effects of these amino acid changes fully explain the red-green color vision in a wide range of mammalian species, goldfish, American chameleon (Anolis carolinensis), and pigeon (Columba livia)...
  70. Choudhuri S, Ogura K, Klaassen C. Cloning, expression, and ontogeny of mouse organic anion-transporting polypeptide-5, a kidney-specific organic anion transporter. Biochem Biophys Res Commun. 2001;280:92-8 pubmed
    ..Phylogenetic analysis reveals that mouse Oatp-5 is an ortholog of rat Oatp-5. ..
  71. Rojo E, Zouhar J, Kovaleva V, Hong S, Raikhel N. The AtC-VPS protein complex is localized to the tonoplast and the prevacuolar compartment in arabidopsis. Mol Biol Cell. 2003;14:361-9 pubmed
    ..VCL1, AtVPS11, and AtVPS33 are the first components of the vacuolar biogenesis machinery to be identified in plants. ..
  72. Karniol B, Vierstra R. The pair of bacteriophytochromes from Agrobacterium tumefaciens are histidine kinases with opposing photobiological properties. Proc Natl Acad Sci U S A. 2003;100:2807-12 pubmed publisher
    ..By using these mutually opposing BphPs, A. tumefaciens presumably has the capacity to simultaneously sense red light-rich and far-red light-rich environments through deactivation of their associated kinase cascades...
  73. Childs J, Poole A, Turner D. Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA. RNA. 2003;9:1437-45 pubmed
    ..Thus, the ODMiR method can be applied to RNAs even when folding is facilitated by a cognate protein. ..
  74. Cronn R, Small R, Haselkorn T, Wendel J. Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution. 2003;57:2475-89 pubmed
    ..Gossypium gossypioides provides a striking example of the previously unsuspected chimeric nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events...
  75. Page K, Connon S, Giovannoni S. Representative freshwater bacterioplankton isolated from Crater Lake, Oregon. Appl Environ Microbiol. 2004;70:6542-50 pubmed
  76. Webb B, Strand M, Dickey S, Beck M, Hilgarth R, Barney W, et al. Polydnavirus genomes reflect their dual roles as mutualists and pathogens. Virology. 2006;347:160-74 pubmed
  77. Todorova S, Costello A. Design of Shewanella-specific 16S rRNA primers and application to analysis of Shewanella in a minerotrophic wetland. Environ Microbiol. 2006;8:426-32 pubmed
    ..The dominant species in the wetland samples at two geochemically distinct zones were phylogenetically related to the iron-reducing microorganism Shewanella oneidensis. ..
  78. Zhong R, Demura T, Ye Z. SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis. Plant Cell. 2006;18:3158-70 pubmed
    ..Together, our results reveal that SND1 is a key transcriptional activator involved in secondary wall biosynthesis in fibers. ..
  79. Wang S, Baumann A, Wilson T. Drosophila melanogaster Methoprene-tolerant (Met) gene homologs from three mosquito species: Members of PAS transcriptional factor family. J Insect Physiol. 2007;53:246-53 pubmed
    ..aegypti and An. gambiae. These results suggest that a gene duplication occurred during the evolution of higher Diptera, resulting in Met and gce. ..
  80. Karimpour Fard A, Hunter L, Gill R. Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling. BMC Genomics. 2007;8:393 pubmed
    ..These studies should prove valuable for future studies seeking to further improve phylogenetic profiling methodologies as well for efforts to efficiently employ such methods to develop new biological insights. ..
  81. Jeyaprakash A, Hoy M. First divergence time estimate of spiders, scorpions, mites and ticks (subphylum: Chelicerata) inferred from mitochondrial phylogeny. Exp Appl Acarol. 2009;47:1-18 pubmed publisher
  82. Ay F, Kahveci T, De Crecy Lagard V. A fast and accurate algorithm for comparative analysis of metabolic pathways. J Bioinform Comput Biol. 2009;7:389-428 pubmed
    ..Our software and the source code in C programming language is available at ..
  83. Gray R, Bayly R, Green S, Agarwala S, Lowe C, Wallingford J. Diversification of the expression patterns and developmental functions of the dishevelled gene family during chordate evolution. Dev Dyn. 2009;238:2044-57 pubmed publisher
    ..These data demonstrate that the expression patterns and developmental functions of specific Dvl genes have diverged significantly during chordate evolution. ..
  84. Cooper W, Parsons K, McIntyre A, Kern B, McGee Moore A, Albertson R. Bentho-pelagic divergence of cichlid feeding architecture was prodigious and consistent during multiple adaptive radiations within African rift-lakes. PLoS ONE. 2010;5:e9551 pubmed publisher
  85. Sukumaran J, Holder M. DendroPy: a Python library for phylogenetic computing. Bioinformatics. 2010;26:1569-71 pubmed publisher, while the active development source code repository is available to the public from GitHub ( ..
  86. Weete J, Abril M, Blackwell M. Phylogenetic distribution of fungal sterols. PLoS ONE. 2010;5:e10899 pubmed publisher
    ..g., Glomeromycota). Data from this study are available from the Assembling the Fungal Tree of Life (AFTOL) Structural and Biochemical Database: ..
  87. Miyashiro T, Wollenberg M, Cao X, Oehlert D, Ruby E. A single qrr gene is necessary and sufficient for LuxO-mediated regulation in Vibrio fischeri. Mol Microbiol. 2010;77:1556-67 pubmed publisher
    ..Our studies contribute to a better understanding of the ancestral state of these pathways in vibrios, as well as to the evolution and divergence of other sRNAs within different bacterial lineages. ..
  88. Liu L, Yu L. Estimating species trees from unrooted gene trees. Syst Biol. 2011;60:661-7 pubmed publisher
    ..In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals. ..
  89. Laney A, Keller K, Martin R, Tzanetakis I. A discovery 70 years in the making: characterization of the Rose rosette virus. J Gen Virol. 2011;92:1727-32 pubmed publisher
    ..Diversity studies using two virus proteins, p3 and p4, demonstrated that the virus has low diversity between isolates as they share nucleotide identities ranging from 97 to 99%. ..
  90. Lack J, Nichols R, Wilson G, Van Den Bussche R. Genetic signature of reproductive manipulation in the phylogeography of the bat fly, Trichobius major. J Hered. 2011;102:705-18 pubmed publisher
    ..16% infection rate) with a novel strain of Rickettsia. We discuss the implications for T. major phylogeography and the necessity of a bigenomic approach in arthropod population genetics...
  91. Saballos A, Sattler S, Sanchez E, Foster T, Xin Z, Kang C, et al. Brown midrib2 (Bmr2) encodes the major 4-coumarate:coenzyme A ligase involved in lignin biosynthesis in sorghum (Sorghum bicolor (L.) Moench). Plant J. 2012;70:818-30 pubmed publisher
    ..Gene expression assays indicated that Bmr2 is under auto-regulatory control, as reduced 4CL activity results in over-expression of the defective gene. Several 4CL paralogs are also up-regulated in response to the mutation...
  92. Bever J, Broadhurst L, Thrall P. Microbial phylotype composition and diversity predicts plant productivity and plant-soil feedbacks. Ecol Lett. 2013;16:167-74 pubmed publisher
    ..Together, this work demonstrates correspondence of phylotype with microbial function, and demonstrates that the dynamics of rhizobia on host species can feed back on plant population performance...