Experts and Doctors on phylogeny in California, United States


Locale: California, United States
Topic: phylogeny

Top Publications

  1. Goldstein D, Ruiz Linares A, Cavalli Sforza L, Feldman M. An evaluation of genetic distances for use with microsatellite loci. Genetics. 1995;139:463-71 pubmed
    ..We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable. ..
  2. Blainey P, Mosier A, Potanina A, Francis C, Quake S. Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE. 2011;6:e16626 pubmed publisher
  3. Werner J, Feng S, Kasten R, Hodzic E, Chomel B, Barthold S. Cloning, characterization, and expression of Bartonella henselae p26. Clin Vaccine Immunol. 2006;13:830-6 pubmed
    ..The p26 protein product is an immunodominant antigen that is expressed during infection in cats as a preprotein and is subsequently cleaved to form mature P26. ..
  4. Rajalingam R, Hong M, Adams E, Shum B, Guethlein L, Parham P. Short KIR haplotypes in pygmy chimpanzee (Bonobo) resemble the conserved framework of diverse human KIR haplotypes. J Exp Med. 2001;193:135-46 pubmed
  5. Adams E, Parham P. Species-specific evolution of MHC class I genes in the higher primates. Immunol Rev. 2001;183:41-64 pubmed
    ..The differing rates at which MHC class I genes have evolved during primate evolution likely reflects their differing functions in the immune response. ..
  6. Meyer M, Trimmer J, Gilthorpe J, Smith S. Characterization of zebrafish PSD-95 gene family members. J Neurobiol. 2005;63:91-105 pubmed
    ..These data are consistent with the idea that PSD-95 family members are involved in synapse assembly and function, and provide a platform for future functional studies in vivo in a highly tractable model organism. ..
  7. Abi Rached L, Moesta A, Rajalingam R, Guethlein L, Parham P. Human-specific evolution and adaptation led to major qualitative differences in the variable receptors of human and chimpanzee natural killer cells. PLoS Genet. 2010;6:e1001192 pubmed publisher
  8. Greenwood A, Butler P, White R, DeMarco U, Pearce D, Fernald R. Multiple corticosteroid receptors in a teleost fish: distinct sequences, expression patterns, and transcriptional activities. Endocrinology. 2003;144:4226-36 pubmed publisher
    ..The identification of four CR subtypes in teleosts suggests a more complicated corticosteroid signaling in fish than previously recognized...
  9. Vrijenhoek R, Duhaime M, Jones W. Subtype variation among bacterial endosymbionts of tubeworms (Annelida: Siboglinidae) from the Gulf of California. Biol Bull. 2007;212:180-4 pubmed

More Information

Publications169 found, 100 shown here

  1. Hershberg R, Lipatov M, Small P, Sheffer H, Niemann S, Homolka S, et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol. 2008;6:e311 pubmed publisher
    ..tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis. ..
  2. Schulz J, Sasaki J, Vacquier V. Increased association of synaptosome-associated protein of 25 kDa with syntaxin and vesicle-associated membrane protein following acrosomal exocytosis of sea urchin sperm. J Biol Chem. 1998;273:24355-9 pubmed
    ..These findings support the involvement of SNAP-25 in the invertebrate sperm acrosome reaction, possibly through increased association with VAMP and syntaxin driving the fusion of plasma and acrosomal membranes...
  3. Huelsenbeck J, Nielsen R, Bollback J. Stochastic mapping of morphological characters. Syst Biol. 2003;52:131-58 pubmed
    ..Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation...
  4. Cummings C, Brinig M, Lepp P, van de Pas S, Relman D. Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J Bacteriol. 2004;186:1484-92 pubmed
  5. Hershberg R, Petrov D. Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet. 2010;6:e1001115 pubmed publisher
  6. Anderson I, Scheuner C, Göker M, Mavromatis K, Hooper S, Porat I, et al. Novel insights into the diversity of catabolic metabolism from ten haloarchaeal genomes. PLoS ONE. 2011;6:e20237 pubmed publisher
    ..The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis...
  7. Ziemert N, Podell S, Penn K, Badger J, Allen E, Jensen P. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS ONE. 2012;7:e34064 pubmed publisher
    ..The results provide a rapid method to assess secondary metabolite biosynthetic gene diversity and richness in organisms or environments and a mechanism to identify genes that may be associated with uncharacterized biochemistry. ..
  8. Palmer R, Fessler L, Edeen P, Madigan S, McKeown M, Hunter T. DFak56 is a novel Drosophila melanogaster focal adhesion kinase. J Biol Chem. 1999;274:35621-9 pubmed
    ..Our results imply a role for DFak56 in adhesion-dependent signaling pathways in vivo during D. melanogaster development. ..
  9. Underhill P, Shen P, Lin A, Jin L, Passarino G, Yang W, et al. Y chromosome sequence variation and the history of human populations. Nat Genet. 2000;26:358-61 pubmed
    ..A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago. ..
  10. Roh J, Chang C, Bhalla A, Klein C, Hsu S. Intermedin is a calcitonin/calcitonin gene-related peptide family peptide acting through the calcitonin receptor-like receptor/receptor activity-modifying protein receptor complexes. J Biol Chem. 2004;279:7264-74 pubmed
  11. Masta S, Boore J. The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Mol Biol Evol. 2004;21:893-902 pubmed publisher
    ..Such mechanisms may have allowed for the minimization of the spider mitochondrial genome...
  12. Goodman C, Casati P, Walbot V. A multidrug resistance-associated protein involved in anthocyanin transport in Zea mays. Plant Cell. 2004;16:1812-26 pubmed
  13. Callahan B, Neher R, Bachtrog D, Andolfatto P, Shraiman B. Correlated evolution of nearby residues in Drosophilid proteins. PLoS Genet. 2011;7:e1001315 pubmed publisher
  14. Ziemert N, Jensen P. Phylogenetic approaches to natural product structure prediction. Methods Enzymol. 2012;517:161-82 pubmed publisher
  15. Rootsi S, Behar D, Järve M, Lin A, Myres N, Passarelli B, et al. Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites. Nat Commun. 2013;4:2928 pubmed publisher
  16. Session A, Uno Y, Kwon T, Chapman J, Toyoda A, Takahashi S, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016;538:336-343 pubmed publisher
    ..The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression. ..
  17. Orphan V, Hinrichs K, Ussler W, Paull C, Taylor L, Sylva S, et al. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol. 2001;67:1922-34 pubmed
  18. Suzuki M, Zheng H, Takasaka T, Sugimoto C, Kitamura T, Beutler E, et al. Asian genotypes of JC virus in Japanese-Americans suggest familial transmission. J Virol. 2002;76:10074-8 pubmed
    ..This finding provides support for the hypothesis that JCV is transmitted mainly within the family through long-term cohabitation. ..
  19. Song Y, Liu C, McTeague M, Finegold S. 16S ribosomal DNA sequence-based analysis of clinically significant gram-positive anaerobic cocci. J Clin Microbiol. 2003;41:1363-9 pubmed
    ..This finding is in contrast to the phenotypic identification results, by which only 56% of isolates were correctly identified to species level. ..
  20. Johnson S, Jang S, Gulland F, Miller M, Casper D, Lawrence J, et al. Characterization and clinical manifestations of Arcanobacterium phocae infections in marine mammals stranded along the central California coast. J Wildl Dis. 2003;39:136-44 pubmed
    ..phocae isolates may have been misidentified as Listeria ivanovii. Arcanobacterium phocae was commonly isolated from superficial abscesses, was often present in mixed infections, and was susceptible to all antimicrobial agents tested. ..
  21. Dehal P, Boore J. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 2005;3:e314 pubmed
    ..Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage...
  22. Zapata J, Martínez García V, Lefebvre S. Phylogeny of the TRAF/MATH domain. Adv Exp Med Biol. 2007;597:1-24 pubmed
    ..However, the available information allows us to get a glimpse on the origins, distribution and evolution of the TRAF/MATH domain, which will be overviewed in this chapter. ..
  23. Semyonov J, Park J, Chang C, Hsu S. GPCR genes are preferentially retained after whole genome duplication. PLoS ONE. 2008;3:e1903 pubmed publisher
    ..These results demonstrate that gene retention is not uniform after WGD in vertebrates, and suggest a Darwinian selection of GPCR-mediated intercellular communication in metazoan organisms. ..
  24. Koop D, Holland L. The basal chordate amphioxus as a simple model for elucidating developmental mechanisms in vertebrates. Birth Defects Res C Embryo Today. 2008;84:175-87 pubmed publisher
    ..Thus, studies of amphioxus development can shed light on similar, but more complex, development of vertebrates. Such studies are especially interesting for their insights into the genetic basis of craniofacial birth defects in humans...
  25. O Maille P, Malone A, Dellas N, Andes Hess B, Smentek L, Sheehan I, et al. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat Chem Biol. 2008;4:617-23 pubmed publisher
    ..These results provide a measure of the mutational accessibility of phenotypic variability in a diverging lineage of terpene synthases...
  26. Hagey L, Møller P, Hofmann A, Krasowski M. Diversity of bile salts in fish and amphibians: evolution of a complex biochemical pathway. Physiol Biochem Zool. 2010;83:308-21 pubmed publisher
    ..Analysis of the evolution of bile salt synthetic pathways provides a rich model system for the molecular evolution of a complex biochemical pathway in vertebrates...
  27. Freel K, Millán Aguiñaga N, Jensen P. Multilocus sequence typing reveals evidence of homologous recombination linked to antibiotic resistance in the genus Salinispora. Appl Environ Microbiol. 2013;79:5997-6005 pubmed publisher
  28. Myburg A, Grattapaglia D, Tuskan G, Hellsten U, Hayes R, Grimwood J, et al. The genome of Eucalyptus grandis. Nature. 2014;510:356-62 pubmed publisher
    ..This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology. ..
  29. Gardner S, McLoughlin K, Be N, Allen J, Weaver S, Forrester N, et al. Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. PLoS ONE. 2016;11:e0152604 pubmed publisher
    ..Finally, we identified genomic variants associated with serotypes and host species, revealing a complex relationship between genotype and phenotype. ..
  30. Chaillon A, Nakazawa M, Wertheim J, Little S, Smith D, Mehta S, et al. No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men. J Virol. 2017;91: pubmed publisher
  31. Ozcelik T, Rosenthal A, Francke U. Chromosomal mapping of brain-derived neurotrophic factor and neurotrophin-3 genes in man and mouse. Genomics. 1991;10:569-75 pubmed
    ..BDNF has been mapped to human chromosome 11p15.5-p11.2 and to mouse chromosome 2, and NTF3 to human chromosome 12p and mouse chromosome 6. ..
  32. Heisterkamp N, Mulder M, Langeveld A, ten Hoeve J, Wang Z, Roe B, et al. Localization of the human mitochondrial citrate transporter protein gene to chromosome 22Q11 in the DiGeorge syndrome critical region. Genomics. 1995;29:451-6 pubmed
    ..Deletion of this gene in DiGeorge syndrome and velocardio-facial syndrome may contribute to the mental deficiency seen in the patients. ..
  33. Nusse R, Samos C, Brink M, Willert K, Cadigan K, Wodarz A, et al. Cell culture and whole animal approaches to understanding signaling by Wnt proteins in Drosophila. Cold Spring Harb Symp Quant Biol. 1997;62:185-90 pubmed
  34. Holland L, Rached L, Tamme R, Holland N, Kortschak D, Inoko H, et al. Characterization and developmental expression of the amphioxus homolog of Notch (AmphiNotch): evolutionary conservation of multiple expression domains in amphioxus and vertebrates. Dev Biol. 2001;232:493-507 pubmed
  35. Angata T, Varki A. Chemical diversity in the sialic acids and related alpha-keto acids: an evolutionary perspective. Chem Rev. 2002;102:439-69 pubmed
  36. Yeung K, Miller J, Savage A, Husband B, Igic B, Kohn J. Association of ploidy and sexual system in Lycium californicum (Solanaceae). Evolution. 2005;59:2048-55 pubmed
    ..The correspondence between ploidy and sex expression is consistent with the hypothesis that polyploidization triggers the evolution of gender dimorphism in this and other Lycium species...
  37. Goldstein T, Lowenstine L, Lipscomb T, Mazet J, Novak J, Stott J, et al. Infection with a novel gammaherpesvirus in northern elephant seals (Mirounga angustirostris). J Wildl Dis. 2006;42:830-5 pubmed
    ..Identical herpesviral DNA was also detected in blood and mucosal swabs collected from five healthy elephant seal pups. ..
  38. Cunnac S, Wilson A, Nuwer J, Kirik A, Baranage G, Mudgett M. A conserved carboxylesterase is a SUPPRESSOR OF AVRBST-ELICITED RESISTANCE in Arabidopsis. Plant Cell. 2007;19:688-705 pubmed
    ..These data indicate that the carboxylesterase inhibits AvrBsT-triggered phenotypes in Arabidopsis. Here, we present the cloning and characterization of the SUPPRESSOR OF AVRBST-ELICITED RESISTANCE1. ..
  39. Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Comput Biol. 2011;7:e1002318 pubmed publisher
    ..It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families. ..
  40. De Ingeniis J, Kazanov M, Shatalin K, Gelfand M, Osterman A, Sorci L. Glutamine versus ammonia utilization in the NAD synthetase family. PLoS ONE. 2012;7:e39115 pubmed publisher
    ..Further evolution of the NADS family included lineage-specific loss of one of the two alternative forms and horizontal gene transfer events. Lastly, we identified NADS structural elements associated with glutamine-utilizing capabilities...
  41. McMurdie P, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8:e61217 pubmed publisher
    ..The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor. ..
  42. Yim H, Cho Y, Guang X, Kang S, Jeong J, Cha S, et al. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet. 2014;46:88-92 pubmed publisher
  43. Freedman A, Gronau I, Schweizer R, Ortega Del Vecchyo D, Han E, Silva P, et al. Genome sequencing highlights the dynamic early history of dogs. PLoS Genet. 2014;10:e1004016 pubmed publisher
    ..This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary. ..
  44. Sawake S, Tajima N, Mortimer J, Lao J, Ishikawa T, Yu X, et al. KONJAC1 and 2 Are Key Factors for GDP-Mannose Generation and Affect l-Ascorbic Acid and Glucomannan Biosynthesis in Arabidopsis. Plant Cell. 2015;27:3397-409 pubmed publisher
    ..These results suggest that KJCs are key factors for the generation of GDP-Man and affect AsA level and glucomannan accumulation through the stimulation of VTC1 GMPP activity. ..
  45. Huguet Tapia J, Lefebure T, Badger J, Guan D, Pettis G, Stanhope M, et al. Genome Content and Phylogenomics Reveal both Ancestral and Lateral Evolutionary Pathways in Plant-Pathogenic Streptomyces Species. Appl Environ Microbiol. 2016;82:2146-2155 pubmed publisher
    ..In contrast, S. turgidiscabies and S. acidiscabies, two relatively unrelated pathogens, possess highly similar thaxtomin biosynthesis clusters, which suggests that the acquisition of these genes was through lateral gene transfer. ..
  46. Fu Z, Epstein B, Kelley J, Zheng Q, Bergland A, Castillo Carrillo C, et al. Using NextRAD sequencing to infer movement of herbivores among host plants. PLoS ONE. 2017;12:e0177742 pubmed publisher
    ..We demonstrate that emerging sequencing technologies that detect genome-wide SNPs of a vector can be used to infer such localized movement. ..
  47. Ezran C, Karanewsky C, Pendleton J, Sholtz A, Krasnow M, Willick J, et al. The Mouse Lemur, a Genetic Model Organism for Primate Biology, Behavior, and Health. Genetics. 2017;206:651-664 pubmed publisher
  48. Hoffmann I, Ang H, Duester G. Alcohol dehydrogenases in Xenopus development: conserved expression of ADH1 and ADH4 in epithelial retinoid target tissues. Dev Dyn. 1998;213:261-70 pubmed
  49. Bowman A, Patel King R, Benashski S, McCaffery J, Goldstein L, King S. Drosophila roadblock and Chlamydomonas LC7: a conserved family of dynein-associated proteins involved in axonal transport, flagellar motility, and mitosis. J Cell Biol. 1999;146:165-80 pubmed
    ..We propose that roadblock/LC7 family members may modulate specific dynein functions. ..
  50. Zapata J, Pawlowski K, Haas E, Ware C, Godzik A, Reed J. A diverse family of proteins containing tumor necrosis factor receptor-associated factor domains. J Biol Chem. 2001;276:24242-52 pubmed
    ..We propose the moniker TEFs (TD-encompassing factors) for this large family of proteins. ..
  51. Scheeff E, Axelrod H, Miller M, Chiu H, Deacon A, Wilson I, et al. Genomics, evolution, and crystal structure of a new family of bacterial spore kinases. Proteins. 2010;78:1470-82 pubmed publisher
    ..Several classes of BSKs have apparently independently lost catalytic activity to become pseudokinases, indicating that the family also has a major noncatalytic function. ..
  52. Shulse C, Allen E. Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages. PLoS ONE. 2011;6:e20146 pubmed publisher
  53. Stolc V, Shmygelska A, Griko Y. Adaptation of organisms by resonance of RNA transcription with the cellular redox cycle. PLoS ONE. 2011;6:e25270 pubmed publisher
    ..This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation. ..
  54. McElwain M, Ko D, Gordon M, Fyrst H, Saba J, Nusse R. A suppressor/enhancer screen in Drosophila reveals a role for wnt-mediated lipid metabolism in primordial germ cell migration. PLoS ONE. 2011;6:e26993 pubmed publisher
    ..Our data are consistent with a model in which the activity of lipid phosphate phosphatases shapes a concentration gradient of ceramide-1-phosphate (C1P), the product of Dcerk, allowing proper PGC migration. ..
  55. Martin L, Meier M, Lyons S, Sit R, Marzluff W, Quake S, et al. Systematic reconstruction of RNA functional motifs with high-throughput microfluidics. Nat Methods. 2012;9:1192-4 pubmed publisher
    ..The functional motif reconstructed in a single experiment on our platform uncovers new binding specificities and enriches interpretation of phylogenetic data. ..
  56. Stanley D, Raines C, Kerfeld C. Comparative analysis of 126 cyanobacterial genomes reveals evidence of functional diversity among homologs of the redox-regulated CP12 protein. Plant Physiol. 2013;161:824-35 pubmed publisher
    ..Moreover, our findings substantiate the proposal that this small protein may have multiple roles in photosynthetic organisms. ..
  57. Leyn S, Kazanov M, Sernova N, Ermakova E, Novichkov P, Rodionov D. Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. J Bacteriol. 2013;195:2463-73 pubmed publisher
    ..The inferred collection of regulons is available in the RegPrecise database ( and can be used in genetic experiments, metabolic modeling, and evolutionary analysis. ..
  58. Rasmussen M, Anzick S, Waters M, Skoglund P, DeGiorgio M, Stafford T, et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 2014;506:225-9 pubmed publisher
    ..Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual. ..
  59. Lloyd Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall A, et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. 2017;550:61-66 pubmed publisher
    ..This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics...
  60. Mateos M, Vrijenhoek R. Ancient versus reticulate origin of a hemiclonal lineage. Evolution. 2002;56:985-92 pubmed
    ..monacha and therefore support the hypothesis of a recent origin. Additionally, our findings suggest that this unisexual fish may serve as a vehicle for introgression between two allopatric sexual species. ..
  61. Conkright M, Guzman E, Flechner L, Su A, Hogenesch J, Montminy M. Genome-wide analysis of CREB target genes reveals a core promoter requirement for cAMP responsiveness. Mol Cell. 2003;11:1101-8 pubmed
    ..These results illustrate a mechanism by which subsets of target genes for a transcription factor are differentially regulated depending on core promoter configuration. ..
  62. Pankow S, Bamberger C. The p53 tumor suppressor-like protein nvp63 mediates selective germ cell death in the sea anemone Nematostella vectensis. PLoS ONE. 2007;2:e782 pubmed
    ..The genotoxic stress induced and nvp63 mediated apoptosis in N. vectensis gametes reveals an evolutionary ancient germ cell protective pathway which relies on p63-like proteins and is conserved from cnidarians to vertebrates...
  63. Stenger D, Lee M. Phylogeny of replication initiator protein TrfA reveals a highly divergent clade of incompatibility group P1 plasmids. Appl Environ Microbiol. 2011;77:2522-6 pubmed publisher
    ..Replication assays indicated that TrfA of recently discovered IncP-1 plasmids from Xylella fastidiosa and Verminephrobacter eiseniae initiated plasmid replication using cognate or heterologous origins of replication. ..
  64. Gianella S, Mehta S, Strain M, Young J, Vargas M, Little S, et al. Impact of seminal cytomegalovirus replication on HIV-1 dynamics between blood and semen. J Med Virol. 2012;84:1703-9 pubmed publisher
    ..In conclusion, the effects of CMV replication on HIV-1 viral and immunologic dynamics within the male genital tract are not significant enough to perturb evolution or disrupt compartmentalization in the genital tract. ..
  65. Toller W, Rowan R, Knowlton N. Zooxanthellae of the Montastraea annularis species complex: patterns of distribution of four taxa of Symbiodinium on different reefs and across depths. Biol Bull. 2001;201:348-59 pubmed
    ..Experimental bleaching of Symbiodinium C supported this interpretation. Thus sequences from natural samples should be interpreted cautiously. ..
  66. Kelley S, Theisen U, Angenent L, St Amand A, Pace N. Molecular analysis of shower curtain biofilm microbes. Appl Environ Microbiol. 2004;70:4187-92 pubmed
    ..Frequent cleaning or disposal of shower curtains is indicated, particularly in households with immune-compromised individuals. ..
  67. Woyke T, Xie G, Copeland A, Gonzalez J, Han C, Kiss H, et al. Assembling the marine metagenome, one cell at a time. PLoS ONE. 2009;4:e5299 pubmed publisher
    ..A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa. ..
  68. McMurdie P, Behrens S, Müller J, Goke J, Ritalahti K, Wagner R, et al. Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet. 2009;5:e1000714 pubmed publisher
    ..This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism. ..
  69. Han J, Lee J, Jiang Y, Li Z, Feng L, Ulevitch R. Characterization of the structure and function of a novel MAP kinase kinase (MKK6). J Biol Chem. 1996;271:2886-91 pubmed
    ..This suggests novel mechanisms regulating activation and/or function of various forms of MKK6. ..
  70. Canavez F, Moreira M, Simon F, Parham P, Seu nez H. Phylogenetic relationships of the Callitrichinae (Platyrrhini, primates) based on beta2-microglobulin DNA sequences. Am J Primatol. 1999;48:225-36 pubmed publisher
    ..The inclusion of Cebuella in the genus Callithrix is suggested. These studies indicated that tamarins are more plesiomorphic than marmosets in agreement with the phyletic dwarfism hypothesis...
  71. Coleman M, Eisen J, Mohrenweiser H. Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse. Genomics. 2000;65:274-82 pubmed
    ..HARP/SMARCAL1 transcripts are ubiquitously expressed in human and mouse tissues, with testis presenting the highest levels of mRNA expression in humans...
  72. Pivetti C, Yen M, Miller S, Busch W, Tseng Y, Booth I, et al. Two families of mechanosensitive channel proteins. Microbiol Mol Biol Rev. 2003;67:66-85, table of contents pubmed
    ..The presence of a conserved residue pattern for the putative channel-forming TMSs in the MscL and MscS family proteins suggests a common structural organization, gating mechanism, and evolutionary origin. ..
  73. Conti M, Beavo J. Biochemistry and physiology of cyclic nucleotide phosphodiesterases: essential components in cyclic nucleotide signaling. Annu Rev Biochem. 2007;76:481-511 pubmed
  74. Jeon M, Nguyen H, Bahri S, Zinn K. Redundancy and compensation in axon guidance: genetic analysis of the Drosophila Ptp10D/Ptp4E receptor tyrosine phosphatase subfamily. Neural Dev. 2008;3:3 pubmed publisher
    ..Strong phenotypes are only observed in triple mutants in which both type III RPTPs are eliminated together with Ptp69D or Ptp52F. Our results allow us to construct a complete genetic interaction matrix for all six of the RPTPs. ..
  75. Karmin M, Saag L, Vicente M, Wilson Sayres M, Järve M, Talas U, et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 2015;25:459-66 pubmed publisher
    ..We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males. ..
  76. Mosier A, Francis C. Determining the distribution of marine and coastal ammonia-oxidizing archaea and bacteria using a quantitative approach. Methods Enzymol. 2011;486:205-21 pubmed publisher
    ..We also describe quantitative measures designed to target two specific clades of marine AOA: the "shallow" (group A) and "deep" (group B) water column AOA. ..
  77. Yu J, Holland N, Holland L. An amphioxus winged helix/forkhead gene, AmphiFoxD: insights into vertebrate neural crest evolution. Dev Dyn. 2002;225:289-97 pubmed
  78. Bajt M, Schmitz B, Schachner M, Zipser B. Carbohydrate epitopes involved in neural cell recognition are conserved between vertebrates and leech. J Neurosci Res. 1990;27:276-85 pubmed
    ..The superposition of five different mannosidic epitopes on the axons of sensory afferents suggests complex, concerted participation of mannosidic epitopes in neuronal pathfinding and target recognition. ..
  79. Yoder S, Argueta C, Holtzman A, Aronson T, Berlin O, Tomasek P, et al. PCR comparison of Mycobacterium avium isolates obtained from patients and foods. Appl Environ Microbiol. 1999;65:2650-3 pubmed
    ..avium infection. This study demonstrates a rapid, inexpensive method for typing M. avium, possibly replacing pulsed-field gel electrophoresis...
  80. Saburi S, Nadano D, Akama T, Hirama K, Yamanouchi K, Naito K, et al. The trophinin gene encodes a novel group of MAGE proteins, magphinins, and regulates cell proliferation during gametogenesis in the mouse. J Biol Chem. 2001;276:49378-89 pubmed
    ..These results strongly suggest that magphinins regulate cell proliferation during gametogenesis in the mouse. ..
  81. Davidson C, Tirouvanziam R, Herzenberg L, Lipsick J. Functional evolution of the vertebrate Myb gene family: B-Myb, but neither A-Myb nor c-Myb, complements Drosophila Myb in hemocytes. Genetics. 2005;169:215-29 pubmed
    ..Finally, these experiments demonstrate the utility of genetic complementation in Drosophila to explore the functional evolution of duplicated genes in vertebrates. ..
  82. Holland L, Albalat R, Azumi K, Benito Gutiérrez E, Blow M, Bronner Fraser M, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008;18:1100-11 pubmed publisher
    ..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...
  83. Logan D, Marton T, Stowers L. Species specificity in major urinary proteins by parallel evolution. PLoS ONE. 2008;3:e3280 pubmed publisher
  84. Audzijonyte A, Vrijenhoek R. When gaps really are gaps: statistical phylogeography of hydrothermal vent invertebrates. Evolution. 2010;64:2369-84 pubmed publisher
    ..The simulation approaches presented here might be useful for testing the significance of inferred phylogeographic gaps in other species...
  85. Lykidis A, Pérez Pantoja D, Ledger T, Mavromatis K, Anderson I, Ivanova N, et al. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS ONE. 2010;5:e9729 pubmed publisher
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