 Phylogeny
"Phylogeny" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus,
MeSH (Medical Subject Headings). Descriptors are arranged in a hierarchical structure,
which enables searching at various levels of specificity.
The relationships of groups of organisms as reflected by their genetic makeup.
| Descriptor ID |
D010802
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| MeSH Number(s) |
G05.697 G16.100.178.605 L01.100.697
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| Concept/Terms |
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Below are MeSH descriptors whose meaning is more general than "Phylogeny".
Below are MeSH descriptors whose meaning is more specific than "Phylogeny".
This graph shows the total number of publications written about "Phylogeny" by people in UAMS Profiles by year, and whether "Phylogeny" was a major or minor topic of these publications.
To see the data from this visualization as text, click here.
| Year | Major Topic | Minor Topic | Total |
|---|
| 2020 | 1 | 0 | 1 | | 2019 | 2 | 4 | 6 | | 2018 | 0 | 6 | 6 | | 2017 | 1 | 5 | 6 | | 2016 | 0 | 4 | 4 | | 2015 | 0 | 7 | 7 | | 2014 | 2 | 2 | 4 | | 2013 | 1 | 5 | 6 | | 2012 | 2 | 7 | 9 | | 2011 | 4 | 4 | 8 | | 2010 | 1 | 18 | 19 | | 2009 | 5 | 12 | 17 | | 2008 | 1 | 12 | 13 | | 2007 | 1 | 13 | 14 | | 2006 | 1 | 8 | 9 | | 2005 | 0 | 12 | 12 | | 2004 | 1 | 6 | 7 | | 2003 | 1 | 5 | 6 | | 2002 | 2 | 6 | 8 | | 2001 | 0 | 1 | 1 | | 2000 | 0 | 1 | 1 | | 1999 | 1 | 0 | 1 | | 1998 | 0 | 1 | 1 | | 1997 | 0 | 1 | 1 | | 1996 | 0 | 2 | 2 | | 1995 | 1 | 0 | 1 | | 1994 | 1 | 1 | 2 | | 1993 | 0 | 2 | 2 | | 1992 | 1 | 0 | 1 | | 1986 | 0 | 1 | 1 |
To return to the timeline, click here.
Below are the most recent publications written about "Phylogeny" by people in Profiles over the past ten years.
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Darcy JL, Washburne AD, Robeson MS, Prest T, Schmidt SK, Lozupone CA. A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome. ISME J. 2020 06; 14(6):1359-1368.
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Wassenaar TM, Jun SR, Robeson M, Ussery DW. Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species. Microbiologyopen. 2020 02; 9(2):e973.
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Kim JG, Gwak JH, Jung MY, An SU, Hyun JH, Kang S, Rhee SK. Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea. PLoS One. 2019; 14(8):e0221408.
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Alkam D, Jenjaroenpun P, Wongsurawat T, Udaondo Z, Patumcharoenpol P, Robeson M, Haselow D, Mason W, Nookaew I, Ussery D, Jun SR. Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016. Infect Genet Evol. 2019 11; 75:103965.
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Carossino M, Barrandeguy ME, Erol E, Li Y, Balasuriya UBR. Development and evaluation of a one-step multiplex real-time TaqMan® RT-qPCR assay for the detection and genotyping of equine G3 and G14 rotaviruses in fecal samples. Virol J. 2019 04 25; 16(1):49.
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Bird JT, Tague ED, Zinke L, Schmidt JM, Steen AD, Reese B, Marshall IPG, Webster G, Weightman A, Castro HF, Campagna SR, Lloyd KG. Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments. mBio. 2019 04 16; 10(2).
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Lee MD, Ahlgren NA, Kling JD, Walworth NG, Rocap G, Saito MA, Hutchins DA, Webb EA. Marine Synechococcus isolates representing globally abundant genomic lineages demonstrate a unique evolutionary path of genome reduction without a decrease in GC content. Environ Microbiol. 2019 05; 21(5):1677-1686.
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Shaw EI, Voth DE. Coxiella burnetii: A Pathogenic Intracellular Acidophile. Microbiology (Reading). 2019 01; 165(1):1-3.
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Dix SR, Owen HJ, Sun R, Ahmad A, Shastri S, Spiewak HL, Mosby DJ, Harris MJ, Batters SL, Brooker TA, Tzokov SB, Sedelnikova SE, Baker PJ, Bullough PA, Rice DW, Thomas MS. Structural insights into the function of type VI secretion system TssA subunits. Nat Commun. 2018 11 12; 9(1):4765.
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Wankhade UD, Zhong Y, Kang P, Alfaro M, Chintapalli SV, Piccolo BD, Mercer KE, Andres A, Thakali KM, Shankar K. Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice. Sci Rep. 2018 11 07; 8(1):16502.
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Gee JE, Elrod MG, Gulvik CA, Haselow DT, Waters C, Liu L, Hoffmaster AR. Burkholderia thailandensis Isolated from Infected Wound, Arkansas, USA. Emerg Infect Dis. 2018 11; 24(11):2091-2094.
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Owen HJ, Sun R, Ahmad A, Sedelnikova SE, Baker PJ, Thomas MS, Rice DW. TssA from Burkholderia cenocepacia: expression, purification, crystallization and crystallographic analysis. Acta Crystallogr F Struct Biol Commun. 2018 Sep 01; 74(Pt 9):536-542.
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Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. Microb Ecol. 2018 Oct; 76(3):801-813.
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Jung JY, Ahn Y, Khare S, Gokulan K, Piñeiro SA, Cerniglia CE. An in vitro study to assess the impact of tetracycline on the human intestinal microbiome. Anaerobe. 2018 Feb; 49:85-94.
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Jun SR, Wassenaar TM, Wanchai V, Patumcharoenpol P, Nookaew I, Ussery DW. Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us? BMC Bioinformatics. 2017 12 28; 18(Suppl 14):471.
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Martin BE, Sun H, Carrel M, Cunningham FL, Baroch JA, Hanson-Dorr KC, Young SG, Schmit B, Nolting JM, Yoon KJ, Lutman MW, Pedersen K, Lager K, Bowman AS, Slemons RD, Smith DR, DeLiberto T, Wan XF. Feral Swine in the United States Have Been Exposed to both Avian and Swine Influenza A Viruses. Appl Environ Microbiol. 2017 10 01; 83(19).
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Andrei AS, Baricz A, Robeson MS, Pausan MR, Tamas T, Chiriac C, Szekeres E, Barbu-Tudoran L, Levei EA, Coman C, Podar M, Banciu HL. Hypersaline sapropels act as hotspots for microbial dark matter. Sci Rep. 2017 07 21; 7(1):6150.
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Hakkak R, Korourian S, Foley SL, Erickson BD. Assessment of gut microbiota populations in lean and obese Zucker rats. PLoS One. 2017; 12(7):e0181451.
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Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep. 2017 01 19; 7:40712.
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Willyard A, Gernandt DS, Potter K, Hipkins V, Marquardt P, Mahalovich MF, Langer SK, Telewski FW, Cooper B, Douglas C, Finch K, Karemera HH, Lefler J, Lea P, Wofford A. Pinus ponderosa: A checkered past obscured four species. Am J Bot. 2017 Jan; 104(1):161-181.
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Bunyavanich S, Shen N, Grishin A, Wood R, Burks W, Dawson P, Jones SM, Leung DYM, Sampson H, Sicherer S, Clemente JC. Early-life gut microbiome composition and milk allergy resolution. J Allergy Clin Immunol. 2016 10; 138(4):1122-1130.
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Thorell K, Hosseini S, Palacios Gonzáles RV, Chaotham C, Graham DY, Paszat L, Rabeneck L, Lundin SB, Nookaew I, Sjöling Å. Identification of a Latin American-specific BabA adhesin variant through whole genome sequencing of Helicobacter pylori patient isolates from Nicaragua. BMC Evol Biol. 2016 Feb 29; 16:53.
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Gudeta DD, Bortolaia V, Jayol A, Poirel L, Nordmann P, Guardabassi L. Chromobacterium spp. harbour Ambler class A ß-lactamases showing high identity with KPC. J Antimicrob Chemother. 2016 06; 71(6):1493-6.
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Lorenzi H, Khan A, Behnke MS, Namasivayam S, Swapna LS, Hadjithomas M, Karamycheva S, Pinney D, Brunk BP, Ajioka JW, Ajzenberg D, Boothroyd JC, Boyle JP, Dardé ML, Diaz-Miranda MA, Dubey JP, Fritz HM, Gennari SM, Gregory BD, Kim K, Saeij JP, Su C, White MW, Zhu XQ, Howe DK, Rosenthal BM, Grigg ME, Parkinson J, Liu L, Kissinger JC, Roos DS, Sibley LD. Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. Nat Commun. 2016 Jan 07; 7:10147.
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Jun SR, Wassenaar TM, Nookaew I, Hauser L, Wanchai V, Land M, Timm CM, Lu TY, Schadt CW, Doktycz MJ, Pelletier DA, Ussery DW. Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis. Appl Environ Microbiol. 2016 01 01; 82(1):375-83.
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Espinoza-Valles I, Vora GJ, Lin B, Leekitcharoenphon P, González-Castillo A, Ussery D, Høj L, Gomez-Gil B. Unique and conserved genome regions in Vibrio harveyi and related species in comparison with the shrimp pathogen Vibrio harveyi CAIM 1792. Microbiology (Reading). 2015 Sep; 161(9):1762-1779.
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Garimalla S, Kieber-Emmons T, Pashov AD. The Patterns of Coevolution in Clade B HIV Envelope's N-Glycosylation Sites. PLoS One. 2015; 10(6):e0128664.
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Pearse WD, Chase MW, Crawley MJ, Dolphin K, Fay MF, Joseph JA, Powney G, Preston CD, Rapacciuolo G, Roy DB, Purvis A. Beyond the EDGE with EDAM: Prioritising British Plant Species According to Evolutionary Distinctiveness, and Accuracy and Magnitude of Decline. PLoS One. 2015; 10(5):e0126524.
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Andrei AS, Robeson MS, Baricz A, Coman C, Muntean V, Ionescu A, Etiope G, Alexe M, Sicora CI, Podar M, Banciu HL. Contrasting taxonomic stratification of microbial communities in two hypersaline meromictic lakes. ISME J. 2015 Dec; 9(12):2642-56.
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Land M, Hauser L, Jun SR, Nookaew I, Leuze MR, Ahn TH, Karpinets T, Lund O, Kora G, Wassenaar T, Poudel S, Ussery DW. Insights from 20 years of bacterial genome sequencing. Funct Integr Genomics. 2015 Mar; 15(2):141-61.
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Ali A, Naz A, Soares SC, Bakhtiar M, Tiwari S, Hassan SS, Hanan F, Ramos R, Pereira U, Barh D, Figueiredo HC, Ussery DW, Miyoshi A, Silva A, Azevedo V. Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets. Biomed Res Int. 2015; 2015:139580.
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Haugum K, Johansen J, Gabrielsen C, Brandal LT, Bergh K, Ussery DW, Drabløs F, Afset JE. Comparative genomics to delineate pathogenic potential in non-O157 Shiga toxin-producing Escherichia coli (STEC) from patients with and without haemolytic uremic syndrome (HUS) in Norway. PLoS One. 2014; 9(10):e111788.
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Park SJ, Ghai R, Martín-Cuadrado AB, Rodríguez-Valera F, Chung WH, Kwon K, Lee JH, Madsen EL, Rhee SK. Genomes of two new ammonia-oxidizing archaea enriched from deep marine sediments. PLoS One. 2014; 9(5):e96449.
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Rutledge CE, Lau HT, Mangan H, Hardy LL, Sunnotel O, Guo F, MacNicol AM, Walsh CP, Lees-Murdock DJ. Efficient translation of Dnmt1 requires cytoplasmic polyadenylation and Musashi binding elements. PLoS One. 2014; 9(2):e88385.
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Melchor L, Brioli A, Wardell CP, Murison A, Potter NE, Kaiser MF, Fryer RA, Johnson DC, Begum DB, Hulkki Wilson S, Vijayaraghavan G, Titley I, Cavo M, Davies FE, Walker BA, Morgan GJ. Single-cell genetic analysis reveals the composition of initiating clones and phylogenetic patterns of branching and parallel evolution in myeloma. Leukemia. 2014 Aug; 28(8):1705-15.
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Suvorova ES, Radke JB, Ting LM, Vinayak S, Alvarez CA, Kratzer S, Kim K, Striepen B, White MW. A nucleolar AAA-NTPase is required for parasite division. Mol Microbiol. 2013 Oct; 90(2):338-55.
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Sloan EA, Kearney MF, Gray LR, Anastos K, Daar ES, Margolick J, Maldarelli F, Hammarskjold ML, Rekosh D. Limited nucleotide changes in the Rev response element (RRE) during HIV-1 infection alter overall Rev-RRE activity and Rev multimerization. J Virol. 2013 Oct; 87(20):11173-86.
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Lemos de Matos A, Liu J, McFadden G, Esteves PJ. Evolution and divergence of the mammalian SAMD9/SAMD9L gene family. BMC Evol Biol. 2013 Jun 12; 13:121.
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Chintapalli SV, Bhardwaj G, Babu J, Hadjiyianni L, Hong Y, Todd GK, Boosalis CA, Zhang Z, Zhou X, Ma H, Anishkin A, van Rossum DB, Patterson RL. Reevaluation of the evolutionary events within recA/RAD51 phylogeny. BMC Genomics. 2013 Apr 10; 14:240.
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Vesth T, Lagesen K, Acar Ö, Ussery D. CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One. 2013; 8(4):e60120.
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Yang H, Yung M, Li L, Hoch JA, Ryan CM, Kar UK, Souda P, Whitelegge JP, Miller JH. Evidence that YycJ is a novel 5'-3' double-stranded DNA exonuclease acting in Bacillus anthracis mismatch repair. DNA Repair (Amst). 2013 May 01; 12(5):334-46.
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Jensen DB, Vesth TC, Hallin PF, Pedersen AG, Ussery DW. Bayesian prediction of bacterial growth temperature range based on genome sequences. BMC Genomics. 2012; 13 Suppl 7:S3.
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Kaas RS, Friis C, Ussery DW, Aarestrup FM. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genomics. 2012 Oct 31; 13:577.
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Khodakovskaya MV, Kim BS, Kim JN, Alimohammadi M, Dervishi E, Mustafa T, Cernigla CE. Carbon nanotubes as plant growth regulators: effects on tomato growth, reproductive system, and soil microbial community. Small. 2013 Jan 14; 9(1):115-23.
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Al Rayyan N, Wankhade UD, Bush K, Good DJ. Two single nucleotide polymorphisms in the human nescient helix-loop-helix 2 (NHLH2) gene reduce mRNA stability and DNA binding. Gene. 2013 Jan 01; 512(1):134-42.
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Zhang HY, Liang JJ, Meng XM, Li H, Yang J, Su LJ, Zhang HP, Xie LJ, He XX, Li YS, Yin S, Li XQ, Li XN, Luo TR. Molecular epidemiology of PRRSV from China's Guangxi Province between 2007 and 2009. Virus Genes. 2013 Feb; 46(1):71-80.
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Ali A, Soares SC, Santos AR, Guimarães LC, Barbosa E, Almeida SS, Abreu VA, Carneiro AR, Ramos RT, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Schneider MP, Lage AP, Miyoshi A, Azevedo V. Campylobacter fetus subspecies: comparative genomics and prediction of potential virulence targets. Gene. 2012 Oct 25; 508(2):145-56.
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Ussery DW, Gordon SV. Two novel methods for using genome sequences to infer taxonomy. Microbiology (Reading). 2012 Jun; 158(Pt 6):1414.
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Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB. PHYRN: a robust method for phylogenetic analysis of highly divergent sequences. PLoS One. 2012; 7(4):e34261.
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Leekitcharoenphon P, Lukjancenko O, Friis C, Aarestrup FM, Ussery DW. Genomic variation in Salmonella enterica core genes for epidemiological typing. BMC Genomics. 2012 Mar 12; 13:88.
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Erol E, Sells SF, Williams NM, Kennedy L, Locke SJ, Labeda DP, Donahue JM, Carter CN. An investigation of a recent outbreak of nocardioform placentitis caused abortions in horses. Vet Microbiol. 2012 Aug 17; 158(3-4):425-30.
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Salgado M, Rabi SA, O'Connell KA, Buckheit RW, Bailey JR, Chaudhry AA, Breaud AR, Marzinke MA, Clarke W, Margolick JB, Siliciano RF, Blankson JN. Prolonged control of replication-competent dual- tropic human immunodeficiency virus-1 following cessation of highly active antiretroviral therapy. Retrovirology. 2011 Dec 05; 8:97.
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Lukjancenko O, Ussery DW, Wassenaar TM. Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol. 2012 Apr; 63(3):651-73.
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Darcy JL, Lynch RC, King AJ, Robeson MS, Schmidt SK. Global distribution of Polaromonas phylotypes--evidence for a highly successful dispersal capacity. PLoS One. 2011; 6(8):e23742.
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Özen AI, Ussery DW. Defining the Pseudomonas genus: where do we draw the line with Azotobacter? Microb Ecol. 2012 Feb; 63(2):239-48.
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Papadopoulou A, Anastasiou I, Spagopoulou F, Stalimerou M, Terzopoulou S, Legakis A, Vogler AP. Testing the species--genetic diversity correlation in the Aegean archipelago: toward a haplotype-based macroecology? Am Nat. 2011 Aug; 178(2):241-55.
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Potnis N, Krasileva K, Chow V, Almeida NF, Patil PB, Ryan RP, Sharlach M, Behlau F, Dow JM, Momol M, White FF, Preston JF, Vinatzer BA, Koebnik R, Setubal JC, Norman DJ, Staskawicz BJ, Jones JB. Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics. 2011 Mar 11; 12:146.
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