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Items: 45

1.

Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses.

Campioni F, Cao G, Kastanis G, Janies DA, Bergamini AMM, Rodrigues DDP, Stones R, Brown E, Allard MW, Falcão JP.

Sci Rep. 2018 Jul 11;8(1):10478. doi: 10.1038/s41598-018-28844-6.

2.

A new strategy to infer circularity applied to four new complete frog mitogenomes.

Jacob Machado D, Janies D, Brouwer C, Grant T.

Ecol Evol. 2018 Mar 25;8(8):4011-4018. doi: 10.1002/ece3.3918. eCollection 2018 Apr.

3.

Glucose-6-Phosphate Dehydrogenase Deficiency Genetic Variants in Malaria Patients in Southwestern Ethiopia.

Carter TE, Mekonnen SK, Lopez K, Bonnell V, Damodaran L, Aseffa A, Janies DA.

Am J Trop Med Hyg. 2018 Jan;98(1):83-87. doi: 10.4269/ajtmh.17-0557. Epub 2018 Jan 1.

PMID:
29141760
4.

The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics.

Linchangco GV Jr, Foltz DW, Reid R, Williams J, Nodzak C, Kerr AM, Miller AK, Hunter R, Wilson NG, Nielsen WJ, Mah CL, Rouse GW, Wray GA, Janies DA.

Mol Phylogenet Evol. 2017 Oct;115:161-170. doi: 10.1016/j.ympev.2017.07.022. Epub 2017 Jul 27.

PMID:
28757447
5.

Regeneration in bipinnaria larvae of the bat star Patiria miniata induces rapid and broad new gene expression.

Oulhen N, Heyland A, Carrier TJ, Zazueta-Novoa V, Fresques T, Laird J, Onorato TM, Janies D, Wessel G.

Mech Dev. 2016 Nov;142:10-21. doi: 10.1016/j.mod.2016.08.003. Epub 2016 Aug 20.

6.

Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms.

Clouse RM, Linchangco GV Jr, Kerr AM, Reid RW, Janies DA.

R Soc Open Sci. 2015 Dec 4;2(12):150377. doi: 10.1098/rsos.150377. eCollection 2015 Dec.

7.

Zika Virus: Medical Countermeasure Development Challenges.

Malone RW, Homan J, Callahan MV, Glasspool-Malone J, Damodaran L, Schneider Ade B, Zimler R, Talton J, Cobb RR, Ruzic I, Smith-Gagen J, Janies D, Wilson J; Zika Response Working Group.

PLoS Negl Trop Dis. 2016 Mar 2;10(3):e0004530. doi: 10.1371/journal.pntd.0004530. eCollection 2016 Mar. Review.

8.

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.

Janies DA, Witter Z, Linchangco GV, Foltz DW, Miller AK, Kerr AM, Jay J, Reid RW, Wray GA.

BMC Bioinformatics. 2016 Jan 22;17:48. doi: 10.1186/s12859-016-0883-2.

9.

Identification of a neuropeptide precursor protein that gives rise to a "cocktail" of peptides that bind Cu(II) and generate metal-linked dimers.

Jones CE, Zandawala M, Semmens DC, Anderson S, Hanson GR, Janies DA, Elphick MR.

Biochim Biophys Acta. 2016 Jan;1860(1 Pt A):57-66. doi: 10.1016/j.bbagen.2015.10.008. Epub 2015 Oct 22.

PMID:
26475641
10.

Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application.

Janies D, Witter Z, Gibson C, Kraft T, Senturk IF, Çatalyürek Ü.

Stud Health Technol Inform. 2015;216:766-70.

PMID:
26262155
11.

Phylogeny of Echinoderm Hemoglobins.

Christensen AB, Herman JL, Elphick MR, Kober KM, Janies D, Linchangco G, Semmens DC, Bailly X, Vinogradov SN, Hoogewijs D.

PLoS One. 2015 Aug 6;10(8):e0129668. doi: 10.1371/journal.pone.0129668. eCollection 2015.

12.

Comparative Phylogenetic Studies on Schistosoma japonicum and Its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution.

Attwood SW, Ibaraki M, Saitoh Y, Nihei N, Janies DA.

PLoS Negl Trop Dis. 2015 Jul 31;9(7):e0003935. doi: 10.1371/journal.pntd.0003935. eCollection 2015.

13.

Tracing Origins of the Salmonella Bareilly Strain Causing a Food-borne Outbreak in the United States.

Hoffmann M, Luo Y, Monday SR, Gonzalez-Escalona N, Ottesen AR, Muruvanda T, Wang C, Kastanis G, Keys C, Janies D, Senturk IF, Catalyurek UV, Wang H, Hammack TS, Wolfgang WJ, Schoonmaker-Bopp D, Chu A, Myers R, Haendiges J, Evans PS, Meng J, Strain EA, Allard MW, Brown EW.

J Infect Dis. 2016 Feb 15;213(4):502-8. doi: 10.1093/infdis/jiv297. Epub 2015 May 20.

PMID:
25995194
14.

Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies.

Handelman SK, Aaronson JM, Seweryn M, Voronkin I, Kwiek JJ, Sadee W, Verducci JS, Janies DA.

Comput Biol Med. 2015 Mar;58:1-13. doi: 10.1016/j.compbiomed.2014.12.013. Epub 2014 Dec 24.

15.

Genotypic and phenotypic heterogeneity in the U3R region of HIV type 1 subtype C.

Mates JM, Kumar SB, Bazan J, Mefford M, Voronkin I, Handelman S, Mwapasa V, Ackerman W 4th, Janies D, Kwiek JJ.

AIDS Res Hum Retroviruses. 2014 Jan;30(1):102-12. doi: 10.1089/AID.2013.0026. Epub 2013 Aug 12.

16.

Eco-virological approach for assessing the role of wild birds in the spread of avian influenza H5N1 along the Central Asian Flyway.

Newman SH, Hill NJ, Spragens KA, Janies D, Voronkin IO, Prosser DJ, Yan B, Lei F, Batbayar N, Natsagdorj T, Bishop CM, Butler PJ, Wikelski M, Balachandran S, Mundkur T, Douglas DC, Takekawa JY.

PLoS One. 2012;7(2):e30636. doi: 10.1371/journal.pone.0030636. Epub 2012 Feb 7.

17.

Reassortment Networks and the evolution of pandemic H1N1 swine-origin influenza.

Bokhari SH, Pomeroy LW, Janies DA.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jan-Feb;9(1):214-27. doi: 10.1109/TCBB.2011.95.

PMID:
22076498
18.

Global spread and evolution of viral haemorrhagic septicaemia virus.

Studer J, Janies DA.

J Fish Dis. 2011 Oct;34(10):741-7. doi: 10.1111/j.1365-2761.2011.01290.x.

PMID:
21916899
19.

CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome.

Griffen AL, Beall CJ, Firestone ND, Gross EL, Difranco JM, Hardman JH, Vriesendorp B, Faust RA, Janies DA, Leys EJ.

PLoS One. 2011 Apr 22;6(4):e19051. doi: 10.1371/journal.pone.0019051.

20.

Different regions of HIV-1 subtype C env are associated with placental localization and in utero mother-to-child transmission.

Kumar SB, Handelman SK, Voronkin I, Mwapasa V, Janies D, Rogerson SJ, Meshnick SR, Kwiek JJ.

J Virol. 2011 Jul;85(14):7142-52. doi: 10.1128/JVI.01955-10. Epub 2011 May 4.

21.

Echinoderm phylogeny including Xyloplax, a progenetic asteroid.

Janies DA, Voight JR, Daly M.

Syst Biol. 2011 Jul;60(4):420-38. doi: 10.1093/sysbio/syr044. Epub 2011 Apr 27.

PMID:
21525529
22.

Health-care hit or miss?

Hersh W, Jacko JA, Greenes R, Tan J, Janies D, Embi PJ, Payne PR.

Nature. 2011 Feb 17;470(7334):327-9. doi: 10.1038/470327a. No abstract available.

PMID:
21331020
23.

Bacterial 16S sequence analysis of severe caries in young permanent teeth.

Gross EL, Leys EJ, Gasparovich SR, Firestone ND, Schwartzbaum JA, Janies DA, Asnani K, Griffen AL.

J Clin Microbiol. 2010 Nov;48(11):4121-8. doi: 10.1128/JCM.01232-10. Epub 2010 Sep 8.

24.

Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: genetic diversity and relationships from 1976 to 2007.

Bulach D, Halpin R, Spiro D, Pomeroy L, Janies D, Boyle DB.

J Virol. 2010 Oct;84(19):9957-66. doi: 10.1128/JVI.00930-10. Epub 2010 Jul 28.

25.

Genome informatics of influenza A: from data sharing to shared analytical capabilities.

Janies DA, Voronkin IO, Das M, Hardman J, Treseder TW, Studer J.

Anim Health Res Rev. 2010 Jun;11(1):73-9. doi: 10.1017/S1466252310000083. Review.

PMID:
20591214
26.

Reassortment networks for investigating the evolution of segmented viruses.

Bokhari SH, Janies DA.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):288-98. doi: 10.1109/TCBB.2008.73.

PMID:
20431148
27.

Selection for resistance to oseltamivir in seasonal and pandemic H1N1 influenza and widespread co-circulation of the lineages.

Janies DA, Voronkin IO, Studer J, Hardman J, Alexandrov BB, Treseder TW, Valson C.

Int J Health Geogr. 2010 Feb 24;9:13. doi: 10.1186/1476-072X-9-13.

28.

Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza.

Hill AW, Guralnick RP, Wilson MJ, Habib F, Janies D.

Infect Genet Evol. 2009 Mar;9(2):169-78. doi: 10.1016/j.meegid.2008.10.006. Epub 2008 Oct 30.

PMID:
19022400
29.

GRASSIUS: a platform for comparative regulatory genomics across the grasses.

Yilmaz A, Nishiyama MY Jr, Fuentes BG, Souza GM, Janies D, Gray J, Grotewold E.

Plant Physiol. 2009 Jan;149(1):171-80. doi: 10.1104/pp.108.128579. Epub 2008 Nov 5.

30.

Genomic analysis and geographic visualization of H5N1 and SARS-CoV.

Hill AW, Alexandrov B, Guralnick RP, Janies D.

AMIA Annu Symp Proc. 2007 Oct 11:975.

PMID:
18694075
31.

Genome analysis linking recent European and African influenza (H5N1) viruses.

Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM, Brown IH, Couacy-Hymann E, De Mia GM, Dung do H, Guercio A, Joannis T, Maken Ali AS, Osmani A, Padalino I, Saad MD, Savić V, Sengamalay NA, Yingst S, Zaborsky J, Zorman-Rojs O, Ghedin E, Capua I.

Emerg Infect Dis. 2007 May;13(5):713-8.

32.

Genomic analysis and geographic visualization of the spread of avian influenza (H5N1).

Janies D, Hill AW, Guralnick R, Habib F, Waltari E, Wheeler WC.

Syst Biol. 2007 Apr;56(2):321-9. No abstract available.

PMID:
17464886
33.

Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation.

Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Vlasova A, Janies D, Jones LR, Ghedin E, Saif LJ.

Virology. 2007 Jun 20;363(1):1-10. Epub 2007 Apr 16.

34.

Large scale genotype-phenotype correlation analysis based on phylogenetic trees.

Habib F, Johnson AD, Bundschuh R, Janies D.

Bioinformatics. 2007 Apr 1;23(7):785-8. Epub 2007 Jan 31.

PMID:
17267431
35.
36.

An XML-based system for synthesis of data from disparate databases.

Kurc T, Janies DA, Johnson AD, Langella S, Oster S, Hastings S, Habib F, Camerlengo T, Ervin D, Catalyurek UV, Saltz JH.

J Am Med Inform Assoc. 2006 May-Jun;13(3):289-301. Epub 2006 Feb 24.

37.
38.

Genetic diversity and recombination of porcine sapoviruses.

Wang QH, Han MG, Funk JA, Bowman G, Janies DA, Saif LJ.

J Clin Microbiol. 2005 Dec;43(12):5963-72.

39.

Molecular phylogeny of coral-reef sea cucumbers (Holothuriidae: Aspidochirotida) based on 16S mitochondrial ribosomal DNA sequence.

Kerr AM, Janies DA, Clouse RM, Samyn Y, Kuszak J, Kim J.

Mar Biotechnol (NY). 2005 Jan-Feb;7(1):53-60. Epub 2004 Dec 30.

PMID:
15997365
40.

Efficiency of parallel direct optimization.

Janies DA, Wheeler WC.

Cladistics. 2001 Mar;17(1 Pt 2):S71-82.

PMID:
12240679
41.

Theory and practice of parallel direct optimization.

Janies DA, Wheeler WC.

EXS. 2002;(92):115-23.

PMID:
11924490
42.

Multiple sequence alignment in phylogenetic analysis.

Phillips A, Janies D, Wheeler W.

Mol Phylogenet Evol. 2000 Sep;16(3):317-30. Review.

PMID:
10991785
43.

Development, evolution, and corroboration.

Janies D, DeSalle R.

Anat Rec. 1999 Feb 15;257(1):6-14. Review.

PMID:
10333399
44.

Highly Derived Coelomic and Water-Vascular Morphogenesis in a Starfish with Pelagic Direct Development.

Janies DA, McEdward LR.

Biol Bull. 1993 Aug;185(1):56-76. doi: 10.2307/1542130.

PMID:
29300605
45.

Life Cycle Evolution in Asteroids: What is a Larva?

McEdward LR, Janies DA.

Biol Bull. 1993 Jun;184(3):255-268. doi: 10.2307/1542444.

PMID:
29300539

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