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Items: 1 to 50 of 55

1.

Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors.

Nelson CW, Sibley SD, Kolokotronis SO, Hamer GL, Newman CM, Anderson TK, Walker ED, Kitron UD, Brawn JD, Ruiz MO, Goldberg TL.

Virus Evol. 2018 Jun 12;4(1):vey013. doi: 10.1093/ve/vey013. eCollection 2018 Jan.

2.

Transient influence of blood meal and natural environment on blacklegged tick bacterial communities.

Zolnik CP, Falco RC, Daniels TJ, Kolokotronis SO.

Ticks Tick Borne Dis. 2018 Mar;9(3):563-572. doi: 10.1016/j.ttbdis.2018.01.007. Epub 2018 Jan 31.

PMID:
29409718
3.

Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens.

Anco C, Kolokotronis SO, Henschel P, Cunningham SW, Amato G, Hekkala E.

Mitochondrial DNA A DNA Mapp Seq Anal. 2018 Apr;29(3):455-473. doi: 10.1080/24701394.2017.1307973. Epub 2017 Apr 19.

PMID:
28423965
4.

Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

Brown TS, Narechania A, Walker JR, Planet PJ, Bifani PJ, Kolokotronis SO, Kreiswirth BN, Mathema B.

BMC Genomics. 2016 Nov 21;17(1):947.

5.

Bats, Primates, and the Evolutionary Origins and Diversification of Mammalian Gammaherpesviruses.

Escalera-Zamudio M, Rojas-Anaya E, Kolokotronis SO, Taboada B, Loza-Rubio E, Méndez-Ojeda ML, Arias CF, Osterrieder N, Greenwood AD.

MBio. 2016 Nov 8;7(6). pii: e01425-16. doi: 10.1128/mBio.01425-16.

6.

Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets.

Narechania A, Baker R, DeSalle R, Mathema B, Kolokotronis SO, Kreiswirth B, Planet PJ.

Gigascience. 2016 Oct 24;5(1):44.

7.

The mitogenome of the bed bug Cimex lectularius (Hemiptera: Cimicidae).

Kolokotronis SO, Foox J, Rosenfeld JA, Brugler MR, Reeves D, Benoit JB, Booth W, Robison G, Steffen M, Sakas Z, Palli SR, Schal C, Richards S, Narechania A, Baker RH, Sorkin LN, Amato G, Mason CE, Siddall ME, DeSalle R.

Mitochondrial DNA B Resour. 2016;1(1):425-427. doi: 10.1080/23802359.2016.1180268. Epub 2016 Jun 20.

8.

Microbiome changes through ontogeny of a tick pathogen vector.

Zolnik CP, Prill RJ, Falco RC, Daniels TJ, Kolokotronis SO.

Mol Ecol. 2016 Oct;25(19):4963-77. doi: 10.1111/mec.13832. Epub 2016 Sep 18.

PMID:
27588381
9.

Genetic identification of mammalian meal source in dung beetle gut contents.

Gómez A, Kolokotronis SO.

Mitochondrial DNA A DNA Mapp Seq Anal. 2017 Jul;28(4):612-615. doi: 10.3109/24701394.2016.1155120. Epub 2016 Mar 12.

PMID:
27159706
10.

Combining genetic and distributional approaches to sourcing introduced species: a case study on the Nile monitor (Varanus niloticus) in Florida.

Dowell SA, Wood JP, Campbell TS, Kolokotronis SO, Hekkala ER.

R Soc Open Sci. 2016 Apr 20;3(4):150619. doi: 10.1098/rsos.150619. eCollection 2016 Apr.

11.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):97-97.e3. doi: 10.1016/j.cels.2015.07.006. Epub 2015 Jul 29. No abstract available.

12.

Modern Methods for Delineating Metagenomic Complexity.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):6-7. doi: 10.1016/j.cels.2015.07.007. Epub 2015 Jul 29. No abstract available.

13.

Erratum for Alfano et al., Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses.

Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD.

J Virol. 2016 Mar 28;90(8):4254. doi: 10.1128/JVI.00210-16. Print 2016 Apr. No abstract available.

14.

Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius.

Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE.

Nat Commun. 2016 Feb 2;7:10164. doi: 10.1038/ncomms10164.

15.

Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses.

Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD.

J Virol. 2015 Dec 4;90(4):1757-72. doi: 10.1128/JVI.02745-15. Print 2016 Feb 15. Erratum in: J Virol. 2016 Apr;90(8):4254.

16.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE.

Cell Syst. 2015 Jul 29;1(1):72-87. Epub 2015 Mar 3.

17.

Molecular data from contemporary and historical collections reveal a complex story of cryptic diversification in the Varanus (Polydaedalus) niloticus Species Group.

Dowell SA, Portik DM, de Buffrénil V, Ineich I, Greenbaum E, Kolokotronis SO, Hekkala ER.

Mol Phylogenet Evol. 2016 Jan;94(Pt B):591-604. doi: 10.1016/j.ympev.2015.10.004. Epub 2015 Oct 22.

PMID:
26475616
18.

No Observed Effect of Landscape Fragmentation on Pathogen Infection Prevalence in Blacklegged Ticks (Ixodes scapularis) in the Northeastern United States.

Zolnik CP, Falco RC, Kolokotronis SO, Daniels TJ.

PLoS One. 2015 Oct 2;10(10):e0139473. doi: 10.1371/journal.pone.0139473. eCollection 2015.

19.

To beat or not to beat a tick: comparison of DNA extraction methods for ticks (Ixodes scapularis).

Ammazzalorso AD, Zolnik CP, Daniels TJ, Kolokotronis SO.

PeerJ. 2015 Aug 13;3:e1147. doi: 10.7717/peerj.1147. eCollection 2015.

20.

Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes.

Ganu RS, Ishida Y, Koutmos M, Kolokotronis SO, Roca AL, Garrow TA, Schook LB.

PLoS One. 2015 Jul 27;10(7):e0134084. doi: 10.1371/journal.pone.0134084. eCollection 2015.

21.

Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America.

Planet PJ, Diaz L, Kolokotronis SO, Narechania A, Reyes J, Xing G, Rincon S, Smith H, Panesso D, Ryan C, Smith DP, Guzman M, Zurita J, Sebra R, Deikus G, Nolan RL, Tenover FC, Weinstock GM, Robinson DA, Arias CA.

J Infect Dis. 2015 Dec 15;212(12):1874-82. doi: 10.1093/infdis/jiv320. Epub 2015 Jun 5.

22.

Fine-scale genetic analysis of the exploited Nile monitor (Varanus niloticus) in Sahelian Africa.

Dowell SA, de Buffrénil V, Kolokotronis SO, Hekkala ER.

BMC Genet. 2015 Mar 28;16:32. doi: 10.1186/s12863-015-0188-x.

23.

Evolution of the indoor biome.

NESCent Working Group on the Evolutionary Biology of the Built Environment, Martin LJ, Adams RI, Bateman A, Bik HM, Hawks J, Hird SM, Hughes D, Kembel SW, Kinney K, Kolokotronis SO, Levy G, McClain C, Meadow JF, Medina RF, Mhuireach G, Moreau CS, Munshi-South J, Nichols LM, Palmer C, Popova L, Schal C, Täubel M, Trautwein M, Ugalde JA, Dunn RR.

Trends Ecol Evol. 2015 Apr;30(4):223-32. doi: 10.1016/j.tree.2015.02.001. Epub 2015 Mar 11. Review.

PMID:
25770744
24.

Changes in the Mitogenome Announcement manuscript category.

DeSalle R, Kolokotronis SO.

Mitochondrial DNA. 2015 Feb;26(1):1. doi: 10.3109/19401736.2015.1013392. Epub 2015 Feb 19. No abstract available.

PMID:
25693712
25.

Negative purifying selection drives prion and doppel protein evolution.

Tsangaras K, Kolokotronis SO, Ulrich RG, Morand S, Michaux J, Greenwood AD.

J Mol Evol. 2014 Aug;79(1-2):12-20. doi: 10.1007/s00239-014-9632-1. Epub 2014 Jul 20.

26.

In the wake of invasion: tracing the historical biogeography of the South American cricetid radiation (Rodentia, Sigmodontinae).

Leite RN, Kolokotronis SO, Almeida FC, Werneck FP, Rogers DS, Weksler M.

PLoS One. 2014 Jun 25;9(6):e100687. doi: 10.1371/journal.pone.0100687. eCollection 2014. Erratum in: PLoS One. 2014;9(10):e110081.

27.

Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element.

Benson MA, Ohneck EA, Ryan C, Alonzo F 3rd, Smith H, Narechania A, Kolokotronis SO, Satola SW, Uhlemann AC, Sebra R, Deikus G, Shopsin B, Planet PJ, Torres VJ.

Mol Microbiol. 2014 Aug;93(4):664-81. doi: 10.1111/mmi.12682. Epub 2014 Jul 16.

28.

Mycobacterial phylogenomics: an enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families.

Librado P, Vieira FG, Sánchez-Gracia A, Kolokotronis SO, Rozas J.

Genome Biol Evol. 2014 Jun 5;6(6):1454-65. doi: 10.1093/gbe/evu117.

29.

Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology.

Scheel DM, Slater GJ, Kolokotronis SO, Potter CW, Rotstein DS, Tsangaras K, Greenwood AD, Helgen KM.

Zookeys. 2014 May 14;(409):1-33. doi: 10.3897/zookeys.409.6244. eCollection 2014.

30.

Emergence of the epidemic methicillin-resistant Staphylococcus aureus strain USA300 coincides with horizontal transfer of the arginine catabolic mobile element and speG-mediated adaptations for survival on skin.

Planet PJ, LaRussa SJ, Dana A, Smith H, Xu A, Ryan C, Uhlemann AC, Boundy S, Goldberg J, Narechania A, Kulkarni R, Ratner AJ, Geoghegan JA, Kolokotronis SO, Prince A.

MBio. 2013 Dec 17;4(6):e00889-13. doi: 10.1128/mBio.00889-13.

31.

Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

Mendez M, Jefferson TA, Kolokotronis SO, Krützen M, Parra GJ, Collins T, Minton G, Baldwin R, Berggren P, Särnblad A, Amir OA, Peddemors VM, Karczmarski L, Guissamulo A, Smith B, Sutaria D, Amato G, Rosenbaum HC.

Mol Ecol. 2013 Dec;22(23):5936-48. doi: 10.1111/mec.12535. Epub 2013 Oct 29.

PMID:
24268046
32.

Molecular surveillance of low pathogenic avian influenza viruses in wild birds across the United States: inferences from the hemagglutinin gene.

Piaggio AJ, Shriner SA, VanDalen KK, Franklin AB, Anderson TD, Kolokotronis SO.

PLoS One. 2012;7(12):e50834. doi: 10.1371/journal.pone.0050834. Epub 2012 Dec 4.

33.

Testing the effectiveness of an international conservation agreement: marketplace forensics and CITES caviar trade regulation.

Doukakis P, Pikitch EK, Rothschild A, DeSalle R, Amato G, Kolokotronis SO.

PLoS One. 2012;7(7):e40907. doi: 10.1371/journal.pone.0040907. Epub 2012 Jul 25.

34.

Zoonotic viruses associated with illegally imported wildlife products.

Smith KM, Anthony SJ, Switzer WM, Epstein JH, Seimon T, Jia H, Sanchez MD, Huynh TT, Galland GG, Shapiro SE, Sleeman JM, McAloose D, Stuchin M, Amato G, Kolokotronis SO, Lipkin WI, Karesh WB, Daszak P, Marano N.

PLoS One. 2012;7(1):e29505. doi: 10.1371/journal.pone.0029505. Epub 2012 Jan 10.

35.

A functional phylogenomic view of the seed plants.

Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R.

PLoS Genet. 2011 Dec;7(12):e1002411. doi: 10.1371/journal.pgen.1002411. Epub 2011 Dec 15.

36.

Random Addition Concatenation Analysis: a novel approach to the exploration of phylogenomic signal reveals strong agreement between core and shell genomic partitions in the cyanobacteria.

Narechania A, Baker RH, Sit R, Kolokotronis SO, DeSalle R, Planet PJ.

Genome Biol Evol. 2012;4(1):30-43. doi: 10.1093/gbe/evr121. Epub 2011 Nov 16.

37.

The Fish Barcode of Life (FISH-BOL) special issue.

Hanner R, Desalle R, Ward RD, Kolokotronis SO.

Mitochondrial DNA. 2011 Oct;22 Suppl 1:1-2. doi: 10.3109/19401736.2011.598767. No abstract available.

PMID:
21980984
38.

Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants.

Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL.

PLoS One. 2011;6(6):e20642. doi: 10.1371/journal.pone.0020642. Epub 2011 Jun 8.

39.

Bayesian estimation of substitution rates from ancient DNA sequences with low information content.

Ho SY, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis SO, Shapiro B.

Syst Biol. 2011 May;60(3):366-75. doi: 10.1093/sysbio/syq099. Epub 2011 Feb 4. No abstract available.

PMID:
21296909
40.

Genetic variation in avocado stem weevils Copturus aguacatae (Coleoptera: Curculionidae) in Mexico.

Engstrand RC, Cibrián Tovar J, Cibrián-Jaramillo A, Kolokotronis SO.

Mitochondrial DNA. 2010 Dec;21 Suppl 1:38-43. doi: 10.3109/19401736.2010.536226.

PMID:
21271857
41.

The MexBOL initiative.

Escalante P, Desalle R, Kolokotronis SO.

Mitochondrial DNA. 2010 Dec;21 Suppl 1:1-2. doi: 10.3109/19401736.2010.551715. No abstract available.

PMID:
21271851
42.

Evolutionary dynamics of endogenous feline leukemia virus proliferation among species of the domestic cat lineage.

Polani S, Roca AL, Rosensteel BB, Kolokotronis SO, Bar-Gal GK.

Virology. 2010 Sep 30;405(2):397-407. doi: 10.1016/j.virol.2010.06.010. Epub 2010 Jul 7.

43.

Wild bird's-eye view of influenza virus A(H1N1) phylogenetic evolution.

Piaggio AJ, Clark L, Franklin AB, Kolokotronis SO.

Ecohealth. 2009 Sep;6(3):346-50. doi: 10.1007/s10393-009-0270-9. Epub 2010 May 11. Erratum in: Ecohealth. 2010 Sep;7(3):408-9.

PMID:
20458519
44.

DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers.

Lowenstein JH, Burger J, Jeitner CW, Amato G, Kolokotronis SO, Gochfeld M.

Biol Lett. 2010 Oct 23;6(5):692-5. doi: 10.1098/rsbl.2010.0156. Epub 2010 Apr 21.

45.

The real maccoyii: identifying tuna sushi with DNA barcodes--contrasting characteristic attributes and genetic distances.

Lowenstein JH, Amato G, Kolokotronis SO.

PLoS One. 2009 Nov 18;4(11):e7866. doi: 10.1371/journal.pone.0007866.

46.

The Diploblast-Bilateria Sister hypothesis: parallel revolution of a nervous systems may have been a simple step.

Schierwater B, Kolokotronis SO, Eitel M, DeSalle R.

Commun Integr Biol. 2009 Sep;2(5):403-5.

47.

Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

Roca AL, Ishida Y, Nikolaidis N, Kolokotronis SO, Fratpietro S, Stewardson K, Hensley S, Tisdale M, Boeskorov G, Greenwood AD.

BMC Evol Biol. 2009 Sep 11;9:232. doi: 10.1186/1471-2148-9-232.

48.

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R.

PLoS One. 2009 Jun 2;4(6):e5764. doi: 10.1371/journal.pone.0005764.

49.

Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis.

Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R.

PLoS Biol. 2009 Jan 27;7(1):e20. doi: 10.1371/journal.pbio.1000020.

50.

Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease.

Wyatt KB, Campos PF, Gilbert MT, Kolokotronis SO, Hynes WH, DeSalle R, Ball SJ, Daszak P, MacPhee RD, Greenwood AD.

PLoS One. 2008;3(11):e3602. doi: 10.1371/journal.pone.0003602. Epub 2008 Nov 5. Erratum in: PLoS ONE. 2009;4(1). doi: doi.org/10.1371/annotation/9fbe9687-682e-4010-97e4-139b33343d34. Ball, Stanley J [added].

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