publications
#undergraduate *graduate
The copyrights for all non-Open Access articles below are held by their respective publishers. By clicking on the pdf link you are requesting a single copy for personal use or study. Reproduction or commercial use of these works in whole or edited form is prohibited by law.
2022
Lin YP, Tufts DM, Combs M, Dupuis AP 2nd, Marcinkiewicz AL, Hirsbrunner AD, Diaz AJ, Stout JL, Blom AM, Strle K, Davis AD, Kramer LD, Kolokotronis SO, Diuk-Wasser MA. (2022) Cellular and immunological mechanisms influence host-adapted phenotypes in a vector-borne microparasite. Proceedings Biological Sciences 289(1969):20212087. [pdf]
2021
Hart TM, Dupuis AP 2nd, Tufts DM, Blom AM, Starkey SR, Rego ROM, Ram S, Kraiczy P, Kramer LD, Diuk-Wasser MA, Kolokotronis SO, Lin YP. (2021) Host tropism determination by convergent evolution of immunological evasion in the Lyme disease system. PLoS Pathogens 17(7):e1009801. [pdf]
Quinlan JR, O'Leary SJ, Fields AT, Benavides M, Stumpf E, Carcamo R, Cruz J, Lewis D, Wade B, Amato G, Kolokotronis SO, Clementi GM, Chapman DD. (2021) Using fisher-contributed secondary fins to fill critical shark-fisheries data gaps. Conservation Biology 35(3):991-1001. [pdf]
[Phys.org]
2020
Nelson CW, Ardern Z, Goldberg TL, Meng C, Kuo CH, Ludwig C, Kolokotronis SO, Wei X. (2020) Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic. eLife 9:e59633. [pdf]
[The Telegraph | ScienceDaily]
Rios R, Reyes J, Carvajal LP, Rincon S, Panesso D, Echeverri AM, Dinh A, Kolokotronis SO, Narechania A, Tran TT, Munita JM, Murray BE, Planet PJ, Arias CA, Diaz L. (2020) Genomic epidemiology of vancomycin-resistant Enterococcus faecium (VREfm) in Latin America: revisiting the global VRE population structure. Scientific Reports 10(1):5636. [pdf]
2019
Brown TS, Challagundla L, Baugh EH, Omar SV, Mustaev A, Auld SC, Shah NS, Kreiswirth BN, Brust JCM, Nelson KN, Narechania A, Kurepina N, Mlisana K, Bonneau R, Eldholm V, Ismail N, Kolokotronis SO, Robinson DA, Gandhi NR, Mathema B. (2019) Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa. Proceedings of the National Academy of Sciences of the USA 116(46):23284-23291. [pdf]
Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. (2019) Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Scientific Reports 9(1):5602. [pdf]
Tufts DM, Hart TM, Chen GF, Kolokotronis SO, Diuk-Wasser MA, Lin YP. (2019) Outer surface protein polymorphisms linked to host-spirochete association in Lyme borreliae. Molecular Microbiology 111(4):868-882. [pdf]
Botelho AMN, Cerqueira e Costa MO, Moustafa AM, Beltrame CO, Ferreira FA, Côrtes MF, Costa BSS, Silva DNS, Bandeira PT, Lima NCB, Souza RC, Almeida LGdP, Vasconcelos ATR, Narechania A, Ryan C, O’Brien K, Kolokotronis SO, Planet PJ, Nicolás MF, Figueiredo AMS. (2019) Local Diversification of methicillin- resistant Staphylococcus aureus ST239 in South America after its rapid worldwide dissemination. Frontiers in Microbiology 10:82. [pdf]
2018
Nelson CW, Sibley SD, Kolokotronis SO, Hamer GL, Newman CM, Anderson TA, Walker ED, Kitron UD, Brawn JD, Ruiz MO, Goldberg TL. (2018) Selective constraint and adaptive potential of West Nile virus within and among naturally infected avian hosts and mosquito vectors. Virus Evolution 4(1):vey013. [pdf]
Zolnik CP*, Falco, RC, Daniels TJ, Kolokotronis SO. (2018) Transient influence of blood meal and natural environment on blacklegged tick bacterial communities. Ticks and Tick-borne Diseases 9(3):563-572. [pdf]
2017
Anco C*, Kolokotronis SO, Henschel P, Cunningham SW*, Amato G, Hekkala E. (2017) Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens. Mitochondrial DNA 29(3):455-473. [pdf]
Gómez A, Kolokotronis SO. (2017) Genetic identification of mammalian meal source in dung beetle gut contents. Mitochondrial DNA 28(4):612-615. [pdf]
2016
Brown TS, Narechania A, Walker JR, Planet PJ, Bifani PJ, Kolokotronis SO, Kreiswirth BN, Mathema B. (2016) Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York city and New Jersey, 1999-2009. BMC Genomics 17(1):947. [pdf]
Escalera-Zamudio M*, Rojas-Anaya E, Kolokotronis SO, Taboada B, Loza-Rubio E, Méndez-Ojeda ML, Arias CF, Osterrieder N, Greenwood AD. (2016) Bats, primates, and the evolutionary origin and diversification of mammalian gammaherpesviruses. mBio 7(6):e01425-16. [pdf]
Narechania A, Baker R, DeSalle R, Mathema B, Kolokotronis SO, Kreiswirth B, Planet PJ. (2016) Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets. GigaScience 5:44. [pdf] [video]
Zolnik CP*, Prill RJ, Falco RC, Daniels TJ, Kolokotronis SO. (2016) Microbiome changes through ontogeny of a tick pathogen vector. Molecular Ecology 25(19):4963-4977. [pdf]
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. (2016) The mitogenome of the bed bug Cimex lectularius (Hemiptera: Cimicidae). Mitochondrial DNA: Resources 1(1):425-427. [pdf]
Dowell SA*, Wood JP, Campbell TS, Kolokotronis SO, Hekkala ER. (2016) Combining genetic and distributional approaches to sourcing introduced species: a case study on the Nile monitor (Varanus niloticus) in Florida. Royal Society Open Science 3:150619. [pdf]
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, Sabghini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M*, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE. (2016) Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nature Communications 7:10164. [pdf]
Alfano N*, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD. (2016) Episodic diversifying selection shaped the genomes of gibbon ape leukemia virus and related gammaretroviruses. Journal of Virology 90(4):1757-1772. [pdf] [erratum]
Dowell SA*, Portik DM, Buffrénil V, Ineich I, Greenbaum E, Kolokotronis SO, Hekkala ER. (2016) Molecular data from contemporary and historical collections reveal a complex story of cryptic diversification in the Varanus (Polydaedalus) niloticus Species Group. Molecular Phylogenetics & Evolution 94(B):591-604 [pdf]
2015
Zolnik CP*, Falco RC, Kolokotronis SO, Daniels TJ. (2015) No observed effect of landscape fragmentation on pathogen infection prevalence in blacklegged ticks (Ixodes scapularis) in the Northeastern United States. PLoS ONE 10(10):e0139473. [pdf]
Ammazzalorso AD#, Zolnik CP*, Falco RC, Daniels TJ, Kolokotronis SO. (2015) To beat or not to beat a tick: Comparison of DNA extraction methods from ticks (Ixodes scapularis). PeerJ 3:e1147. [pdf]
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, Schneider Paolantonio K, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. (2015) Modern methods for delineating metagenomic complexity. Cell Systems 1:6-7. [pdf]
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. (2015) Parallel epidemics of community-associated methicillin-resistant Staphylococcus aureus USA300 in North and South America. Journal of Infectious Diseases 212(12):1874-1882. [pdf]
Ganu RS, Ishida Y, Roca AL, Kolokotronis SO, Garrow TA, Schook LB. (2015) Evolutionary analyses and natural selection of betaine–homocysteine S-methyltransferase (BHMT) and BHMT2 genes. PLoS ONE 10(7):e0134084. [pdf]
Dowell SA*, de Buffrénil, Kolokotronis SO, Hekkala ER. (2015) Fine-scale genetic analysis of the exploited Nile monitor (Varanus niloticus) in Sahelian Africa. BMC Genetics 16:32. [pdf]
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, Schneider Paolantonio K, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. (2015) Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Systems 1:72-87. [pdf]
[WSJ 1 | WSJ 2 | New York Times] [interactive maps: WSJ | PathoMap]
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. (2015) Evolution of the indoor biome. Trends in Ecology & Evolution 30(4):223-232. [pdf]
DeSalle R, Kolokotronis SO. (2015) Changes in the Mitogenome Announcement manuscript category. Mitochondrial DNA 26(1):1.[pdf]
2014
Tsangaras K¶, Kolokotronis SO¶, Ulrich RG, Morand S, Michaux J, Greenwood AD. (2014) Negative purifying selection drives Prion and Doppel protein evolution. Journal of Molecular Evolution 79(1-2):12-20. [pdf] ¶co-first authors
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. (2014) Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element. Molecular Microbiology 93(4):664-681. [pdf]
Leite RN, Kolokotronis SO, Almeida FC, Werneck FP, Rogers DS, Weksler M. (2014) In the wake of invasion: Tracing the historical biogeography of the South American cricetid radiation (Rodentia, Sigmodontinae). PLoS ONE 9(6):e100687. [pdf]
Librado P¶, Vieira FG¶, Sánchez-Gracia A¶, Kolokotronis SO¶, Rozas J. (2014) Mycobacterial phylogenomics: An enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families. Genome Biology and Evolution 6(6):1454-1465. [pdf] ¶co-first authors
Scheel DM, Slater GJ, Kolokotronis SO, Potter CW, Rotstein DS, Tsangaras K, Greenwood AD, Helgen KM. (2014) Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. ZooKeys 409:1-33. [pdf] [National Geographic Magazine | Smithsonian Magazine | Smithsonian Science | Phys.org]
2013
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. (2013) 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. mBio 4(6):e00889-13. [pdf]
[Times of India | ScienceDaily]
Mendez M, Jefferson TJ, 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 H. (2013) 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? Molecular Ecology 22(23):5936-5948. [pdf]
[Washington Post | New York Times | National Geographic | BBC | Reuters | LA Times | CBS | NBC | Scientific American | Smithsonian Magazine]
2012
Piagio PJ, Shriner SA, VanDalen KK, Franklin AB, Anderson TD, Kolokotronis SO. (2012) Molecular surveillance of low pathogenic avian influenza viruses in wild birds across the United States: Inferences from the hemagglutinin gene. PLoS ONE 7(12):e50834. [pdf]
Doukakis P, Pikitch EK, Rothschild A, Desalle R, Amato G, Kolokotronis SO. (2012) Testing the effectiveness of an international conservation agreement: Marketplace forensics and CITES caviar trade regulation. PLoS ONE 7(7):e40907. [pdf]
[New York Times by Florence Fabricant]
Smith KS, 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. (2012) Zoonotic viruses associated with illegally imported wildlife products. PLoS ONE 7(1): e29505. [pdf]
[Discover by Carl Zimmer | TIME Science | BBC News | New York Times | Conservation Magazine]
Narechania A, Baker RH, Sit R, Kolokotronis SO, DeSalle R, Planet PJ. (2012) 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. Genome Biology and Evolution 4(1):30-43. [pdf]
2011
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. (2011) A functional phylogenomics view of the seed plants. PLoS Genetics 7(12):e1002411. [pdf] ¶co-first authors
[New York Times | Genome Technology]
Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL. (2011) Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants. PLoS ONE 6(6):e20642. [pdf]
[Audubon Magazine]
Hanner R, DeSalle R, Ward RD, Kolokotronis SO. [editors] (2011) The Fish Barcode of Life (FISH-BOL) special issue. Mitochondrial DNA 22(S1):1-2. [pdf]
Ho SYW, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis SO, Shapiro B. (2011) Bayesian estimation of substitution rates from ancient DNA sequences from low information content. Systematic Biology 60(3):366-375. [pdf]
2010
Engstrand RC, Cibrián Tovar J, Cibrián-Jaramillo A, Kolokotronis SO. (2010) Genetic variation in avocado stem weevils Copturus aguacatae (Coleoptera: Curculionidae) in Mexico. Mitochondrial DNA 21(S1):38-43. [pdf]
Escalante P, DeSalle R, Kolokotronis SO. [editors] (2010) The MexBOL initiative. Mitochondrial DNA 21(S1):1-2. [pdf]
Polani S, Roca AL, Rosensteel B, Kolokotronis SO, Bar-Gal GK. (2010) Evolutionary dynamics of endogenous feline leukemia virus proliferation among species of the domestic cat lineage. Virology 405(2):397-407. [pdf]
Lowenstein JH, Burger J, Jeitner CW, Amato G, Kolokotronis SO, Gochfeld M. (2010) DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers. Biology Letters 6(5):692-695. [pdf]
[CBC News]
Gonçalves da Silva A, Kolokotronis SO, Wharton D. (2010) Modeling the eradication of invasive mammals using the sterile male technique. Biological Invasions 12(4):751-759. [pdf]
Eaton MJ, Meyers GL, Kolokotronis SO, Leslie MS, Martin AP, Amato G. (2010) Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates. Conservation Genetics 11(14):1389-1404. [pdf]
[NPR | BBC | GenomeWeb | Conservation Magazine | New Scientist]
2009
Piaggio AJ, Clark L, Franklin AB, Kolokotronis SO. (2009) Wild bird’s-eye view of influenza virus A(H1N1) phylogenetic evolution. EcoHealth 6(3):346-350. [pdf]
Lowenstein JH*, Amato G, Kolokotronis SO. (2009) The real maccoyii: identifying tuna sushi with DNA barcodes – contrasting characteristic attributes and genetic distances. PLoS ONE 4(11):e7866. [pdf]
[Popular Science | Wall Street Journal | WIRED | Slashdot | Discovery | Live Science | Rockefeller BOL blog]
Roca AL, Ishida Y, Nikolaidis N, Kolokotronis SO, Fratpietro S, Stewardson K, Hensley S, Tisdale M, Boeskorov G, Greenwood AD. (2009) Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth. BMC Evolutionary Biology 9:232. [pdf]
Schierwater B, Kolokotronis SO, Eitel M, DeSalle R. (2009) The Diploblast-Bilateria Sister hypothesis: parallel evolution of a nervous system may have been a simple step. Communicative and Integrative Biology 2(5):1-3. [pdf]
de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R. (2009) The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS ONE 4(6):e5764. [pdf]
Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, DeSalle R. (2009) Concatenated analysis sheds light on early metazoan evolution and fuels a modern “urmetazoon” hypothesis. PLoS Biology 7(1):e1000020. [pdf]
2008
Wyatt KB, Campos PF, Gilbert MT, Kolokotronis SO, Hynes WH, DeSalle R, Daszak P, MacPhee RD, Greenwood AD. (2008) Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease. PLoS ONE 3(11):e3602. [pdf]
[Science | ScienceDaily]
Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AH, Bray SE, O’Brien SJ, Rabeder G, Matheus P, Cooper A, Slatkin M, Pääbo S, Hofreiter M. (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evolutionary Biology 8:220. [pdf]
[Science]
Baillie GJ, Kolokotronis SO, Waltari E, Maffei JG, Kramer LD, Perkins SL. (2008) Phylogenetic and evolutionary analyses of St. Louis encephalitis virus genomes. Molecular Phylogenetics and Evolution 47(2):717-728. [pdf]
[Genome Technology | ScienceDaily]
2007
Ho SYW, Kolokotronis SO, Allaby RG. (2007) Elevated substitution rates estimated from ancient DNA sequences. Biology Letters 3(6):702-705. [pdf]
Kolokotronis SO, MacPhee RDE, Greenwood AD. (2007) Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen. BMC Evolutionary Biology 7:67. [pdf]
2005
Amor DC, Kolokotronis SO, Medellín RA, Ramey Jr. R, Ryder OA. (2005) Genética de la conservación. In: El Berrendo en México, Acciones de conservación. Valdes M, de la Cruz E, Peters E, Pallares E, Editors. Agrupación Sierra Madre & Instituto Nacional de Ecología (INE-SEMARNAT), México DF. pp. 27-33.
2003
Shykoff JA, Kolokotronis SO, Collin CL, López-Villavicencio M. (2003) Effects of male sterility on reproductive traits in gynodioecious plants: A meta-analysis. Oecologia 135(1):1-9. [pdf]
