Sergios-Orestis Kolokotronis, Ph.D. - Publications

Affiliations: 
2011-2012 Biology Barnard College, Columbia University, New York, NY, United States 
 2012-2016 Biological Sciences Fordham University, Bronx, NY, United States 
 2016- School of Public Health SUNY Downstate Medical Center, Brooklyn, NY, United States 
Area:
molecular evolution, evolutionary genomics, conservation genetics, endangered species, disease vectors, pathogens
Website:
http://kolokolab.org

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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, ... ... Kolokotronis SO, et al. Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa. Proceedings of the National Academy of Sciences of the United States of America. PMID 31659018 DOI: 10.1073/pnas.1906636116  1
2019 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. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Scientific Reports. 9: 5602. PMID 30944370 DOI: 10.1038/s41598-019-41967-8  1
2019 Botelho AMN, Cerqueira E Costa MO, Moustafa AM, Beltrame CO, Ferreira FA, Côrtes MF, Costa BSS, Silva DNS, Bandeira PT, Lima NCB, Souza RC, de Almeida LGP, Vasconcelos ATR, Narechania A, Ryan C, ... ... Kolokotronis SO, et al. Local Diversification of Methicillin- Resistant ST239 in South America After Its Rapid Worldwide Dissemination. Frontiers in Microbiology. 10: 82. PMID 30873127 DOI: 10.3389/fmicb.2019.00082  1
2018 Zolnik CP, Falco RC, Daniels TJ, Kolokotronis SO. Transient influence of blood meal and natural environment on blacklegged tick bacterial communities. Ticks and Tick-Borne Diseases. PMID 29409718 DOI: 10.1016/j.ttbdis.2018.01.007  1
2017 Anco C, Kolokotronis SO, Henschel P, Cunningham SW, Amato G, Hekkala E. Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens. Mitochondrial Dna. Part a, Dna Mapping, Sequencing, and Analysis. 1-19. PMID 28423965 DOI: 10.1080/24701394.2017.1307973  1
2016 Brown TS, Narechania A, Walker JR, Planet PJ, Bifani PJ, Kolokotronis SO, Kreiswirth BN, Mathema B. Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York city and New Jersey, 1999-2009. Bmc Genomics. 17: 947. PMID 27871225 DOI: 10.1186/s12864-016-3298-6  1
2016 Escalera-Zamudio M, Rojas-Anaya E, Kolokotronis SO, Taboada B, Loza-Rubio E, Méndez-Ojeda ML, Arias CF, Osterrieder N, Greenwood AD. Bats, Primates, and the Evolutionary Origins and Diversification of Mammalian Gammaherpesviruses. Mbio. 7. PMID 27834200 DOI: 10.1128/mBio.01425-16  1
2016 Narechania A, Baker R, DeSalle R, Mathema B, Kolokotronis SO, Kreiswirth B, Planet PJ. Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets. Gigascience. 5: 44. PMID 27776538 DOI: 10.1186/s13742-016-0152-3  1
2016 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, et al. The mitogenome of the bed bug Cimex lectularius (Hemiptera: Cimicidae). Mitochondrial Dna. Part B, Resources. 1: 425-427. PMID 27617305 DOI: 10.1080/23802359.2016.1180268  1
2016 Zolnik CP, Prill RJ, Falco RC, Daniels TJ, Kolokotronis SO. Microbiome changes through ontogeny of a tick pathogen vector. Molecular Ecology. PMID 27588381 DOI: 10.1111/mec.13832  1
2016 Dowell SA, Wood JP, Campbell TS, Kolokotronis SO, Hekkala ER. 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. PMID 27152204 DOI: 10.1098/rsos.150619  1
2016 Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD. Erratum for Alfano et al., Episodic Diversifying Selection Shaped the Genomes of Gibbon Ape Leukemia Virus and Related Gammaretroviruses. Journal of Virology. 90: 4254. PMID 27022099 DOI: 10.1128/JVI.00210-16  1
2016 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, ... ... Kolokotronis SO, et al. Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. Nature Communications. 7: 10164. PMID 26836631 DOI: 10.1038/ncomms10164  1
2015 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, ... ... Kolokotronis SO, et al. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Systems. 1: 97-97.e3. PMID 27135689 DOI: 10.1016/j.cels.2015.07.006  1
2015 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, ... ... Kolokotronis SO, et al. Modern Methods for Delineating Metagenomic Complexity. Cell Systems. 1: 6-7. PMID 27135684 DOI: 10.1016/j.cels.2015.07.007  1
2015 Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD. Episodic diversifying selection shaped the genomes of gibbon ape leukemia virus and related gammaretroviruses. Journal of Virology. PMID 26637454 DOI: 10.1128/JVI.02745-15  1
2015 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, ... ... Kolokotronis SO, et al. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Systems. 1: 72-87. PMID 26594662 DOI: 10.1016/j.cels.2015.01.001  1
2015 Dowell SA, Portik DM, de Buffrénil V, Ineich I, Greenbaum E, Kolokotronis SO, Hekkala ER. Molecular data from contemporary and historical collections reveal a complex story of cryptic diversification in the Varanus (Polydaedalus) niloticus Species Group. Molecular Phylogenetics and Evolution. PMID 26475616 DOI: 10.1016/j.ympev.2015.10.004  1
2015 Zolnik CP, Falco RC, Kolokotronis SO, Daniels TJ. No Observed Effect of Landscape Fragmentation on Pathogen Infection Prevalence in Blacklegged Ticks (Ixodes scapularis) in the Northeastern United States. Plos One. 10: e0139473. PMID 26430734 DOI: 10.1371/journal.pone.0139473  1
2015 Ammazzalorso AD, Zolnik CP, Daniels TJ, Kolokotronis SO. To beat or not to beat a tick: comparison of DNA extraction methods for ticks (Ixodes scapularis). Peerj. 3: e1147. PMID 26290800 DOI: 10.7717/peerj.1147  1
2015 Ganu RS, Ishida Y, Koutmos M, Kolokotronis SO, Roca AL, Garrow TA, Schook LB. Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes. Plos One. 10: e0134084. PMID 26213999 DOI: 10.1371/journal.pone.0134084  1
2015 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, et al. Parallel Epidemics of Community-Associated Methicillin-Resistant Staphylococcus aureus USA300 Infection in North and South America. The Journal of Infectious Diseases. PMID 26048971 DOI: 10.1093/infdis/jiv320  1
2015 Dowell SA, de Buffrénil V, Kolokotronis SO, Hekkala ER. Fine-scale genetic analysis of the exploited Nile monitor (Varanus niloticus) in Sahelian Africa. Bmc Genetics. 16: 32. PMID 25884730 DOI: 10.1186/s12863-015-0188-x  1
2015 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, et al. Evolution of the indoor biome. Trends in Ecology & Evolution. 30: 223-32. PMID 25770744 DOI: 10.1016/j.tree.2015.02.001  1
2015 DeSalle R, Kolokotronis SO. Changes in the Mitogenome Announcement manuscript category. Mitochondrial Dna. 26: 1. PMID 25693712 DOI: 10.3109/19401736.2015.1013392  1
2015 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, ... ... Kolokotronis SO, et al. Modern Methods for Delineating Metagenomic Complexity Cell Systems. 1: 6-7. DOI: 10.1016/j.cels.2015.07.007  1
2015 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, ... ... Kolokotronis SO, et al. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Cell Systems. 1: 72-87. DOI: 10.1016/j.cels.2015.01.001  1
2014 Tsangaras K, Kolokotronis SO, Ulrich RG, Morand S, Michaux J, Greenwood AD. Negative purifying selection drives prion and doppel protein evolution. Journal of Molecular Evolution. 79: 12-20. PMID 25038839 DOI: 10.1007/s00239-014-9632-1  1
2014 Leite RN, Kolokotronis SO, Almeida FC, Werneck FP, Rogers DS, Weksler M. In the wake of invasion: tracing the historical biogeography of the South American cricetid radiation (Rodentia, Sigmodontinae). Plos One. 9: e100687. PMID 24963664 DOI: 10.1371/journal.pone.0100687  1
2014 Benson MA, Ohneck EA, Ryan C, Alonzo F, Smith H, Narechania A, Kolokotronis SO, Satola SW, Uhlemann AC, Sebra R, Deikus G, Shopsin B, Planet PJ, Torres VJ. Evolution of hypervirulence by a MRSA clone through acquisition of a transposable element. Molecular Microbiology. 93: 664-81. PMID 24962815 DOI: 10.1111/mmi.12682  1
2014 Librado P, Vieira FG, Sánchez-Gracia A, Kolokotronis SO, Rozas J. 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: 1454-65. PMID 24904011 DOI: 10.1093/gbe/evu117  1
2014 Scheel DM, Slater GJ, Kolokotronis SO, Potter CW, Rotstein DS, Tsangaras K, Greenwood AD, Helgen KM. Biogeography and taxonomy of extinct and endangered monk seals illuminated by ancient DNA and skull morphology. Zookeys. 1-33. PMID 24899841 DOI: 10.3897/zookeys.409.6244  1
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. 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: e00889-13. PMID 24345744 DOI: 10.1128/mBio.00889-13  1
2013 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, et al. 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: 5936-48. PMID 24268046 DOI: 10.1111/mec.12535  1
2012 Piaggio AJ, Shriner SA, VanDalen KK, Franklin AB, Anderson TD, Kolokotronis SO. Molecular surveillance of low pathogenic avian influenza viruses in wild birds across the United States: inferences from the hemagglutinin gene. Plos One. 7: e50834. PMID 23226543 DOI: 10.1371/journal.pone.0050834  1
2012 Doukakis P, Pikitch EK, Rothschild A, DeSalle R, Amato G, Kolokotronis SO. Testing the effectiveness of an international conservation agreement: marketplace forensics and CITES caviar trade regulation. Plos One. 7: e40907. PMID 22848410 DOI: 10.1371/journal.pone.0040907  1
2012 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, et al. Zoonotic viruses associated with illegally imported wildlife products. Plos One. 7: e29505. PMID 22253731 DOI: 10.1371/journal.pone.0029505  1
2012 Narechania A, Baker RH, Sit R, Kolokotronis SO, DeSalle R, Planet PJ. 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: 30-43. PMID 22094860 DOI: 10.1093/gbe/evr121  1
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. A functional phylogenomic view of the seed plants. Plos Genetics. 7: e1002411. PMID 22194700 DOI: 10.1371/journal.pgen.1002411  1
2011 Hanner R, Desalle R, Ward RD, Kolokotronis SO. The Fish Barcode of Life (FISH-BOL) special issue. Mitochondrial Dna. 22: 1-2. PMID 21980984 DOI: 10.3109/19401736.2011.598767  1
2011 Ishida Y, Oleksyk TK, Georgiadis NJ, David VA, Zhao K, Stephens RM, Kolokotronis SO, Roca AL. Reconciling apparent conflicts between mitochondrial and nuclear phylogenies in African elephants. Plos One. 6: e20642. PMID 21701575 DOI: 10.1371/journal.pone.0020642  1
2011 Ho SY, Lanfear R, Phillips MJ, Barnes I, Thomas JA, Kolokotronis SO, Shapiro B. Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Systematic Biology. 60: 366-75. PMID 21296909 DOI: 10.1093/sysbio/syq099  1
2010 Engstrand RC, Cibrián Tovar J, Cibrián-Jaramillo A, Kolokotronis SO. Genetic variation in avocado stem weevils Copturus aguacatae (Coleoptera: Curculionidae) in Mexico. Mitochondrial Dna. 21: 38-43. PMID 21271857 DOI: 10.3109/19401736.2010.536226  1
2010 Escalante P, Desalle R, Kolokotronis SO. The MexBOL initiative. Mitochondrial Dna. 21: 1-2. PMID 21271851 DOI: 10.3109/19401736.2010.551715  1
2010 Polani S, Roca AL, Rosensteel BB, Kolokotronis SO, Bar-Gal GK. Evolutionary dynamics of endogenous feline leukemia virus proliferation among species of the domestic cat lineage. Virology. 405: 397-407. PMID 20615520 DOI: 10.1016/j.virol.2010.06.010  1
2010 Lowenstein JH, Burger J, Jeitner CW, Amato G, Kolokotronis SO, Gochfeld M. DNA barcodes reveal species-specific mercury levels in tuna sushi that pose a health risk to consumers. Biology Letters. 6: 692-5. PMID 20410032 DOI: 10.1098/rsbl.2010.0156  1
2010 Eaton MJ, Meyers GL, Kolokotronis SO, Leslie MS, Martin AP, Amato G. Barcoding bushmeat: Molecular identification of Central African and South American harvested vertebrates Conservation Genetics. 11: 1389-1404. DOI: 10.1007/s10592-009-9967-0  1
2010 da Silva AG, Kolokotronis SO, Wharton D. Modeling the eradication of invasive mammals using the sterile male technique Biological Invasions. 12: 751-759. DOI: 10.1007/s10530-009-9477-5  1
2009 Piaggio AJ, Clark L, Franklin AB, Kolokotronis SO. Wild bird's-eye view of influenza virus A(H1N1) phylogenetic evolution. Ecohealth. 6: 346-50. PMID 20458519 DOI: 10.1007/s10393-009-0270-9  1
2009 Lowenstein JH, Amato G, Kolokotronis SO. The real maccoyii: identifying tuna sushi with DNA barcodes--contrasting characteristic attributes and genetic distances. Plos One. 4: e7866. PMID 19924239 DOI: 10.1371/journal.pone.0007866  1
2009 Schierwater B, Kolokotronis SO, Eitel M, DeSalle R. The Diploblast-Bilateria Sister hypothesis: parallel revolution of a nervous systems may have been a simple step. Communicative & Integrative Biology. 2: 403-5. PMID 19907700  1
2009 Roca AL, Ishida Y, Nikolaidis N, Kolokotronis SO, Fratpietro S, Stewardson K, Hensley S, Tisdale M, Boeskorov G, Greenwood AD. Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth. Bmc Evolutionary Biology. 9: 232. PMID 19747392 DOI: 10.1186/1471-2148-9-232  1
2009 de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R. The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. Plos One. 4: e5764. PMID 19503618 DOI: 10.1371/journal.pone.0005764  1
2009 Schierwater B, Eitel M, Jakob W, Osigus HJ, Hadrys H, Dellaporta SL, Kolokotronis SO, Desalle R. Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis. Plos Biology. 7: e20. PMID 19175291 DOI: 10.1371/journal.pbio.1000020  1
2009 Schierwater B, Kolokotronis SO, Eitel M, DeSalle R. The Diploblast-Bilateria Sister hypothesis: Parallel evolution of a nervous systems may have been a simple step Communicative and Integrative Biology. 2: 403-405. DOI: 10.4161/cib.2.5.8763  1
2008 Wyatt KB, Campos PF, Gilbert MT, Kolokotronis SO, Hynes WH, DeSalle R, Ball SJ, Daszak P, MacPhee RD, Greenwood AD. Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease. Plos One. 3: e3602. PMID 18985148 DOI: 10.1371/journal.pone.0003602  1
2008 Krause J, Unger T, Noçon A, Malaspinas AS, Kolokotronis SO, Stiller M, Soibelzon L, Spriggs H, Dear PH, Briggs AW, Bray SC, O'Brien SJ, Rabeder G, Matheus P, Cooper A, et al. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. Bmc Evolutionary Biology. 8: 220. PMID 18662376 DOI: 10.1186/1471-2148-8-220  1
2008 Baillie GJ, Kolokotronis SO, Waltari E, Maffei JG, Kramer LD, Perkins SL. Phylogenetic and evolutionary analyses of St. Louis encephalitis virus genomes. Molecular Phylogenetics and Evolution. 47: 717-28. PMID 18374605 DOI: 10.1016/j.ympev.2008.02.015  1
2007 Ho SY, Kolokotronis SO, Allaby RG. Elevated substitution rates estimated from ancient DNA sequences. Biology Letters. 3: 702-5. PMID 17785261 DOI: 10.1098/rsbl.2007.0377  1
2007 Kolokotronis SO, Macphee RD, Greenwood AD. Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen. Bmc Evolutionary Biology. 7: 67. PMID 17466066 DOI: 10.1186/1471-2148-7-67  1
2003 Shykoff JA, Kolokotronis SO, Collin CL, López-Villavicencio M. Effects of male sterility on reproductive traits in gynodioecious plants: a meta-analysis. Oecologia. 135: 1-9. PMID 12647098 DOI: 10.1007/s00442-002-1133-z  1
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