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Sergios-Orestis Kolokotronis, PhD

Assistant Professor

Department of Epidemiology and Biostatistics

Tel: (347) 557-1108 • Fax: (347) 557-1127


  • About
  • Publications
Academic Qualifications:
  • PhD: Columbia University
  • MPhil & MA: Columbia University
  • Adv. Certif. in Environmental Policy: Columbia University
  • BS: Université Paris-Sud XI
Background and Expertise:

Dr. Sergios-Orestis Kolokotronis is an Assistant Professor in the Department of Epidemiology and Biostatistics in the School of Public Health at SUNY Downstate Medical Center, Brooklyn, NY. Dr. Kolokotronis graduated from Université Paris-Sud XI (BS, Biology; Minor: Mathematical Biology) and Columbia University (MA/MPhil/PhD, Ecology & Evolutionary Biology). As a postdoctoral fellow at the American Museum of Natural History’s Sackler Institute for Comparative Genomics he researched the evolution through time of pathogens and their close relatives (funded by DARPA) and served as the Research Coordinator of the DNA Barcoding Initiative (funded by the Alfred P. Sloan Foundation). He applies evolutionary thinking to questions on the evolution and adaptation of microbial pathogens, their vectors, and reservoir species using genomics and bioinformatics. Organismal systems of interest include RNA viruses, Mycobacterium tuberculosis, MRSA, and eukaryotic parasites, such as malaria and trypanosomes. His latest interests include the microbial ecological context of pathogen transmission and persistence, e.g. microbiomes of ticks and urban birds, and how the urban and industrial environment intensifies natural selection for antibiotic, metal, and pollutant resistance of microbial communities (employing metagenomics). Before joining the SUNY Downstate community he was a faculty member at Fordham University and Barnard College, Columbia University, where he taught a variety of undergraduate and graduate courses and supervised students.

Google Scholar:
  • Kolokotronis SO, Foox J, Rosenfeld JA, Brugler MR, Reeves D, Benoit JB, Booth W, Robison G, Steffen M, Palli SR, Schal C, Richards S, Narechania A, Baker RH, Sorkin LN, Amato G, Mason CE, Siddall ME, DeSalle R, Sakas Z. (2016) The mitogenome of the bed bug Cimex lectularius (Hemiptera: Cimicidae). Mitochondrial DNA: Resources 1(1):425-427.
  • 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.
  • Alfano N, Kolokotronis SO, Tsangaras K, Roca AL, Xu W, Eiden MV, Greenwood AD. (2016) Episodic diversifying selection shaped the genomes of gibbon ape 1 leukemia virus and related gammaretroviruses. Journal of Virology 90(4):1757-1772.
  • 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.
  • 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.
  • 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.
  • Afshinnekoo E, et al. (2015) Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Systems 1:72-87. [interactive maps: PathoMap, Wall Street Journal]
  • 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.  *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.
  • 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.  *co-first authors
  • 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.
  • 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.
  • 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.