PDF 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. {New York Times (by Florence Fabricant)}

PDF 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. {Discover Magazine (by Carl Zimmer)} {Conservation Magazine} {TIME Science} {BBC News} {New York Times}

PDF 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 Biol Evol 4(1):30-43.

PDF 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. *equal contribution {press release} {New York Times} {NSF Science360} {Genome Technology}

PDF 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. {Audubon Magazine}

PDF 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 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.
{CBC News} {France24} {Yahoo! News}

PDF 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.
{npr} {BBC} {Scientific American} {GenomeWeb} {Conservation Magazine} {New Scientist}

PDF 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.
{Wall Street Journal} {Wired Science} {Slashdot} {Rockefeller BoL blog} {LiveScience} {Discovery News} {Yahoo! News}

PDF BMC Highly Accessed 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. {Suppl. Mat.}
{MSNBC} {Nature News} {LiveScience} {Discovery Channel News} {Wired Science} {GenomeWeb} {ScienceDaily} {ScientificBlogging}

PDF Faculty 1000 Factor 6.0 Must Read 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. {Suppl. Mat.}
{ScienceNOW} {Discovery Channel News} {ScienceDaily}

PDF BMC Highly Accessed 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. {Suppl. Mat.}
{Science News}

PDF 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.
{ScienceDaily} {Genome Technology}

PDF Ho SYW, Kolokotronis SO, Allaby RG. (2007) Elevated substitution rates estimated from ancient DNA sequences. Biology Letters 3(6):702-705. {Suppl. Mat.}

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.

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.

PDF 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.


Gymnosperm and monocot clades from BigPlant v1.0 ML tree - Fig. 1 from PLoS Genetics paper

publication: Seed plant phylogenomics @ PLoS Genetics.   Read more

conference: Health & Environment @ AMNH.   Read more

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