Publications

30. de Sanctis B., Krukov I., and APJ de Koning (2017). Allele age under non-classical assumptions is clarified by an exact computational Markov chain approach. Scientific Reports 7: 11869.
29.  Czeczko P., Greenway S., and APJ de Koning (2017). EzMap: a simple pipeline for reproducible analysis of the human virome. Bioinformatics 33(16):2573–2574.
28.  Krukov I.*, de Sanctis B.*, and APJ de Koning (2016). Wright–Fisher Exact Solver (WFES): scalable analysis of population genetic models without simulation or diffusion theory. Bioinformatics 33(9): 1416–1417.

27.  Castoe TA., de Koning APJ, et al. (2013). The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc. Natl. Acad. Sci. USA: Early Edition, Dec 2 2013.

Featured in the press: special News Feature in Science Magazine (Dec. 6, 2013 issue), Science NOW News, Huffington Post, etc.

26.  Vonk FJ, et al. (including de Koning APJ; 2013). The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc. Natl. Acad. Sci. USA: Early Edition, Dec 2 2013.

Featured in the press: special News Feature in Science Magazine (Dec. 6, 2013 issue), Science NOW News, Huffington Post, etc.



25.  Shaffer HB et al. (including de Koning APJ; 2013). The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineageGenome Biology (In Press).

Featured in the press: GenomeWeb, New Scientist, Los Angeles Times, CTV News, etc.

Featured in: S. Gilbert and I. Corfe (2013). "Turtle origins: Picking up Speed." Developmental Cell 25(4).
24.  Castoe, T.A., J.W. Streicher, J.M. Meik, M.J. Ingrasci, A.W. Poole, de Koning APJ, J.A. Campbell, C.L. Parkinson, E.N. Smith, and D.D. Pollock (2012). Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related speciesMolecular Ecology Resources 12(6): 1105-1113. 
23.  de Koning APJ, Gu W, Castoe TA, and DD Pollock (2012). Phylogenetics, Likelihood, Evolution, and Complexity (PLEX)Bioinformatics 28(22): 2989-2990. 
22.  Liberles D, Teichmann S, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell L, de Koning APJ, Dokholyan N, Echave J, Elofsson A, Gerloff D, Goldstein R, Grahnen J, Holder M, Lakner C, Lartillot N, Lovell S, Naylor G, Perica T, Pollock D, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel A, Thorne J, Thornton J, Weinreich D, and S Whelan (2012). The interface of protein structure, protein biophysics, and molecular evolution.  Protein Science 21(6):769-85. 

21.  St. John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Iguchi T, Bed'Hom B, Burgess SC, Cooksey AM, Castoe TA, Abzhanov A, Densmore LD, Venegas-Anya M, Greenwold MJ, Sawyer RH, Hoffmann FG, Crawford NG, Drew JC, Edwards SV, Fujita MK, Howard JM, Faircloth BC, Janes DE, Khan SY, Kohno S, de Koning APJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Schmidt CJ, Triplett EW, Tuberville TD, Jarvis ED, Guillette Jr LJ, Glenn TC, Green RE and DA Ray (2012). Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotesGenome Biology v13: 415.

Featured in the press: RedOrbit
 
20.  Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Streicher JW, Smith EN, and DD Pollock (2012).  Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.  PLoS ONE 7(2): e30953. 

19.  de Koning APJ, Gu W, Castoe TA, Batzer MA, and DD Pollock (2011). Repetitive elements may comprise over two-thirds of the human genome.  PLoS Genetics 7(12): e1002384.

Featured in: D Burgess (2012).  “Genomics: repetitive elements under-estimated?”  Nature Reviews in Genetics 13(74). 
18.  Castoe TA, Fox SE, de Koning APJ, Poole AW, Daza JM, Smith EN, Mockler T, Secor SM and DD Pollock (2011).  A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus)BMC Research Notes 4: 310. 
17.  Pollock DD, de Koning APJ, Kim H, Castoe TA, Churchill M, and K Kechris (2011).  Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS ONE v6(11): e26105. 

16.  Castoe TA, de Koning APJ, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor S, and DD Pollock (2011).  Sequencing the genome of the Burmese python (Python molurus bivittatus) - a model for studying extreme adaptations in snakes.  Genome Biology 12(7): 406.

Featured in the press:  PBS Newshour, Scientific American blog, New Scientist

 

15.  Castoe TA, Hall KT, Guibotsy Mboulas ML, Gu W, de Koning APJ, Fox SE, Poole AW, Vemulapalli V, Daza JM, Mockler T, Smith EN, Feschotte C, Pollock DD (2011).  Discovery of highly divergent repeat landscapes in snake genomes using high throughput sequencing.  Genome Biol Evol. 2011 May 13. [Epub ahead of print]. 

14.  de Koning APJ, Gu W, and DD Pollock (2010).  Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories.  Molecular Biology and Evolution 27(2): 249-265. 
13.  Castoe TA, Gu W, de Koning APJ, Daza JM, Jiang ZZ, Parkinson CL, and DD Pollock (2010).  Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes.  Cytogenomics and Genome Research (Genomes of Reptiles, special issue) v127(2-4): 112-27. 
12.  Castoe TA, de Koning APJ, and DD Pollock (2010).  Adaptive molecular convergence: molecular evolution versus molecular phylogenetics.  Communicative and Integrative Biology 3(1):1-3. 
11.  Castoe TA, de Koning APJ, and DD Pollock (2010)  “Molecular structure and evolution of genomes”.  Chapter in Evolutionary Genomics and Systems Biology.  Gustavo Caetano-Anolles ed., Wiley & Sons. 
10.  Castoe TA, Poole AW, Gu W, de Koning APJ, Daza JM, Smith EN, and DD Pollock (2009).  Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.  Molecular Ecology Resources, published online 30 July 2009 (doi: 10.1111/j.1755-0998.2009.02750.x). 
9.   de Koning APJ, Gu W, and DD Pollock (2009)  Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference (erratum). Mol. Biol. Evol. 26:481. 

8.   Castoe TA★, de Koning APJ★, Kim H-K, Gu W, Noonan BP, Jiang ZJ, Naylor G, Parkinson CL, and DD Pollock (2009).  From the Cover:  Evidence for an ancient adaptive episode of convergent molecular evolutionProc. Natl. Acad. Sci. USA 2009 106:8986-8991; published online before print April 28, 2009.
★Shared primary authorship

Featured in: S. V. Edwards (2009) “Natural selection and phylogenetic analysis.” Proc. Natl. Acad. Sci. USA 2009 106:8799-8800.

 

7.   de Koning APJ (2007)  Experimental Design and the Detection of Adaptive Divergence in Phylogenetics and Genomics.  Doctoral dissertation, University at Albany, SUNY. 
6.   Bradley MD, Beach MB, de Koning APJ, Pratt TS, and R Osuna (2007)  Global effects of Fis on Escherichia coli gene expression during growth.  Microbiology 153: 2922-2940. 
5.   Krishnan NM, Seligmann H, Stewart C-B, de Koning APJ, and DD Pollock (2004)  Ancestral sequence reconstruction in primate mitochondrial DNA:  Compositional bias and effect on functional inference. Mol. Biol. Evol. 21(10): 1871-83. 
4.   Bidochka MJ, Kamp AM, Lavender TM, de Koning APJ, De Croos JN (2001)  Habitat association in two genetic groups of the insect-pathogenic fungus Metarhizium anisopliae: uncovering cryptic species? Applied and Environmental Microbiology 67(3):  1335-1342. 
3.   Bidochka MJ, de Koning APJ, St. Leger RJ  (2001)  Analysis of a genomic clone of hydrophobin (ssgA) from the entomopathogenic fungus Metarhizium anisopliae.  Mycological Research 105: 360-364. 
2.   Bidochka MJ, and de Koning APJ (2001)  Are teleomorphs really necessary?: modelling the potential effects of Muller's Ratchet on deuteromycetous entomopathogenic fungi. Mycological Research 105:  1014-1019. 
1.  Hickie B, Mackay D, and de Koning APJ (1999)  Lifetime pharmacokinetic model for hydrophobic contaminants in marine mammals.  Environmental Toxicology and Chemistry 18:  2622-2633.