Publications
1992. Copia-like retrotransposons in plants: a brief introduction. The Plant Genetics NewsletterThe Plant Genetics Newsletter. 8
1991. Review of Fundamentals of Molecular Evolution, by Li. W.-H. and D. Graur. CladisticsCladistics. 7
1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol EvolMol Biol Evol. 12
1994. Slipped-strand mispairing in a plastid gene: ıt rpoC2 in grasses (Poaceae). Mol Biol EvolMol Biol Evol. 11
2004. A book like its cover –- The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny, Edited by M. Salemi and A.-M. Vandamme. Heredity. 93:234-235.
2013. AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite. Dictionary of Bioinformatics.
2005. Magic bullets and golden rules: data sampling in molecular phylogenetics. Zoology (Jena)Zoology (Jena). 108
2004. Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC BioinformaticsBMC Bioinformatics. 5
1994. Transmission patterns of eukaryotic transposable elements - arguments for and against horizontal transfer. Trends Ecol EvolTrends Ecol Evol. 9
2004. Few amino acid positions in ıt rpoB are associated with most of the rifampin resistance in ıt Mycobacterium tuberculosis. BMC BioinformaticsBMC Bioinformatics. 5
1998. Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (ıt Hordeum vulgare ssp. ıt spontaneum): an evaluation of the background selection hypothesis. Proc Natl Acad Sci USAProc Natl Acad Sci USA. 95
1997. Hardness of flip-cut problems from optical mapping. Journal of Computational BiologyJournal of Computational Biology. 4
2006. Procrastination leads to efficient filtration for local multiple alignment. International Workshop on Algorithms in Bioinformatics.
2007. Analyzing patterns of microbial evolution using the mauve genome alignment system. Comparative Genomics. :135–152.
2014. Developmental expression of chicken FOXN1 and putative target genes during feather development.. Int J Dev Biol. 58(1):57-64.
2015. Bayesian integration of genetics and epigenetics detects causal regulatory SNPs underlying expression variability. Nature Communications. 6:8555.
2016. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.. PLoS One. 11(9):e0160574.
2011. Population Dynamics of Vibrio Cholerae and Cholera in the Bangladesh Sundarbans: Role of Zooplankton Diversity. Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol..
2008. Environmental signatures associated with cholera epidemics. Proceedings of the National Academy of SciencesProceedings of the National Academy of Sciences. 105
2009. Predicting the distribution of Vibrio spp. in the Chesapeake Bay: a Vibrio cholerae case study. EcoHealthEcoHealth. 6