Christopher N. Balakrishnan

Title: Assistant Professor
Area of Study: Evolutionary and Behavioral Genomics
Phone: (252) 328-2910
Fax: (252) 328-4178
Website: Balakrishnan Lab Website
Office: N212B Howell Science Complex
Address: East Carolina University
Department of Biology
N212B Howell Science Complex
Mailstop 551
Greenville, NC 27858


Ph.D.: Biology, Boston University, 2005

B.A.: Biology, University of Pennsylvania 1997

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Research Interests:

Work in the Balakrishnan Lab is aimed at understanding how genes and the environment interact to generate biodiversity. By combining a historical perspective with functional and comparative genomics, we seek to uncover both the genomic basis of evolutionary adaptation and the ecological and demographic processes responsible for population divergence. Our work revolves around four central research themes:

Speciation Biology: We are interested in understanding both ecological and genomic aspects of the speciation process using birds as a model system. Indigobirds represent a remarkable case of sympatric speciation and the evolution of morphological mimicry.

Behavioral Genomics: The zebra finch has long been an important system for the study of behavior. We are expanding on this system, using the diversity of behavior displayed by birds. By combining a comparative evolutionary approach with modern genomic approaches we aim to learn more about how changes in the genome and gene regulation relate to behavioral variation.

Comparative Genomics: We use comparative genomic approaches to study the evolution of avian (and other) genomes. This includes detailed, targeted studies of genes and gene families of interest (for example, the MHC), and also genome-wide comparisons of rates and patterns of sequence evolution and gene duplication.

Phylogeography: To put patterns of behavioral and functional genomic change in an evolutionary context, it is essential to understand the timing and demography of divergence. We study patterns of divergence in African and Australian finches using modern multi-locus approaches.


Balakrishnan, C.N., Y. Lin, S.E. London, D.F. Clayton. 2012. RNA-seq transcriptome analysis of zebra finch cell lines. Genomics in press.

Itoh, Y., K. Kampf, C.N. Balakrishnan & A. P. Arnold. 2011. Karyoptypic polymorphism of the zebra finch Z chromosome. Chromosoma 120(3): 255-264

Janes, D. E., C. Chapus, Y. Gondo, D. F. Clayton, S. Sinha, C. Blatti, C.N. Balakrishnan and S.V. Edwards.2011 Reptiles and mammals have differentially retained long non-coding sequences from the amniote ancestor. Genome Biology and Evolution 3: 102- 13.

Balakrishnan, C.N., Lee, J. & S.V. Edwards. 2010. Phylogeography and phylogenetics in the nuclear age. Pp. 65-88. In: P.R. and B.R. Grant (eds.) In search of the causes of evolution: from field observations to mechanisms. Princeton University Press

Balakrishnan, C.N, S.V. Edwards & D.F. Clayton. 2010. The zebra finch genome and avian genomics in the wild. Emu Austral Ornithology 110: 233-241.

Nam, K. N., C. Mugal, B. Nabholz, H. Schielzerth , J. Wolf, N.Backström, A. Künstner, C.N. Balakrishnan, A. Heger,C. Ponting, D.F. Clayton and H. Ellegren. 2010. Comparative genomics and gene sequence evolution in birds. Genome Biology 11: R68.

Warren et al. 2010 (C.N Balakrishnan; author 20 of 84). The genome of a songbird. Nature 464: 757-762.

Balakrishnan, C.N., R. Ekblom, R. Godinez, M. Volker, H. Kotkiewicz, H. Westerdahl, D. Burt, T. Graves, D. Griffin, W. Warren and S.V. Edwards. 2010. Gene duplication and fragmentation of the songbird major histocompatibility complex (MHC). BMC Biology 8: 29.

Ekblom R., C.N. Balakrishnan, T. Burke, J. Slate. 2010. Digital gene expression analysis of the zebra finch genome. BMC Genomics 11: 219.

Künster, A., J.B. Wolf, N. Backström, O. Whitney, C.N. Balakrishnan, L. Day, S.V. Edwards, B.A. Schlinger, R.K. Wilson, E. Jarvis, W.C. Warren and H. Ellegren. 2010. Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species. Molecular Ecology 19: 266-276.

Clayton, D.F., C.N. Balakrishnan, & S.E. London. 2009. Integrating genomes, brain and behavior in the study of songbirds. Current Biology 19: R865-873.

Balakrishnan, C.N. & S.V. Edwards. 2009. Nucleotide variation, linkage disequilibrium and founder-facilitated speciation in wild populations of the zebra finch (Taeniopygia guttata). Genetics 181: 645-660.

Balakrishnan, C.N., K.M. Sefc & M.D. Sorenson. 2009. Incomplete reproductive isolation following host shift in brood parasitic indigobirds. Proceedings of the Royal Society, Series B 276: 219-228.

Courses Taught:

BIOL 4240/7240 Genome Evolution

BIOL 6992/6993 – Next Generation Sequencing Techniques and Analysis

Laboratory Personnel:


Allison Lansverk,
Ph.D. Student


Daniel Newhouse, 
Masters Student


Bin Luo, 
Laboratory Technician


Shaivya Pathak,