2019
*Newhouse, D.J., M.B. Serra, E.A. Tuttle, R. Gonser and C.N. Balakrishnan. Parent and offspring genotypes influence gene expression in early life. In press at Molecular Ecology (preprint available: bioRxiv 488684)
Kernbach, M.E., D.J. Newhouse*, J.M. Miller, R.J. Hall, J. Gibbons, J. Oberstaller, D. Selechnik, R. Jiang, T.R. Unnasch, C.N. Balakrishnan and L.B. Martin. 2019. Light pollution increases West Nile virus competence of a ubiquitous passerine reservoir species. Proceedings of the Royal Society, Series B. 286: 20191051.
*Lansverk, A.L., K. Schroeder*,. S.E. London, S.C. Griffith, D.F. Clayton and C.N. Balakrishnan. 2019. The variability of song variability in wild and domesticated zebra finches Taeniopygia guttata. Royal Society Open Science 6: 190273.
Louder, M.I.M, S. Lawson, K.S. Lynch, C.N. Balakrishnan and M.E. Hauber. 2019. Neural mechanisms of auditory species recognition in birds. Online Early, Biological Reviews.
Louder M.I.M and C.N. Balakrishnan. 2019.”Transcriptome” entry in the Encyclopedia of Animal Cognition and Behavior (J. Vonk and T.K. Shackelford, eds.), Springer Nature Switzerland.
Horton, B.H., T.B. Ryder, I.T. Moore and C.N. Balakrishnan. 2019. Gene expression in the social behavior network of the wire‐tailed manakin (Pipra filicauda) brain. Genes, Brains and Behavior, e12560.
Lynch, K.S., L.A. O’Connell, M.I.M. Louder, C.N. Balakrishnan and E.K. Fisher. 2019. Understanding the loss of maternal care in avian brood parasites using preoptic area transcriptome comparisons in brood parasitic and non-parasitic blackbirds. G3: Genes, Genomes & Genetics 4, 1075-1084
Kernbach, M.E., D.J. Newhouse*, J.M. Miller, R.J. Hall, J. Gibbons, J. Oberstaller, D. Selechnik, R. Jiang, T.R. Unnasch, C.N. Balakrishnan and L.B. Martin. 2019. Light pollution increases West Nile virus competence of a ubiquitous passerine reservoir species. Proceedings of the Royal Society, Series B. 286: 20191051.
*Lansverk, A.L., K. Schroeder*,. S.E. London, S.C. Griffith, D.F. Clayton and C.N. Balakrishnan. 2019. The variability of song variability in wild and domesticated zebra finches Taeniopygia guttata. Royal Society Open Science 6: 190273.
Louder, M.I.M, S. Lawson, K.S. Lynch, C.N. Balakrishnan and M.E. Hauber. 2019. Neural mechanisms of auditory species recognition in birds. Online Early, Biological Reviews.
Louder M.I.M and C.N. Balakrishnan. 2019.”Transcriptome” entry in the Encyclopedia of Animal Cognition and Behavior (J. Vonk and T.K. Shackelford, eds.), Springer Nature Switzerland.
Horton, B.H., T.B. Ryder, I.T. Moore and C.N. Balakrishnan. 2019. Gene expression in the social behavior network of the wire‐tailed manakin (Pipra filicauda) brain. Genes, Brains and Behavior, e12560.
Lynch, K.S., L.A. O’Connell, M.I.M. Louder, C.N. Balakrishnan and E.K. Fisher. 2019. Understanding the loss of maternal care in avian brood parasites using preoptic area transcriptome comparisons in brood parasitic and non-parasitic blackbirds. G3: Genes, Genomes & Genetics 4, 1075-1084
2018
Hofmeister E.K., C.N. Balakrishnan & C.T. Atkinson. Population differences in susceptibility to Plasmodium relictum in zebra finches Taeniopygia guttata. Avian Diseases, Online Early.
Louder, M.I.M., M.E. Hauber & C.N. Balakrishnan Early social experience modulates transcriptomic responses to species-specific song stimuli in female songbirds. Behavioural Brain Research 347: 69-76.
M. Kopp, M.S. Servedio, T.C. Mendelson, R.J. Safran, R.L. Rodriguez, E.C. Scordato, L.B. Symes, C.N. Balakrishnan, M.E. Hauber, D.M. Zonana, G.S. van Doorn. 2018. Mechanisms of assortative mating in speciation: connecting theory and empirical research. The American Naturalist 191(1).
Louder, M.I.M., M.E. Hauber & C.N. Balakrishnan Early social experience modulates transcriptomic responses to species-specific song stimuli in female songbirds. Behavioural Brain Research 347: 69-76.
M. Kopp, M.S. Servedio, T.C. Mendelson, R.J. Safran, R.L. Rodriguez, E.C. Scordato, L.B. Symes, C.N. Balakrishnan, M.E. Hauber, D.M. Zonana, G.S. van Doorn. 2018. Mechanisms of assortative mating in speciation: connecting theory and empirical research. The American Naturalist 191(1).
2017
*Newhouse, D.J., E. Hofmeister & C.N. Balakrishnan. Transcriptional response to West Nile Virus infection in the zebra finch, a songbird model for immunity. Royal Society Open Science 4: 170296.
Hofmeister, E., M. Lund, V. Shearn-Boschler & C.N. Balakrishnan. Susceptibility and antibody response of the laboratory model zebra finch (Taeniopygia guttata) to West Nile virus. PLoS One 12(1): e0167876.2016
2016
*Davidson, J.D. & C.N. Balakrishnan. 2016. Gene regulatory divergence during speciation in a songbird. G3: Genes, Genomes & Genetics 6:1357-1364
Louder, M.I.M., H.U. Voss, T.J. Manna, S.S. Carryl, S.E. London, C.N. Balakrishnan & M.E. Hauber. 2016. Shared neural substrates of species recognition in parental and brood parasitic songbirds.. Neuroscience Letters 622: 49-54.
Hebets, E.A., A.B. Barron, C.N. Balakrishnan, M.E. Hauber, P.H. Mason & K.L. Hoke. 2016. A systems approach to animal signaling. Proceeding of the Royal Society B 283(1826): 20152889
Tuttle, E.A., A.O. Bergland, M.S. Brewer, D.J. Newhouse*, Z.C. Cheviron, M. Stager. W.C. Warren, R. Gonser, C.N. Balakrishnan. 2016. Divergence and functional degradation of a sex chromosome-like supergene. Current Biology 26(3):344-350.
Toews, D.P.L, L.Campagna, S.A. Taylor, C.N. Balakrishnan, D.T. Baldassarre, P.E. Deane-Coe, M.G. Harvey, D.M. Hooper, D.E. Irwin, C.D. Judy, N. A. Mason, J.E. McCormack, K.G. McCracken, C.H. Oliveros, R.J. Safran, E.S.C. Scordato, K. Faust Stryjewski, A.Tigano, J.A.C. Uy & B.M. Winger. 2016. Genomic approaches to understanding population divergence and speciation in birds. The Auk: Ornithological Advances. 133: 13-30.
2016
*Davidson, J.D. & C.N. Balakrishnan. 2016. Gene regulatory divergence during speciation in a songbird. G3: Genes, Genomes & Genetics 6:1357-1364
Louder, M.I.M., H.U. Voss, T.J. Manna, S.S. Carryl, S.E. London, C.N. Balakrishnan & M.E. Hauber. 2016. Shared neural substrates of species recognition in parental and brood parasitic songbirds.. Neuroscience Letters 622: 49-54.
Hebets, E.A., A.B. Barron, C.N. Balakrishnan, M.E. Hauber, P.H. Mason & K.L. Hoke. 2016. A systems approach to animal signaling. Proceeding of the Royal Society B 283(1826): 20152889
Tuttle, E.A., A.O. Bergland, M.S. Brewer, D.J. Newhouse*, Z.C. Cheviron, M. Stager. W.C. Warren, R. Gonser, C.N. Balakrishnan. 2016. Divergence and functional degradation of a sex chromosome-like supergene. Current Biology 26(3):344-350.
Toews, D.P.L, L.Campagna, S.A. Taylor, C.N. Balakrishnan, D.T. Baldassarre, P.E. Deane-Coe, M.G. Harvey, D.M. Hooper, D.E. Irwin, C.D. Judy, N. A. Mason, J.E. McCormack, K.G. McCracken, C.H. Oliveros, R.J. Safran, E.S.C. Scordato, K. Faust Stryjewski, A.Tigano, J.A.C. Uy & B.M. Winger. 2016. Genomic approaches to understanding population divergence and speciation in birds. The Auk: Ornithological Advances. 133: 13-30.
2015
*Lansverk, A.L, J.B. Dongmo, J.C. Schuetz & C.N. Balakrishnan. 2015.Parasitism of the black-crowned waxbill Estrilda nonnula by pin-tailed whydahs Vidua macroura: implications for coevolution. Wilson Journal of Ornithology 127(4):733-739.
*Newhouse, D.J. & C.N. Balakrishnan. 2015. High MHC diversity despite bottlenecks in wild and domesticated zebra finches. BMC Evolutionary Biology 15:256.
Singhal, S. E.M. Leffler, K. Sannareddy, I. Turner, O. Venn, D.M. Hooper, A.I. Strand, Q. Li, B. Raney, C.N. Balakrishnan, S.C. Griffith, G. McVean, M. Przeworski. 2015. Stable recombination hotspots in birds. Science 350: 928-932.
2014
Lin, Y., C.N. Balakrishnan & D.F. Clayton. 2014. Functional genomic analysis and neuroanatomical localization of mir-2954, a song responsive, sex-linked microRNA. Frontiers in Neuroscience 8:409.
Balakrishnan, C.N., M. Mukai, R.A. Gonser, J.C. Wingfield, S.E. London, E.M. Tuttle & D.F. Clayton. 2014. Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior. PeerJ: e396 -selected as PeerJ “Pick of the Year” 2015
Bade L.M, C.N. Balakrishnan, E.M. Pilgrim, S.B. McRae, J.J. Luczkovich. 2014. A genetic technique to identify the diet of cownose rays, Rhinoptera bonasus: analysis of shellfish prey items from North Carolina and Virginia. Environmental Biology of Fishes 97: 999-1012.
2013
Balakrishnan C.N., C. Chapus, M.S. Brewer,* & D.F. Clayton. 2013. Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome. Open Biology 3(9):130063. doi: 10.1098/rsob.130063
Balakrishnan, C.N., Y. Lin, D.F. Clayton. 2012. RNA-seq transcriptome analysis of male and female zebra finch cell lines. Genomics 100:363-369.
The Pre-ECU Era
Itoh, Y.K., Kampf, C.N. Balakrishnan and A.P. Arnold. 2011. Karyotypic polymorphism of the zebra finch Z chromosome. Chromosoma 120:255-264. doi: 10.1007/s00412-010-0308-3.
Janes D.E., C. Chapus, Y. Gondo, D.F. Clayton, S. Sinha, C. Blatti, M. Fujita, 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: 102-113.
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. Princeton, NJ.
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.
Warren et al. 2010 (C.N Balakrishnan; author 20 of 84). The genome of a songbird. Nature 464: 757-762.
Ekblom R., C.N. Balakrishnan, T. Burke, J. Slate. 2010. Digital gene expression analysis of the zebra finch genome. BMC Genomics 11: 219.
Balakrishnan, C.N, S.V. Edwards & D.F. Clayton. 2010. The zebra finch genome and avian genomics in the wild. Emu 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.
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.
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.
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., 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.
Balakrishnan, C.N. and M.D. Sorenson. 2007. Dispersal ecology versus host specialization as determinants of ectoparasite distribution in brood parasitic indigobirds and their estrildid finch hosts. Molecular Ecology 16: 217-229.
Balakrishnan, C.N. and M.D. Sorenson. 2006. Premating reproductive isolation among sympatric indigobird species and host races. Behavioral Ecology 17: 473-478.
Edwards, S.V., S.B. Kingan, J.D. Calkins, C.N. Balakrishnan, W.B. Jennings, W.J. Swanson, M.D. Sorenson. 2005. Speciation in birds: Genes, geography, and sexual selection. Proceedings of the National Academy of Sciences USA 102: 6550-6557.
Payne, R.B., C.R. Barlow, C.N. Balakrishnan, M.D. Sorenson. 2005. Song mimicry by brood-parasitic indigobirds Vidua camerunensis of Black-bellied Firefinch Lagonosticta rara and other finches in West Africa. Ibis 147: 130-143.
Sorenson M.D., C.N. Balakrishnan, and R.B. Payne. 2004. Clade-limited colonization in brood parasitic finches (Vidua spp.). Systematic Biology 53(1): 140-153.
Balakrishnan, C.N., S.L. Monfort, A. Gaur, L. Singh, M.D. Sorenson. 2003. Phylogeography and conservation genetics of the Eld’s deer (Cervus eldi). Molecular Ecology 12:1-10.
Ayyanathan, K., W. J. Fredericks, C. Berking, M. Herlyn, C. Balakrishnan, E. Gunter, F. J. Rauscher, III. 2000. Hormone-dependent tumor regression in vivo by an inducible transcriptional repressor directed at the PAX3-FKHR oncogene. Cancer Research 60 (20): 5803-5814.
Rauscher, F.J., J. F. Morris, W. J. Fredericks, J. L. Guisa, C. Balakrishnan, M. Jost, M. Heerlyn, and U. Rodeck. 1998. Characterization of monoclonal antibodies directed to the amino terminus of the WT-1 Wilms Tumor suppressor protein. Hybridoma 17: 191-197.
*Lansverk, A.L, J.B. Dongmo, J.C. Schuetz & C.N. Balakrishnan. 2015.Parasitism of the black-crowned waxbill Estrilda nonnula by pin-tailed whydahs Vidua macroura: implications for coevolution. Wilson Journal of Ornithology 127(4):733-739.
*Newhouse, D.J. & C.N. Balakrishnan. 2015. High MHC diversity despite bottlenecks in wild and domesticated zebra finches. BMC Evolutionary Biology 15:256.
Singhal, S. E.M. Leffler, K. Sannareddy, I. Turner, O. Venn, D.M. Hooper, A.I. Strand, Q. Li, B. Raney, C.N. Balakrishnan, S.C. Griffith, G. McVean, M. Przeworski. 2015. Stable recombination hotspots in birds. Science 350: 928-932.
2014
Lin, Y., C.N. Balakrishnan & D.F. Clayton. 2014. Functional genomic analysis and neuroanatomical localization of mir-2954, a song responsive, sex-linked microRNA. Frontiers in Neuroscience 8:409.
Balakrishnan, C.N., M. Mukai, R.A. Gonser, J.C. Wingfield, S.E. London, E.M. Tuttle & D.F. Clayton. 2014. Brain transcriptome sequencing and assembly of three songbird model systems for the study of social behavior. PeerJ: e396 -selected as PeerJ “Pick of the Year” 2015
Bade L.M, C.N. Balakrishnan, E.M. Pilgrim, S.B. McRae, J.J. Luczkovich. 2014. A genetic technique to identify the diet of cownose rays, Rhinoptera bonasus: analysis of shellfish prey items from North Carolina and Virginia. Environmental Biology of Fishes 97: 999-1012.
2013
Balakrishnan C.N., C. Chapus, M.S. Brewer,* & D.F. Clayton. 2013. Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome. Open Biology 3(9):130063. doi: 10.1098/rsob.130063
Balakrishnan, C.N., Y. Lin, D.F. Clayton. 2012. RNA-seq transcriptome analysis of male and female zebra finch cell lines. Genomics 100:363-369.
The Pre-ECU Era
Itoh, Y.K., Kampf, C.N. Balakrishnan and A.P. Arnold. 2011. Karyotypic polymorphism of the zebra finch Z chromosome. Chromosoma 120:255-264. doi: 10.1007/s00412-010-0308-3.
Janes D.E., C. Chapus, Y. Gondo, D.F. Clayton, S. Sinha, C. Blatti, M. Fujita, 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: 102-113.
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. Princeton, NJ.
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.
Warren et al. 2010 (C.N Balakrishnan; author 20 of 84). The genome of a songbird. Nature 464: 757-762.
Ekblom R., C.N. Balakrishnan, T. Burke, J. Slate. 2010. Digital gene expression analysis of the zebra finch genome. BMC Genomics 11: 219.
Balakrishnan, C.N, S.V. Edwards & D.F. Clayton. 2010. The zebra finch genome and avian genomics in the wild. Emu 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.
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.
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.
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., 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.
Balakrishnan, C.N. and M.D. Sorenson. 2007. Dispersal ecology versus host specialization as determinants of ectoparasite distribution in brood parasitic indigobirds and their estrildid finch hosts. Molecular Ecology 16: 217-229.
Balakrishnan, C.N. and M.D. Sorenson. 2006. Premating reproductive isolation among sympatric indigobird species and host races. Behavioral Ecology 17: 473-478.
Edwards, S.V., S.B. Kingan, J.D. Calkins, C.N. Balakrishnan, W.B. Jennings, W.J. Swanson, M.D. Sorenson. 2005. Speciation in birds: Genes, geography, and sexual selection. Proceedings of the National Academy of Sciences USA 102: 6550-6557.
Payne, R.B., C.R. Barlow, C.N. Balakrishnan, M.D. Sorenson. 2005. Song mimicry by brood-parasitic indigobirds Vidua camerunensis of Black-bellied Firefinch Lagonosticta rara and other finches in West Africa. Ibis 147: 130-143.
Sorenson M.D., C.N. Balakrishnan, and R.B. Payne. 2004. Clade-limited colonization in brood parasitic finches (Vidua spp.). Systematic Biology 53(1): 140-153.
Balakrishnan, C.N., S.L. Monfort, A. Gaur, L. Singh, M.D. Sorenson. 2003. Phylogeography and conservation genetics of the Eld’s deer (Cervus eldi). Molecular Ecology 12:1-10.
Ayyanathan, K., W. J. Fredericks, C. Berking, M. Herlyn, C. Balakrishnan, E. Gunter, F. J. Rauscher, III. 2000. Hormone-dependent tumor regression in vivo by an inducible transcriptional repressor directed at the PAX3-FKHR oncogene. Cancer Research 60 (20): 5803-5814.
Rauscher, F.J., J. F. Morris, W. J. Fredericks, J. L. Guisa, C. Balakrishnan, M. Jost, M. Heerlyn, and U. Rodeck. 1998. Characterization of monoclonal antibodies directed to the amino terminus of the WT-1 Wilms Tumor suppressor protein. Hybridoma 17: 191-197.
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