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The list below contains publications of research performed by current Biology Department Graduate Students while at Penn State.  Graduate student authors are noted in bold.


  • Duarte J, Wall PK, Leebens-Mack JH, and dePamphilis CW. 2007. Utility of Amborella trichopoda and Nuphar advena ESTs for phylogeny and comparative sequence analysis. Taxon. In press.
  • Dunham E, and Holmes E. 2007. Inferring the timescale of dengue virus evolution under realistic models of DNA substitution. J. Molec. Evol. 64: 656-661.
  • Rhesus Macaque Genome Sequencing and Analysis Consortium (Addo-Quaye C). 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 316: 222-234.
  • Hedges SB, and Heinicke MP. 2007. Molecular phylogeny and biogeography of West Indian frogs of the genus Leptodactylus (Anura, Leptodactylidae). Mol. Phylogenet. Evol. 44: 308.
  • Heinicke MP, Duellman WE, and Hedges SB. 2007. Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal. Proc. Natl. Acad. Sci. U.S.A. 104: 10092-10097.
  • Hou M, Berman, P, Hsu CH and Harris RS. 2007. HomologMiner: looking for homologous genomic groups in whole genomes. Bioinformatics 23:917-925.
  • Kvikstad EM, Tyekucheva S, Chiaromonte F, and Makova KD. 2007 A macaque’s-eye view of human insertions and deletions: differences in mechanisms. PLoS Comp Bio 3: e176.
  • Li X, Wang X-J, Tannenhauser J, Podell S, Mukherjee P, Hertel M, Biane J, Masuda S, Nottebohm F, and Gaasterland T. 2007. Genomic resources for songbird research and their use in characterizing gene expression during brain development. Proc. Natl. Acad. Sci. U.S.A. 104: 6834-6839.
  • McSteen P, Malcomber S, Skirpan A, Lunde C, Wu X, Kellogg E, and Hake S. 2007. barren inflorescence2 encodes a co-ortholog of the PINOID serine/threonine kinase and is required for organogenesis during inflorescence and vegetative development in maize. Plant Physiol. 144: 1000-1011.
  • Meisel R, and Scheaffer S. 2007. Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements. PLoS ONE. 2: e530.
  • Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B,  Burhans R, King DC, Baertsch R, Blankenberg D, Pond SLK, Nekrutenko A, Giardine B, Harris RSTyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 2007. 28-Way Vertebrate Alignment and Conservation Track in the UCSC Genome Browser. Genome Research In Press.
  • Nelson MI, and Holmes EC. 2007. The evolution of epidemic influenza. Nat Rev Genet. 8: 196-205.
  • Nelson MI, Simonsen L, Viboud C, Miller MA, and Holmes EC. 2007. Phylogenetic analysis reveals the global migration of seasonal influenza A viruses.  PLoS Pathogens. In press.
  • Nikolaidis N, Chalkia D, Watkins DN, Barrow RK, Snyder SH, van Rossum DB, and Patterson RL. 2007. Ancient origin of the new developmental superfamily DANGER. PLoS ONE. 2: e204.
  • Nilson SE, and Assmann SM. 2007. The control of transpiration. Insights from Arabidopsis. Plant Physiol. 143: 19-27.
  • Savtchouk IA, Mattie FJ, and Ollis AA. 2007. Ceramide: from embryos to tumors. Sci. STKE. 2007: jc1.
  • Sun L and Liu SJ. 2007. Activation of extrasynaptic NMDA receptors induces a PKC-dependent switch in AMPA receptor subtypes in mouse cerebellar stellate cells. J. Physiol. 583: 537-553.
  • Sun Y, Zhou X, and Ma H. 2007. Genome-wide analysis of Kelch repeat-containing F-box family. J. Integr. Plant Biol. 49: 940-952.
  • Zhou Y, and Holmes EC. 2007. Bayesian estimates of the evolutionary rate and age of hepatitis B virus. J. Molec. Evol. In press.



  • Akashi H, Ko W-Y, Piao S, John A, Goel P, Lin C-F, and Vitins AP. 2006. Molecular evolution in the Drosophila melanogaster species subgroup: frequent parameter fluctuations on the timescale of molecular divergence. Genetics. 172: 1711-1726.
  • Braun DM, Ma Y, Inada N, Muszynski MG, and Baker RF. 2006. tie-dyed1 regulates carbohydrate accumulation in maize leaves. Plant Physiol. 142: 1511-1522.
  • Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, and Makova KD. 2006. Genomic environment predicts expression patterns on the human inactive X chromosome. PLoS Genetics. 2: e151.
  • Chen R, and Holmes EC. 2006. Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol. 23: 2336-2341.
  • Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, and dePamphilis CW. 2006. ChloroplastDB: the chloroplast genome database. Nucl. Acids Res. 34: D692-696.
  • Dobson A, Cattadori I, Holt RD, Ostfeld RS, Keesing F, Krichbaum K, Rohr JR, Perkins SE, and Hudson PJ. 2006. Sacred cows and sympathetic squirrels: the importance of biological diversity to human health. PLoS Medicine. 3: e231.
  • Duarte JM, Cui L, Wall PK, Zhang Q, Zhang X, Leebens-Mack J, Ma H, Altman N, and dePamphilis CW. 2006. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol. 23: 469-478.
  • Hedges SB, Battistuzzi FU, and Blair. JE. 2006. Molecular timescale of evolution in the Proterozoic. Pp. 199-229 in Neoproterozoic Geobiology and Paleobiology. S Xioa and AJ Kaufman, ed. Springer, New York.
  • Jiang M, and Chen G. 2006. High Ca2+-phosphate transfection efficiency in low-density neuronal cultures. Nat. Protocols. 1: 695-700.
  • Kim S, Soltis PS, Wall K, and Soltis DE. 2006. Phylogeny and domain evolution in the APETALA2-like gene family. Mol Biol Evol. 23: 107-120.
  • Li S, Assmann SM, and Albert R. 2006. Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling. PLoS Biology. 4: e312.
  • Lin Z, Kong H, Nei M, and Ma H. 2006. Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Proc. Natl. Acad. Sci. U.S.A. 103: 10328-10333.
  • Luis A, and Hudson P. 2006. Hibernation patterns in mammals: a role for bacterial growth? Functional Ecology. 20: 471-477.
  • Nelson MI, Simonsen L, Viboud C, Miller MA, Taylor J, George KS, Griesemer SB, Ghedin E, Sengamalay NA, Spiro DJ, Volkov I, Grenfell BT, Lipman DJ, Taubenberger JK, and Holmes EC. 2006. Stochastic processes are key determinants of short-term evolution in influenza A virus. PLoS Pathogens. 2: e125.
  • Qi J, Wang Y, Jiang M, Warren P, and Chen G. 2006. Cyclothiazide induces robust epileptiform activity in rat hippocampal neurons both in vitro and in vivo. J Physiol. 571: 605-618.
  • Riccardi A, Domagal-Goldman S, Battistuzzi FU, and Cameron V. 2006. Astrobiology influx or in flux? Astrobiology. 6: 397-399.
  • Zahn L, Feng B, and Ma. H. 2006. Beyond the ABC model: regulation of floral homeotic genes. Adv. Bot. Res. 44: 161-205.
  • Zhao D, Yang X, Quan L, Timofejeva L, Rigel N, Ma H, and Makaroff C. 2006. ASK1, a SKP1 homolog, is required for nuclear reorganization, presynaptic homolog juxtaposition and the proper distribution of cohesin during meiosis in Arabidopsis. Plant Mol. Biol. 62: 99-110.


  • Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Solow TM, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo MJ, Frohlich MW, Perl-Treves R, Schlarbaum SE, Bliss BJ, Zhang X, Tanksley SD, Oppenheimer DG, Soltis PS, Ma H, DePamphilis CW, and Leebens-Mack JH. 2005. Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol. 5: 5.
  • Lai Z-C, Wei X, Shimizu T, Ramos E, Rohrbaugh M, Nikolaidis N, Ho L-L, and Li Y. 2005. Control of cell proliferation and apoptosis by Mob as tumor suppressor, Mats. Cell. 120: 675-685.
  • Li W, Yang X, Lin Z, Timofejeva L, Xiao R, Makaroff CA, and Ma H. 2005. The AtRAD51C gene is required for normal meiotic chromosome synapsis and double-stranded break repair in Arabidopsis. Plant Physiol. 138: 965-976.
  • Makalowska I, Lin C-F, and Makalowski W. 2005. Overlapping genes in vertebrate genomes. Computational Biology and Chemistry. 29: 1-12.
  • Nikolaidis N, Makalowska I, Chalkia D, Makalowski W, Klein J, and Nei M. 2005. Origin and evolution of the chicken leukocyte receptor complex. Proc. Natl. Acad. Sci. U.S.A. 102: 4057-4062.
  • Pandey S, Perfus-Barbeoch L, Taylor J, and Zhao Z. 2005. Plant cell signaling: in vivo and -omics approaches. J. Plant Growth Regul. 24: 46-54.
  • Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, and Gibbs RA. 2005. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 15: 1-18.
  • Soltis DE, Albert V, Kim S, Yoo M, Soltis PS, Frohlich M, Leebens-Mack J, Kong H, Wall K, dePamphilis CW, and Ma H. 2005. Evolution of the flower in Diversity and Evolution of Plants: Genotypic and Phenotypic Variation in Higher Plants. R Henry, ed. CABI Publishers.
  • Waters JR, Van Meter P, Perrotti W, Drogo S, and Cyr RJ. 2005. Cat dissection vs. sculpting human structures in clay: an analysis of two approaches to undergraduate human anatomy laboratory education. Advan. Physiol. Edu. 29: 27-34.
  • Zhang X, Feng B, Zhang Q, Zhang D, Altman N, and Ma H. 2005. Genome-wide expression profiling and identification of gene activities during early flower development in Arabidopsis. Plant Mol. Biol. 58: 401-419.



  • Battistuzzi FU, Feijao A, and Hedges SB. 2004. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol. Biol. 4: 44.
  • Fan L-M, Zhao Z, and Assmann SM. 2004. Guard cells: a dynamic signaling model. Current Opinion in Plant Biology. 7: 537-546.
  • Jiang M, Deng L, and Chen G. 2004. High Ca(2+)-phosphate transfection efficiency enables single neuron gene analysis. Gene Ther. 11: 1303-1311.
  • Lewandowska D, Simpson CG, Clark GP, Jennings NS, Barciszewska-Pacak M, Lin C-F, Makalowski W, Brown JWS, and Jarmolowski A. 2004. Determinants of plant U12-dependent intron splicing efficiency. Plant Cell. 16: 1340-1352.
  • Ni W, Xie D, Hobbie L, Feng B, Zhao D, Akkara J, and Ma H. 2004. Regulation of flower development in Arabidopsis by SCF complexes. Plant Physiol. 134: 1574-1585.
  • Wang J-PZ, Lindsay BG, Leebens-Mack J, Cui L, Wall K, Miller WC, and dePamphilis CW. 2004. EST clustering error evaluation and correction. Bioinformatics. 20: 2973-2984.



  • Mahalingam R, Gomez-Buitrago A, Eckardt N, Shah N, Guevara-Garcia A, Day P, Raina R, and Fedoroff N. 2003. Characterizing the stress/defense transcriptome of Arabidopsis. Genome Biology. 4: R20.
  • Molbak L, Tett A, Ussery DW, Wall K, Turner S, Bailey M, and Field D. 2003. The plasmid genome database. Microbiology. 149: 3043-3045.
  • Zhao D, Ni W, Feng B, Han T, Petrasek MG, and Ma H. 2003. Members of the Arabidopsis-SKP1-like gene family exhibit a variety of expression patterns and may play diverse roles in Arabidopsis. Plant Physiol. 133: 203-217.