Selected Publications
Colbourne JK, Eads BD, Shaw J, Bohuski E, Bauer D, Andrews, J (2007) Sampling Daphnia’s expressed genes: preservation, expansion, and invention of crustacean genes with reference to insect genomes. BMC Genomics 8:217
Eads BD, Colbourne JK, Bohuski E, Andrews J (2007) Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex. BMC Genomics 8:464
Eads BD, Cash A, Bogart K, Costello J, Andrews J (2006) Microarray hybridization troubleshooting. Methods Enzymol 411:31-49.
Andrews J, Oliver B (2002) Sex determination signals control ovo-B transcription in Drosophila melanogaster germ cells. Genetics 160:537-545
Andrews, J, Bouffard GG, Cheadle C, Lü J, Becker K, Oliver B (2000) Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis. Genome Research 10:2030-2043
Andrews J, Garcia-Estefania D, Delon I, Lü J, Mével-Ninio M, Spierer A, Payre F, Pauli D, Oliver B (2000) OVO transcription factors function antagonistically in the Drosophila female germline. Development 127:881-982
Mehrotra S, Maqbool SB, Kolpakas A, Murnen K, Calvi BR (2008) Endocycling cells do not apoptose in response to DNA re-replication genotoxic stress. Genes & Development 22:3158-3171 [cover article]
Calvi BR, Byrnes BA, Kolpakas AJ (2007) Conservation of epigenetic regulation, ORC binding, and developmental timing of DNA replication origins in the genus Drosophila. Genetics 177:1291-1301
Clark et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218
Bandura JL, Beall E, Bell M, Silver H, Botchan M, Calvi BR (2005) humpty dumpty is required for developmental DNA amplification and cell proliferation in Drosophila. Current Biology 15: 755-759
Aggarwal BD, Calvi BR (2004) Chromatin regulates origin activity in Drosophila follicle cells. Nature 430: 372-376
Thomer M, May NR, Aggarwal BD, Kwok G, Calvi BR (2004) Drosophila double-parked is sufficient for re-replication during development and is regulated by Cyclin E / CDK2. Development 131(19): 4807-4818
Cherbas L, Cherbas P (2007) Transformation of Drosophila cell lines: an alternative approach to exogenous protein expression. Methods Mol Biol. 388:317-40
Brown HLD, Cherbas L, Cherbas P, Truman JW (2006) Use of time-lapse imaging and dominant negative receptors to dissect the steroid receptor control of neuronal remodeling in Drosophila. Development 133: 275-285
Badenhorst P, Xiao H, Cherbas L, Kwon SY, Voas M, Rebay I, Cherbas P, Wu C (2005) The Drosophila nucleosome remodeling factor NURF is required for ecdysteroid signaling and metamorphosis. Genes & Development 19: 2540-2545
Sedkov Y, Cho-Fertikh E, Petruk S, Cherbas L, Smith ST, Jones RS, Cherbas P, Canaani E, Jaynes JB, Mazo A (2003) Methylation at lysine 4 of histone H3 in ecdysone-dependent development of Drosophila. Nature 2003 426:78-83
Hu X, Cherbas L, Cherbas P (2003) Transcription activation by the ecdysone receptor (EcR/USP): identification of activation functions. Mol Endocrinol 17(4):716-31
Cherbas L, Hu X, Zhimulev I, Belyaeva E, Cherbas P(2003) EcR isoforms in Drosophila: testing tissue-specific requirements by targeted blockade and rescue. Development 130(2):271-84
Marygold, S.J., Roote, J., Reuter, G., Lambertsson, A., Ashburner, M., Millburn, G.H., Harrison, P.M., Yu, Z., Kenmochi, N., Kaufman, T.C., Leevers, S.J., Cook, K.R. (2007). The ribosomal protein genes and Minute loci of Drosophila melanogaster. Genome Biol. 8(10): R216 
Parks, A.L., Cook, K.R., Belvin, M., Dompe, N.A., Fawcett, R., Huppert, K., Tan, L.R., Winter, C.G., Bogart, K.P., Deal, J.E., Deal-Herr, M.E., Grant, D., Marcinko, M., Miyazaki, W.Y., Robertson, S., Shaw, K.J., Tabios, M., Vysotskaia, V., Zhao, L., Andrade, R.S., Edgar, K.A., Howie, E., Killpack, K., Milash, B., Norton, A., Thao, D., Whittaker, K., Winner, M.A., Friedman, L., Margolis, J., Singer, M.A., Kopczynski, C., Curtis, D., Kaufman, T.C., Plowman, G.D., Duyk, G., Francis-Lang, H.L. (2004). Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome. Nature Genetics 36(3): 288--292
Hahn MW, Kern AD (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Molecular Biology and Evolution 22:803-806
Hahn, MW (2006) Accurate inference and estimation in population genomics. Molecular Biology and Evolution 23:911-918
Begun DJ, Holloway AK, Stephens K, Hillier LW, Poh Y-P, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey C, Pachter L, Myers E, Langley CH (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biology 5:e310
Hahn MW, Han MV, Han S-G (2007) Gene family evolution across 12 Drosophila genomes. PLoS Genetics 3:e197
Drosophila Comparative Genome Sequencing and Analysis Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218
Nuzhdin SV, Tufts DM, Hahn MW (2008) Abundant genetic variation in transcript level during early Drosophila development. Evolution & Development 10:683-689
A. Stark, M. F. Lin, P. Kheradpour, J. S. Pedersen, L. Parts, J. W. Carlson, M. A. Crosby, M. D. Rasmussen, S. Roy, A. N. Deoras, J. G. Ruby, J. Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, E. Hodges, A. S. Hinrichs, A. Caspi, B. Paten, S.-W. Park, M. V. Han, M. L. Maeder, B. J. Polansky, B. E. Robson, S. Aerts, J. van Helden, B. Hassan, D. G. Gilbert, D. A. Eastman, Michael Rice, M. Weir, M. W. Hahn, Y. Park, C. N. Dewey, L. Pachter, W. J. Kent, D. Haussler, E. C. Lai, D. P. Bartel, G. J. Hannon, T. C. Kaufman, M. B. Eisen, A. G. Clark, D. Smith, S. E. Celniker, W. M. Gelbart and M. Kellis (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-32
Drosophila 12 Genomes Consortium* (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-18 * Project Leaders A. G. Clark, M. B. Eisen, D. R. Smith, C. M. Bergman, B. Oliver, T. A. Markow, T. C. Kaufman, M. Kellis and William Gelbart
Sowell RA, Hersberger KE, Kaufman TC, Clemmer DE (2007) Examining the Proteome of Drosophila across Organism Lifespan. J Proteome Res 6:3637-3647
Eisman R, Kaufman TC (2008) Cytological investigation of the mechanism of parthenogenesis in Drosophila mercatorum. FLY 1:317-329
Schaeffer, S. W., A. Bhutkar, B. F. McAllister, M. Matsuda, L. M. Matzkin, P. M. O' Grady, C. Rohde, V. L. S. Valente, M. Aguadé, W. W. Anderson, K. Edwards, A. C. L. Garcia, J. Goodman, J. Hartigan, E. Kataoka, R. T. Lapoint, E. R. Lozovsky, C. A. Machado, M. A. F. Noor, M. Papaceit, L. K. Reed, S. Richards, T. T. Rieger, S. M. Russo, H. Sato, C. Segarra, D. R. Smith, T. F. Smith, V. Strelets, Y. N. Tobari, Y. Tomimura, M. Wasserman, T. Watts, R. Wilson, K. Yoshida, T. A. Markow, W. M. Gelbart and T. C. Kaufman (2008) Polytene Chromosomal Maps of 11 Drosophila species: The order of genomic scaffolds inferred from genetic and physical maps. Genetics 179:1601-1655
Xun Z, Sowell RA, Kaufman TC, Clemmer DE (2008) Quantitative Proteomics of a Presymptomatic A53T -Synuclein Drosophila Model of Parkinson Disease. Mol Cell Proteomics 7:1191-1203
Kumar JP (2008) The molecular circuitry governing eye development in Drosophila. BBA (in press)
Kumar JP (2008) The Sine Oculis Homeobox (SIX) family of transcription factors as regulators of development and disease. Cellular and Molecular Life Sciences (in press)
Salzer CL, Kumar JP (2008) Position dependent responses to discontinuities in the retinal determination network. Developmental Biology (in press)
Yao JG, Weasner BM, Wang LH, Jang CC, Weasner BP, Tang CY, Salzer CS, Chen CH, Sun YH, Kumar JP (2008) Differential Requirements for the Pax6(5a) genes eyegone and twin of eyegone during eye development in Drosophila. Developmental Biology 315:535-551
Weasner BP, Salzer CL, Kumar JP (2007) Sine oculis, a member of the SIX family of transcription factors directs eye development. Developmental Biology 303:756-771
Anderson JL, Salzer CL, Kumar JP (2006) Regulation of the retinal determination gene, dachshund, in the embryonic head and developing eye of Drosophila. Developmental Biology 297:536-549
Matthews KA, Kaufman TC, Gelbart WM (2005) Research resources for Drosophila: the expanding universe. Nature Rev Genet 6(3): 179-193
Matthews KA (1994) Care and feeding of Drosophila melanogaster. In: Methods in Cell Biology 44: 13-32
Matthews KA, Rees D, Kaufman TC (1993) A functionally specialized alpha-tubulin is required for oocyte meiosis and cleavage mitoses in Drosophila. Development 117(3):977-991
Matthews KA, Miller DF, Kaufman TC (1990) Functional implications of the unusual spatial distribution of a minor alpha-tubulin isotype in Drosophila: a common thread among chordotonal ligaments, developing muscle, and testis cyst cells. Dev Biol 137(1):171-183
Matthews KA, Miller DF, Kaufman TC (1989) Developmental distribution of RNA and protein products of the Drosophila alpha-tubulin gene family. Dev Biol 132(1):45-61
Griswold A, Chang KT, Runko A, Knight M, Min K-T (2008) Sir2 mediates apoptosis through JNK-dependent pathway in Drosophila. Proc Natl Acad Sci USA105:8673-8678 
Chang KT, Min K-T (2005) Drosophila melanogaster homolog of Down Syndrome Critical Region 1 is critical for mitochondrial function. Nature Neuroscience8:1577-1585
Menzies F, Yenisetti S, Min K-T (2005) Roles of Drosophila DJ-1 in oxidative stress and survival of dopaminergic neurons. Current Biology 6:1578-1582
Chang KT, Shi YJ, Min K-T (2003) The Drosophila homolog of human Down’s Syndrome Critical Region 1 gene regulates learning: Implications for mental retardation. Proc Natl Acad Sci USA 100:15794-15799
Taylor JP, Taye AA, Campbell C, Kazemi-Esfarjani P, Fischbeck KH, Min K-T (2003) Aberrant histone acetylation, altered transcription, and retinal degeneration in a Drosophila model of polyglutamine disease are rescued by CREB-binding protein. Genes & Development 17:1463-1468
Pramatarova A, Ochalski PW, Chen K, Gropman A, Myers S, Min K-T, Howell BW (2003) Nck-b interacts with tyrosine phosphorylated disabled 1 and redistributes in reelin-stimulated neurons. Mol Cell Biol 23:7210-7221
Montooth KL, Abt DN, Hofmann JW, Rand DM (2008) Comparative genomics of the Drosophila mtDNA: variation in evolutionary rates across regulatory elements, oxidative phosphorylation complexes and lineages. Submitted to J Mol Evol
Montooth KL, Rand DM (2008) The Spectrum of Mitochondrial Mutation Differs across Species. PLoS Biol 6(8): e213
Drosophila Comparative Genome Sequencing and Analysis Consortium (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218
Meiklejohn CD, Montooth KL, Rand DM (2007) Positive and negative selection on the mitochondrial genome. Trends in Genetics 23(6): 259-263
Montooth KL, Siebenthall KT, Clark AG (2006) Membrane lipid physiology and toxin catabolism underlie ethanol and acetic acid tolerance in Drosophila melanogaster. J Exp Biol 209(19): 3837-3850
Montooth KL, Marden JH, Clark AG (2003) Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila. Genetics 165(2): 623-635
Sokol NS. An overview of the identification, detection, and functional analysis of Drosophila microRNAs. Methods in Molecular Biology (2008) 420:319-34
Sokol NS, Xu P, Jan Y-N, Ambros, V. Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. Genes and Development (2008); 22: 1591-6
Sokol NS, Ambros V. Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes and Development (2005) 19: 2343-2354
Sempere LF, Sokol NS, Dubrovsky EB, Berger EM, Ambros V. Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity. Developmental Biology (2003) 259:9-18
Zelhof, A.C., E. Koundakjian, A.L. Scully, R.W. Hardy, L. Pounds. (2003) Mutation of the photoreceptor specific homeodomain gene Pph13 results in defects in phototransduction and rhabdomere morphogenesis. Development. 130: 4393-4403
Zelhof, A.C. and R.W. Hardy. (2004) WASp is required for the correct temporal morphogenesis of rhabdomere microvilli. J. Cell Biology. 164(3): 417-426
Zelhof, A.C., R.W. Hardy, A. Becker, C. Zuker (2006) Transforming the architecture of compound eyes. Nature 443: 696-699.
Cook, B and A.C. Zelhof (2008) Photoreceptors in evolution and disease. Nature Genetics 40(11): 1275-1276