Publication List

2009

  1. Costello, J., Dalkilic, M., Beason, S., Gehlhausen, J., Patwardhan, R., Middha, S., Eads, B. and Andrews, J.
    Gene Networks in Drosophila melanogaster: Integrating Experimental Data to Predict Gene Function.
    Genome Biology 10(9): R97.
  2. Kijimoto, T., Rose, D., Costello, J., Tang, Z., Moczek, A. and Andrews, J.
    Expressed sequence tag resources and their application in horned beetles, an emerging model system in evolutionary developmental biology.
    BMC Genomics (In Review).

2008

  1. Eads, B., Schurko, A., and J. Logsdon.
    Meiosis genes in Daphnia pulex and the role of cyclical parthenogenesis in genome evolution.
    BMC Evol Biol 9: 78
  2. Costello, J., Cash, A., Dalkilic, M., and Andrews, J.
    Data Pushing: a Fly-centric guide to Bioinformatics tools
    Fly 2(1):1-18. 2008.

2007

  1. Drosophila Comparative Genome Sequencing and Analysis Consortium.
    Evolution of genes and genomes on the Drosophila phylogeny.
    Nature 450(7167):203-218. 2007.
  2. Eads, B. D., Bohuski, E., Colbourne, J., and Andrews, J.
    Profiling parthenogenetic and sex-biased gene expression in Daphnia pulex.
    BMC Genomics 8(1):464. 2007.
  3. Colbourne, J. K., Eads, B. D., Shaw, J., Bohuski, E., Bauer, D., and Andrews, J.
    Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes.
    BMC Genomics 8(1):217. 2007.
  4. Eads, B. D., Andrews, J., and Colbourne, J.
    Ecological genomics in Daphnia: stress responses and environmental sex determination.
    Heredity 100: 184-190. 2007.
  5. Moczek, A.P., Andrews, J., Kijimoto, T., Yerushalmi, Y., and Rose, D.
    Emerging model systems in evo-devo: horned beetles and the origins of diversity.
    Evolution and Development. 9(4):323-328. 2007.
  6. Costello, J., Buchannan-Carter, J., Dalkilic, M., and Andrews, J.
    Integrating Drosophila Data to Discover Disease-Related Protein Interactions in Human
    In Proceedings of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. 2007.

2006

  1. Costello, J., Dalkilic, M., Patwardhan, R., Middha, S., Eads, B., Colbourne, J., Hur, J., Mehta, K., and Andrews, J.
    Network Properties of a Gene Network Built from Drosophila melanogaster Data
    NetSci. 2006. (Short Paper)
  2. Cherbas, L, Bogart, K., Zhao, Y, Cherbas, P. and Andrews, J.
    DGRC-2: Spotted oligonucleotide transcriptome microarrays for the Drosophila community.
    CGB Technical Report 2006-01. The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana
  3. Costello, J. and Andrews, J.
    Re-Annotation of DGRC-1 Amplicon Microarrays from Drosophila melanogaster Annotation version 3.1 to version 4.1.
    CGB Technical Report 2006-06. The Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana
  4. Eads, B. D., Cash, A., Bogart, K., Costello, J., and Andrews, J.
    Microarray hybridization troubleshooting.
    Methods Enzymol. 411: 34-49. 2006.
  5. Burr, A., Bogart, K., Conaty, J. and Andrews, J.
    Automated liquid handling and high-throughput preparation of PCR amplified probes for microarray fabrication.
    Methods in Enzymol. 410: 99- 120. 2006.
  6. Lai, Z., Gross, B., Zou, Y., Andrews, J. and Rieseberg, L.
    Microaray analysis reveals differential gene expression in hybrid sunflower species.
    Molecular Ecology 15: 1213-1227. 2006.

Through 2005

  1. Lai, Z., Livingstone, K., Zou, Y., Church, S., Knapp, S., Andrews, J. and Rieseberg, L.
    Identification and mapping of SNPs and candidate genes in sunflower: towards a functional map.
    Theor Appl Genet. 111:1532-1544. 2005.
  2. Parisi, M., Nuttall, R., Naiman, D., Bouffard, G., Malley, J., Andrews, J., Eastman, S. and Oliver, B.
    Paucity of genes on the Drosophila X Chromosome showing male-biased expression.
    Science 299: 697-700. 2003.
  3. Andrews, J. and Oliver, B.
    Sex determination signals control ovo-B transcription in Drosophila melanogaster germ cells.
    Genetics 160: 537-545. 2002.
  4. Andrews, J., Bouffard, G.G., Cheadle, C., Lu J., Becker, K., and Oliver, B.
    Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis.
    Genome Research 10: 2030-2043. 2002.
  5. Andrews, J., Garcia-Estefania, D., Delon, I., Lu J., Mevel-Ninio, M., Spierer, A., Payre, F., Pauli, D., and Oliver, B.
    OVO transcription factors function antagonistically in the Drosophila female germline.
    Development 127: 881-982. 2000.
  6. Andrews, J., Levenson, I. and Oliver, B.
    New AUG initiation codons in a long 5\222-UTR create four dominant negative alleles of the Drosophila C2H2 zinc-finger gene ovo.
    Dev. Genes Evol. 207: 482-487. 1998.
  7. Lu J., Andrews, J., Pauli, D. and Oliver, B.
    Drosophila OVO zinc-finger protein regulates ovo and ovarian tumor target promoters.
    Dev. Genes Evol. 208: 213-222. 1998.
  8. Andrews, J., Smith, M., Merakovsky, J., Coulson, M., Hannan, F., and Kelly, L. E.
    The stoned locus of Drosophila melanogaster produces a dicistronic transcript and encodes two distinct polypeptides.
    Genetics 143: 1699-1711. 1996.
  9. Batterham, P., Crew, J. R., Sokac, A. M., Andrews, J. R., Pasquini, G. M. F., Davies, A. G., Stocker, R. F. and Pollock, J. A.
    Genetic analysis of the lozenge gene complex in Drosophila melanogaster: Adult visual system phenotypes.
    J. Neurogenetics 10: 193-220. 1996.