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5 results on '"Andrews, Justen"'

1. The Ecoresponsive Genome of "Daphnia pulex"

Author

Colbourne, John K., Pfrender, Michael E., Gilbert, Donald, Thomas, W. Kelley, Tucker, Abraham, Oakley, Todd H., Tokishita, Shinichi, Aerts, Andrea, Arnold, Georg J., Basu, Malay Kumar, Bauer, Darren J., Cáceres, Carla E., Carmel, Liran, Casola, Claudio, Choi, Jeong-Hyeon, Detter, John C., Dong, Qunfeng, Dusheyko, Serge, Eads, Brian D., Fröhlich, Thomas, Geiler-Samerotte, Kerry A., Gerlach, Daniel, Hatcher, Phil, Jogdeo, Sanjuro, Krijgsveld, Jeroen, Kriventseva, Evgenia V., Kültz, Dietmar, Laforsch, Christian, Lindquist, Erika, Lopez, Jacqueline, Manak, J. Robert, Muller, Jean, Pangilinan, Jasmyn, Patwardhan, Rupali P., Pitluck, Samuel, Pritham, Ellen J., Rechtsteiner, Andreas, Rho, Mina, Rogozin, Igor B., Sakarya, Onur, Salamov, Asaf, Schaack, Sarah, Shapiro, Harris, Shiga, Yasuhiro, Skalitzky, Courtney, Smith, Zachary, Souvorov, Alexander, Sung, Way, Tang, Zuojian, Tsuchiya, Dai, Tu, Hank, Vos, Harmjan, Wang, Mei, Wolf, Yuri I., Yamagata, Hideo, Yamada, Takuji, Ye, Yuzhen, Shaw, Joseph R., Andrews, Justen, Crease, Teresa J., Tang, Haixu, Lucas, Susan M., Robertson, Hugh M., Bork, Peer, Koonin, Eugene V., Zdobnov, Evgeny M., Grigoriev, Igor V., Lynch, Michael, and Boore, Jeffrey L.

Published
2011
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2. Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Author

The modeENCODE Consortium, Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia, Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah C. R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., and Kellis, Manolis

Published
2010

3. Identification of functional elements and regulatory circuits by Drosophila modENCODE

Author

Roy, Sushmita, Ernst, Jason, Kharchenko, Peter V., Kheradpour, Pouya, Negre, Nicolas, Eaton, Matthew L., Landolin, Jane M., Bristow, Christopher A., Ma, Lijia, Lin, Michael F., Washietl, Stefan, Arshinoff, Bradley I., Ay, Ferhat, Meyer, Patrick E., Robine, Nicolas, Washington, Nicole L., Di Stefano, Luisa, Berezikov, Eugene, Brown, Christopher D., Candeias, Rogerio, Carlson, Joseph W., Carr, Adrian, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel, Tolstorukov, Michael Y., Will, Sebastian, Alekseyenko, Artyom A., Artieri, Carlo, Booth, Benjamin W., Brooks, Angela N., Dai, Qi, Davis, Carrie A., Duff, Michael O., Feng, Xin, Gorchakov, Andrey A., Gu, Tingting, Henikoff, Jorja G., Kapranov, Philipp, Li, Renhua, MacAlpine, Heather K., Malone, John, Minoda, Aki, Nordman, Jared, Okamura, Katsutomo, Perry, Marc, Powell, Sara K., Riddle, Nicole C., Sakai, Akiko, Samsonova, Anastasia A., Sandler, Jeremy E., Schwartz, Yuri B., Sher, Noa, Spokony, Rebecca, Sturgill, David, van Baren, Marijke, Wan, Kenneth H., Yang, Li, Yu, Charles, Feingold, Elise, Good, Peter, Guyer, Mark, Lowdon, Rebecca, Ahmad, Kami, Andrews, Justen, Berger, Bonnie, Brenner, Steven E., Brent, Michael R., Cherbas, Lucy, Elgin, Sarah C.R., Gingeras, Thomas R., Grossman, Robert, Hoskins, Roger A., Kaufman, Thomas C., Kent, William, Kuroda, Mitzi I., Orr-Weaver, Terry, Perrimon, Norbert, Pirrotta, Vincenzo, Posakony, James W., Ren, Bing, Russell, Steven, Cherbas, Peter, Graveley, Brenton R., Lewis, Suzanna, Micklem, Gos, Oliver, Brian, Park, Peter J., Celniker, Susan E., Henikoff, Steven, Karpen, Gary H., Lai, Eric C., MacAlpine, David M., Stein, Lincoln D., White, Kevin P., Kellis, Manolis, Booth, Benjamin, Comstock, Charles L.G., Dobin, Alex, Drenkow, Jorg, Dudoit, Sandrine, Dumais, Jacqueline, Fagegaltier, Delphine, Ghosh, Srinka, Hansen, Kasper D., Jha, Sonali, Langton, Laura, Lin, Wei, Miller, David, Tenney, Aaron E., Wang, Huaien, Willingham, Aarron T., Zaleski, Chris, Zhang, Dayu, Acevedo, David, Bishop, Eric P., Gadel, Sarah E., Jung, Youngsook L., Kennedy, Cameron D., Lee, Ok Kyung, Linder-Basso, Daniela, Marchetti, Sarah E., Shanower, Gregory, Nègre, Nicolas, Grossman, Robert L., Auburn, Richard, Bellen, Hugo J., Chen, Jia, Domanus, Marc H., Hanley, David, Heinz, Elizabeth, Li, Zirong, Meyer, Folker, Miller, Steven W., Morrison, Carolyn A., Scheftner, Douglas A., Senderowicz, Lionel, Shah, Parantu K., Suchy, Sarah, Tian, Feng, Venken, Koen J.T., White, Robert, Wilkening, Jared, Zieba, Jennifer, Nordman, Jared T., Orr-Weaver, Terry L., DeNapoli, Leyna C., Ding, Queying, Eng, Thomas, Kashevsky, Helena, Li, Sharon, Prinz, Joseph A., Hannon, Gregory J., Hirst, Martin, Marra, Marco, Rooks, Michelle, Zhao, Yongjun, Bryson, Terri D., Perry, Marc D., Kent, William J., Lewis, Suzanna E., Barber, Galt, Chateigner, Aurelien, Clawson, Hiram, Contrino, Sergio, Guillier, Francois, Hinrichs, Angie S., Kephart, Ellen T., Lloyd, Paul, Lyne, Rachel, McKay, Sheldon, Moore, Richard A., Mungall, Chris, Rutherford, Kim M., Ruzanov, Peter, Smith, Richard, Stinson, E. O., Zha, Zheng, Artieri, Carlo G., Malone, John H., Jiang, Lichun, Mattiuzzo, Nicolas, Feingold, Elise A., Good, Peter J., Guyer, Mark S., Lowdon, Rebecca F., Stem Cell Aging Leukemia and Lymphoma (SALL), and Restoring Organ Function by Means of Regenerative Medicine (REGENERATE)

Subjects
Transcription, Genetic, Genome, Insect, Gene regulatory network, Genomics, Genes, Insect, Computational biology, Biology, Genome, Article, Epigenesis, Genetic, Histones, Nucleosome, Animals, Drosophila Proteins, Gene Regulatory Networks, Promoter Regions, Genetic, Gene, Genetics, Multidisciplinary, Binding Sites, REDfly, Computational Biology, Molecular Sequence Annotation, Chromatin, Nucleosomes, Drosophila melanogaster, Gene Expression Regulation, RNA, Small Untranslated, Drosophila Protein, Transcription Factors
Abstract

From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation is still needed to characterize how the genome is used to help to produce a functional organism (see the Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for the Caenorhabditis elegans genome, and The modENCODE Consortium (p. 1787 ) summarize for the Drosophila melanogaster genome, full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites, and high-resolution maps of chromatin organization. Both studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized. Overall, the studies provide insights into the organization, structure, and function of the two genomes and provide basic information needed to guide and correlate both focused and genome-wide studies.

Published
2010

4. EST and microarray analysis of horn development in Onthophagus beetles.

Author

Kijimoto, Teiya, Costello, James, Zuojian Tang, Moczek, Armin P., and Andrews, Justen

Subjects
BEETLES, ECOLOGY, HORNS (Anatomy), GENOMICS, DNA microarrays
Abstract

Background: The origin of novel traits and their subsequent diversification represent central themes in evo-devo and evolutionary ecology. Here we explore the genetic and genomic basis of a class of traits that is both novel and highly diverse, in a group of organisms that is ecologically complex and experimentally tractable: horned beetles. Results: We developed two high quality, normalized cDNA libraries for larval and pupal Onthophagus taurus and sequenced 3,488 ESTs that assembled into 451 contigs and 2,330 singletons. We present the annotation and a comparative analysis of the conservation of the sequences. Microarrays developed from the combined libraries were then used to contrast the transcriptome of developing primordia of head horns, prothoracic horns, and legs. Our experiments identify a first comprehensive list of candidate genes for the evolution and diversification of beetle horns. We find that developing horns and legs show many similarities as well as important differences in their transcription profiles, suggesting that the origin of horns was mediated partly, but not entirely, by the recruitment of genes involved in the formation of more traditional appendages such as legs. Furthermore, we find that horns developing from the head and prothorax differ in their transcription profiles to a degree that suggests that head and prothoracic horns are not serial homologs, but instead may have evolved independently from each other. Conclusion: We have laid the foundation for a systematic analysis of the genetic basis of horned beetle development and diversification with the potential to contribute significantly to several major frontiers in evolutionary developmental biology. [ABSTRACT FROM AUTHOR]

Published
2009
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5. Paucity of Genes on the Drosophila X Chromosome Showing Male-Biased Expression.

Author

Parisi, Michael, Nuttall, Rachel, Naiman, Daniel, Bouffard, Gerard, Malley, James, Andrews, Justen, Eastman, Scott, and Oliver, Brian

Subjects
*SEX chromosomes, *SEXUAL dimorphism in animals, *BIOLOGICAL divergence, *GENOMICS
Abstract

Sex chromosomes are primary determinants of sexual dimorphism in many organisms. These chromosomes are thought to arise via the divergence of an ancestral autosome pair and are almost certainly influenced by differing selection in males and females. Exploring how sex chromosomes differ from autosomes is highly amenable to genomic analysis. We examined global gene expression in Drosophila melanogaster and report a dramatic underrepresentation of X-chromosome genes showing high relative expression in males. Using comparative genomics, we find that these same X-chromosome genes are exceptionally poorly conserved in the mosquito Anopheles gambiae. These data indicate that the X chromosome is a disfavored location for genes selectively expressed in males. [ABSTRACT FROM AUTHOR]

Published
2003
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