Ecological genomics seminar
Contents
The Ecological Genomics page
This page is for use of participants in EEB 6485 Seminar in Ecological Genomics
- To upload a pdf use this form (note that this form requires authentication; contact Eric Schultz for the username and password)
- To add a link to an uploaded journal article pdf, review the instructions that will arrive in an email following each successful use of the upload form (more help on hypertext links in Help).
The Spring 2010 Edition
February 3
- Rokas, A. and P. Abbot. 2009 Harnessing genomics for evolutionary insights. Trends in Ecology and Evolution 24:192-200.
- Ungerer, M.C., L.C. Johnson and M.A. Herman. 2008. Ecological genomics: understanding gene and genome function in the natural environment. Heredity 100: 178-183.
February 10
- Snow day.
February 17
- Place et al 2008 MEPS.pdf Gene expression in the intertidal mussel Mytilus californianus: physiological response to environmental factors on a biogeographic scale
February 24
- Hahn et al 2009.pdf Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis
March 3
- Vera, J. C., C. W. Wheat, H. W. Fescemyer, M. J. Frilander, D. L. Crawford, I. Hanski, and J. H. Marden. 2008. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Molecular Ecology 17: 1636-1647.
March 17
- Metzker, M. L. 2010. Sequencing technologies - the next generation. Nature Reviews Genetics 11: 31-46.
March 24
- Cummings, M. E., J. Larkins-Ford, C. R. L. Reilly, R. Y. Wong, M. Ramsey, and H. A. Hofmann. 2008. Sexual and social stimuli elicit rapid and contrasting genomic responses. Proceedings of the Royal Society B-Biological Sciences 275: 393-402.
March 31
- Hegedus, Z., A. Zakrzewska, V.C. Agoston, A. Ordas, P. Racz, M. Mink, H.P. Spaink and A.H. Meijer. 2009. Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Molecular Immunology 46: 2918–2930.
April 7
- Goetz, F., D. Rosauer, S. Sitar, G. Goetz, C. Simchick, S. Roberts, R. Johnson, C. Murphy, C. R. Bronte, and S. Mackenzie. 2010. A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush). Molecular Ecology 19: 176-196.
April 14
- Aubin-Horth, N., and S. C. P. Renn. 2009. Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity. Molecular Ecology 18: 3763-3780.
- Aubin-Horth, N., Letcher, B.H., and Hofmann, H.A. 2009. Gene-expression signatures of Atlantic salmon's plastic life cycle. General and Comparative Endocrinology 163(3): 278-284.
April 21
- Ellegren, H. 2008. Comparative genomics and the study of evolution by natural selection. Molecular Ecology 17: 4586-4596.
April 28
Topics of interest
Toyshop: overview of next generation sequencing technologies (Rachel O'Neill, rescheduled tentatively for 3/3)
Functional variability in gene expression; response to abiotic factors, social factors, other species
Linking intra- and interspecific genomic variability to morphological variability
Environmentally-mediated modification of the genome; epigenetics
Metagenomics: genetic variability at the community level
Genomics and community/ecosystem-scale processes
Genomics and development: how regulatory pathways shape morphology
Genomics and systematics: discovery of informative loci
Reference compilations
Methods-oriented overview papers
- Metzker, M. L. 2010. Sequencing technologies - the next generation. Nature Reviews Genetics 11: 31-46.
- Morozova, O., M. Hirst, and M. A. Marra. 2009. Applications of New Sequencing Technologies for Transcriptome Analysis. Annual Review of Genomics and Human Genetics 10: 135-151.
- Mortazavi, A., B. A. Williams, K. McCue, L. Schaeffer, and B. Wold. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5: 621-628.
- Rothberg, J. M., and J. H. Leamon. 2008. The development and impact of 454 sequencing. Nature Biotechnology 26: 1117-1124.
- Schuster, S. C. 2008. Next-generation sequencing transforms today's biology. Nature Methods 5: 16-18.
- Shendure, J., and H. L. Ji. 2008. Next-generation DNA sequencing. Nature Biotechnology 26: 1135-1145.
- Weber, A. P. M., K. L. Weber, K. Carr, C. Wilkerson, and J. B. Ohlrogge. 2007. Sampling the arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiology 144: 32-42.