Ecological genomics seminar

From eebedia

(Difference between revisions)
Jump to: navigation, search
 
(33 intermediate revisions by 5 users not shown)
Line 1: Line 1:
 
=The Ecological Genomics page=
 
=The Ecological Genomics page=
 
This page is for use of participants in EEB 6485 Seminar in Ecological Genomics<br/>
 
This page is for use of participants in EEB 6485 Seminar in Ecological Genomics<br/>
:To upload a pdf use [http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/upload.html this form] (note that this form requires authentication; contact [mailto:eric.schultz@uconn.edu] for the username and password)
+
:To upload a pdf use [http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/upload.html this form] (note that this form requires authentication; contact [mailto:eric.schultz@uconn.edu Eric Schultz] for the username and password)
:To add a link to a journal article, review the instructions for hypertext links in [[Help:Contents|Help]].
+
: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:Contents|Help]]).
 
[[Image:454.JPG|thumb|Overview of the 454 sequencing technology. From Rothberg, J.M. and J.H. Leamon. 2008. Nature Biotechnology 26: 1117-1124 ]]
 
[[Image:454.JPG|thumb|Overview of the 454 sequencing technology. From Rothberg, J.M. and J.H. Leamon. 2008. Nature Biotechnology 26: 1117-1124 ]]
 
==The Spring 2010 Edition==
 
==The Spring 2010 Edition==
Line 9: Line 9:
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Ungerer_et_al_2008_heredity.pdf}}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.
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Ungerer_et_al_2008_heredity.pdf}}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<br/>
 
February 10<br/>
 +
:Snow day.
 
<br/>
 
<br/>
 
February 17<br/>
 
February 17<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Place%20et%20al%202008%20MEPS.pdf}} Place et al 2008 MEPS.pdf  Gene expression in the intertidal mussel Mytilus californianus: physiological response to environmental factors on a biogeographic scale
 
<br/>
 
<br/>
 
February 24<br/>
 
February 24<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Hahn%20et%20al%202009.pdf}} Hahn et al 2009.pdf Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis
 
<br/>
 
<br/>
 
March 3<br/>
 
March 3<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Vera_et_al_Molecular_ecology.pdf}} 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.
 +
<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/vera%20et%20al%202008%20supplementary%20material.pdf}} vera et al 2008 supplementary material.pdf
 
<br/>
 
<br/>
 
March 17<br/>
 
March 17<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Metzker%202010%20Nature%20Reviews%20Genetics.pdf}} Metzker, M. L. 2010. Sequencing technologies - the next generation. Nature Reviews Genetics 11: 31-46.
 
<br/>
 
<br/>
 
March 24<br/>
 
March 24<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/cummings_et_al_2008_proc_roy_soc.pdf}} 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.
 
<br/>
 
<br/>
 
March 31<br/>
 
March 31<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Hegedus%202009.pdf}} 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.
 
<br/>
 
<br/>
 
April 7<br/>
 
April 7<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Goetz_et_al_2010_molec_ecol.pdf}} 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.
 
<br/>
 
<br/>
 
April 14<br/>
 
April 14<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/aubin-horth%20and%20renn%202009%20molec%20ecol.pdf}} 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.
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Aubin-Horth%20et%20al%202009%20gen%20comp%20endocr.pdf}} 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.
 
<br/>
 
<br/>
 
April 21<br/>
 
April 21<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Ellegren_2008_molec_ecol.pdf}} Ellegren, H. 2008. Comparative genomics and the study of evolution by natural selection. Molecular Ecology 17: 4586-4596.
 
<br/>
 
<br/>
 
April 28<br/>
 
April 28<br/>
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Rubin%20et%20al.%202010.pdf}} Rubin et al. 2010. Whole genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-593.
 +
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Turner%20et%20al.%202010.pdf}} Turner et al. 2010. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics 42: 260-264.
 
<br/>
 
<br/>
==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++==++
+
 
 +
==Topics of interest==
 +
Toyshop: overview of next generation sequencing technologies (Rachel O'Neill, rescheduled tentatively for 3/3)<br/>
 +
Functional variability in gene expression; response to abiotic factors, social factors, other species<br/>
 +
Linking intra- and interspecific genomic variability to morphological variability<br/>
 +
Environmentally-mediated modification of the genome; epigenetics<br/>
 +
Metagenomics: genetic variability at the community level<br/>
 +
Genomics and community/ecosystem-scale processes<br/>
 +
Genomics and development: how regulatory pathways shape morphology<br/>
 +
Genomics and systematics: discovery of informative loci<br/>
 +
 
 +
==Reference compilations==
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/bibliography.pdf}}An ecological genomics bibliography
 
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/bibliography.pdf}}An ecological genomics bibliography
 
<br/>
 
<br/>
 +
:[http://www3.interscience.wiley.com/journal/117989598/home March 2010 Special Issue of Molecular Ecology on NEXT GENERATION MOLECULAR ECOLOGY]
 +
<br/>
 +
==Methods-oriented overview papers==
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Metzker%202010%20Nature%20Reviews%20Genetics.pdf}} Metzker, M. L. 2010. Sequencing technologies - the next generation. Nature Reviews Genetics 11: 31-46.
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/morozova%20et%20al%202009%20annu%20rev%20genomics%20hum%20genet.pdf}}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.
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Mortazavi%202008%20Nature%20Methods.pdf}} 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.
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Rothberg%20and%20Leamon%202008%20Nature%20Biotech.pdf}} Rothberg, J. M., and J. H. Leamon. 2008. The development and impact of 454 sequencing. Nature Biotechnology 26: 1117-1124.
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Schuster%202008%20Nature%20Methods.pdf}} Schuster, S. C. 2008. Next-generation sequencing transforms today's biology. Nature Methods 5: 16-18.
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Shendure%20and%20Ji%202008%20Nature%20Biotech.pdf}} Shendure, J., and H. L. Ji. 2008. Next-generation DNA sequencing. Nature Biotechnology 26: 1135-1145.
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/Weber%202007%20Plant%20Physiology.pdf}} 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.
 +
<br/>
 +
==Brief reviews and alerts==
 +
:{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/EEB6485/restricted/martinez%20and%20nelson%202010%20plos%20genetics.pdf}} Martinez, D.A. and M.A. Nelson. 2010. The Next Generation Becomes the Now Generation. PLOS Genetics.
 +
 
[[Category:EEB Seminars]]
 
[[Category:EEB Seminars]]

Latest revision as of 14:16, 23 April 2010

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).
Overview of the 454 sequencing technology. From Rothberg, J.M. and J.H. Leamon. 2008. Nature Biotechnology 26: 1117-1124

The Spring 2010 Edition

February 3

Pdficon small.gifRokas, A. and P. Abbot. 2009 Harnessing genomics for evolutionary insights. Trends in Ecology and Evolution 24:192-200.
Pdficon small.gifUngerer, 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

Pdficon small.gif 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

Pdficon small.gif Hahn et al 2009.pdf Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis


March 3

Pdficon small.gif 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.


Pdficon small.gif vera et al 2008 supplementary material.pdf


March 17

Pdficon small.gif Metzker, M. L. 2010. Sequencing technologies - the next generation. Nature Reviews Genetics 11: 31-46.


March 24

Pdficon small.gif 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

Pdficon small.gif 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

Pdficon small.gif 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

Pdficon small.gif 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.
Pdficon small.gif 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

Pdficon small.gif Ellegren, H. 2008. Comparative genomics and the study of evolution by natural selection. Molecular Ecology 17: 4586-4596.


April 28

Pdficon small.gif Rubin et al. 2010. Whole genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-593.
Pdficon small.gif Turner et al. 2010. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics 42: 260-264.


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

Pdficon small.gifAn ecological genomics bibliography


March 2010 Special Issue of Molecular Ecology on NEXT GENERATION MOLECULAR ECOLOGY


Methods-oriented overview papers

Pdficon small.gif Metzker, M. L. 2010. Sequencing technologies - the next generation. Nature Reviews Genetics 11: 31-46.
Pdficon small.gifMorozova, 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.
Pdficon small.gif 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.
Pdficon small.gif Rothberg, J. M., and J. H. Leamon. 2008. The development and impact of 454 sequencing. Nature Biotechnology 26: 1117-1124.
Pdficon small.gif Schuster, S. C. 2008. Next-generation sequencing transforms today's biology. Nature Methods 5: 16-18.
Pdficon small.gif Shendure, J., and H. L. Ji. 2008. Next-generation DNA sequencing. Nature Biotechnology 26: 1135-1145.
Pdficon small.gif 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.


Brief reviews and alerts

Pdficon small.gif Martinez, D.A. and M.A. Nelson. 2010. The Next Generation Becomes the Now Generation. PLOS Genetics.
Personal tools