This web page is for the Metagenomics Journal Club. Current, past and future journal articles can be found here.
Location: UC Santa Cruz, Earth and Marine Sciences Building, Institute of Geophysics and Planetary Physics, C332
Time: TBA
Date: TBA
To Recommend A Paper, send the citation and link to Jeff:
jlong@soe.ucsc.edu
| Date | Recommender | Paper |
|---|---|---|
| 23 Apr 2010 | Jonathan Magasin |
Use of simulated data sets to evaluate the
fidelity of metagenomic processing methods, Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice C McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Paul Richardson, Philip Hugenholtz and Nikos C Kyrpides, Nature Methods 4, 495-500 (2007) http://dx.doi.org/10.1038/nmeth1043 |
| 30 Apr 2010 | Jeffrey Long |
ShotgunFunctionalizeR: an R-package for functional comparison of metgenomes
Bioinformatics Vol. 25, no.20, 2009 Application Note: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/20/2737 Supplementary Data 1 - Methods Supplementary Data 2 - User Manual http://bioinformatics.oxfordjournals.org/cgi/content/full/btp508/DC1 Package Availability http://shotgun.zool.gu.se |
| 14 May 2010 | Thomas Juettemann | Metagenomic Sequencing of an In Vitro-Simulated Microbial
Community, Morgan JL, Darling AE, Eisen JA, PLoS ONE 5(4): e10209, doi:10.1371/journal.pone.0010209 http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010209 |
| 21 May 2010 | Jeffrey Long |
The metagenomics RAST server -- a public resource for the
automatic phylogenetic and functional analysis of
metagenomes Meyer, F. and Paarmann, D. and D'Souza, M. and Olson, R. and Glass, EM and Kubal, M. and Paczian, T. and Rodriguez, A. and Stevens, R. and Wilke, A. and others BMC bioinformatics 2008 vol. 9, no. 1, pp 386, http://www.biomedcentral.com/1471-2105/9/386/ |
| 4 Jun 2010 | Jonathan Magasin and Jeffrey Long |
MEGAN analysis of metagenomic data, Huson, D.H. and Auch, A.F. and Qi, J. and Schuster, S.C. Genome Research 2007 vol. 17, no. 3, pp 377 http://serine.umiacs.umd.edu/teaching/computational_biology/syllabus/files/huson_et_al_2007.pdf AND Visual and statistical comparison of metagenomes Mitra, S. and Klar, B. and Huson, D.H. Bioinformatics 2009, vol. 25, no. 15, pp 1849 http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/15/1849 |
| Date | Recommender | Paper |
|---|---|---|
| 12 Feb 2010 | Jeff Long | Identifying biologically relevant differences between metagenomic communities, Donovan Parks and Robert Beiko, Bioinformatics published 3 February 2010, http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq041v1?etoc |
| 5 Mar 2010 | Pia Moisander | A supervised learning approach for taxonomic classification of
core-photosystem-II genes and transcripts in the marine environment, Shani Tzahor, Dikla Man-Aharonovich, Benjamin Kirkup, Tali Yogev, Ilana Berman-Frank, Martin Polz, Oded Béjà and Yael Mandel-Gutfreund BMC Genomics published 16 May 2009, http://www.biomedcentral.com/1471-2164/10/229 |
| 9 Apr 2010 | Jim Tripp | Quantifying environmental adaptation of metabolic pathways in
metagenomics, Gianoulis, T.A. and Raes, J. and Patel, P.V. and Bjornson, R. and Korbel, J.O. and Letunic, I. and Yamada, T. and Paccanaro, A. and Jensen, L.J. and Snyder, M. and others Proceedings of the National Academy of Sciences published 3 February 2009, http://www.pnas.org/content/106/5/1374.abstract |