General Topics

2009-02-12T02:33:24Z

MK: /* Educational resources */ Added VADLO search engine

=General S. cerevisiae information=

*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast

*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].

*Information about wine making, from [http://www.wine-oenology.com Wine High School of The Champagne region].

*Information about yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.

*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].

*An [http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/Index.html introduction] to yeast, the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.

*An updated version the yeast primer [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html Getting Started with Yeast] written by Fred Sherman.

*[http://biochemie.web.med.uni-muenchen.de/Yeast_Biol/ Yeast Molecular Biology: A Short Compendium on Basic Features and Novel Aspects] written by Horst Feldmann at the University of Munich

*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to S.cerevisiae nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].

*A [[Polymerase_targets|table]] describing the gene targets of the different RNA polymerases in S. cerevisiae.

*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.

*[http://www.yeastgenome.org/ SGD] maintains a [http://www.yeastgenome.org/ExternalContents.shtml list] of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.

*Search the [http://www.bio.net/hypermail/yeast/ Yeast BioSci] (a.k.a. BioNet) Electronic Conference

*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]

=Educational resources=

*[http://www.phys.ksu.edu/gene/ Genetics Education Network] Tom Manney's (Kansas State University) yeast experiments for undergrads and high school students. A well-done and informative web site for yeast in the classroom.

*[http://www.cur.org/reslink2000.html Research Link 2000] Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.

*[http://www.woodrow.org/teachers/bi/1993/using.html Using Yeast As An Ultraviolet Light Measurement Tool.] This is a Tom Manney protocol rewritten by Kevin Conant, a participant in the Woodrow Wilson Biology Institute 1993.

*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.

*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.

*[http://www.nabt.org National Association of Biology Teachers] High school teachers predominate in this organization, but there are resources for post-secondary education as well.

*[http://www.asm.org American Society for Microbiology.] The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.

*[http://www.bio.davidson.edu/courses/genomics/genomics.html Discovering Genomics, Proteomics, and Bioinformatics] This website describes a course and the accompanying textbook written by A. Malcolm Campbell and Laurie J. Heyer.

*[http://www.bio.davidson.edu/projects/GCAT/gcat.html Genome Consortium for Active Teaching (GCAT)] Description of the consortium and how it is working to bring functional genomics methods into the undergraduate biology curriculum.

*[http://www.actionbioscience.org/genomic/index.html Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.

*[http://www.bio.davidson.edu/projects/magic/magic.html MicroArray Genome Imaging and Clustering Tool (MAGIC)] Open source software for analysis of large-scale gene expression datasets; developed by Laurie Heyer and her undergraduate students at Davidson College, North Carolina.

*[http://Vadlo.com VADLO Life Sciences Search Engine] from Life in Research, LLC. Provides search for life sciences research methods, databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases], [http://search.vadlo.com/b/q?k=Cerevisiae&rel=2 S. cerevisiae Powerpoints].

=Schizosaccharomyces pombe information=

*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html S. pombe genomic sequence] published by V. Wood et al., [http://www.nature.com Nature] 415, 871-880 (2002)

*[http://www.genedb.org/genedb/pombe/index.jsp PomBase] S. pombe database compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for S. pombe compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]

*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European Schizosaccharomyces genome sequencing project]

*[http://www-rcf.usc.edu/~forsburg/ General information about S. pombe] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/vectors.html S. pombe molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab

*[http://www-rcf.usc.edu/~forsburg/genetable.html An S. pombe nomenclature guide]: S. pombe genes mapped to S. cerevisiae genes from the Forsburg Lab

=Candida albicans information=

*[http://candida.bri.nrc.ca/candida/index.cfm Candida albicans pages] at the NRC/BRI

*[http://www.candidagenome.org/ Candida Genome Database] at Stanford

*[http://www-sequence.stanford.edu/group/candida/ Candida information] from the Stanford Genome Technology Center

*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for C. albicans, part of the Galar Fungail Consortium project

*[http://albicansmap.ahc.umn.edu/ Institute for Candida experimentation] at the University of Minnesota

*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus

*[http://agabian.ucsf.edu/ Annotation of the C. albicans genome] from the Agabian Lab

=Links to other fungal information=

*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]

*[http://www.doctorfungus.org/ Doctor Fungus]

=Fungal genome sequencing projects=

==Euascomycota==
*[http://www.tigr.org/tdb/e2k1/afu1/ Aspergillus fumigatus]
*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ Aspergillus nidulans]
*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ Magnaporthe grisea]
*[http://www.broad.mit.edu/annotation/fungi/neurospora/ Neurospora crassa]

==Basidiomycota==

* ''Cryptococcus''
**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
** ''Cryptococcus neoformans'' var. ''grubii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]

* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].

==Archiascomycota==
* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']

==Hemiascomycota==
* The [http://cbi.labri.fr/Genolevures/ Génolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species

==Links==
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.

=Fungal genome database projects=

* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
*[http://fungal.genome.duke.edu fungal.genome.duke.edu], a scientific database resource at [http://www.duke.edu Duke University] providing Genome Browser, BLAST, and downloadable genome annotations for many fungal genomes.

Methods

2009-02-12T02:26:52Z

MK: Added Vadlo search engine

*[http://www.fhcrc.org/labs/breeden/Methods_BreedenLab.html| Yeast Lab Protocols] from the Breeden Lab, Fred Hutchinson Cancer Research Center.

*[http://www.fhcrc.org/labs/gottschling/ Yeast Lab Protocols] from the Gottschling Lab, Fred Hutchinson Cancer Research Center.

*[http://gasch.genetics.wisc.edu/protocols.html Yeast & Microarray Protocols] from the Gasch Lab, University of Wisconsin-Madison.

*[http://www.umanitoba.ca/faculties/medicine/biochem/gietz/Trafo.html The Definitive Yeast Transformation Homepage] from the University of Manitoba.

*[http://fangman-brewer.genetics.washington.edu/index.html DNA Replication Protocols] from the Fangman and Brewer Labs, University of Washington.

*[http://www.fccc.edu/research/labs/golemis/InteractionTrapInWork.html Interaction Trap at Work] information page from Erica Golemis's laboratory at the Fox Chase Cancer Center.

*[http://cmgm.stanford.edu/pbrown/mguide/index.html The MGuide. Version 2.0], a complete guide to microarraying for the molecular biologist, from the Brown Lab, Stanford University.

*[http://gasch.genetics.wisc.edu/protocols/Gasch_MethEnzym.pdf Guide to Yeast Microarray Experiments], by Audrey Gasch, from Guide to Yeast Genetics and Molecular and Cellular Biology, Methods in Enzymology (2002)

*The [http://depts.washington.edu/yeastrc/ NCRR Yeast Resource Center] at the University of Washington facilitates the study of yeast protein complexes by providing access to techniques such as mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction.

*Full text of the paper (Erdeniz et al. (1997) Genome Res. 7:1174-1183) describing [http://www.genome.org/cgi/content/full/7/12/1174 PCR-Based Allele Replacement]. Available to the public without password restriction and at no charge, through a special arrangement with Genome Research arranged by Rodney Rothstein.

*[http://genomics.princeton.edu/dunham/chemostat.html Chemostat Manual] from Maitreya Dunham's lab, Princeton University. See her [http://genomics.princeton.edu/dunham/protocols.shtml other protocols].

*[http://www.phys.ksu.edu/gene/chapters.html A Classroom Guide To Yeast Experiments] from The GENE project at Kansas State University.

*[http://openwetware.org/wiki/The_mRNA_Decay_Resource:Protocols_and_Resources Protocols and Resources] from the RNA Decay Resource, a resource for the sharing of information, know-how, and wisdom among researchers who study mRNA decay.

*[[SGA]] SGA protocols and scoring software.

*[http://Vadlo.com Molecular Biology Protocols Search Engine] from Life in Research, LLC. Also life sciences databases, online tools, software, and powerpoints. For example [http://search.vadlo.com/b/q?k=Yeast+Protocols&rel=0 Yeast protocols], [http://search.vadlo.com/b/q?k=Yeast&rel=3 Yeast databases]

SGD-Wiki - User contributions [en]

General Topics

Methods