Difference between revisions of "General Topics"

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This page has replaced the Virtual Library.
 
=General <i>S. cerevisiae</i> information=
 
=General <i>S. cerevisiae</i> information=
  
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*Generally speaking:[http://www.yeastgenome.org/VL-what_are_yeast.html What are yeasts]?
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*Generally speaking:
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**[[What_are_yeast?|What are yeast?]]
 
**Here are some [http://www.yeastgenome.org/yeast_images.shtml pictures] of yeast
 
**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].
 
*The [http://www.yeastgenome.org/community/ArtOfBrewing.htm Art of Brewing], courtesy of [http://www.millerbrewing.com/ Miller Brewing Company].
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*Information about winemaking, 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 yeast and bread baking, from [http://www.breadworld.com/ Fleischmann's] and [http://www.redstaryeast.com/ Red Star Yeast] companies.
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*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].
 
*Information about the yeast-based foods [http://www.accomodata.co.uk/marmite.htm Marmite] and [http://www.vegemite.com.au/ Vegemite].
  
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*An [http://dbb.urmc.rochester.edu/labs/Sherman_f/yeast/Index.html introduction] to yeast, the most ideal eukaryotic microorganism for biological studies.
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*An [http://www.urmc.rochester.edu/labs/Sherman-Lab/publications/pdfs/Saccharomyces-Cerevisiae-Yeast-Intro.pdf introduction to yeast], the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.
  
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*An updated version the yeast primer [http://dbb.urmc.rochester.edu/labs/sherman_f/StartedYeast.html Getting Started with Yeast] written by Fred Sherman.
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*An updated version of the yeast primer [http://www.urmc.rochester.edu/labs/Sherman-Lab/publications/pdfs/Getting-Started-With-Yeast.pdf 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
 
*[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 <i>S.cerevisiae</i> nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].
 
*Download a [http://www.yeastgenome.org/sgdpub/Saccharomyces_cerevisiae.pdf guide to <i>S.cerevisiae</i> nomenclature], published in [http://www.sciencedirect.com/science/journal/01689525 Trends in Genetics].
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*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 <i>S. cerevisiae</i> molecular biology and genetics.
 
*A [http://www.usask.ca/biology/sgd/sgd1.html tutorial] from the University of Saskatchewan provides an introduction to SGD and to <i>S. cerevisiae</i> molecular biology and genetics.
  
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*[http://www.yeastgenome.org/ SGD] maintains a [http://www.yeastgenome.org/ExternalContents.shtml list] of websites with relevance to <i>S. cerevisiae</i> molecular biology and genetics and to general molecular biology.
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*A [[External_Links|list]] of websites with relevance to <i>S. cerevisiae</i> 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
 
*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]
 
*Usenet group on yeast molecular biology: [http://www.bio.net/hypermail/yeast/ bionet.molbio.yeast]
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*Curated publications at SGD describing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Industrial%20Applications industrial uses of yeast], such as biofuels, winemaking, brewing.
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*Curated publications at SGD addressing [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Infection%20and%20Antifungals infections and antifungals] and [http://www.yeastgenome.org/cgi-bin/reference/reference.pl?topic=Disease%20Gene%20Related genes associated with diseases]
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=Educational resources=
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*[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.
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*[http://faculty.bsc.edu/phanson/yen/ Yeast Education Network] An archive of yeast-based teaching tools for the undergraduate classroom and laboratory.  This site also includes most of the Education Workshop talks from YGM 2008.
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*[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.
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*[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.
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*[http://www.mendelweb.org/ MendelWeb], an educational resource on the origins of classical genetics.
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*[http://www.nsta.org National Science Teachers Association.] Resources for all science teachers from kindergarten to college.
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*[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.
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*[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.
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*[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.
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*[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.
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*[http://www.actionbioscience.org/genomic/index.html  Issues in Genomics] ActionBioscience.org lists a number of articles on genomics topics.
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*[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.
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*[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].
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*[http://www.nature.com/scitable Scitable] A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.
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*[http://www.guidetohealthcareschools.com/library/human-genetics The Human Genetics Education Resource] A general guide to resources in human genomics, inheritance, molecular genetics, genetic interactions, gene expression and evolution.
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*[http://genetics.thetech.org/book-titles When Will Broccoli Taste Like Chocolate?: Your Questions on Genetic Traits Answered by Stanford University Scientists] A collection of general genetics questions and answers from the Ask a Geneticist section of [http://www.thetech.org/ The Tech Museum website].
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=<i>Schizosaccharomyces pombe</i> information=
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*[http://www.nature.com/nature/journal/v415/n6874/abs/nature724.html <i>S. pombe</i> genomic sequence] published by V. Wood <i>et al.</i>, [http://www.nature.com Nature] <b>415,</b> 871-880 (2002)
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*[http://www.pombase.org/ PomBase] The scientific resource for fission yeast. <i>S. pombe</i> database compiled at the [http://www.cam.ac.uk/ University of Cambridge, UK]
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*[http://www.sanger.ac.uk/cgi-bin/blast/submitblast/s_pombe Blast Server] for <i>S. pombe</i> compiled at the [http://www.sanger.ac.uk/ Sanger Centre, UK]
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*[http://www.sanger.ac.uk/Projects/S_pombe/EUseqgrp.shtml European <i>Schizosaccharomyces</i> genome sequencing project]
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*[http://www-rcf.usc.edu/~forsburg/ General information about <i>S. pombe</i>] from the Forsburg Lab
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*[http://www-rcf.usc.edu/~forsburg/vectors.html <i>S. pombe</i> molecular genetics: plasmids, markers, maps and references] from the Forsburg Lab
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*[http://www-rcf.usc.edu/~forsburg/genetable.html An <i>S. pombe</i> nomenclature guide]: <i>S. pombe</i> genes mapped to <i>S. cerevisiae</i> genes from the Forsburg Lab
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=<i>Candida albicans</i> information=
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*[http://candida.bri.nrc.ca/candida/index.cfm <i>Candida albicans</i> pages] at the NRC/BRI
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*[http://www.candidagenome.org/ <i>Candida</i> Genome Database] at Stanford
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*[http://www-sequence.stanford.edu/group/candida/ <i>Candida</i> information] from the Stanford Genome Technology Center
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*[http://genolist.pasteur.fr/CandidaDB/ CandidaDB], a genomic database for <i>C. albicans</i>, part of the Galar Fungail Consortium project
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*[http://albicansmap.ahc.umn.edu/ Institute for <i>Candida</i> experimentation] at the University of Minnesota
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*[http://www.nlm.nih.gov/medlineplus/candidiasis.html Candidiasis information] at MEDLINE plus
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*[http://agabian.ucsf.edu/ Annotation of the <i>C. albicans</i> genome] from the Agabian Lab
  
 
=Links to other fungal information=
 
=Links to other fungal information=
  
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=Biology related career resources=
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*[http://botit.botany.wisc.edu/toms_fungi/ Tom Volk's Fungi]
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*[http://www.doctorfungus.org/ Doctor Fungus]
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*[http://www.fgsc.net/ The Fungal Genetics Stock Center]
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=Fungal genome sequencing projects=
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==Euascomycota==
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*[http://www.tigr.org/tdb/e2k1/afu1/ <i>Aspergillus fumigatus</i>]
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*[http://www.broad.mit.edu/annotation/fungi/aspergillus/ <i>Aspergillus nidulans</i>]
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*[http://www.broad.mit.edu/annotation/fungi/magnaporthe/ <i>Magnaporthe grisea</i>]
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*[http://www.broad.mit.edu/annotation/fungi/neurospora/ <i>Neurospora crassa</i>]
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==Basidiomycota==
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* ''Cryptococcus''
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**[http://sequence-www.stanford.edu/group/C.neoformans/index.html ''Cryptococcus neoformans'' var. ''neoformans'' strain B3501]
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** [http://www.tigr.org/tdb/e2k1/cna1/ ''Cryptococcus neoformans'' var. ''neoformans'' strain JEC21]
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** ''Cryptococcus neoformans'' var. ''grubii'' H99 - [http://cneo.genetics.duke.edu/ Duke University], [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans Fungal Genome Initiative]
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** ''Cryptococcus gattii'' R265 - [http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans_b Fungal Genome Initiative]
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** ''Cryptococcus gattii'' WM276 - [http://www.bcgsc.ca/project/cryptococcus/ Kronstad Lab/British Columbia Genome Sequencing Centre]
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* [http://www.broad.mit.edu/annotation/genome/coprinus_cinereus/ ''Coprinus cinereus'']
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* [http://www.broad.mit.edu/annotation/genome/puccinia_graminis ''Puccinia graminis f. sp. tritici'']
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* [http://www.broad.mit.edu/annotation/genome/ustilago_maydis/ ''Ustilago maydis''], [http://mips.gsf.de/genre/proj/ustilago/ MIPS resources].
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==Archiascomycota==
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* [http://pgp.cchmc.org/ ''Pneumocystis carinii'']
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* [http://www.broad.mit.edu/annotation/genome/schizosaccharomyces_japonicus ''Schizosaccharomyces japonicus'']
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==Hemiascomycota==
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* The [http://cbi.labri.fr/Genolevures/ G&eacute;nolevures] project, featuring partial genomic sequence for 13 Hemiascomycete species
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 +
==Links==
 +
* There is also [http://fungalgenomes.org/wiki/Fungal_Genome_Links list] of currently sequenced or in progress fungal genome projects with references.
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 +
=Fungal genome database projects=
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 +
*[http://www.aspgd.org/ Aspergillus Genome Database], a database for <i>A. nidulans, A. fumigatus, A. niger</i> and related species.
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* [http://cryptogenome.ucsf.edu/ CryptoBase], a scientific database resource at [http://www.ucsf.edu UCSF] for ''C. neoformans'' var. ''grubii'' (serotype A)
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*[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.

Latest revision as of 04:44, 10 December 2015

This page has replaced the Virtual Library.

General S. cerevisiae information

  • An introduction to yeast, the most ideal eukaryotic microorganism for biological studies, written by Fred Sherman.
  • A table describing the gene targets of the different RNA polymerases in S. cerevisiae.
  • A tutorial from the University of Saskatchewan provides an introduction to SGD and to S. cerevisiae molecular biology and genetics.
  • A list of websites with relevance to S. cerevisiae molecular biology and genetics and to general molecular biology.
  • Search the Yeast BioSci (a.k.a. BioNet) Electronic Conference

Educational resources

  • 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.
  • Yeast Education Network An archive of yeast-based teaching tools for the undergraduate classroom and laboratory. This site also includes most of the Education Workshop talks from YGM 2008.
  • Research Link 2000 Aimed at undergraduate classrooms, this is an offshoot of Tom Manney's yeast experiments. It also lists other model organisms.
  • MendelWeb, an educational resource on the origins of classical genetics.
  • American Society for Microbiology. The ASM website lists resources in its education section. The ASM publishes numerous books on microbiology education at various levels.
  • Scitable A free library providing overviews of key science concepts, with a focus on genetics, compiled by the Nature Publishing Group.

Schizosaccharomyces pombe information

Candida albicans information

  • CandidaDB, a genomic database for C. albicans, part of the Galar Fungail Consortium project

Links to other fungal information

Fungal genome sequencing projects

Euascomycota

Basidiomycota

Archiascomycota

Hemiascomycota

  • The Génolevures project, featuring partial genomic sequence for 13 Hemiascomycete species

Links

  • There is also list of currently sequenced or in progress fungal genome projects with references.

Fungal genome database projects

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