New & Noteworthy
Exploring the Global Yeast Genetic Interaction Network
April 17, 2017
Global yeast genetic interaction profile similarity network. Image from TheCellMap.org.
With the construction of a global genetic interaction network in S. cerevisiae, it’s not hard to see why yeast genetic interactions remain a treasure trove for biological discovery. When combined with tools for visualization and analysis, these data can be used to draw powerful functional maps of the cell and infer potential functions for uncharacterized genes.
In a recent paper published in G3: Genes|Genomes|Genetics, Usaj et al. describe a web-based resource for exploring the global yeast genetic interaction network: TheCellMap.org. TheCellMap.org is an online database and visualization tool for quantitative yeast genetic interaction data. It provides an interactive version of the global yeast genetic interaction similarity network described by Costanzo et al., enabling users to scroll through and zoom in on different clusters of functionally related genes within the network. Users can search for specific genes or alleles, extract and re-organize sub-networks for genes of interest, functionally annotate genetic interactions, and more. Further, if more details about a gene are needed, users can even double-click on the gene to be taken to its respective locus summary page at SGD!
For more information about this resource, see http://TheCellMap.org/about/ or access the publication at https://doi.org/10.1534/g3.117.040220.
Categories: Announcements
Apply Now for the 2017 Yeast Genetics & Genomics Course
March 17, 2017
For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory.
For almost 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, the name didn’t include “Genomics” in the beginning…). The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.
The application deadline is April 15th, so don’t miss your chance! Find all the details and application form here.
This year’s instructors – Grant Brown, Maitreya Dunham, and Elçin Ünal – have designed a course (July 25 – August 14) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:
- How to Find and Analyze Yeast Information Using SGD
- Isolation and Characterization of Mutants
- Transformation of Plasmids & Integrating DNAs
- Meiosis & Tetrad Dissection as well as mitotic recombination
- Synthetic Genetic Array Analysis
- Next-Gen. whole-genome and multiplexed DNA barcode sequencing
- Genome-based methods of analysis
- Visualization of yeast using light and fluorescence microscopy
- Exploring synthetic biology with CRISPR/CAS9-directed engineering of biosynthetic pathways
Techniques have been summarized in a completely updated course manual, which was recently published by CSHL Press.
There’s fierce competition between students at CSHL courses in the Plate Race, a relay in which teams carry stacks of 40 Petri dishes (used, of course).
Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.
Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!
The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!
Categories: Announcements
Don’t miss Fungal Pathogen Genomics!
January 30, 2017
The application deadline for the Fungal Pathogen Genomics workshop to be held May 11-17, 2017 at the Wellcome Genome Campus in Hinxton, Cambridge, UK is fast approaching! Be sure to apply by this Friday, February 3!
This exciting new week-long course aims to provide experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis; including genome browsers and comparison tools, data mining using resources such as FungiDB, Ensembl/PhytoPathDB, PomBase, SGD/CGD, MycoCosm, analysis of genome annotation, and next generation sequence analysis and visualization (including RNA sequence analysis and variant calling). An important aim is that the participants should understand the origin of data available in public resources and how to analyse it in conjunction with their own.
The course is taught as a collaborative effort between available fungal informatics resources. The majority of this intensive course will be based on hands-on exercises, supplemented by lectures on genomics and bioinformatics techniques and keynote presentations by distinguished guest speakers.
Don’t miss out – apply now!
Categories: Announcements
Happy Holidays from SGD!
December 20, 2016
Happy Holidays from SGD!
We want to take this opportunity to wish you and your family, friends and lab mates the best during the upcoming holidays.
Stanford University will be closed for two weeks from Wednesday, December 21, 2016 through Tuesday, January 3, 2017. Regular operations will resume on Wednesday, January 4, 2017.
Although SGD staff members will be taking time off, please rest assured that the website will remain up and running throughout the winter break, and we will attempt to keep connected via email should you have any questions.
Happy Holidays and best wishes for all good things in the coming New Year!
Categories: Announcements
Sign Up Now! Next SGD Webinar: December 14, 2016
December 12, 2016
Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, disease associations, alleles and phenotype variants, and functional complementation relationships.
Join our upcoming webinar on December 14th, 9:30 AM PST to learn about homology and disease data in SGD. In this quick 15 minute session, we will demonstrate the best ways to research this information on our website and provide a helpful tutorial on related SGD tools and features. Our webinars are always an excellent opportunity to connect with the SGD team–be sure to bring questions if you have them!
All are welcome to this event. If you are interested attending, please register here: http://bit.ly/SGDwebinar6
This is the sixth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Homologs, Tutorial, Yeast and Human Disease
New SGD Help Video: Finding Human Homology & Disease Information
October 24, 2016
Looking for human disease-related information in SGD? There is so much to find! Active areas of curation at SGD include yeast-human homology, alleles and phenotype variants, functional complementation relationships, and disease associations. There are plenty of ways to find this information on our website, and it takes just 90 seconds to learn how – what are you waiting for?
For more SGD Help Videos, visit our YouTube channel, and be sure to subscribe so you don’t miss anything!
Categories: Announcements, Homologs, Tutorial, Yeast and Human Disease
Sign Up Now for the Next SGD Webinar: September 7, 2016
September 02, 2016
The SPELL expression analysis tool at SGD makes it easy to find expression datasets and coexpressed genes that are relevant to your genes of interest. Just plug in a set of genes and go! Once given a query, SGD’s instance of SPELL locates informative expression datasets from over 270 published studies and identifies additional genes with similar expression profiles.
Find out how to use SPELL in our upcoming webinar on September 7th, 9:30 AM PDT. This quick 10-minute tutorial will explain how to run a multi-gene query in SPELL, locate expression datasets relevant to your query, and find genes with similar expression profiles.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar5
This is the fifth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Tutorial
SGD: New Search, New Style
August 22, 2016
- Superior search box functionality: New autocomplete options connect to information faster than ever
- Sorting options: Results sorted alphabetically, by relevance, and by number of annotations
- Download gene lists: Export gene lists from search results into a text file with the “Wrapped” and “Download” options
- Faceted searching: Narrow search results by using categories like Genes, Molecular Functions, Phenotypes, and more!
Categories: Announcements, Website changes
Coming Soon – New Search and New Styling
August 15, 2016
SGD is planning to release a new faceted search on Monday, August 22, 2016, along with some new site styling optimized for mobile use. The refactored search has been available for the last few months on our beta site: sgd-beta.stanford.edu.
New features of the search include:
- an expanded selection of fields included in the autocomplete list
- the ability to enter the SGD site and explore data and pages without an initial query – just click the Explore button and go!
- narrowing of search results by categories such as genes, molecular functions, and phenotypes (and more!)
Navigating SGD will soon be easier than ever. Please explore the new search, try some different queries, view the new styling on your favorite pages, and send us your feedback via email, or through this short survey.
Categories: Announcements, Website changes
Sign Up Now for the Next SGD Webinar: August 3, 2016
July 28, 2016
SGD’s Variant Viewer is an easy-to-learn web application that allows visualization of differences in both gene and protein sequences. With Variant Viewer, you can compare the nucleotide and amino acid sequences of your favorite genes in twelve widely-used S. cerevisiae strains. Our upcoming webinar on August 3rd, 9:30 AM PDT will provide a quick 10 minute tutorial on how to use Variant Viewer. We will demonstrate how to compare nucleotide and amino acid sequences of different S. cerevisiae genomes, and how to visualize strain-specific single nucleotide polymorphisms, insertions, and deletions contained within a given open reading frame.
If you are interested in attending this event, please register using this online form: http://bit.ly/SGDwebinar4
This is the fourth episode in the SGD Webinar Series. For more information on the SGD Webinar Series, please visit our wiki page: SGD Webinar Series.
Categories: Announcements, Sequence, Tutorial