Difference between revisions of "SGD Newsletter, Spring 2025"
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[[Category: Newsletter]] | [[Category: Newsletter]] | ||
| − | '''About this newsletter:''' <br> This is the | + | '''About this newsletter:''' <br> This is the Spring 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. |
| − | ==Give a Gift / Support SGD: Credit Cards | + | ==Give a Gift / Support SGD: Credit Cards Now Accepted== |
[[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]] | [[Image:gift.png|link=https://www.yeastgenome.org|thumb|left|upright=.5]] | ||
| − | Budget cuts from NIH continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. ''Donations are now critical for our work to continue'' | + | Budget cuts from NIH continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. ''Donations are now critical for our work to continue''. |
Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. | Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card. | ||
| − | To contribute using a credit card, please use this form: give.stanford.edu. | + | To contribute using a credit card, please use this form: [https://give.stanford.edu/ give.stanford.edu]. |
* Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu | * Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu | ||
| Line 18: | Line 18: | ||
Thank you for your support! | Thank you for your support! | ||
| − | == | + | ==SGD's Latest Genetics Publication== |
| + | [[File:genetics_229_3cover.jpeg|link=https://academic.oup.com/genetics/article-abstract/229/3/iyae185/7895713|thumb|left|upright=.5]] | ||
| + | [https://www.yeastgenome.org/reference/S000377741 ''Saccharomyces'' Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements] has now been published in GENETICS and is available in the [https://academic.oup.com/genetics/issue/229/3 March 2025 issue]. Check out the most recent updates at SGD, including: | ||
| + | <blockquote> | ||
| + | * Two most recent reference genome annotation updates | ||
| + | * Expanded biochemical pathways representation | ||
| + | * Changes to SGD search and data files | ||
| + | * Other enhancements to the SGD website and user interface | ||
| + | </blockquote> | ||
| + | <br><br> | ||
| − | == | + | ==Pathway Annotations Now Available as GO Annotations== |
| + | [[File:figure1GENETICS2025.jpg|thumb|left|upright=.75]][https://pathway.yeastgenome.org/ YeastPathways], the database of metabolic pathways and enzymes in the budding yeast ''Saccharomyces cerevisiae'', is manually curated and maintained by the biocuration team at SGD. | ||
| − | + | This resource is jam-packed with information, but was somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Initially, we added a new section with pathways links on the relevant gene pages (ex. [https://yeastgenome.org/locus/S000005762#pathway DFR1]). Additionally, we made the pathways available in SGD Search. Now, we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. [https://yeastgenome.org/locus/S000005762/go#comp DFR1]). | |
| + | Because many fundamental molecular processes and pathways are evolutionarily conserved between yeast and higher eukaryotes, including humans, the curated metabolic pathway information has great value for the transfer of knowledge to other organisms. It is for this reason that the YeastPathways data were exported in BioPAX ([https://pubmed.ncbi.nlm.nih.gov/20829833/ Demir et al. 2010]) format for import into Noctua, a tool for collaborative curation of biological pathways and gene annotations that was developed by the GO Consortium ([https://www.yeastgenome.org/reference/S000250248 Thomas et al. 2019]). BioPAX provides a standardized format for representing biological pathways, allowing researchers to integrate pathway information from different sources and databases. Noctua can import pathway data encoded in BioPAX format to populate the pathway editor with molecular interactions, biological processes, and regulatory relationships, and can utilize BioPAX files to combine pathway data from multiple datasets for pathway curation and analysis. | ||
| − | ==microPublications - | + | Pathways curated and edited in Noctua can be exported both as GO annotations for yeast and orthologous genes in other species, or as pathway annotations in BioPAX, facilitating the sharing of curated pathways with other researchers, databases, and analysis tools using a standard format, promoting data exchange, and collaboration within the scientific community. |
| + | |||
| + | ==New Yeast Phenome Links in Phenotype Resources== | ||
| + | [[File:calico_life_sciences_llc_logo.jpg|link=https://www.calicolabs.com/|thumb|left|upright=.4]] | ||
| + | |||
| + | The [https://www.yeastphenome.org/ Yeast Phenome] is a collaborative project from the Baryshnikova lab at Calico Life Sciences to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast ''Saccharomyces cerevisiae''. | ||
| + | |||
| + | The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection. | ||
| + | |||
| + | Locus-specific links to the Yeast Phenome are now available in the Resources section of the Phenotype tab and will take you directly to the corresponding page of the Yeast Phenome data library. Try it now: the SGD phenotype page for [https://yeastgenome.org/locus/S000001171/phenotype#resources ARP1], and the linked [https://www.yeastphenome.org/genes/1096/ ARP1] page at Yeast Phenome. | ||
| + | |||
| + | ==microPublications - Latest Yeast Papers== | ||
[[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]] | [[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]] | ||
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Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]: | Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]: | ||
| + | |||
| + | *[https://www.yeastgenome.org/reference/S100000262 Andrade Latino A, Biggins S (2025)] Analysis of a cancer-associated mutation in the budding yeast Nuf2 kinetochore protein. MicroPubl Biol 2025 | ||
| + | |||
| + | *[https://www.yeastgenome.org/reference/S100000243 Butcher C, VanderVen K, Li J (2025)] Proteasome condensates repeatedly "contact and release" at the nuclear periphery during dissolution. MicroPubl Biol 2025 | ||
| + | |||
| + | *[https://www.yeastgenome.org/reference/S100000186 Eftimie A, Meyer D (2025)] Transcription Regulatory Protein ''SIN3'' (YOL004W) Influences Mutation Rates in ''Saccharomyces cerevisiae''. MicroPubl Biol 2025 | ||
| + | |||
| + | *[https://www.yeastgenome.org/reference/S100000338 James M, Klain GK, Brito SO, Trejo L, Okello TMA, Segarra VA (2025)] Autophagy-deficient budding yeast cells are sensitive to freeze-thaw stress. MicroPubl Biol 2025 | ||
| + | |||
| + | *[https://www.yeastgenome.org/reference/S000378976 Law S, et al. (2024)] The Role of hBRCA2 in the Repair of Spontaneous and UV DNA Damage in Saccharomyces cerevisiae. MicroPubl Biol 2024 | ||
| + | |||
| + | *[https://www.yeastgenome.org/reference/S100000138 Pfliegler WP, Imre A, Biotechnology BSc Class Of UOD, Pócsi I (2025)] PCR-fingerprinting of culturable yeasts from commercially obtained beers: a simple and engaging applied microbiological laboratory exercise. MicroPubl Biol 2025 | ||
| + | |||
| + | *[https://www.yeastgenome.org/reference/S100000150 Thota K, Fredette-Roman JD, Sharp NP (2025)] Yeast mutation rates in alternative carbon sources reflect the influence of reactive oxygen species. MicroPubl Biol 2025 | ||
All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD]. | All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD]. | ||
| − | ==Alliance of Genome Resources - Latest Release 8. | + | ==Alliance of Genome Resources - Latest Release 8.1.0== |
[[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]] | [[Image:alliance_logo.png|link=https://www.alliancegenome.org|thumb|right|upright=.725]] | ||
| − | The 8. | + | The 8.1.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements. |
| − | + | Recent changes in 8.0.0 and 8.1.0 include: | |
* Redesign of the legend corrects issues with casual relationship representation; interface visuals have been refined; all defined causal relationships are now depicted using standardized glyphs with a matching color legend. | * Redesign of the legend corrects issues with casual relationship representation; interface visuals have been refined; all defined causal relationships are now depicted using standardized glyphs with a matching color legend. | ||
| Line 48: | Line 84: | ||
There is now an Event Calendar with the schedule of upcoming Alliance office hours and webinars: https://www.alliancegenome.org/event-calendar | There is now an Event Calendar with the schedule of upcoming Alliance office hours and webinars: https://www.alliancegenome.org/event-calendar | ||
| − | ==Upcoming | + | * View the video of the latest Alliance of Genome Resources webinar: |
| − | + | **[https://www.youtube.com/watch?v=iaOE8-kbxqo How AI informs literature curation at the Alliance] | |
| + | **Presented on April 17, 2025 by Kimberly Van Auken and Valerio Arnaboldi of WormBase, and Chris Tabone of FlyBase. | ||
| + | |||
| + | ==Upcoming Conferences & Courses== | ||
| + | *[https://geneontology.org/ Gene Ontology Consortium Spring 2025 Meeting] | ||
| + | **May 5-8, 2025 | ||
| + | **Geneva, Switzerland | ||
| + | **''SGD will be attending'' | ||
| + | |||
| + | *[https://www.csh-asia.org/?content/2721 CSH Asia: Yeast and Life Sciences] | ||
| + | **June 02 to June 06, 2025 - | ||
| + | **Suzhou, China | ||
| + | |||
| + | *[https://www.pnwyc.net/ PNWYC 2025: Pacific Northwest Yeast Club] | ||
| + | **June 20, 2025 | ||
| + | **Vancouver, Canada | ||
| + | |||
| + | *[https://premc.org/yeast2025/about-paris/ Yeast2025: 32nd International Conference on Yeast Genetics and Molecular Biology ICYGMB32] | ||
| + | **July 21 to July 24, 2025 | ||
| + | **Sorbonne University, Paris, France | ||
| + | **''SGD will be attending'' | ||
| + | |||
| + | *[https://meetings.cshl.edu/courses.aspx?course=C-YEAS Yeast Genetics & Genomics] | ||
| + | **July 22 to August 12, 2025 | ||
| + | **Cold Spring Harbor Laboratory, Cold Spring Harbor, NY | ||
| + | **''SGD will be attending'' | ||
| − | + | *[https://issy38.com.pl/ 38th International Specialized Symposium on Yeasts (ISSY38)] | |
| + | **September 01 to September 05, 2025 - | ||
| + | **Warsaw University, Warsaw, Poland | ||
| − | + | *[https://genetics-gsa.org/fungal/ 33rd Fungal Genetics Conference] | |
| + | **March 17 to March 22, 2026 - | ||
| + | **Asilomar Conference Grounds, Pacific Grove, CA | ||
Latest revision as of 13:27, 30 April 2025
About this newsletter:
This is the Spring 2025 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community.
Contents
[hide]- 1 Give a Gift / Support SGD: Credit Cards Now Accepted
- 2 SGD's Latest Genetics Publication
- 3 Pathway Annotations Now Available as GO Annotations
- 4 New Yeast Phenome Links in Phenotype Resources
- 5 microPublications - Latest Yeast Papers
- 6 Alliance of Genome Resources - Latest Release 8.1.0
- 7 Upcoming Conferences & Courses
Give a Gift / Support SGD: Credit Cards Now Accepted
Budget cuts from NIH continue to strain SGD's finances. Despite our efforts at reducing costs, we still have significant ongoing budgetary challenges. Donations are now critical for our work to continue.
Your generous gift to SGD enables us to continue providing essential information for your research and teaching efforts. We are now able to accept gifts via credit card.
To contribute using a credit card, please use this form: give.stanford.edu.
- Under ‘Direct your gift,’ select ‘Other Stanford Designation’ from the pulldown menu
- In the ‘Other’ text box, specify SGD by including the text “Saccharomyces Genome Database - Account : GHJKO, Genetics : WAZC”
- Complete the form and payment to donate to SGD
If you’d like to contribute by check, please contact us at: sgd-helpdesk@lists.stanford.edu
Thank you for your support!
SGD's Latest Genetics Publication
Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements has now been published in GENETICS and is available in the March 2025 issue. Check out the most recent updates at SGD, including:
- Two most recent reference genome annotation updates
- Expanded biochemical pathways representation
- Changes to SGD search and data files
- Other enhancements to the SGD website and user interface
Pathway Annotations Now Available as GO Annotations
YeastPathways, the database of metabolic pathways and enzymes in the budding yeast Saccharomyces cerevisiae, is manually curated and maintained by the biocuration team at SGD.
This resource is jam-packed with information, but was somewhat hidden from view. We have been doing different things recently to make the pathways more readily accessible. Initially, we added a new section with pathways links on the relevant gene pages (ex. DFR1). Additionally, we made the pathways available in SGD Search. Now, we have transformed the metabolic pathways and associated genes/enzymes into Gene Ontology (GO) annotations (ex. DFR1).
Because many fundamental molecular processes and pathways are evolutionarily conserved between yeast and higher eukaryotes, including humans, the curated metabolic pathway information has great value for the transfer of knowledge to other organisms. It is for this reason that the YeastPathways data were exported in BioPAX (Demir et al. 2010) format for import into Noctua, a tool for collaborative curation of biological pathways and gene annotations that was developed by the GO Consortium (Thomas et al. 2019). BioPAX provides a standardized format for representing biological pathways, allowing researchers to integrate pathway information from different sources and databases. Noctua can import pathway data encoded in BioPAX format to populate the pathway editor with molecular interactions, biological processes, and regulatory relationships, and can utilize BioPAX files to combine pathway data from multiple datasets for pathway curation and analysis.
Pathways curated and edited in Noctua can be exported both as GO annotations for yeast and orthologous genes in other species, or as pathway annotations in BioPAX, facilitating the sharing of curated pathways with other researchers, databases, and analysis tools using a standard format, promoting data exchange, and collaboration within the scientific community.
New Yeast Phenome Links in Phenotype Resources
The Yeast Phenome is a collaborative project from the Baryshnikova lab at Calico Life Sciences to create a comprehensive compendium of systematic loss-of-function phenotypes for the budding yeast Saccharomyces cerevisiae.
The Yeast Phenome systematically tracks, collects, and annotates all published phenotypic screens utilizing the yeast knock-out collection.
Locus-specific links to the Yeast Phenome are now available in the Resources section of the Phenotype tab and will take you directly to the corresponding page of the Yeast Phenome data library. Try it now: the SGD phenotype page for ARP1, and the linked ARP1 page at Yeast Phenome.
microPublications - Latest Yeast Papers
microPublication Biology is part of the emerging genre of rapidly-published research communications. microPublications publishes brief, novel findings, negative and/or reproduced results, and results which may initially lack a broader scientific narrative. Each article is peer-reviewed, assigned a DOI, and indexed through PubMed and PubMedCentral.
Consider microPubublications when you have a result that doesn't necessarily fit into a larger story, but will be of value to others.
Latest yeast microPublications:
- Andrade Latino A, Biggins S (2025) Analysis of a cancer-associated mutation in the budding yeast Nuf2 kinetochore protein. MicroPubl Biol 2025
- Butcher C, VanderVen K, Li J (2025) Proteasome condensates repeatedly "contact and release" at the nuclear periphery during dissolution. MicroPubl Biol 2025
- Eftimie A, Meyer D (2025) Transcription Regulatory Protein SIN3 (YOL004W) Influences Mutation Rates in Saccharomyces cerevisiae. MicroPubl Biol 2025
- James M, Klain GK, Brito SO, Trejo L, Okello TMA, Segarra VA (2025) Autophagy-deficient budding yeast cells are sensitive to freeze-thaw stress. MicroPubl Biol 2025
- Law S, et al. (2024) The Role of hBRCA2 in the Repair of Spontaneous and UV DNA Damage in Saccharomyces cerevisiae. MicroPubl Biol 2024
- Pfliegler WP, Imre A, Biotechnology BSc Class Of UOD, Pócsi I (2025) PCR-fingerprinting of culturable yeasts from commercially obtained beers: a simple and engaging applied microbiological laboratory exercise. MicroPubl Biol 2025
- Thota K, Fredette-Roman JD, Sharp NP (2025) Yeast mutation rates in alternative carbon sources reflect the influence of reactive oxygen species. MicroPubl Biol 2025
All yeast microPublications can be found in SGD.
Alliance of Genome Resources - Latest Release 8.1.0
The 8.1.0 release includes data refreshes from each of the model organism source databases as well as various backend improvements.
Recent changes in 8.0.0 and 8.1.0 include:
- Redesign of the legend corrects issues with casual relationship representation; interface visuals have been refined; all defined causal relationships are now depicted using standardized glyphs with a matching color legend.
There is now an Event Calendar with the schedule of upcoming Alliance office hours and webinars: https://www.alliancegenome.org/event-calendar
- View the video of the latest Alliance of Genome Resources webinar:
- How AI informs literature curation at the Alliance
- Presented on April 17, 2025 by Kimberly Van Auken and Valerio Arnaboldi of WormBase, and Chris Tabone of FlyBase.
Upcoming Conferences & Courses
- Gene Ontology Consortium Spring 2025 Meeting
- May 5-8, 2025
- Geneva, Switzerland
- SGD will be attending
- CSH Asia: Yeast and Life Sciences
- June 02 to June 06, 2025 -
- Suzhou, China
- PNWYC 2025: Pacific Northwest Yeast Club
- June 20, 2025
- Vancouver, Canada
- Yeast2025: 32nd International Conference on Yeast Genetics and Molecular Biology ICYGMB32
- July 21 to July 24, 2025
- Sorbonne University, Paris, France
- SGD will be attending
- Yeast Genetics & Genomics
- July 22 to August 12, 2025
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- SGD will be attending
- 38th International Specialized Symposium on Yeasts (ISSY38)
- September 01 to September 05, 2025 -
- Warsaw University, Warsaw, Poland
- 33rd Fungal Genetics Conference
- March 17 to March 22, 2026 -
- Asilomar Conference Grounds, Pacific Grove, CA
