SGD Newsletter, December 2024 - Revision history

Stacia: /* SGD’s new GENETICS publication */

2024-12-13T18:04:14Z

‎SGD’s new GENETICS publication

Stacia: /* SGD’s new GENETICS publication */

2024-12-13T18:03:05Z

‎SGD’s new GENETICS publication

Suzia: /* SGD’s new GENETICS publication */

2024-12-13T17:48:01Z

‎SGD’s new GENETICS publication

Suzia at 17:30, 13 December 2024

2024-12-13T17:30:27Z

Suzia: Suzia moved page SGD Newsletter, Winter 2024 to SGD Newsletter, December 2024: clarity

2024-12-13T17:22:31Z

Suzia moved page SGD Newsletter, Winter 2024 to SGD Newsletter, December 2024: clarity

Stacia: /* Community wiki shutting down */

2024-12-13T15:04:00Z

‎Community wiki shutting down

Stacia: /* microPublications - latest yeast papers */

2024-12-13T15:02:24Z

‎microPublications - latest yeast papers

Stacia: /* Contribute to the community: Sign open letter for biodata */

2024-12-13T15:01:58Z

‎Contribute to the community: Sign open letter for biodata

Stacia: /* Alliance of Genome Resources - Latest Release 7.4 */

2024-12-13T14:59:30Z

‎Alliance of Genome Resources - Latest Release 7.4

Stacia: /* microPublications - latest yeast papers */

2024-12-13T14:55:37Z

‎microPublications - latest yeast papers

@@ Line 34: / Line 34: @@
 ==SGD’s new GENETICS publication==
-[[File:geneticslogo.png|link=https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyae185/7895713?redirectedFrom=fulltext|thumb|left|upright=.6]]
+[[File:geneticslogo.png|link=https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyae185/7895713|thumb|left|upright=.6]]
 [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 as an accepted manuscript.  Check out the most recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface.

@@ Line 34: / Line 34: @@
 ==SGD’s new GENETICS publication==
-[[File:geneticslogo.png|link=https://www.yeastgenome.org/reference/S000377741|thumb|left|upright=.6]]
+[[File:geneticslogo.png|link=https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyae185/7895713?redirectedFrom=fulltext|thumb|left|upright=.6]]
 [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 as an accepted manuscript.  Check out the most recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface.

@@ Line 34: / Line 34: @@
 ==SGD’s new GENETICS publication==
-[[File:geneticslogo.png|link=https://globalbiodata.org/open-letter-campaign/|thumb|left|upright=.6]]
+[[File:geneticslogo.png|link=https://www.yeastgenome.org/reference/S000377741|thumb|left|upright=.6]]
 [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 as an accepted manuscript.  Check out the most recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface.

@@ Line 1: / Line 1: @@
 [[Category: Newsletter]]
 '''About this newsletter:'''<br>
-This is the Winter 2024 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features from SGD and to foster communication within the yeast community.
+This is the December 2024 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features from SGD and to foster communication within the yeast community.
 ==AlphaFold protein structures now on SGD protein pages==

@@ Line 31: / Line 31: @@
 ==Community wiki shutting down==
-As another casualty of decreased funding, SGD will no longer be able to provide the Community Wiki. Some of the resources hosted on the wiki have been moved to our Help pages, the Alliance Community Forum, or remain available though our SGD-archives downloads. We thank all our past and current Community Wiki contributors, and invite the yeast community to join SGD on our Alliance Community forum.
+As another casualty of decreased funding, SGD will no longer provide the Community Wiki. Some of the resources hosted on the wiki have been moved to our [https://sites.google.com/view/yeastgenome-help/sgd-general-help Help] pages, the [https://community.alliancegenome.org/c/model-organism-yeast/8 Alliance Community Forum], or remain available though the [http://sgd-archive.yeastgenome.org SGD downloads] site. We thank all our past and current Community Wiki contributors, and invite the yeast community to join SGD on the Alliance Community forum.
 ==SGD’s new GENETICS publication==

← Older revision	Revision as of 17:22, 13 December 2024
(No difference)

@@ Line 37: / Line 37: @@
 [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 as an accepted manuscript.  Check out the most recent updates at SGD, including the two most recent reference genome annotation updates, expanded biochemical pathways representation, changes to SGD search and data files, and other enhancements to the SGD website and user interface.
-==microPublications - latest yeast papers==
+==microPublications - Latest yeast papers==
 [[Image:MicroPub.png|link=https://www.micropublication.org/|thumb|right|upright=.4]]

@@ Line 21: / Line 21: @@
 In July 2024, YeastMine was discontinued due to ongoing cuts in funding at SGD. However, we have moved the YeastMine data into [https://www.alliancegenome.org/bluegenes/alliancemine AllianceMine], hosted by the [https://www.alliancegenome.org/ Alliance of Genome Resources], of which SGD is a founding member. You can even access lists like [https://www.alliancegenome.org/bluegenes/alliancemine/results/ALL_Verified_Uncharacterized_Dubious_ORFs “ALL_Verified_Uncharacterized_Dubious_ORFs”] through the [https://www.alliancegenome.org/bluegenes/alliancemine/lists AllianceMine ''Lists''] just as you could in the previous versions of YeastMine. Ensure any bookmarks to YeastMine have been updated to match the new URL: '''https://www.alliancegenome.org/bluegenes/alliancemine'''. User documentation for the new YeastMine interface is [http://intermine.org/intermine-user-docs/ available from InterMine].
-==Contribute to the community: Sign open letter for biodata==
+==Help maintain your genomic databases! Sign open letter supporting funding for biodata resources==
 [[Image:FkAzFtQWIAExhDl.jpeg|link=https://globalbiodata.org/open-letter-campaign/|thumb|left|upright=.5]]

@@ Line 61: / Line 61: @@
 The 7.4.0 release includes ~2.5 million variants of clinical significance from ClinVar.
-The Alliance dropped 400 million human variants (at least temporarily), mostly of unknown or uncertain clinical significance, in favor of over 2.5 million human variants of known clinical significance from ClinVar. This should speed up the performance of the site and improve site stability. The Alliance will address inclusion of the other high throughput human variants in the future. More detailed information about the 7.4 Alliance release can be found in the [https://www.alliancegenome.org/release-notes release notes].
+The Alliance removed 400 million human variants from the search because their inclusion was hampering site performance. The removed variants are mostly of unknown or uncertain clinical significance.  The Alliance has instead included over 2.5 million human variants of known clinical significance from ClinVar. This should speed up the performance of the search function and improve site stability. The Alliance will address inclusion of the other high throughput human variants in the future. More detailed information about the 7.4 Alliance release can be found in the [https://www.alliancegenome.org/release-notes release notes].
 ==Give a Gift / Support SGD==

@@ Line 45: / Line 45: @@
 Latest [https://www.micropublication.org/journals/biology/species/s-cerevisiae yeast microPublications]:
-* [https://www.yeastgenome.org/reference/S000350355 Pinto J, Tavakolian N, Li CB, Stelkens R (2024)] The relationship between cell density and cell count differs among ''Saccharomyces'' yeast species. MicroPubl Biol 2024
+* [https://www.yeastgenome.org/reference/S000377792 Beard JS, Francis LK, Forrest RC, Kalinowski A, Parks JC, Griffin WH, Tackett CL, Duina AA (2024)] Trapping of yFACT at 3' ends of genes is not a universal characteristic of yeast versions of Bryant-Li-Bhoj syndrome histone H3 mutants. MicroPubl Biol 2024
 * [https://www.yeastgenome.org/reference/S000376719 Mucelli X, Huang LS (2024)] Naming internal insertion alleles created using CRISPR in ''Saccharomyces cerevisiae''. MicroPubl Biol 2024
 * [https://www.yeastgenome.org/reference/S000375481 Owutey SL, Procuniar KA, Akoto E, Davis JC, Vachon RM, O'Malley LF, Schneider HO, Smaldino PJ, True JD, Kalinski AL, Rubenstein EM (2024)] Endoplasmic reticulum and inner nuclear membrane ubiquitin-conjugating enzymes Ubc6 and Ubc7 confer resistance to hygromycin B in ''Saccharomyces cerevisiae''. MicroPubl Biol 2024
-* [https://www.yeastgenome.org/reference/S000350461 Hill JM, Pedersen RT, Drubin DG (2024)] Myosin-I's motor and actin assembly activation activities are modular and separable in budding yeast clathrin-mediated endocytosis. MicroPubl Biol 2024
+* [https://www.yeastgenome.org/reference/S000350355 Pinto J, Tavakolian N, Li CB, Stelkens R (2024)] The relationship between cell density and cell count differs among ''Saccharomyces'' yeast species. MicroPubl Biol 2024
 * [https://www.yeastgenome.org/reference/S000377291 Ramakrishnan P, Keeney J (2024)] The yeast gene ECM9 regulates cell wall maintenance and cell division in stress conditions. MicroPubl Biol 2024
 All yeast microPublications can be found in [https://www.yeastgenome.org/search?category=reference&journal=microPublication.%20Biology&page=0&q= SGD].