R3N313 last accessed: 2022-11-04

SGD - Saccharomyces Genome Database
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Saccharomyces genome database (SGD)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

sgd
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

Other names: SGD, SGD - Saccharomyces Genome Database, Saccharomyces genome database (SGD), sgd

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.

Webpage:

http://www.yeastgenome.org/

Licence:

Name: Stanford University Terms of Use
URL: https://www.stanford.edu/site/terms/

Publications: (46)

Publications
More detailed information about this field from each metasource.

Saccharomyces Genome Database: the genomics resource of budding yeast
PMID: 22110037
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

SGD: Saccharomyces Genome Database
PMID: 9399804
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

Genetic and physical maps of Saccharomyces cerevisiae
PMID: 9169866
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The reference genome sequence of Saccharomyces cerevisiae: then and now
PMID: 24374639
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit
PMID: 22434830
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Gene Ontology annotations at SGD: new data sources and annotation methods
PMID: 17982175
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
PMID: 14681421
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
PMID: 11752257
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Comparison of the complete protein sets of worm and yeast: orthology and divergence
PMID: 9851918
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Yeast as a model organism
PMID: 9297238
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces Genome Database provides mutant phenotype data
PMID: 19906697
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

A guide to best practices for Gene Ontology (GO) manual annotation
PMID: 23842463
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Standardized description of scientific evidence using the Evidence Ontology (ECO)
PMID: 25052702
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome
PMID: 16381907
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis
PMID: 17001629
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Expanded protein information at SGD: new pages and proteome browser
PMID: 17142221
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces Genome Database
PMID: 12073322
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The complex portal--an encyclopaedia of macromolecular complexes
PMID: 25313161
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces genome database: underlying principles and organisation
PMID: 15153302
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces genome database provides new regulation data
PMID: 24265222
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Integrating functional genomic information into the Saccharomyces genome database
PMID: 10592186
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins
PMID: 12519985
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)
PMID: 15608219
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
PMID: 11125055
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae
PMID: 25781462
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure
PMID: 9847146
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database
PMID: 23487186
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns
PMID: 19577472
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

New mutant phenotype data curation system in the Saccharomyces Genome Database
PMID: 20157474
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Saccharomyces Genome Database: A Tool for Discovery
PMID: 26631132
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Saccharomyces Genome Database Variant Viewer
PMID: 26578556
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study
PMID: 21411447
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Molecular linguistics: extracting information from gene and protein sequences
PMID: 9159100
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations
PMID: 22434836
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Biocuration at the Saccharomyces genome database
PMID: 25997651
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Genetic nomenclature guide. Saccharomyces cerevisiae
PMID: 7660459
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

From one to many: expanding the Saccharomyces cerevisiae reference genome panel
PMID: 26989152
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report
PMID: 22434826
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes
PMID: 26631123
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component
PMID: 26631125
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The YeastGenome app: the Saccharomyces Genome Database at your fingertips
PMID: 23396302
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

Expanding yeast knowledge online
PMID: 9885151
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining
PMID: 26631124
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations
PMID: 26631126
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

http://dx.doi.org/10.1002/9780470089941.et1104s01
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

http://dx.doi.org/10.1093/nar/gkt1158
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Saccharomyces Genome Database: the genomics resource of budding yeast PubMed citations: 796.

796 articles citing: Saccharomyces Genome Database: the genomics resource of budding yeast

Physiological and Molecular Characterization of an Oxidative Stress-Resistant Saccharomyces cerevisiae Strain Obtained by Evolutionary Engineering. PMID:35283819
Inter-Species Rescue of Mutant Phenotype-The Standard for Genetic Analysis of Human Genetic Disorders in Drosophila melanogaster Model. PMID:35269756
The evolution, evolvability and engineering of gene regulatory DNA. PMID:35264797
Invertebrate Model Organisms as a Platform to Investigate Rare Human Neurological Diseases. PMID:35256540
Inferring Causation in Yeast Gene Association Networks With Kernel Logistic Regression. PMID:35173404
Comparative Analysis of Type 1 and Type Z Protein Phosphatases Reveals D615 as a Key Residue for Ppz1 Regulation. PMID:35163251
A comprehensive landscape of 60S ribosome biogenesis factors. PMID:35139378
Post-transcriptional control of fungal cell wall synthesis. PMID:35097244
Genetic basis of a spontaneous mutation's expressivity. PMID:35078232
Lactic Acid Permeability of Aquaporin-9 Enables Cytoplasmic Lactate Accumulation via an Ion Trap. PMID:35054513
Identification of periodic attractors in Boolean networks using a priori information. PMID:35030172
Improving carotenoid production in recombinant yeast, Saccharomyces cerevisiae, using ultrasound-irradiated two-phase extractive fermentation. PMID:35024023
Determinants of the temperature adaptation of mRNA degradation. PMID:35018460
The Ceramide Synthase Subunit Lac1 Regulates Cell Growth and Size in Fission Yeast. PMID:35008733
Rhizophagus proliferus genome sequence reiterates conservation of genetic traits in AM fungi, but predicts higher saprotrophic activity. PMID:34967937
Functional analysis of a Phytophthora host-translocated effector using the yeast model system. PMID:34966585
What 'Omics can tell us about antifungal adaptation. PMID:34958354
YPK9 and WHI2 Negatively Interact during Oxidative Stress. PMID:34946185
Three topological features of regulatory networks control life-essential and specialized subsystems. PMID:34930908
The economics of organellar gene loss and endosymbiotic gene transfer. PMID:34930424
Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. PMID:34922010
Yeast Double Transporter Gene Deletion Library for Identification of Xenobiotic Carriers in Low or High Throughput. PMID:34903049
The genetic basis of differential autodiploidization in evolving yeast populations. PMID:34849811
Pathways shaping the mitochondrial inner membrane. PMID:34847778
An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes. PMID:34843465
The SPFH Protein Superfamily in Fungi: Impact on Mitochondrial Function and Implications in Virulence. PMID:34835412
The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. PMID:34830359
Nearly 30 Years of Animal Models to Study Amyotrophic Lateral Sclerosis: A Historical Overview and Future Perspectives. PMID:34830115
Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution. PMID:34810219
Protein innovation through template switching in the Saccharomyces cerevisiae lineage. PMID:34799587
Multiple epistatic DNA variants in a single gene affect gene expression in trans. PMID:34791209
Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets. PMID:34764269
An HSP90 cochaperone Ids2 maintains the stability of mitochondrial DNA and ATP synthase. PMID:34763695
Constraint-based modeling of yeast mitochondria reveals the dynamics of protein import and iron-sulfur cluster biogenesis. PMID:34755100
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PMID:34748537
Sex without crossing over in the yeast Saccharomycodes ludwigii. PMID:34732243
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. PMID:34676984
A standard knockout procedure alters expression of adjacent loci at the translational level. PMID:34606617
Low Toxicological Impact of Commercial Pristine Multi-Walled Carbon Nanotubes on the Yeast Saccharomyces cerevisiae. PMID:34578588
Biotechnological Importance of Torulaspora delbrueckii: From the Obscurity to the Spotlight. PMID:34575750
Porin 1 Modulates Autophagy in Yeast. PMID:34572064
Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum. PMID:34554246
Genetic screen for suppressors of increased silencing in rpd3 mutants in Saccharomyces cerevisiae identifies a potential role for H3K4 methylation. PMID:34534290
Restoring fertility in yeast hybrids: Breeding and quantitative genetics of beneficial traits. PMID:34518218
Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae. PMID:34499735
Fur4-mediated uracil-scavenging to screen for surface protein regulators. PMID:34498791
A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. PMID:34494883
Mapping the dynamic transfer functions of eukaryotic gene regulation. PMID:34469745
CO2 enhances the formation, nutrient scavenging and drug resistance properties of C. albicans biofilms. PMID:34385462
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon. PMID:34376148
Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments. PMID:34367085
HSF1 induces RNA polymerase II synthesis of ribosomal RNA in S. cerevisiae during nitrogen deprivation. PMID:34363098
Using Budding Yeast to Identify Molecules That Block Cancer Cell 'Mitotic Slippage' Only in the Presence of Mitotic Poisons. PMID:34360748
Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. PMID:34358317
Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site. PMID:34302485
Harmful R-loops are prevented via different cell cycle-specific mechanisms. PMID:34294712
Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity. PMID:34287034
YPIBP: A repository for phosphoinositide-binding proteins in yeast. PMID:34285772
From the first touch to biofilm establishment by the human pathogen Candida glabrata: a genome-wide to nanoscale view. PMID:34285314
Data integration uncovers the metabolic bases of phenotypic variation in yeast. PMID:34264947
Performance of Regression Models as a Function of Experiment Noise. PMID:34262264
Integrated Multi-Omics Analysis of Mechanisms Underlying Yeast Ethanol Tolerance. PMID:34236875
ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors. PMID:34223816
iTARGEX analysis of yeast deletome reveals novel regulators of transcriptional buffering in S phase and protein turnover. PMID:34197604
A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex. PMID:34162742
Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans. PMID:34154419
Investigating the role of the transcriptional regulator Ure2 on the metabolism of Saccharomyces cerevisiae: a multi-omics approach. PMID:34152451
Tailoring strain construction strategies for muconic acid production in S. cerevisiae and E. coli. PMID:34150501
A small ribosome-associated ncRNA globally inhibits translation by restricting ribosome dynamics. PMID:34121604
R2DT is a framework for predicting and visualising RNA secondary structure using templates. PMID:34108470
A genome-scale yeast library with inducible expression of individual genes. PMID:34096681
Identifying Genes Devoted to the Cell Death Process in the Gene Regulatory Network of Ustilago maydis. PMID:34093501
Discovery of 17 conserved structural RNAs in fungi. PMID:34086938
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. PMID:34072576
A Biochemical and Structural Understanding of TOM Complex Interactions and Implications for Human Health and Disease. PMID:34064787
Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins. PMID:33996892
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast. PMID:33920164
The state of F-BAR domains as membrane-bound oligomeric platforms. PMID:33888395
Selectivity of mRNA degradation by autophagy in yeast. PMID:33875662
Transcriptome Analysis in Yeast Reveals the Externality of Position Effects. PMID:33871622
Data from crosslinking and analysis of cDNAs (CRAC) of Nab3 in yeast cells expressing a circular ncRNA decoy. PMID:33842679
Reasons for 2-furaldehyde and 5-hydroxymethyl-2-furaldehyde resistance in Saccharomyces cerevisiae: current state of knowledge and perspectives for further improvements. PMID:33830300
Multiple nutritional phenotypes of fission yeast mutants defective in genes encoding essential mitochondrial proteins. PMID:33823662
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals. PMID:33790324
Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism. PMID:33790287
Protein interaction potential landscapes for yeast replicative aging. PMID:33785798
Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species. PMID:33772558
Basigin drives intracellular accumulation of l-lactate by harvesting protons and substrate anions. PMID:33770122
A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast. PMID:33757429
A case of convergent-gene interference in the budding yeast knockout library causing chromosome instability. PMID:33724427
RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2'-O-methylation. PMID:33721027
Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast. PMID:33720010
Engineered yeast genomes accurately assembled from pure and mixed samples. PMID:33674578
A Protocol to Map the Spatial Proteome Using HyperLOPIT in Saccharomyces cerevisiae. PMID:33654815
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions. PMID:33616531
Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. PMID:33573382
DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. PMID:33571201
Global mapping of protein-metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. PMID:33568709
Inner-nuclear-membrane-associated degradation employs Dfm1-independent retrotranslocation and alleviates misfolded transmembrane-protein toxicity. PMID:33566711
The actin networks of chytrid fungi reveal evolutionary loss of cytoskeletal complexity in the fungal kingdom. PMID:33561386
Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12. PMID:33561236
Yeast translation elongation factor eEF3 promotes late stages of tRNA translocation. PMID:33555093
Ribosome-bound Get4/5 facilitates the capture of tail-anchored proteins by Sgt2 in yeast. PMID:33542241
Genomic and Targeted Approaches Unveil the Cell Membrane as a Major Target of the Antifungal Cytotoxin Amantelide A. PMID:33527693
A genome-wide screen in Saccharomyces cerevisiae identifies Tannic Acid-sensitive mutants. PMID:33474531
Transportome-wide engineering of Saccharomyces cerevisiae. PMID:33465478
Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae. PMID:33462193
Model systems for studying polyphosphate biology: a focus on microorganisms. PMID:33420907
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. PMID:33402206
The involvement of the Candida glabrata trehalase enzymes in stress resistance and gut colonization. PMID:33356857
Bidirectional Genetic Control of Phenotypic Heterogeneity and Its Implication for Cancer Drug Resistance. PMID:33355660
Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast. PMID:33292418
Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function. PMID:33280256
In silico identification of Drosophila melanogaster genes encoding RNA polymerase subunits. PMID:33274328
A Suggestion of Converting Protein Intrinsic Disorder to Structural Entropy Using Shannon's Information Theory. PMID:33267305
Saccharomyces paradoxus Transcriptional Alterations in Cells of Distinct Phenotype and Viral dsRNA Content. PMID:33266158
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. PMID:33262328
Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid. PMID:33252673
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. PMID:33237311
Cell-cycle phospho-regulation of the kinetochore. PMID:33221975
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross. PMID:33179598
Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress. PMID:33170850
Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates. PMID:33152326
Genetic profiling of protein burden and nuclear export overload. PMID:33146608
Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa. PMID:33138786
Characterization of systemic genomic instability in budding yeast. PMID:33106418
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. PMID:33084874
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions. PMID:33070389
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
Genome Profiling for Aflatoxin B1 Resistance in Saccharomyces cerevisiae Reveals a Role for the CSM2/SHU Complex in Tolerance of Aflatoxin B1-Associated DNA Damage. PMID:32994210
Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism. PMID:32978375
TheCellVision.org: A Database for Visualizing and Mining High-Content Cell Imaging Projects. PMID:32934016
Systematic analysis of nuclear gene function in respiratory growth and expression of the mitochondrial genome in S. cerevisiae. PMID:32904421
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials. PMID:32849484
RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. PMID:32839320
Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media. PMID:32817546
Ribosomal proteins: mutant phenotypes by the numbers and associated gene expression changes. PMID:32810425
Polo kinase recruitment via the constitutive centromere-associated network at the kinetochore elevates centromeric RNA. PMID:32810142
Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping. PMID:32804946
Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. PMID:32732306
Characteristics of Extracellular Vesicles Released by the Pathogenic Yeast-Like Fungi Candida glabrata, Candida parapsilosis and Candida tropicalis. PMID:32708393
COSMO: A dynamic programming algorithm for multicriteria codon optimization. PMID:32695273
Protein Interactions of the Mechanosensory Proteins Wsc2 and Wsc3 for Stress Resistance in Saccharomyces cerevisiae. PMID:32641451
Harnessing sub-organelle metabolism for biosynthesis of isoprenoids in yeast. PMID:32637671
Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes. PMID:32635509
Phosphoproteome Response to Dithiothreitol Reveals Unique Versus Shared Features of Saccharomyces cerevisiae Stress Responses. PMID:32597660
The transcription factor Leu3 shows differential binding behavior in response to changing leucine availability. PMID:32589214
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
Proteomic profiling of the monothiol glutaredoxin Grx3 reveals its global role in the regulation of iron dependent processes. PMID:32525871
Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes. PMID:32522745
The RNA fold interactome of evolutionary conserved RNA structures in S. cerevisiae. PMID:32493961
An Optimized Competitive-Aging Method Reveals Gene-Drug Interactions Underlying the Chronological Lifespan of Saccharomyces cerevisiae. PMID:32477409
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks. PMID:32471360
Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization. PMID:32457798
A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning. PMID:32416068
Budding yeast complete DNA synthesis after chromosome segregation begins. PMID:32385287
Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae. PMID:32376676
A Novel Computational Approach for Identifying Essential Proteins From Multiplex Biological Networks. PMID:32373163
Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. PMID:32369734
Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective. PMID:32336995
A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria. PMID:32332106
Mitochondrial Biogenesis Is Positively Regulated by Casein Kinase I Hrr25 Through Phosphorylation of Puf3 in Saccharomyces cerevisiae. PMID:32317286
Perturbing proteomes at single residue resolution using base editing. PMID:32313011
Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast. PMID:32312967
Growing a circular economy with fungal biotechnology: a white paper. PMID:32280481
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. PMID:32184324
An evaluation of machine-learning for predicting phenotype: studies in yeast, rice, and wheat. PMID:32174648
Yeast as a Model to Understand Actin-Mediated Cellular Functions in Mammals-Illustrated with Four Actin Cytoskeleton Proteins. PMID:32164332
Rpn4 and proteasome-mediated yeast resistance to ethanol includes regulation of autophagy. PMID:32157425
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. PMID:32128557
Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection. PMID:32123323
Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. PMID:32107786
Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9. PMID:32102971
Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets. PMID:32094381
Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast. PMID:32085421
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. PMID:32066524
2'-O-ribose methylation of transfer RNA promotes recovery from oxidative stress in Saccharomyces cerevisiae. PMID:32053677
Sex alters molecular evolution in diploid experimental populations of S. cerevisiae. PMID:32042122
Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom. PMID:32020195
The Key Parameters that Govern Translation Efficiency. PMID:31954660
Vanillin Production in Pseudomonas: Whole-Genome Sequencing of Pseudomonas sp. Strain 9.1 and Reannotation of Pseudomonas putida CalA as a Vanillin Reductase. PMID:31924622
The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae. PMID:31885205
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries. PMID:31856718
The InsP7 phosphatase Siw14 regulates inositol pyrophosphate levels to control localization of the general stress response transcription factor Msn2. PMID:31848224
Phagocytosis-like cell engulfment by a planctomycete bacterium. PMID:31827088
Mapping Ethanol Tolerance in Budding Yeast Reveals High Genetic Variation in a Wild Isolate. PMID:31824552
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. PMID:31799603
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters. PMID:31792407
Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization. PMID:31791228
Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. PMID:31757756
ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps. PMID:31747015
CgSTE11 mediates cross tolerance to multiple environmental stressors in Candida glabrata. PMID:31745168
DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories. PMID:31738765
Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture. PMID:31728200
Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. PMID:31722220
A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin. PMID:31660150
Cellular models of Batten disease. PMID:31655107
Use of Wine and Dairy Yeasts as Single Starter Cultures for Flavor Compound Modification in Fish Sauce Fermentation. PMID:31649641
Transcriptome visualization and data availability at the Saccharomyces Genome Database. PMID:31612944
The CCR4-NOT Complex Maintains Stability and Transcription of rRNA Genes by Repressing Antisense Transcripts. PMID:31611247
Genetic interaction networks mediate individual statin drug response in Saccharomyces cerevisiae. PMID:31602312
A Humanized Yeast Phenomic Model of Deoxycytidine Kinase to Predict Genetic Buffering of Nucleoside Analog Cytotoxicity. PMID:31575041
Comprehensive Analysis of Replication Origins in Saccharomyces cerevisiae Genomes. PMID:31572328
Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae. PMID:31570626
Proteomics-Based Monitoring of Pathway Activity Reveals that Blocking Diacylglycerol Biosynthesis Rescues from Alpha-Synuclein Toxicity. PMID:31521608
Spontaneous whole-genome duplication restores fertility in interspecific hybrids. PMID:31511504
Whole-Genome Sequencing of Yeast Cells. PMID:31503417
Systematical Analysis of the Protein Targets of Lactoferricin B and Histatin-5 Using Yeast Proteome Microarrays. PMID:31466342
Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli. PMID:31464375
fagin: synteny-based phylostratigraphy and finer classification of young genes. PMID:31455236
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
Protein-Protein Interactions in Candida albicans. PMID:31440220
Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome. PMID:31437148
Improving ionic liquid tolerance in Saccharomyces cerevisiae through heterologous expression and directed evolution of an ILT1 homolog from Yarrowia lipolytica. PMID:31428944
Accurate Tracking of the Mutational Landscape of Diploid Hybrid Genomes. PMID:31397846
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach. PMID:31366992
Atg11 tethers Atg9 vesicles to initiate selective autophagy. PMID:31356628
Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. PMID:31341962
Comparative transcriptomics suggest unique molecular adaptations within tardigrade lineages. PMID:31340759
ParaDB: A manually curated database containing genomic annotation for the human pathogenic fungi Paracoccidioides spp. PMID:31306428
Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L-dose dependency in HDAC1-deficient thymic lymphoma. PMID:31304633
Molecular Chaperones Accelerate the Evolution of Their Protein Clients in Yeast. PMID:31297528
Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen. PMID:31283755
Moonlighting proteins are variably exposed at the cell surfaces of Candida glabrata, Candida parapsilosis and Candida tropicalis under certain growth conditions. PMID:31269895
The l-Thr Kinase/l-Thr-Phosphate Decarboxylase (CobD) Enzyme from Methanosarcina mazei Gö1 Contains Metallocenters Needed for Optimal Activity. PMID:31268299
Proteome-wide signatures of function in highly diverged intrinsically disordered regions. PMID:31264965
Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone. PMID:31254414
Screening of Candida albicans GRACE library revealed a unique pattern of biofilm formation under repression of the essential gene ILS1. PMID:31235750
Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. PMID:31216041
DNA sequence influences hexasome orientation to regulate DNA accessibility. PMID:31216039
UV Laser-Induced, Time-Resolved Transcriptome Responses of Saccharomyces cerevisiae. PMID:31213515
Combining learning and constraints for genome-wide protein annotation. PMID:31208327
Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. PMID:31128237
Stop-codon read-through arises largely from molecular errors and is generally nonadaptive. PMID:31120886
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PMID:31112549
The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. PMID:31092540
Yeast expression of mammalian Onzin and fungal FCR1 suggests ancestral functions of PLAC8 proteins in mitochondrial metabolism and DNA repair. PMID:31036870
YeasTSS: an integrative web database of yeast transcription start sites. PMID:31032841
Gene discovery informatics toolkit defines candidate genes for unexplained infertility and prenatal or infantile mortality. PMID:30993004
In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation. PMID:30946741
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
The Endoplasmic Reticulum-Mitochondria Encounter Structure Complex Coordinates Coenzyme Q Biosynthesis. PMID:30937424
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PMID:30897079
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling. PMID:30849073
A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle. PMID:30833602
A synthetic non-histone substrate to study substrate targeting by the Gcn5 HAT and sirtuin HDACs. PMID:30804216
dStruct: identifying differentially reactive regions from RNA structurome profiling data. PMID:30791935
Proteomic characterization of the arsenic response locus in S. cerevisiae. PMID:30739529
Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations. PMID:30715293
Integration of macromolecular complex data into the Saccharomyces Genome Database. PMID:30715277
Primary and Secondary Metabolic Effects of a Key Gene Deletion (ΔYPL062W) in Metabolically Engineered Terpenoid-Producing Saccharomyces cerevisiae. PMID:30683746
Role of the highly conserved G68 residue in the yeast phosphorelay protein Ypd1: implications for interactions between histidine phosphotransfer (HPt) and response regulator proteins. PMID:30665347
Spatial proteomics: a powerful discovery tool for cell biology. PMID:30659282
NommPred: Prediction of Mitochondrial and Mitochondrion-Related Organelle Proteins of Nonmodel Organisms. PMID:30626996
Yeast Models of Prion-Like Proteins That Cause Amyotrophic Lateral Sclerosis Reveal Pathogenic Mechanisms. PMID:30618605
Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions. PMID:30590648
Extension of the yeast metabolic model to include iron metabolism and its use to estimate global levels of iron-recruiting enzyme abundance from cofactor requirements. PMID:30578666
Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection. PMID:30576464
A resource of variant effect predictions of single nucleotide variants in model organisms. PMID:30573687
Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes. PMID:30553725
A biosensor-based approach reveals links between efflux pump expression and cell cycle regulation in pleiotropic drug resistance of yeast. PMID:30514758
Decoupling the Variances of Heterosis and Inbreeding Effects Is Evidenced in Yeast's Life-History and Proteomic Traits. PMID:30509954
The subcellular organisation of Saccharomyces cerevisiae. PMID:30503867
Updating genome annotation for the microbial cell factory Aspergillus niger using gene co-expression networks. PMID:30496528
The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. PMID:30425417
i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks. PMID:30393778
Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans. PMID:30377286
Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions. PMID:30376562
Genomic and Transcriptomic Basis of Hanseniaspora vineae's Impact on Flavor Diversity and Wine Quality. PMID:30366992
YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries. PMID:30357397
Functional Mapping of Transcription Factor Grf10 That Regulates Adenine-Responsive and Filamentation Genes in Candida albicans. PMID:30355670
Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health. PMID:30338244
Analysis of impact metrics for the Protein Data Bank. PMID:30325351
Genome-wide identification of the fatty acid desaturases gene family in four Aspergillus species and their expression profile in Aspergillus oryzae. PMID:30324529
Substrate priming enhances phosphorylation by the budding yeast kinases Kin1 and Kin2. PMID:30305396
Critical Role for Saccharomyces cerevisiae Asc1p in Translational Initiation at Elevated Temperatures. PMID:30285306
Oxidative stress-induced structural changes in the microtubule-associated flavoenzyme Irc15p from Saccharomyces cerevisiae. PMID:30267443
Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host. PMID:30254120
Identifying Drivers of Parallel Evolution: A Regression Model Approach. PMID:30252076
POSTAR2: deciphering the post-transcriptional regulatory logics. PMID:30239819
Network analysis of membranous glomerulonephritis based on metabolomics data. PMID:30221719
Knockout of the Hmt1p Arginine Methyltransferase in Saccharomyces cerevisiae Leads to the Dysregulation of Phosphate-associated Genes and Processes. PMID:30206180
Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts. PMID:30195436
Effects of Acetylation and Phosphorylation on Subunit Interactions in Three Large Eukaryotic Complexes. PMID:30181345
Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. PMID:30181241
Astaxanthin overproduction in yeast by strain engineering and new gene target uncovering. PMID:30159030
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. PMID:30152809
A High-Throughput Candida albicans Two-Hybrid System. PMID:30135223
Structure analysis of yeast glutaredoxin Grx6 protein produced in Escherichia coli. PMID:30123389
Poor codon optimality as a signal to degrade transcripts with frameshifts. PMID:30105929
Resistance to the Plant Defensin NaD1 Features Modifications to the Cell Wall and Osmo-Regulation Pathways of Yeast. PMID:30087664
Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells. PMID:30072377
Tracing the De Novo Origin of Protein-Coding Genes in Yeast. PMID:30065088
Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes. PMID:30053068
Genetics of trans-regulatory variation in gene expression. PMID:30014850
Structure Optimization for Large Gene Networks Based on Greedy Strategy. PMID:30013615
Decoding the chromatin proteome of a single genomic locus by DNA sequencing. PMID:30005073
Patterns of Conservation and Diversification in the Fungal Polarization Network. PMID:29931311
A novel chimaeric flocculation protein enhances flocculation in Saccharomyces cerevisiae. PMID:29896447
Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER. PMID:29889214
Peptide inhibitors of the anaphase promoting-complex that cause sensitivity to microtubule poison. PMID:29883473
Repeated Cis-Regulatory Tuning of a Metabolic Bottleneck Gene during Evolution. PMID:29788479
Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks. PMID:29777105
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. PMID:29738528
Yeast Cell Wall Chitin Reduces Wine Haze Formation. PMID:29703738
YAAM: Yeast Amino Acid Modifications Database. PMID:29688347
Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins. PMID:29686995
Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi. PMID:29679020
A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. PMID:29661190
Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle. PMID:29654251
Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks. PMID:29641998
Predicting essential proteins by integrating orthology, gene expressions, and PPI networks. PMID:29634727
Comparative analysis of transcriptomic responses to sub-lethal levels of six environmentally relevant pesticides in Saccharomyces cerevisiae. PMID:29611082
Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry. PMID:29606352
Promoter architecture determines cotranslational regulation of mRNA. PMID:29567675
Yeast can accommodate phosphotyrosine: v-Src toxicity in yeast arises from a single disrupted pathway. PMID:29546391
Integrative structure and functional anatomy of a nuclear pore complex. PMID:29539637
Yeast screen for modifiers of C9orf72 poly(glycine-arginine) dipeptide repeat toxicity. PMID:29528392
Toolbox: Creating a systematic database of secretory pathway proteins uncovers new cargo for COPI. PMID:29527758
Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. PMID:29521624
The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants. PMID:29495437
Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PMID:29494600
Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance. PMID:29474395
The PUF Protein Family: Overview on PUF RNA Targets, Biological Functions, and Post Transcriptional Regulation. PMID:29385744
Hsp70-associated chaperones have a critical role in buffering protein production costs. PMID:29377792
Non-B-Form DNA Is Enriched at Centromeres. PMID:29365169
Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. PMID:29361467
nextPARS: parallel probing of RNA structures in Illumina. PMID:29358234
High-resolution transcription maps reveal the widespread impact of roadblock termination in yeast. PMID:29351914
Gene regulation in Kluyveromyces marxianus in the context of chromosomes. PMID:29346402
Assigning function to natural allelic variation via dynamic modeling of gene network induction. PMID:29335276
Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. PMID:29330519
The elongation factor Spn1 is a multi-functional chromatin binding protein. PMID:29300974
CUFID-query: accurate network querying through random walk based network flow estimation. PMID:29297279
Serine-Dependent Sphingolipid Synthesis Is a Metabolic Liability of Aneuploid Cells. PMID:29281829
Put3 Positively Regulates Proline Utilization in Candida albicans. PMID:29242833
Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PMID:29240790
YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules. PMID:29220473
A comprehensive evaluation of constraining amino acid biosynthesis in compartmented models for metabolic flux analysis. PMID:29188182
Regulation of lipid droplets by metabolically controlled Ldo isoforms. PMID:29187528
High-resolution mapping of cis-regulatory variation in budding yeast. PMID:29183975
Fast batch searching for protein homology based on compression and clustering. PMID:29162030
Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems. PMID:29149186
Negative Epistasis in Experimental RNA Fitness Landscapes. PMID:29127445
Mms1 is an assistant for regulating G-quadruplex DNA structures. PMID:29098365
Metabolic differentiation of surface and invasive cells of yeast colony biofilms revealed by gene expression profiling. PMID:29061122
The role of PKA in the translational response to heat stress in Saccharomyces cerevisiae. PMID:29045428
YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae. PMID:29036684
Engineering species-like barriers to sexual reproduction. PMID:29026112
GWIPS-viz: 2018 update. PMID:28977460
Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D. PMID:28961779
The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source. PMID:28957510
Similarity-Based Segmentation of Multi-Dimensional Signals. PMID:28955039
Determinants and Regulation of Protein Turnover in Yeast. PMID:28918244
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Proteomic and genetic analysis of the response of S. cerevisiae to soluble copper leads to improvement of the antimicrobial function of cellulosic copper nanoparticles. PMID:28869270
Transcription factor clusters regulate genes in eukaryotic cells. PMID:28841133
Fungal lifestyle reflected in serine protease repertoire. PMID:28831173
Physiology, ecology and industrial applications of aroma formation in yeast. PMID:28830094
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response. PMID:28829420
Landscape of submitochondrial protein distribution. PMID:28819139
Evolutionary dynamics in the fungal polarization network, a mechanistic perspective. PMID:28812259
Constraints and consequences of the emergence of amino acid repeats in eukaryotic proteins. PMID:28805808
Iron affects Ire1 clustering propensity and the amplitude of endoplasmic reticulum stress signaling. PMID:28794014
A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis. PMID:28754723
ProtozoaDB 2.0: A Trypanosoma Brucei Case Study. PMID:28726736
Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model. PMID:28704374
The yeast noncoding RNA interaction network. PMID:28701522
Habitat Predicts Levels of Genetic Admixture in Saccharomyces cerevisiae. PMID:28696926
Whole Genome Sequence of the Heterozygous Clinical Isolate Candida krusei 81-B-5. PMID:28696923
Genetic variation and expression changes associated with molybdate resistance from a glutathione producing wine strain of Saccharomyces cerevisiae. PMID:28683117
Gene2Function: An Integrated Online Resource for Gene Function Discovery. PMID:28663344
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale. PMID:28658629
Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction. PMID:28651538
Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of De Novo Gene Birth. PMID:28642936
Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PMID:28628618
Fusion, fission, and transport control asymmetric inheritance of mitochondria and protein aggregates. PMID:28615194
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. PMID:28604659
Cellular Consequences of Diminished Protein O-Mannosyltransferase Activity in Baker's Yeast. PMID:28598353
Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress. PMID:28592509
Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. PMID:28589392
Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast). PMID:28575451
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. PMID:28502612
NuA4 Lysine Acetyltransferase Complex Contributes to Phospholipid Homeostasis in Saccharomyces cerevisiae. PMID:28455416
PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes. PMID:28429714
PopNet: A Markov Clustering Approach to Study Population Genetic Structure. PMID:28383661
Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence. PMID:28369658
Loss of Heterozygosity Drives Adaptation in Hybrid Yeast. PMID:28369610
Molecular Regulation of Alternative Polyadenylation (APA) within the Drosophila Nervous System. PMID:28366829
Curated protein information in the Saccharomyces genome database. PMID:28365727
Outreach and online training services at the Saccharomyces Genome Database. PMID:28365719
SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance. PMID:28361708
From the baker to the bedside: yeast models of Parkinson's disease. PMID:28357302
The autophagy interaction network of the aging model Podospora anserina. PMID:28347269
Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions. PMID:28335026
Meta-analytic framework for liquid association. PMID:28334340
Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator. PMID:28327289
High-throughput transformation of Saccharomyces cerevisiae using liquid handling robots. PMID:28319150
Integration site selection by retroviruses and transposable elements in eukaryotes. PMID:28286338
A Systems Biology Approach to Understanding the Mechanisms of Action of an Alternative Anticancer Compound in Comparison to Cisplatin. PMID:28250393
The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism. PMID:28250014
Modulation of Replicative Lifespan in Cryptococcus neoformans: Implications for Virulence. PMID:28194146
A method for high-throughput production of sequence-verified DNA libraries and strain collections. PMID:28193641
Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts. PMID:28173099
The structure of the yeast mitochondrial ribosome. PMID:28154081
Extremely fast and incredibly close: cotranscriptional splicing in budding yeast. PMID:28153948
Protein Bioinformatics Databases and Resources. PMID:28150231
An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts. PMID:28135269
Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast. PMID:28122942
Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response. PMID:28079179
Eukaryotic stand-alone pseudouridine synthases - RNA modifying enzymes and emerging regulators of gene expression? PMID:28045575
Characterization of the Candida albicans Amino Acid Permease Family: Gap2 Is the Only General Amino Acid Permease and Gap4 Is an S-Adenosylmethionine (SAM) Transporter Required for SAM-Induced Morphogenesis. PMID:28028545
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans. PMID:27918582
A common bacterial metabolite elicits prion-based bypass of glucose repression. PMID:27906649
Yeast HMO1: Linker Histone Reinvented. PMID:27903656
Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response. PMID:27883312
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data. PMID:27875984
Identification of evolutionarily conserved DNA damage response genes that alter sensitivity to cisplatin. PMID:27863405
Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae. PMID:27846849
A Transcriptome Meta-Analysis Proposes Novel Biological Roles for the Antifungal Protein AnAFP in Aspergillus niger. PMID:27835655
RNAcentral: a comprehensive database of non-coding RNA sequences. PMID:27794554
Inositol polyphosphates intersect with signaling and metabolic networks via two distinct mechanisms. PMID:27791083
Real-time monitoring of the sugar sensing in Saccharomyces cerevisiae indicates endogenous mechanisms for xylose signaling. PMID:27776527
IPC - Isoelectric Point Calculator. PMID:27769290
The Local Edge Machine: inference of dynamic models of gene regulation. PMID:27760556
European derived Saccharomyces cerevisiae colonisation of New Zealand vineyards aided by humans. PMID:27744274
Determining the Mitochondrial Methyl Proteome in Saccharomyces cerevisiae using Heavy Methyl SILAC. PMID:27696855
Functional Metabolomics Describes the Yeast Biosynthetic Regulome. PMID:27693354
The fail-safe mechanism of post-transcriptional silencing of unspliced HAC1 mRNA. PMID:27692069
Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. PMID:27690225
Identification of Non-Coding RNAs in the Candida parapsilosis Species Group. PMID:27658249
In Vivo Analysis of NH4+ Transport and Central Nitrogen Metabolism in Saccharomyces cerevisiae during Aerobic Nitrogen-Limited Growth. PMID:27637876
Development of a prediction system for tail-anchored proteins. PMID:27634135
Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. PMID:27614020
Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. PMID:27601190
Predicting essential proteins based on subcellular localization, orthology and PPI networks. PMID:27586883
Validation of Reference Genes for Robust qRT-PCR Gene Expression Analysis in the Rice Blast Fungus Magnaporthe oryzae. PMID:27560664
The interplay between chromosome stability and cell cycle control explored through gene-gene interaction and computational simulation. PMID:27530428
Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome. PMID:27508123
Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation. PMID:27492286
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PMID:27487245
Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects. PMID:27479122
Investigating the Combinatory Effects of Biological Networks on Gene Co-expression. PMID:27445830
Global deceleration of gene evolution following recent genome hybridizations in fungi. PMID:27440871
Gene-Environment Interactions in Stress Response Contribute Additively to a Genotype-Environment Interaction. PMID:27437938
Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources. PMID:27432472
Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PMID:27428627
Methods for causal inference from gene perturbation experiments and validation. PMID:27382150
Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution. PMID:27380265
Nuclear import sequence identification in hOAS3 protein. PMID:27379722
Model organism databases: essential resources that need the support of both funders and users. PMID:27334346
Promotion of Cell Viability and Histone Gene Expression by the Acetyltransferase Gcn5 and the Protein Phosphatase PP2A in Saccharomyces cerevisiae. PMID:27317677
A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast. PMID:27297467
Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor. PMID:27291296
Diverse genetic architectures lead to the same cryptic phenotype in a yeast cross. PMID:27248513
BicNET: Flexible module discovery in large-scale biological networks using biclustering. PMID:27213009
Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae. PMID:27194750
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. PMID:27161996
Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. PMID:27159373
Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PMID:27152522
Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens. PMID:27148247
Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae. PMID:27143390
Requirements for Carnitine Shuttle-Mediated Translocation of Mitochondrial Acetyl Moieties to the Yeast Cytosol. PMID:27143389
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data. PMID:27137891
Gene-nutrient interaction markedly influences yeast chronological lifespan. PMID:27125759
Positive Selection and Centrality in the Yeast and Fly Protein-Protein Interaction Networks. PMID:27119079
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
Computational Analysis Reveals a Key Regulator of Cryptococcal Virulence and Determinant of Host Response. PMID:27094327
A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers. PMID:27071721
Alternative Glycerol Balance Strategies among Saccharomyces Species in Response to Winemaking Stress. PMID:27064588
Characterization of the Probiotic Yeast Saccharomyces boulardii in the Healthy Mucosal Immune System. PMID:27064405
Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi. PMID:27018804
Partial Decay of Thiamine Signal Transduction Pathway Alters Growth Properties of Candida glabrata. PMID:27015653
A dual approach for improving homogeneity of a human-type N-glycan structure in Saccharomyces cerevisiae. PMID:26983412
An extended set of yeast-based functional assays accurately identifies human disease mutations. PMID:26975778
Characterisation of the broad substrate specificity 2-keto acid decarboxylase Aro10p of Saccharomyces kudriavzevii and its implication in aroma development. PMID:26971319
Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems. PMID:26949740
Functions for diverse metabolic activities in heterochromatin. PMID:26936955
MTE1 Functions with MPH1 in Double-Strand Break Repair. PMID:26920759
Flux Control in Glycolysis Varies Across the Tree of Life. PMID:26920685
Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. PMID:26911370
A common mechanism involving the TORC1 pathway can lead to amphotericin B-persistence in biofilm and planktonic Saccharomyces cerevisiae populations. PMID:26903175
Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions. PMID:26869583
Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components. PMID:26831523
Global translational impacts of the loss of the tRNA modification t6A in yeast. PMID:26798630
Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae. PMID:26782936
Identification and Characterization of Wor4, a New Transcriptional Regulator of White-Opaque Switching. PMID:26772749
Combinatorial Cis-regulation in Saccharomyces Species. PMID:26772747
Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae. PMID:26764011
Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution. PMID:26758516
Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA. PMID:26751567
Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress. PMID:26748095
BioGRID: A Resource for Studying Biological Interactions in Yeast. PMID:26729913
Use of the BioGRID Database for Analysis of Yeast Protein and Genetic Interactions. PMID:26729909
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. PMID:26714768
A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. PMID:26700642
Genome-wide screen uncovers novel pathways for tRNA processing and nuclear-cytoplasmic dynamics. PMID:26680305
Disentangling the multigenic and pleiotropic nature of molecular function. PMID:26678917
A comprehensive comparison of general RNA-RNA interaction prediction methods. PMID:26673718
The European Bioinformatics Institute in 2016: Data growth and integration. PMID:26673705
Protein disorder reduced in Saccharomyces cerevisiae to survive heat shock. PMID:26673203
Discovery of a nucleocytoplasmic O-mannose glycoproteome in yeast. PMID:26644575
The Saccharomyces Genome Database: A Tool for Discovery. PMID:26631132
Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR. PMID:26609959
Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae. PMID:26602688
Arabidopsis Rab Geranylgeranyltransferases Demonstrate Redundancy and Broad Substrate Specificity in Vitro. PMID:26589801
TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation in Saccharomyces cerevisiae. PMID:26582391
Biomass composition: the "elephant in the room" of metabolic modelling. PMID:26491422
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Alternative Splicing in Next Generation Sequencing Data of Saccharomyces cerevisiae. PMID:26469855
Efforts to make and apply humanized yeast. PMID:26462863
Divergent Evolution of the Transcriptional Network Controlled by Snf1-Interacting Protein Sip4 in Budding Yeasts. PMID:26440109
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models. PMID:26426067
Protein biogenesis machinery is a driver of replicative aging in yeast. PMID:26422514
Stimulation of Chromosomal Rearrangements by Ribonucleotides. PMID:26400612
Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. PMID:26399295
Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response. PMID:26391581
Targeted single molecule mutation detection with massively parallel sequencing. PMID:26384417
RNA regulatory networks diversified through curvature of the PUF protein scaffold. PMID:26364903
Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress. PMID:26359986
A toolbox of endogenous and heterologous nuclear localization sequences for the methylotrophic yeast Pichia pastoris. PMID:26347503
K-Profiles: A Nonlinear Clustering Method for Pattern Detection in High Dimensional Data. PMID:26339652
Applications of comparative evolution to human disease genetics. PMID:26338499
Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi. PMID:26327315
Crystallographic studies of the structured core domain of Knr4 from Saccharomyces cerevisiae. PMID:26323295
Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine Aggregates. PMID:26317359
Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions. PMID:26314830
Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes. PMID:26286535
Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data. PMID:26275099
The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts. PMID:26269586
MESSI: metabolic engineering target selection and best strain identification tool. PMID:26255308
ERC analysis: web-based inference of gene function via evolutionary rate covariation. PMID:26243019
Draft Genome Sequence of Saccharomyces cerevisiae Strain NCIM3186 Used in the Production of Bioethanol from Sweet Sorghum. PMID:26227595
Utilizing Chemical Genomics to Identify Cytochrome b as a Novel Drug Target for Chagas Disease. PMID:26186534
Assembly of Slx4 signaling complexes behind DNA replication forks. PMID:26113155
Metabolic engineering of yeast to produce fatty acid-derived biofuels: bottlenecks and solutions. PMID:26106371
Cross-organism analysis using InterMine. PMID:26097192
Amino Acid Flux from Metabolic Network Benefits Protein Translation: the Role of Resource Availability. PMID:26056817
Site-specific processing of Ras and Rap1 Switch I by a MARTX toxin effector domain. PMID:26051945
Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions. PMID:26047845
Databases for Microbiologists. PMID:26013493
The Recent De Novo Origin of Protein C-Termini. PMID:26002864
A graph modification approach for finding core-periphery structures in protein interaction networks. PMID:26000032
Biocuration at the Saccharomyces genome database. PMID:25997651
A BAYESIAN NONPARAMETRIC MIXTURE MODEL FOR SELECTING GENES AND GENE SUBNETWORKS. PMID:25984253
Plasma Membrane Proteolipid 3 Protein Modulates Amphotericin B Resistance through Sphingolipid Biosynthetic Pathway. PMID:25965669
Spindle Checkpoint Factors Bub1 and Bub2 Promote DNA Double-Strand Break Repair by Nonhomologous End Joining. PMID:25963654
Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast. PMID:25950722
Loss of the RNA polymerase III repressor MAF1 confers obesity resistance. PMID:25934505
Co-regulation of translation in protein complexes. PMID:25909184
Measuring semantic similarities by combining gene ontology annotations and gene co-function networks. PMID:25886899
Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences. PMID:25884379
Essentiality and centrality in protein interaction networks revisited. PMID:25880655
An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. PMID:25880651
Deconstructing the genetic basis of spent sulphite liquor tolerance using deep sequencing of genome-shuffled yeast. PMID:25866561
Computational prediction of protein-protein interactions. PMID:25859943
Rio1 promotes rDNA stability and downregulates RNA polymerase I to ensure rDNA segregation. PMID:25851096
Biochemical functional predictions for protein structures of unknown or uncertain function. PMID:25848497
Cooperative stabilization of the SIR complex provides robust epigenetic memory in a model of SIR silencing in Saccharomyces cerevisiae. PMID:25830651
AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae. PMID:25781462
Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeast Saccharomyces cerevisiae. PMID:25759377
Recent advances in the genome-wide study of DNA replication origins in yeast. PMID:25745419
Saccharomyces cerevisiae: a nomadic yeast with no niche? PMID:25725024
IAOseq: inferring abundance of overlapping genes using RNA-seq data. PMID:25707673
Fgk3 glycogen synthase kinase is important for development, pathogenesis, and stress responses in Fusarium graminearum. PMID:25703795
Quantitative proteomics and network analysis of SSA1 and SSB1 deletion mutants reveals robustness of chaperone HSP70 network in Saccharomyces cerevisiae. PMID:25689132
Genome Sequence of Saccharomyces cerevisiae NCIM3107, Used in Bioethanol Production. PMID:25676764
Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. PMID:25662576
Global mRNA selection mechanisms for translation initiation. PMID:25650959
BicPAM: Pattern-based biclustering for biomedical data analysis. PMID:25649207
Fungal mediator tail subunits contain classical transcriptional activation domains. PMID:25645928
PRIMED: PRIMEr database for deleting and tagging all fission and budding yeast genes developed using the open-source genome retrieval script (GRS). PMID:25643023
Negative feedback buffers effects of regulatory variants. PMID:25634765
Differential phosphorylation of a regulatory subunit of protein kinase CK2 by target of rapamycin complex 1 signaling and the Cdc-like kinase Kns1. PMID:25631054
Lagging-strand replication shapes the mutational landscape of the genome. PMID:25624100
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. PMID:25586221
Genetic mapping of MAPK-mediated complex traits Across S. cerevisiae. PMID:25569670
Identification and computational analysis of gene regulatory elements. PMID:25561628
The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast. PMID:25522035
An ontology for microbial phenotypes. PMID:25433798
Surveying the floodgates: estimating protein flux into the endoplasmic reticulum lumen in Saccharomyces cerevisiae. PMID:25431559
The BioGRID interaction database: 2015 update. PMID:25428363
Community structure detection for overlapping modules through mathematical programming in protein interaction networks. PMID:25412367
Pathway connectivity and signaling coordination in the yeast stress-activated signaling network. PMID:25411400
Maintenance of sex-related genes and the co-occurrence of both mating types in Verticillium dahliae. PMID:25383550
Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. PMID:25378625
Genome-wide analyses and functional classification of proline repeat-rich proteins: potential role of eIF5A in eukaryotic evolution. PMID:25364902
Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production. PMID:25364804
Characterization of the mutagenic spectrum of 4-nitroquinoline 1-oxide (4-NQO) in Aspergillus nidulans by whole genome sequencing. PMID:25352541
Compromised RNA polymerase III complex assembly leads to local alterations of intergenic RNA polymerase II transcription in Saccharomyces cerevisiae. PMID:25348158
GBshape: a genome browser database for DNA shape annotations. PMID:25326329
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
Gene network biological validity based on gene-gene interaction relevance. PMID:25295303
FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. PMID:25294921
CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining. PMID:25268582
Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. PMID:25253284
An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. PMID:25244077
Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes. PMID:25237741
Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. PMID:25217615
De-novo learning of genome-scale regulatory networks in S. cerevisiae. PMID:25215507
Causal variation in yeast sporulation tends to reside in a pathway bottleneck. PMID:25211152
Multi-capillary column-ion mobility spectrometry of volatile metabolites emitted by Saccharomyces cerevisiae. PMID:25197771
Average oxidation state of carbon in proteins. PMID:25165594
Rational and combinatorial approaches to engineering styrene production by Saccharomyces cerevisiae. PMID:25162943
Identifying transcription factor complexes and their roles. PMID:25161228
Tombusvirus-yeast interactions identify conserved cell-intrinsic viral restriction factors. PMID:25157258
Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton. PMID:25138357
Starvation-response may not involve Atg1-dependent autophagy induction in non-unikont parasites. PMID:25059978
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. PMID:25055984
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Codon-by-codon modulation of translational speed and accuracy via mRNA folding. PMID:25051069
Biophysical fitness landscapes for transcription factor binding sites. PMID:25010228
Relationship between gene duplicability and diversifiability in the topology of biochemical networks. PMID:25005725
Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes in Ascomycota. PMID:25002674
Discovery of Chromatin-Associated Proteins via Sequence-Specific Capture and Mass Spectrometric Protein Identification in Saccharomyces cerevisiae. PMID:24999558
Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. PMID:24995982
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models. PMID:24980894
Strep-tag II and Twin-Strep based cassettes for protein tagging by homologous recombination and characterization of endogenous macromolecular assemblies in Saccharomyces cerevisiae. PMID:24969434
High throughput screening identifies modulators of histone deacetylase inhibitors. PMID:24968945
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program. PMID:24962434
The Chlamydomonas genome project: a decade on. PMID:24950814
The yeast deletion collection: a decade of functional genomics. PMID:24939991
The calcineurin signaling network evolves via conserved kinase-phosphatase modules that transcend substrate identity. PMID:24930733
Network-dosage compensation topologies as recurrent network motifs in natural gene networks. PMID:24929807
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs. PMID:24894379
Inferring host gene subnetworks involved in viral replication. PMID:24874113
A novel antifungal is active against Candida albicans biofilms and inhibits mutagenic acetaldehyde production in vitro. PMID:24867320
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. PMID:24861622
Budding yeast for budding geneticists: a primer on the Saccharomyces cerevisiae model system. PMID:24807111
VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery. PMID:24753414
Regulation of clathrin-mediated endocytosis by dynamic ubiquitination and deubiquitination. PMID:24746795
Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. PMID:24721214
Modeling the transcriptional regulatory network that controls the early hypoxic response in Candida albicans. PMID:24681685
Tetrahymena thermophila: a divergent perspective on membrane traffic. PMID:24634411
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. PMID:24622611
Heterochronic meiotic misexpression in an interspecific yeast hybrid. PMID:24608322
Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins. PMID:24603469
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. PMID:24573882
Corbi: a new R package for biological network alignment and querying. PMID:24565104
GOLink: Finding Cooccurring Terms across Gene Ontology Namespaces. PMID:24524070
Enhanced enzymatic activity of glycerol-3-phosphate dehydrogenase from the cryophilic Saccharomyces kudriavzevii. PMID:24498063
Acetylation dynamics and stoichiometry in Saccharomyces cerevisiae. PMID:24489116
Deletion of conserved protein phosphatases reverses defects associated with mitochondrial DNA damage in Saccharomyces cerevisiae. PMID:24474773
Draft Genome Sequence of Saccharomyces cerevisiae NAM34-4C, a Lactic Acid-Assimilating Industrial Yeast Strain. PMID:24459259
The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant. PMID:24453040
Draft Genome Sequence of Saccharomyces cerevisiae IR-2, a Useful Industrial Strain for Highly Efficient Production of Bioethanol. PMID:24435865
Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. PMID:24432138
Topology and control of the cell-cycle-regulated transcriptional circuitry. PMID:24395825
Whi3, an S. cerevisiae RNA-binding protein, is a component of stress granules that regulates levels of its target mRNAs. PMID:24386330
Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters. PMID:24386279
An extensive evaluation of read trimming effects on Illumina NGS data analysis. PMID:24376861
POMO--Plotting Omics analysis results for Multiple Organisms. PMID:24365393
A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. PMID:24360959
Intergenic transcriptional interference is blocked by RNA polymerase III transcription factor TFIIIB in Saccharomyces cerevisiae. PMID:24336746
Hierarchical clustering of high-throughput expression data based on general dependences. PMID:24334400
Evolution at two levels of gene expression in yeast. PMID:24318729
Heterodimeric protein complex identification by naïve Bayes classifiers. PMID:24299017
MycoCosm portal: gearing up for 1000 fungal genomes. PMID:24297253
Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs. PMID:24283849
Lysine and arginine content of proteins: computational analysis suggests a new tool for solubility design. PMID:24283752
NeXO Web: the NeXO ontology database and visualization platform. PMID:24271398
Saccharomyces genome database provides new regulation data. PMID:24265222
Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. PMID:24259309
Activities at the Universal Protein Resource (UniProt). PMID:24253303
Integrating in silico resources to map a signaling network. PMID:24233784
Variance heterogeneity in Saccharomyces cerevisiae expression data: trans-regulation and epistasis. PMID:24223957
Decoding the ubiquitin-mediated pathway of arthropod disease vectors. PMID:24205097
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. PMID:24194595
GWIPS-viz: development of a ribo-seq genome browser. PMID:24185699
The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny. PMID:24185697
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. PMID:24170807
Puf3p induces translational repression of genes linked to oxidative stress. PMID:24163252
Integrated module and gene-specific regulatory inference implicates upstream signaling networks. PMID:24146602
The one hour yeast proteome. PMID:24143002
Saccharomyces cerevisiae genes involved in survival of heat shock. PMID:24142923
Fungal zinc metabolism and its connections to virulence. PMID:24133658
Functional analyses of NSF1 in wine yeast using interconnected correlation clustering and molecular analyses. PMID:24130853
Advances in understanding the complex mechanisms of DNA interstrand cross-link repair. PMID:24086043
yApoptosis: yeast apoptosis database. PMID:24082050
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. PMID:24059635
Integration of new genes into cellular networks, and their structural maturation. PMID:24056411
Characterization and prediction of haploinsufficiency using systems-level gene properties in yeast. PMID:24048642
Inferring the effective TOR-dependent network: a computational study in yeast. PMID:24005029
Web Apollo: a web-based genomic annotation editing platform. PMID:24000942
Global linkage map connects meiotic centromere function to chromosome size in budding yeast. PMID:23979930
Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii. PMID:23977017
Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts. PMID:23963700
Towards precision medicine: advances in computational approaches for the analysis of human variants. PMID:23962656
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. PMID:23935056
Genome-wide identification and analysis of membrane-bound O-acyltransferase (MBOAT) gene family in plants. PMID:23928653
Identification of yeast cell cycle regulated genes based on genomic features. PMID:23895232
Sporulation genes associated with sporulation efficiency in natural isolates of yeast. PMID:23874994
Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. PMID:23851338
A guide to best practices for Gene Ontology (GO) manual annotation. PMID:23842463
Evolution of uni- and bifactorial sexual compatibility systems in fungi. PMID:23838688
Mapping the functional yeast ABC transporter interactome. PMID:23831759
The Saccharomyces cerevisiae transcriptome as a mirror of phytochemical variation in complex extracts of Equisetum arvense from America, China, Europe and India. PMID:23826764
Towards systematic discovery of signaling networks in budding yeast filamentous growth stress response using interventional phosphorylation data. PMID:23825934
A protein domain-centric approach for the comparative analysis of human and yeast phenotypically relevant mutations. PMID:23819456
Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes. PMID:23814130
GoSynthetic database tool to analyse natural and engineered molecular processes. PMID:23813641
Compressive genomics for protein databases. PMID:23812995
GeneMANIA prediction server 2013 update. PMID:23794635
Genome Sequences of Industrially Relevant Saccharomyces cerevisiae Strain M3707, Isolated from a Sample of Distillers Yeast and Four Haploid Derivatives. PMID:23792743
Rate-limiting steps in yeast protein translation. PMID:23791185
Improving biobutanol production in engineered Saccharomyces cerevisiae by manipulation of acetyl-CoA metabolism. PMID:23760499
FSRD: fungal stress response database. PMID:23757396
The modest beginnings of one genome project. PMID:23733847
System-wide analysis reveals intrinsically disordered proteins are prone to ubiquitylation after misfolding stress. PMID:23716602
Interface-resolved network of protein-protein interactions. PMID:23696724
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update. PMID:23674503
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
InterMOD: integrated data and tools for the unification of model organism research. PMID:23652793
Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. PMID:23636942
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. PMID:23631471
Extensive transcriptional heterogeneity revealed by isoform profiling. PMID:23615609
The challenge of increasing Pfam coverage of the human proteome. PMID:23603847
Rtt109 prevents hyper-amplification of ribosomal RNA genes through histone modification in budding yeast. PMID:23593017
Systematic curation of protein and genetic interaction data for computable biology. PMID:23587305
Comparative transcriptomics of infectious spores from the fungal pathogen Histoplasma capsulatum reveals a core set of transcripts that specify infectious and pathogenic states. PMID:23563482
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. PMID:23562153
Statistical analysis reveals co-expression patterns of many pairs of genes in yeast are jointly regulated by interacting loci. PMID:23555313
Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output. PMID:23554854
In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae. PMID:23514624
Mobilomics in Saccharomyces cerevisiae strains. PMID:23514613
A natural polymorphism in rDNA replication origins links origin activation with calorie restriction and lifespan. PMID:23505383
Comparative genome analysis and gene finding in Candida species using CGOB. PMID:23486613
Assembling a COMPASS. PMID:23470558
The amidation step of diphthamide biosynthesis in yeast requires DPH6, a gene identified through mining the DPH1-DPH5 interaction network. PMID:23468660
From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization. PMID:23436988
An analysis and prediction of nucleosome positioning based on information content. PMID:23435498
Quantitative analysis of chaperone network throughput in budding yeast. PMID:23420633
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
A novel algorithm for validating peptide identification from a shotgun proteomics search engine. PMID:23402659
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302
Global transcriptome profile of Cryptococcus neoformans during exposure to hydrogen peroxide induced oxidative stress. PMID:23383070
Repeat-encoded poly-Q tracts show statistical commonalities across species. PMID:23374135
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. PMID:23368932
FitSearch: a robust way to interpret a yeast fitness profile in terms of drug's mode-of-action. PMID:23368702
Expanding the boundaries of local similarity analysis. PMID:23368516
Approaching the functional annotation of fungal virulence factors using cross-species genetic interaction profiling. PMID:23300468
Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. PMID:23275543
Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions. PMID:23268696
A gene ontology inferred from molecular networks. PMID:23242164
Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations. PMID:23233838
Chromatin-dependent and -independent regulation of DNA replication origin activation in budding yeast. PMID:23222539
The yeast SR-like protein Npl3 links chromatin modification to mRNA processing. PMID:23209445
The BioGRID interaction database: 2013 update. PMID:23203989
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. PMID:23203867
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs. PMID:23180791
A complex network framework for unbiased statistical analyses of DNA-DNA contact maps. PMID:23175602
GraphAlignment: Bayesian pairwise alignment of biological networks. PMID:23171476
Opportunities for text mining in the FlyBase genetic literature curation workflow. PMID:23160412
Genomic analysis of Saccharomyces cerevisiae isolates that grow optimally with glucose as the sole carbon source. PMID:23135695
Dynamic hubs show competitive and static hubs non-competitive regulation of their interaction partners. PMID:23118954
MODOMICS: a database of RNA modification pathways--2013 update. PMID:23118484
Spliceosome database: a tool for tracking components of the spliceosome. PMID:23118483
Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae. PMID:23079308
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
COG6 interacts with a subset of the Golgi SNAREs and is important for the Golgi complex integrity. PMID:23057818
Protein stickiness, rather than number of functional protein-protein interactions, predicts expression noise and plasticity in yeast. PMID:23017156
Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage. PMID:23013770
Intermembrane space proteome of yeast mitochondria. PMID:22984289
The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt. PMID:22977733
The architecture of eukaryotic translation. PMID:22965119
Identification of unknown protein function using metabolite cocktail screening. PMID:22940582
DExD/H-box RNA helicases in ribosome biogenesis. PMID:22922795
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. PMID:22898448
Role of social wasps in Saccharomyces cerevisiae ecology and evolution. PMID:22847440
Profiling lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and proteome microarrays. PMID:22843995
The yeast magmas ortholog pam16 has an essential function in fermentative growth that involves sphingolipid metabolism. PMID:22808036
The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. PMID:22754563
MC EMiNEM maps the interaction landscape of the Mediator. PMID:22737066
Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. PMID:22696683
Differences in local genomic context of bound and unbound motifs. PMID:22692006
MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. PMID:22669910
SAVoR: a server for sequencing annotation and visualization of RNA structures. PMID:22492627
Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PMID:22442681
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. PMID:22434836
YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. PMID:22434830
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. PMID:22434826
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
SGD: Saccharomyces Genome Database PubMed citations: 398.

398 articles citing: SGD: Saccharomyces Genome Database

SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability. PMID:35664227
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms. PMID:35314699
Predicting Essential Proteins Based on Integration of Local Fuzzy Fractal Dimension and Subcellular Location Information. PMID:35205217
An Iterative Method for Predicting Essential Proteins Based on Multifeature Fusion and Linear Neighborhood Similarity. PMID:35140599
Yeast Crf1p: An activator in need is an activator indeed. PMID:34976315
QTL mapping of a Brazilian bioethanol strain links the cell wall protein-encoding gene GAS1 to low pH tolerance in S. cerevisiae. PMID:34915919
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
TSSr: an R package for comprehensive analyses of TSS sequencing data. PMID:34805991
A Novel Collaborative Filtering Model-Based Method for Identifying Essential Proteins. PMID:34745230
Suppression of telomere capping defects of Saccharomyces cerevisiae yku70 and yku80 mutants by telomerase. PMID:34718547
Systems-level effects of allosteric perturbations to a model molecular switch. PMID:34646016
Charting Shifts in Saccharomyces cerevisiae Gene Expression across Asynchronous Time Trajectories with Diffusion Maps. PMID:34607457
Analysis of the Putative Nucleoporin POM33 in the Filamentous Fungus Sordaria macrospora. PMID:34575720
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. PMID:34496745
Development of an Haa1-based biosensor for acetic acid sensing in Saccharomyces cerevisiae. PMID:34477863
A Novel Method for Identifying Essential Proteins Based on Non-negative Matrix Tri-Factorization. PMID:34422014
A Novel Model for Identifying Essential Proteins Based on Key Target Convergence Sets. PMID:34394201
Parameter Estimation and Variable Selection for Big Systems of Linear Ordinary Differential Equations: A Matrix-Based Approach. PMID:34385718
Spatiotemporal coordination of transcription preinitiation complex assembly in live cells. PMID:34375585
Method for Identifying Essential Proteins by Key Features of Proteins in a Novel Protein-Domain Network. PMID:34267785
Performance of Regression Models as a Function of Experiment Noise. PMID:34262264
Inferring transcriptomic cell states and transitions only from time series transcriptome data. PMID:34131182
Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes. PMID:33850038
Quantifying evolutionary importance of protein sites: A Tale of two measures. PMID:33826605
Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network. PMID:33815480
The Descent of Databases. PMID:33789353
CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate. PMID:33568224
Impacts of fludioxonil resistance on global gene expression in the necrotrophic fungal plant pathogen Sclerotinia sclerotiorum. PMID:33516198
CorkOakDB-The Cork Oak Genome Database Portal. PMID:33382885
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. PMID:33262328
Computational tools for geroscience. PMID:33241167
Transforming the study of organisms: Phenomic data models and knowledge bases. PMID:33232313
Extraction and Integration of Genetic Networks from Short-Profile Omic Data Sets. PMID:33137869
Dynamic transcriptional response of Saccharomyces cerevisiae cells to copper. PMID:33116258
PartCrafter: find, generate and analyze BioParts. PMID:32995539
Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes. PMID:32522745
Genetic interactions derived from high-throughput phenotyping of 6589 yeast cell cycle mutants. PMID:32376972
A novel method to predict essential proteins based on tensor and HITS algorithm. PMID:32252824
Challenges and opportunities for strain verification by whole-genome sequencing. PMID:32245992
Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia. PMID:32228450
Learning causal networks using inducible transcription factors and transcriptome-wide time series. PMID:32181581
Multi-kinase control of environmental stress responsive transcription. PMID:32160258
De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. PMID:32034123
DeepEP: a deep learning framework for identifying essential proteins. PMID:31787076
The CCR4-NOT Complex Maintains Stability and Transcription of rRNA Genes by Repressing Antisense Transcripts. PMID:31611247
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. PMID:31521132
CDAP: An Online Package for Evaluation of Complex Detection Methods. PMID:31485005
An Evaluation of Machine Learning Approaches for the Prediction of Essential Genes in Eukaryotes Using Protein Sequence-Derived Features. PMID:31312416
Comparative genome analysis of Phyllosticta citricarpa and Phyllosticta capitalensis, two fungi species that share the same host. PMID:31277573
An iteration method for identifying yeast essential proteins from heterogeneous network. PMID:31234779
Boolean gene regulatory network model of centromere function in Saccharomyces cerevisiae. PMID:31175490
The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. PMID:31092540
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks. PMID:30925866
GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness. PMID:30917779
Functional protein representations from biological networks enable diverse cross-species inference. PMID:30847485
Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. PMID:30834327
Identification of Essential Proteins Based on Improved HITS Algorithm. PMID:30823614
Investigating Common Pathogenic Mechanisms between Homo sapiens and Different Strains of Candida albicans for Drug Design: Systems Biology Approach via Two-Sided NGS Data Identification. PMID:30769958
A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein⁻Protein Interactive Networks. PMID:30626157
Identification of essential proteins based on a new combination of topological and biological features in weighted protein-protein interaction networks. PMID:30472688
GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms. PMID:30305653
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells. PMID:30072377
Feature Selection via Swarm Intelligence for Determining Protein Essentiality. PMID:29958434
A new method for predicting essential proteins based on participation degree in protein complex and subgraph density. PMID:29894517
Improved flower pollination algorithm for identifying essential proteins. PMID:29745838
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. PMID:29490019
PANDA: Protein function prediction using domain architecture and affinity propagation. PMID:29472600
The extent of ribosome queuing in budding yeast. PMID:29377894
Prediction of essential proteins based on subcellular localization and gene expression correlation. PMID:29219067
A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks. PMID:29219066
Protein complex prediction via dense subgraphs and false positive analysis. PMID:28937982
Protein Complexes Prediction Method Based on Core-Attachment Structure and Functional Annotations. PMID:28878201
Mitochondrial genome evolution in the Saccharomyces sensu stricto complex. PMID:28813471
A new two-stage method for revealing missing parts of edges in protein-protein interaction networks. PMID:28493910
The anatomy of phenotype ontologies: principles, properties and applications. PMID:28387809
Curated protein information in the Saccharomyces genome database. PMID:28365727
Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii. PMID:28336969
The post-genomic era of biological network alignment. PMID:28194172
Misincorporation by RNA polymerase is a major source of transcription pausing in vivo. PMID:28180286
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. PMID:28143396
Transcriptomic responses of a simplified soil microcosm to a plant pathogen and its biocontrol agent reveal a complex reaction to harsh habitat. PMID:27784266
Protein complex detection based on partially shared multi-view clustering. PMID:27623844
Predicting essential proteins based on subcellular localization, orthology and PPI networks. PMID:27586883
An ensemble framework for identifying essential proteins. PMID:27557880
Selection for reduced translation costs at the intronic 5' end in fungi. PMID:27260512
Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. PMID:27252399
Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. PMID:27172212
Utilizing yeast chemogenomic profiles for the prediction of pharmacogenomic associations in humans. PMID:27025271
A two-layer integration framework for protein complex detection. PMID:26911324
Pathway Analysis: State of the Art. PMID:26733877
Circulating microbial RNA and health. PMID:26576508
Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover. PMID:26544557
Identifying binary protein-protein interactions from affinity purification mass spectrometry data. PMID:26438428
Prior knowledge driven Granger causality analysis on gene regulatory network discovery. PMID:26316173
The value of protein structure classification information-Surveying the scientific literature. PMID:26313554
Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi. PMID:26246046
ATP-binding cassette transporters and sterol O-acyltransferases interact at membrane microdomains to modulate sterol uptake and esterification. PMID:26220175
Function of a p24 Heterodimer in Morphogenesis and Protein Transport in Penicillium oxalicum. PMID:26149342
Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes. PMID:26125187
Integrative random forest for gene regulatory network inference. PMID:26072483
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints. PMID:26000633
Biocuration at the Saccharomyces genome database. PMID:25997651
A quantitative imaging-based screen reveals the exocyst as a network hub connecting endocytosis and exocytosis. PMID:25947137
Similarity-based search of model organism, disease and drug effect phenotypes. PMID:25763178
Identifying essential proteins from active PPI networks constructed with dynamic gene expression. PMID:25707432
Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle. PMID:25527639
The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast. PMID:25522035
Reverse engineering gene regulatory networks: coupling an optimization algorithm with a parameter identification technique. PMID:25474560
The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite. PMID:25425642
Cdc42p-interacting protein Bem4p regulates the filamentous-growth mitogen-activated protein kinase pathway. PMID:25384973
DEOP: a database on osmoprotectants and associated pathways. PMID:25326239
Yeast systems biology: our best shot at modeling a cell. PMID:25316779
Pulsatile dynamics in the yeast proteome. PMID:25220054
Purifying selection against gene conversions between the polyamine transport (TPO) genes of Saccharomyces species. PMID:25135753
DFA7, a new method to distinguish between intron-containing and intronless genes. PMID:25036549
Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys. PMID:25015739
Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae. PMID:24968317
Identifying dynamic protein complexes based on gene expression profiles and PPI networks. PMID:24963481
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. PMID:24947676
Detecting overlapping protein complexes based on a generative model with functional and topological properties. PMID:24928559
IFIM: a database of integrated fitness information for microbial genes. PMID:24923821
An unsupervised approach to predict functional relations between genes based on expression data. PMID:24800208
Training-free atomistic prediction of nucleosome occupancy. PMID:24733939
Systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875
Identifying protein complexes based on density and modularity in protein-protein interaction network. PMID:24565048
Review of biological network data and its applications. PMID:24465231
Different levels of catabolite repression optimize growth in stable and variable environments. PMID:24453942
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
Balony: a software package for analysis of data generated by synthetic genetic array experiments. PMID:24305553
Prediction of essential proteins based on gene expression programming. PMID:24267033
Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis. PMID:24188869
Molecular mechanisms of system responses to novel stimuli are predictable from public data. PMID:24185701
Gleaning evolutionary insights from the genome sequence of a probiotic yeast Saccharomyces boulardii. PMID:24148866
Inferring evolutionary histories of pathway regulation from transcriptional profiling data. PMID:24130471
Clustering based on multiple biological information: approach for predicting protein complexes. PMID:24067423
A temperature-responsive network links cell shape and virulence traits in a primary fungal pathogen. PMID:23935449
Statistical significance of combinatorial regulations. PMID:23882073
Re-annotation of protein-coding genes in the genome of saccharomyces cerevisiae based on support vector machines. PMID:23874379
An integrative, translational approach to understanding rare and orphan genetically based diseases. PMID:23853703
Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins. PMID:23785265
Phylogenetic portrait of the Saccharomyces cerevisiae functional genome. PMID:23749449
Genome-scale modeling of the protein secretory machinery in yeast. PMID:23667601
Protein complex detection via weighted ensemble clustering based on Bayesian nonnegative matrix factorization. PMID:23658709
Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production. PMID:23608777
Computational discovery of transcriptional regulatory modules in fungal ribosome biogenesis genes reveals novel sequence and function patterns. PMID:23555806
Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PMID:23516347
Quantitative residue-level structure-evolution relationships in the yeast membrane proteome. PMID:23512408
Predicting physical interactions between protein complexes. PMID:23438732
Extensive transcript diversity and novel upstream open reading frame regulation in yeast. PMID:23390610
Drug uptake, lipid rafts, and vesicle trafficking modulate resistance to an anticancer lysophosphatidylcholine analogue in yeast. PMID:23335509
Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics. PMID:23282200
A hybrid method for the exact planted (l, d) motif finding problem and its parallelization. PMID:23281969
Calculation of nucleosomal DNA deformation energy: its implication for nucleosome positioning. PMID:23247720
Identifying complexes from protein interaction networks according to different types of neighborhood density. PMID:23210476
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
On the contributions of topological features to transcriptional regulatory network robustness. PMID:23194062
Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PMID:23166516
Interactome-wide prediction of protein-protein binding sites reveals effects of protein sequence variation in Arabidopsis thaliana. PMID:23077539
Bayesian correlated clustering to integrate multiple datasets. PMID:23047558
Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes. PMID:23046642
RNA polymerase II collision interrupts convergent transcription. PMID:23041286
Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. PMID:23025710
Comparison of targeted maximum likelihood and shrinkage estimators of parameters in gene networks. PMID:23023699
Modeling coding-sequence evolution within the context of residue solvent accessibility. PMID:22967129
Exploring overlapping functional units with various structure in protein interaction networks. PMID:22916212
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. PMID:22844089
Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. PMID:22832247
The yeast Hsp70 Ssa1 is a sensor for activation of the heat shock response by thiol-reactive compounds. PMID:22809627
Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks. PMID:22808943
A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions. PMID:22798493
Predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using short polypeptide clusters. PMID:22759581
Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis. PMID:22697265
Is 'forward' the same as 'plus'?…and other adventures in SNP allele nomenclature. PMID:22658725
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. PMID:22621308
Regulatory Snapshots: integrative mining of regulatory modules from expression time series and regulatory networks. PMID:22563474
Network evolution: rewiring and signatures of conservation in signaling. PMID:22438796
A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data. PMID:22405054
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. PMID:22369646
Yeast transcription termination factor Rtt103 functions in DNA damage response. PMID:22355353
La-motif-dependent mRNA association with Slf1 promotes copper detoxification in yeast. PMID:22271760
A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon. PMID:22219511
HKC: an algorithm to predict protein complexes in protein-protein interaction networks. PMID:22174556
Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae. PMID:22093685
GeneWeaver: a web-based system for integrative functional genomics. PMID:22080549
Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors. PMID:22060676
Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry. PMID:22046265
An in silico approach combined with in vivo experiments enables the identification of a new protein whose overexpression can compensate for specific respiratory defects in Saccharomyces cerevisiae. PMID:22027258
Learning cellular sorting pathways using protein interactions and sequence motifs. PMID:21999284
Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging. PMID:21963608
Protein expression regulation under oxidative stress. PMID:21933953
Dominating biological networks. PMID:21887225
Categorizing biases in high-confidence high-throughput protein-protein interaction data sets. PMID:21876202
Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome. PMID:21858014
PILGRM: an interactive data-driven discovery platform for expert biologists. PMID:21653547
Evidence of association between nucleosome occupancy and the evolution of transcription factor binding sites in yeast. PMID:21627806
Improved functional overview of protein complexes using inferred epistatic relationships. PMID:21605386
Evolutionary plasticity determination by orthologous groups distribution. PMID:21586164
Understanding and predicting synthetic lethal genetic interactions in Saccharomyces cerevisiae using domain genetic interactions. PMID:21586150
The effects of network neighbours on protein evolution. PMID:21532755
HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PMID:21423752
The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis. PMID:21378103
The multiple personalities of Watson and Crick strands. PMID:21303550
COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. PMID:21298793
Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PMID:21203484
Cross-species Functionome analysis identifies proteins associated with DNA repair, translation and aerobic respiration as conserved modulators of UV-toxicity. PMID:21195161
Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. PMID:21190591
Novel genes exhibit distinct patterns of function acquisition and network integration. PMID:21187012
New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. PMID:21176124
Genome-wide screen for inositol auxotrophy in Saccharomyces cerevisiae implicates lipid metabolism in stress response signaling. PMID:21136082
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PMID:21124865
Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. PMID:21119627
Identification of protein complexes from co-immunoprecipitation data. PMID:21115439
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. PMID:20939868
Genome-wide model for the normal eukaryotic DNA replication fork. PMID:20876092
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. PMID:20796282
Precursor charge state prediction for electron transfer dissociation tandem mass spectra. PMID:20731383
The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data. PMID:20684785
The function of communities in protein interaction networks at multiple scales. PMID:20649971
The evolutionary rate variation among genes of HOG-signaling pathway in yeast genomes. PMID:20618989
FuncBase: a resource for quantitative gene function annotation. PMID:20495000
Protein evolution in yeast transcription factor subnetworks. PMID:20466810
The Zymomonas mobilis regulator hfq contributes to tolerance against multiple lignocellulosic pretreatment inhibitors. PMID:20459639
Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry. PMID:20445003
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
High-content, image-based screening for drug targets in yeast. PMID:20418956
Missing value imputation for epistatic MAPs. PMID:20406472
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. PMID:20395639
Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. PMID:20393576
Fragile genomic sites are associated with origins of replication. PMID:20333204
Integrated cellular network of transcription regulations and protein-protein interactions. PMID:20211003
Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data. PMID:20198642
Predicting the protein-protein interactions using primary structures with predicted protein surface. PMID:20122202
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. PMID:20122162
Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PMID:20098497
Genome-wide computational prediction of tandem gene arrays: application in yeasts. PMID:20092627
Functional characterization of the Chlamydomonas reinhardtii ERG3 ortholog, a gene involved in the biosynthesis of ergosterol. PMID:20084111
Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data. PMID:20066130
A phenotypic profile of the Candida albicans regulatory network. PMID:20041210
Towards accurate imputation of quantitative genetic interactions. PMID:20003301
Quantitative proteomics by metabolic labeling of model organisms. PMID:19955089
Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis. PMID:19897511
In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean. PMID:19884168
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. PMID:19857274
Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways. PMID:19854949
Evidence of highly regulated genes (in-Hubs) in gene networks of Saccharomyces cerevisiae. PMID:19812784
Biogenesis of tail-anchored proteins: the beginning for the end? PMID:19812306
Proteomics data repositories. PMID:19795424
Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. PMID:19787074
A novel scoring approach for protein co-purification data reveals high interaction specificity. PMID:19779545
Yeast Ste23p shares functional similarities with mammalian insulin-degrading enzymes. PMID:19750477
An ensemble model of competitive multi-factor binding of the genome. PMID:19720867
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. PMID:19714207
Impact of chromatin structures on DNA processing for genomic analyses. PMID:19693276
Distinguishing direct versus indirect transcription factor-DNA interactions. PMID:19652015
The tRNA modification complex elongator regulates the Cdc42-dependent mitogen-activated protein kinase pathway that controls filamentous growth in yeast. PMID:19633267
Integrated assessment of genomic correlates of protein evolutionary rate. PMID:19521505
Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PMID:19503594
Role of the cell wall integrity and filamentous growth mitogen-activated protein kinase pathways in cell wall remodeling during filamentous growth. PMID:19502582
The histone deacetylase Rpd3p is required for transient changes in genomic expression in response to stress. PMID:19470158
The signaling mucins Msb2 and Hkr1 differentially regulate the filamentation mitogen-activated protein kinase pathway and contribute to a multimodal response. PMID:19439450
Core and periphery structures in protein interaction networks. PMID:19426456
Database resources in metabolomics: an overview. PMID:19418229
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. PMID:19401680
Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways. PMID:19399174
Evolutionary rates and centrality in the yeast gene regulatory network. PMID:19358738
A microfluidic device to acquire high-magnification microphotographs of yeast cells. PMID:19317904
Directing experimental biology: a case study in mitochondrial biogenesis. PMID:19300515
A census of human transcription factors: function, expression and evolution. PMID:19274049
Uncovering biological network function via graphlet degree signatures. PMID:19259413
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. PMID:19208812
Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae. PMID:19180179
A complex-based reconstruction of the Saccharomyces cerevisiae interactome. PMID:19176519
Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. PMID:19128476
Reconstruction of biochemical networks in microorganisms. PMID:19116616
Up-to-date catalogues of yeast protein complexes. PMID:19095691
The DNA-encoded nucleosome organization of a eukaryotic genome. PMID:19092803
Identification of functional modules based on transcriptional regulation structure. PMID:19091051
Systematic identification of yeast cell cycle transcription factors using multiple data sources. PMID:19061501
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. PMID:19032748
Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast. PMID:19023413
Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PMID:18989395
A relation based measure of semantic similarity for Gene Ontology annotations. PMID:18983678
Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PMID:18927628
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. PMID:18836191
Identifying gene regulatory modules of heat shock response in yeast. PMID:18811975
MitoP2: an integrative tool for the analysis of the mitochondrial proteome. PMID:18780189
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions. PMID:18628749
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. PMID:18586710
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. PMID:18562662
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions. PMID:18556670
VisANT: an integrative framework for networks in systems biology. PMID:18463131
Uncovering signal transduction networks from high-throughput data by integer linear programming. PMID:18411207
Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. PMID:18364712
Co-evolutionary rates of functionally related yeast genes. PMID:18345352
Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. PMID:18215224
MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. PMID:18171474
Trm9-catalyzed tRNA modifications link translation to the DNA damage response. PMID:18082610
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. PMID:18053250
PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. PMID:18039369
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. PMID:17978194
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. PMID:17947326
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PMID:17912365
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Information theory applied to the sparse gene ontology annotation network to predict novel gene function. PMID:17646340
Specific transcriptional responses induced by 8-methoxypsoralen and UVA in yeast. PMID:17608707
oPOSSUM: integrated tools for analysis of regulatory motif over-representation. PMID:17576675
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. PMID:17537814
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. PMID:17535793
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks. PMID:17437029
Inferring condition-specific transcription factor function from DNA binding and gene expression data. PMID:17437025
Identification and characterization of insect-specific proteins by genome data analysis. PMID:17407609
Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PMID:17389913
Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. PMID:17316440
Pseudolipasin A is a specific inhibitor for phospholipase A2 activity of Pseudomonas aeruginosa cytotoxin ExoU. PMID:17178785
Exploration of yeast alkali metal cation/H+ antiporters: sequence and structure comparison. PMID:17176761
Functional analysis of gene duplications in Saccharomyces cerevisiae. PMID:17151249
PROPHECY--a yeast phenome database, update 2006. PMID:17148481
Functional studies of aldo-keto reductases in Saccharomyces cerevisiae. PMID:17140678
PlasmID: a centralized repository for plasmid clone information and distribution. PMID:17132831
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. PMID:17032457
Characterization of binding sites of eukaryotic transcription factors. PMID:16970547
Global analysis of protein palmitoylation in yeast. PMID:16751107
Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. PMID:16648358
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. PMID:16643658
Predicting disease genes using protein-protein interactions. PMID:16611749
Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock. PMID:16584550
Development of an unbiased statistical method for the analysis of unigenic evolution. PMID:16545116
Protein protein interactions, evolutionary rate, abundance and age. PMID:16533385
A flexible representation of omic knowledge for thorough analysis of microarray data. PMID:16509996
Further understanding human disease genes by comparing with housekeeping genes and other genes. PMID:16504025
Subtelomeric factors antagonize telomere anchoring and Tel1-independent telomere length regulation. PMID:16467853
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. PMID:16381908
Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. PMID:16381905
Preferential attachment in the evolution of metabolic networks. PMID:16281983
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs. PMID:16207357
Statistical methods for identifying yeast cell cycle transcription factors. PMID:16157877
DynGO: a tool for visualizing and mining of Gene Ontology and its associations. PMID:16091147
The rarity of gene shuffling in conserved genes. PMID:15960802
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures. PMID:15833139
New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. PMID:15687288
MILANO--custom annotation of microarray results using automatic literature searches. PMID:15661078
PROPHECY--a database for high-resolution phenomics. PMID:15608218
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. PMID:15575972
GOToolBox: functional analysis of gene datasets based on Gene Ontology. PMID:15575967
Protein kinase A regulates constitutive expression of small heat-shock genes in an Msn2/4p-independent and Hsf1p-dependent manner in Saccharomyces cerevisiae. PMID:15545649
Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. PMID:15371544
Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. PMID:15306656
Metalloregulation of yeast membrane steroid receptor homologs. PMID:15060275
Calculating the statistical significance of physical clusters of co-regulated genes in the genome: the role of chromatin in domain-wide gene regulation. PMID:15034148
Diverse and specific gene expression responses to stresses in cultured human cells. PMID:15004229
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts. PMID:14681422
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. PMID:14578455
Predicting protein functions from redundancies in large-scale protein interaction networks. PMID:14566057
Asymmetric sequence divergence of duplicate genes. PMID:12952876
The computational analysis of scientific literature to define and recognize gene expression clusters. PMID:12888516
Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii. PMID:12844361
GeneLynx mouse: integrated portal to the mouse genome. PMID:12819149
Predicting gene function from patterns of annotation. PMID:12695322
Assessing experimentally derived interactions in a small world. PMID:12676999
A literature-based method for assessing the functional coherence of a gene group. PMID:12584126
FunSpec: a web-based cluster interpreter for yeast. PMID:12431279
Using text analysis to identify functionally coherent gene groups. PMID:12368251
Parallel identification of new genes in Saccharomyces cerevisiae. PMID:12176929
The human genome browser at UCSC. PMID:12045153
Isolation and mapping of self-assembling protein domains encoded by the Saccharomyces cerevisiae genome using lambda repressor fusions. PMID:11967834
Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites. PMID:11937640
The Saccharomyces cerevisiae 14-3-3 protein Bmh2 is required for regulation of the phosphorylation status of Fin1, a novel intermediate filament protein. PMID:11931638
Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. PMID:11779846
A receptor tyrosine kinase from choanoflagellates: molecular insights into early animal evolution. PMID:11752452
euGenes: a eukaryote genome information system. PMID:11752277
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). PMID:11752257
GeneLynx: a gene-centric portal to the human genome. PMID:11731507
A large family of endosome-localized proteins related to sorting nexin 1. PMID:11485546
yMGV: a database for visualization and data mining of published genome-wide yeast expression data. PMID:11433039
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. PMID:11433035
Genome-wide responses to mitochondrial dysfunction. PMID:11179416
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. PMID:11125055
Understanding the growth phenotype of the yeast gcr1 mutant in terms of global genomic expression patterns. PMID:10940042
Principal components analysis to summarize microarray experiments: application to sporulation time series. PMID:10902193
Luv1p/Rki1p/Tcs3p/Vps54p, a yeast protein that localizes to the late Golgi and early endosome, is required for normal vacuolar morphology. PMID:10888679
Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae. PMID:10710427
Integrating functional genomic information into the Saccharomyces genome database. PMID:10592186
Global response of Saccharomyces cerevisiae to an alkylating agent. PMID:9990050
Expanding yeast knowledge online. PMID:9885151
Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. PMID:9872985
A trans-activation domain in yeast heat shock transcription factor is essential for cell cycle progression during stress. PMID:9858564
Multiple domains of repressor activator protein 1 contribute to facilitated binding of glycolysis regulatory protein 1. PMID:9826662
A computer program for aligning a cDNA sequence with a genomic DNA sequence. PMID:9750195
Chromatin components as part of a putative transcriptional repressing complex. PMID:9636147
Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. PMID:9620854
Rpp2, an essential protein subunit of nuclear RNase P, is required for processing of precursor tRNAs and 35S precursor rRNA in Saccharomyces cerevisiae. PMID:9618478
AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative. PMID:9399805
SET1, a yeast member of the trithorax family, functions in transcriptional silencing and diverse cellular processes. PMID:9398665
Genetic and physical maps of Saccharomyces cerevisiae PubMed citations: 186.

186 articles citing: Genetic and physical maps of Saccharomyces cerevisiae

Genetic basis of a spontaneous mutation's expressivity. PMID:35078232
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
Clonal evolution in serially passaged Cryptococcus neoformans × deneoformans hybrids reveals a heterogenous landscape of genomic change. PMID:34849836
An HSP90 cochaperone Ids2 maintains the stability of mitochondrial DNA and ATP synthase. PMID:34763695
High-throughput functional characterization of protein phosphorylation sites in yeast. PMID:34663920
Estimating the time since admixture from phased and unphased molecular data. PMID:34599646
The Descent of Databases. PMID:33789353
Perspective: Linkage Maps, Communities of Geneticists, and Genome Databases. PMID:33023927
Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri. PMID:33004914
Manifold passages in an assorted infection in a host could improve virulence of Helicoverpa armigera Nucleopolyhedrovirus (HaNPV). PMID:32489276
Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker. PMID:32051233
Molecular signatures of aneuploidy-driven adaptive evolution. PMID:32001709
Whole-Genome Sequencing of Yeast Cells. PMID:31503417
Multicellular group formation in Saccharomyces cerevisiae. PMID:31480977
Trajectories of Aging: How Systems Biology in Yeast Can Illuminate Mechanisms of Personalized Aging. PMID:31385433
A polyploid admixed origin of beer yeasts derived from European and Asian wine populations. PMID:30835725
Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. PMID:30052927
PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. PMID:30049792
A High-Resolution Map of Meiotic Recombination in Cryptococcus deneoformans Demonstrates Decreased Recombination in Unisexual Reproduction. PMID:29625994
Gene regulation in Kluyveromyces marxianus in the context of chromosomes. PMID:29346402
Genome-scale modeling of yeast: chronology, applications and critical perspectives. PMID:28899034
Post-Translational Dosage Compensation Buffers Genetic Perturbations to Stoichiometry of Protein Complexes. PMID:28121980
Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information. PMID:28116287
Effect of sex, age and genetics on crossover interference in cattle. PMID:27892966
Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. PMID:27252399
Sporadic, Global Linkage Disequilibrium Between Unlinked Segregating Sites. PMID:26715671
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models. PMID:26426067
The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen. PMID:26392286
Low-Rank and Sparse Matrix Decomposition for Genetic Interaction Data. PMID:26273633
An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome. PMID:25880651
Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy. PMID:25752599
Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast. PMID:25349286
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Viral RNAs are unusually compact. PMID:25188030
Topoisomerase II mediates meiotic crossover interference. PMID:25043020
Improved linkage analysis of Quantitative Trait Loci using bulk segregants unveils a novel determinant of high ethanol tolerance in yeast. PMID:24640961
MULTI-WAY BLOCKMODELS FOR ANALYZING COORDINATED HIGH-DIMENSIONAL RESPONSES. PMID:24587846
RANKING RELATIONS USING ANALOGIES IN BIOLOGICAL AND INFORMATION NETWORKS. PMID:24587838
Crossover patterning by the beam-film model: analysis and implications. PMID:24497834
Yeast Nkp2 is required for accurate chromosome segregation and interacts with several components of the central kinetochore. PMID:24385296
Heterodimeric protein complex identification by naïve Bayes classifiers. PMID:24299017
Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. PMID:23821616
The modest beginnings of one genome project. PMID:23733847
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions. PMID:23651452
The role of protein interactions in mediating essentiality and synthetic lethality. PMID:23638160
Under-dominance constrains the evolution of negative autoregulation in diploids. PMID:23555226
System for automatically inferring a genetic netwerk from expression profiles. PMID:23345788
A structural-based strategy for recognition of transcription factor binding sites. PMID:23320072
Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions. PMID:23268696
Cell-cycle and DNA damage regulation of the DNA mismatch repair protein Msh2 occurs at the transcriptional and post-transcriptional level. PMID:23261051
Evolution of cis-regulatory elements in yeast de novo and duplicated new genes. PMID:23256513
The secretory pathway in control of endoplasmic reticulum homeostasis. PMID:23235440
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. PMID:23176165
The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae. PMID:23172850
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. PMID:23089682
Natural genetic variation in yeast longevity. PMID:22955140
Recruitment of Rpd3 to the telomere depends on the protein arginine methyltransferase Hmt1. PMID:22953000
Pathogen webs in collapsing honey bee colonies. PMID:22927991
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. PMID:22898396
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
The yeast Rab GTPase Ypt1 modulates unfolded protein response dynamics by regulating the stability of HAC1 RNA. PMID:22844259
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
Most networks in Wagner's model are cycling. PMID:22511935
Diverse forms of RPS9 splicing are part of an evolving autoregulatory circuit. PMID:22479208
Chaperones divide yeast proteins into classes of expression level and evolutionary rate. PMID:22417914
Reducing false-positive prediction of minimotifs with a genetic interaction filter. PMID:22403687
Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis. PMID:22399573
Diversity measures in environmental sequences are highly dependent on alignment quality--data from ITS and new LSU primers targeting basidiomycetes. PMID:22363808
Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age. PMID:22319151
Characterizing peptide neutral losses induced by negative electron-transfer dissociation (NETD). PMID:22290482
Mapping yeast N-glycosites with isotopically recoded glycans. PMID:22261724
Production of amorphadiene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin. PMID:22247290
Similarities and differences between "uncapped" telomeres and DNA double-strand breaks. PMID:22203190
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. PMID:22192575
Visualizing large RNA molecules in solution. PMID:22190747
The UCSC Genome Browser database: extensions and updates 2011. PMID:22086951
OGEE: an online gene essentiality database. PMID:22075992
ReCombine: a suite of programs for detection and analysis of meiotic recombination in whole-genome datasets. PMID:22046241
Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways. PMID:21980306
Disruption of Yarrowia lipolytica TPS1 gene encoding trehalose-6-P synthase does not affect growth in glucose but impairs growth at high temperature. PMID:21931609
Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. PMID:21901739
Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments. PMID:21791067
Access to DNA establishes a secondary target site bias for the yeast retrotransposon Ty5. PMID:21788500
Fungal enzyme sets for plant polysaccharide degradation. PMID:21785931
The Candida albicans GAP gene family encodes permeases involved in general and specific amino acid uptake and sensing. PMID:21764911
Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data. PMID:21760653
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning. PMID:21685095
Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences. PMID:21635751
Methods and strategies for gene structure curation in WormBase. PMID:21543339
Major prospects for exploring canine vector borne diseases and novel intervention methods using 'omic technologies. PMID:21489242
Customizable views on semantically integrated networks for systems biology. PMID:21414991
Evolutionary origins of STIM1 and STIM2 within ancient Ca2+ signaling systems. PMID:21288721
Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications. PMID:21176163
Discovery of mutations in Saccharomyces cerevisiae by pooled linkage analysis and whole-genome sequencing. PMID:20923977
Genome-wide model for the normal eukaryotic DNA replication fork. PMID:20876092
Genetic analysis of baker's yeast Msh4-Msh5 reveals a threshold crossover level for meiotic viability. PMID:20865162
Proteome-wide search reveals unexpected RNA-binding proteins in Saccharomyces cerevisiae. PMID:20844764
Integration of metabolic reactions and gene regulation. PMID:20737299
A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities. PMID:20686707
G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae. PMID:20676380
Genome-wide association data reveal a global map of genetic interactions among protein complexes. PMID:20041197
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays. PMID:20003312
Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression. PMID:19888207
A comparative analysis of DNA barcode microarray feature size. PMID:19825181
The Gene Wiki: community intelligence applied to human gene annotation. PMID:19755503
Two-parameter characterization of chromosome-scale recombination rate. PMID:19752285
Aneuploidy and improved growth are coincident but not causal in a yeast cancer model. PMID:19636358
A strategy for constructing aneuploid yeast strains by transient nondisjunction of a target chromosome. PMID:19594932
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data. PMID:19401402
ANNIE: integrated de novo protein sequence annotation. PMID:19389726
O-GlcNAc modifications regulate cell survival and epiboly during zebrafish development. PMID:19383152
An improved ontological representation of dendritic cells as a paradigm for all cell types. PMID:19243617
An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast. PMID:19061486
Emerging roles for centromeres in meiosis I chromosome segregation. PMID:18981989
QuantPrime--a flexible tool for reliable high-throughput primer design for quantitative PCR. PMID:18976492
Chromosome-scale genetic mapping using a set of 16 conditionally stable Saccharomyces cerevisiae chromosomes. PMID:18832360
MitoP2: an integrative tool for the analysis of the mitochondrial proteome. PMID:18780189
A catalog of neutral and deleterious polymorphism in yeast. PMID:18769710
Global analysis of the meiotic crossover landscape. PMID:18691940
High-resolution mapping of meiotic crossovers and non-crossovers in yeast. PMID:18615017
Protein complex identification by supervised graph local clustering. PMID:18586722
A genetic screen for increased loss of heterozygosity in Saccharomyces cerevisiae. PMID:18562670
Meiotic recombination at the ends of chromosomes in Saccharomyces cerevisiae. PMID:18562657
Onto-CC: a web server for identifying Gene Ontology conceptual clusters. PMID:18544607
Gene Ontology annotations: what they mean and where they come from. PMID:18460184
Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data. PMID:18426580
Data capture in bioinformatics: requirements and experiences with Pedro. PMID:18402673
Systematic identification of cell cycle regulated transcription factors from microarray time series data. PMID:18315882
Predicted functional RNAs within coding regions constrain evolutionary rates of yeast proteins. PMID:18270559
The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. PMID:18073433
A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies. PMID:18003902
Smy2p participates in COPII vesicle formation through the interaction with Sec23p/Sec24p subcomplex. PMID:17973654
Chromosome mobility during meiotic prophase in Saccharomyces cerevisiae. PMID:17939997
Integration of known transcription factor binding site information and gene expression data to advance from co-expression to co-regulation. PMID:17893074
Functional characterization of pathogenic human MSH2 missense mutations in Saccharomyces cerevisiae. PMID:17720936
Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. PMID:17683642
3D-partner: a web server to infer interacting partners and binding models. PMID:17517763
RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features. PMID:17478517
High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. PMID:17244705
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. PMID:16968785
An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity. PMID:16877712
Integrated assessment and prediction of transcription factor binding. PMID:16789814
Determination of strongly overlapping signaling activity from microarray data. PMID:16507110
Proteomic analysis of the yeast mitochondrial outer membrane reveals accumulation of a subclass of preproteins. PMID:16407407
MitoP2: the mitochondrial proteome database--now including mouse data. PMID:16381964
Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system. PMID:16286509
Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. PMID:16012843
PatMatch: a program for finding patterns in peptide and nucleotide sequences. PMID:15980466
The rarity of gene shuffling in conserved genes. PMID:15960802
Hypervariable noncoding sequences in Saccharomyces cerevisiae. PMID:15956668
The functioning of mammalian ClC-2 chloride channel in Saccharomyces cerevisiae cells requires an increased level of Kha1p. PMID:15926887
Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. PMID:15905473
Functional specificity of shuttling hnRNPs revealed by genome-wide analysis of their RNA binding profiles. PMID:15703440
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. PMID:15611189
Competing crossover pathways act during meiosis in Saccharomyces cerevisiae. PMID:15611158
Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. PMID:15457216
TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. PMID:14724320
Binding of the essential Saccharomyces cerevisiae kinetochore protein Ndc10p to CDEII. PMID:13679521
Optimizing spotting solutions for increased reproducibility of cDNA microarrays. PMID:12954785
MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences. PMID:12824360
Ceramide/long-chain base phosphate rheostat in Saccharomyces cerevisiae: regulation of ceramide synthesis by Elo3p and Cka2p. PMID:12684378
The Ume6 regulon coordinates metabolic and meiotic gene expression in yeast. PMID:12370439
The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae. PMID:12084816
A physical interaction between Gar1p and Rnt1pi is required for the nuclear import of H/ACA small nucleolar RNA-associated proteins. PMID:12052886
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. PMID:12034841
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). PMID:11752257
Molecular population genetics and evolution of a prion-like protein in Saccharomyces cerevisiae. PMID:11606530
RNA polymerase III and RNA polymerase II promoter complexes are heterochromatin barriers in Saccharomyces cerevisiae. PMID:11157758
The sodium/proton exchanger Nhx1p is required for endosomal protein trafficking in the yeast Saccharomyces cerevisiae. PMID:11102523
Computational identification of cis-acting elements affecting post-transcriptional control of gene expression in Saccharomyces cerevisiae. PMID:10710427
Cloning and expression of kinesins from the thermophilic fungus Thermomyces lanuginosus. PMID:10631986
Integrating functional genomic information into the Saccharomyces genome database. PMID:10592186
Tagging chromatin with retrotransposons: target specificity of the Saccharomyces Ty5 retrotransposon changes with the chromosomal localization of Sir3p and Sir4p. PMID:10541559
Collisions between yeast chromosomal loci in vivo are governed by three layers of organization. PMID:10421638
LST1 is a SEC24 homologue used for selective export of the plasma membrane ATPase from the endoplasmic reticulum. PMID:10330397
A mutation in GRS1, a glycyl-tRNA synthetase, affects 3'-end formation in Saccharomyces cerevisiae. PMID:10224248
Identification and characterization of Saccharomyces cerevisiae yapsin 3, a new member of the yapsin family of aspartic proteases encoded by the YPS3 gene. PMID:10191273
Comparison of the complete protein sets of worm and yeast: orthology and divergence. PMID:9851918
Cluster analysis and display of genome-wide expression patterns. PMID:9843981
CNS1 encodes an essential p60/Sti1 homolog in Saccharomyces cerevisiae that suppresses cyclophilin 40 mutations and interacts with Hsp90. PMID:9819421
Nucleolar localization of early tRNA processing. PMID:9716399
Transdominant genetic analysis of a growth control pathway. PMID:9636180
Highly specific protein sequence motifs for genome analysis. PMID:9600885
Yeast nuclei display prominent centromere clustering that is reduced in nondividing cells and in meiotic prophase. PMID:9531545
tRNA genes and retroelements in the yeast genome. PMID:9443958
SGD: Saccharomyces Genome Database. PMID:9399804
The reference genome sequence of Saccharomyces cerevisiae: then and now PubMed citations: 169.

169 articles citing: The reference genome sequence of Saccharomyces cerevisiae: then and now

Telomere-to-Telomere Genome Sequences across a Single Genus Reveal Highly Variable Chromosome Rearrangement Rates but Absolute Stasis of Chromosome Number. PMID:35887427
Using off-gas for insights through online monitoring of ethanol and baker's yeast volatilome using SESI-Orbitrap MS. PMID:35864195
G1-Cyclin2 (Cln2) promotes chromosome hypercondensation in eco1/ctf7 rad61 null cells during hyperthermic stress in Saccharomyces cerevisiae. PMID:35736360
Evolution and functional diversification of catalase genes in the green lineage. PMID:35650553
Animal Models of Neurodegenerative Disease: Recent Advances in Fly Highlight Innovative Approaches to Drug Discovery. PMID:35514431
Contingency and selection in mitochondrial genome dynamics. PMID:35404229
Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. PMID:35384842
Peering Into Candida albicans Pir Protein Function and Comparative Genomics of the Pir Family. PMID:35372132
Domestication reprogrammed the budding yeast life cycle. PMID:35210580
The Ecology and Evolution of the Baker's Yeast Saccharomyces cerevisiae. PMID:35205274
Visualizing the next frontiers in wine yeast research. PMID:35175339
Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes). PMID:35156613
Barcoded bulk QTL mapping reveals highly polygenic and epistatic architecture of complex traits in yeast. PMID:35147078
Contribution of domain structure to the function of the yeast DEDD family exoribonuclease and RNase T functional homolog, Rex1. PMID:35082142
Yeast Crf1p: An activator in need is an activator indeed. PMID:34976315
YPK9 and WHI2 Negatively Interact during Oxidative Stress. PMID:34946185
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
On and Off: Epigenetic Regulation of C. albicans Morphological Switches. PMID:34832617
Efficient breeding of industrial brewing yeast strains using CRISPR/Cas9-aided mating-type switching. PMID:34643787
Signal-based optical map alignment. PMID:34591846
The Siderophore Transporters Sit1 and Sit2 Are Essential for Utilization of Ferrichrome-, Ferrioxamine- and Coprogen-Type Siderophores in Aspergillus fumigatus. PMID:34575806
The amino acid substitution affects cellular response to mistranslation. PMID:34568909
Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae. PMID:34499735
ESA1 regulates meiotic chromosome axis and crossover frequency via acetylating histone H4. PMID:34417612
Peroxiredoxin Asp f3 Is Essential for Aspergillus fumigatus To Overcome Iron Limitation during Infection. PMID:34399627
Comparative Genomics Supports That Brazilian Bioethanol Saccharomyces cerevisiae Comprise a Unified Group of Domesticated Strains Related to Cachaça Spirit Yeasts. PMID:33936002
Unique Brewing-Relevant Properties of a Strain of Saccharomyces jurei Isolated From Ash (Fraxinus excelsior). PMID:33868204
Spt4 Promotes Pol I Processivity and Transcription Elongation. PMID:33809333
Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. PMID:33768233
A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast. PMID:33757429
Regulation of Age-Related Protein Toxicity. PMID:33748125
Perfect Match Genomic Landscape strategy: Refinement and customization of reference genomes. PMID:33737447
A case of convergent-gene interference in the budding yeast knockout library causing chromosome instability. PMID:33724427
Calcium signaling is involved in diverse cellular processes in fungi. PMID:33628605
Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii. PMID:33472617
On the role of transcription in positioning nucleosomes. PMID:33417594
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins. PMID:33237964
Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross. PMID:33179598
The Post-Translational Modifications, Localization, and Mode of Attachment of Non-Covalently Bound Glucanosyltransglycosylases of Yeast Cell Wall as a Key to Understanding their Functioning. PMID:33167499
Rules are made to be broken: a "simple" model organism reveals the complexity of gene regulation. PMID:33130938
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations. PMID:32963084
The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. PMID:32941642
Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP. PMID:32873198
New Perspectives on SNARE Function in the Yeast Minimal Endomembrane System. PMID:32781543
Precise Replacement of Saccharomyces cerevisiae Proteasome Genes with Human Orthologs by an Integrative Targeting Method. PMID:32680853
Differentially Regulated Transcription Factors and ABC Transporters in a Mitochondrial Dynamics Mutant Can Alter Azole Susceptibility of Aspergillus fumigatus. PMID:32528443
Model-driven generation of artificial yeast promoters. PMID:32355169
Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective. PMID:32336995
Resistance Mechanisms of Saccharomyces cerevisiae to Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure. PMID:32299824
Anticipating Xenogenic Pollution at the Source: Impact of Sterilizations on DNA Release From Microbial Cultures. PMID:32232035
High-resolution modeling of the selection on local mRNA folding strength in coding sequences across the tree of life. PMID:32151272
Genomic Considerations for the Modification of Saccharomyces cerevisiae for Biofuel and Metabolite Biosynthesis. PMID:32110897
High Transcriptional Error Rates Vary as a Function of Gene Expression Level. PMID:31841128
Tasting the terroir of wine yeast innovation. PMID:31830254
Suppression of Ribosomal Pausing by eIF5A Is Necessary to Maintain the Fidelity of Start Codon Selection. PMID:31801078
DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories. PMID:31738765
Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO2 levels. PMID:31654410
Rare variants contribute disproportionately to quantitative trait variation in yeast. PMID:31647408
Transcriptome visualization and data availability at the Saccharomyces Genome Database. PMID:31612944
The nucleosome core particle remembers its position through DNA replication and RNA transcription. PMID:31511420
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis. PMID:31439691
Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. PMID:31437442
The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae. PMID:31397853
Accurate Tracking of the Mutational Landscape of Diploid Hybrid Genomes. PMID:31397846
Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. PMID:31292258
Phenotypic and Genotypic Consequences of CRISPR/Cas9 Editing of the Replication Origins in the rDNA of Saccharomyces cerevisiae. PMID:31292210
Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast. PMID:31273196
Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone. PMID:31254414
Differences Between the Raw Material and the Products of de Novo Gene Birth Can Result from Mutational Biases. PMID:31227545
UV Laser-Induced, Time-Resolved Transcriptome Responses of Saccharomyces cerevisiae. PMID:31213515
Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. PMID:31128237
The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. PMID:31092540
DNA Rereplication Is Susceptible to Nucleotide-Level Mutagenesis. PMID:31028114
Prediction and identification of recurrent genomic rearrangements that generate chimeric chromosomes in Saccharomyces cerevisiae. PMID:30962378
ChIPulate: A comprehensive ChIP-seq simulation pipeline. PMID:30897079
Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PMID:30699175
Identification of Suppressor of Clathrin Deficiency-1 (SCD1) and Its Connection to Clathrin-Mediated Endocytosis in Saccharomyces cerevisiae. PMID:30679249
Whole-genome comparisons of Penicillium spp. reveals secondary metabolic gene clusters and candidate genes associated with fungal aggressiveness during apple fruit decay. PMID:30643697
Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions. PMID:30590648
Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing. PMID:30573814
Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans. PMID:30377286
YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries. PMID:30357397
Spt6 Is Required for the Fidelity of Promoter Selection. PMID:30318445
Genotype-by-Environment-by-Environment Interactions in the Saccharomyces cerevisiae Transcriptomic Response to Alcohols and Anaerobiosis. PMID:30301737
Studying Huntington's Disease in Yeast: From Mechanisms to Pharmacological Approaches. PMID:30233317
Engineering Saccharomyces cerevisiae for production of simvastatin. PMID:30213650
Knockout of the Hmt1p Arginine Methyltransferase in Saccharomyces cerevisiae Leads to the Dysregulation of Phosphate-associated Genes and Processes. PMID:30206180
Mitochondrial ribosomal proteins involved in tellurite resistance in yeast Saccharomyces cerevisiae. PMID:30104660
Resistance to the Plant Defensin NaD1 Features Modifications to the Cell Wall and Osmo-Regulation Pathways of Yeast. PMID:30087664
Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. PMID:30045857
Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. PMID:30011030
Inferring Variation in Copy Number Using High Throughput Sequencing Data in R. PMID:29706990
New CRISPR Mutagenesis Strategies Reveal Variation in Repair Mechanisms among Fungi. PMID:29695624
Genome-wide association across Saccharomyces cerevisiae strains reveals substantial variation in underlying gene requirements for toxin tolerance. PMID:29474395
The Yeast Saccharomyces cerevisiae as a Model for Understanding RAS Proteins and their Role in Human Tumorigenesis. PMID:29463063
Association of improved oxidative stress tolerance and alleviation of glucose repression with superior xylose-utilization capability by a natural isolate of Saccharomyces cerevisiae. PMID:29441126
RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments. PMID:29390085
A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes. PMID:29367403
Cdc73 suppresses genome instability by mediating telomere homeostasis. PMID:29320491
Transcriptional Profiling of Saccharomyces cerevisiae Reveals the Impact of Variation of a Single Transcription Factor on Differential Gene Expression in 4NQO, Fermentable, and Nonfermentable Carbon Sources. PMID:29208650
Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs. PMID:29208647
Dynamic localization of a yeast development-specific PP1 complex during prospore membrane formation is dependent on multiple localization signals and complex formation. PMID:29046399
Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells. PMID:28993899
The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source. PMID:28957510
Genetic variation in adaptability and pleiotropy in budding yeast. PMID:28826486
The [PSI +] yeast prion does not wildly affect proteome composition whereas selective pressure exerted on [PSI +] cells can promote aneuploidy. PMID:28814753
Rps26 directs mRNA-specific translation by recognition of Kozak sequence elements. PMID:28759050
CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides. PMID:28751611
Functional Profiling of Transcription Factor Genes in Neurospora crassa. PMID:28696922
Causal Genetic Variation Underlying Metabolome Differences. PMID:28652377
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PMID:28594827
Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of Saccharomyces cerevisiae. PMID:28584079
NuA4 Lysine Acetyltransferase Complex Contributes to Phospholipid Homeostasis in Saccharomyces cerevisiae. PMID:28455416
Inheritance of brewing-relevant phenotypes in constructed Saccharomyces cerevisiae × Saccharomyces eubayanus hybrids. PMID:28431563
PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes. PMID:28429714
Properties of Mitotic and Meiotic Recombination in the Tandemly-Repeated CUP1 Gene Cluster in the Yeast Saccharomyces cerevisiae. PMID:28381587
Loss of Heterozygosity Drives Adaptation in Hybrid Yeast. PMID:28369610
Stress-Triggered Phase Separation Is an Adaptive, Evolutionarily Tuned Response. PMID:28283059
Chromatin Regulation by the NuA4 Acetyltransferase Complex Is Mediated by Essential Interactions Between Enhancer of Polycomb (Epl1) and Esa1. PMID:28108589
Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains. PMID:28000736
Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes. PMID:27991904
Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis. PMID:27855779
Growth conditions that increase or decrease lifespan in Saccharomyces cerevisiae lead to corresponding decreases or increases in rates of interstitial deletions and non-reciprocal translocations. PMID:27769161
Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PMID:27741250
Donor Preference Meets Heterochromatin: Moonlighting Activities of a Recombinational Enhancer in Saccharomyces cerevisiae. PMID:27655944
RNA-DNA sequence differences in Saccharomyces cerevisiae. PMID:27638543
Selection on Position of Nonsense Codons in Introns. PMID:27630196
Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance. PMID:27451446
The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum. PMID:27381095
Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast. PMID:27374328
Pluribus-Exploring the Limits of Error Correction Using a Suffix Tree. PMID:27362987
Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. PMID:27252399
Perspectives in Genomics The Future of Fungi in 'omics, era. PMID:27226764
The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast. PMID:27190003
Ploidy influences the functional attributes of de novo lager yeast hybrids. PMID:27183995
Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. PMID:27172212
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks. PMID:27161996
Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PMID:27152522
Independent Evolution of Winner Traits without Whole Genome Duplication in Dekkera Yeasts. PMID:27152421
Survey of cryptic unstable transcripts in yeast. PMID:27113450
From one to many: expanding the Saccharomyces cerevisiae reference genome panel. PMID:26989152
Structural elements that govern Sec14-like PITP sensitivities to potent small molecule inhibitors. PMID:26921357
MTE1 Functions with MPH1 in Double-Strand Break Repair. PMID:26920759
Global translational impacts of the loss of the tRNA modification t6A in yeast. PMID:26798630
Reduced Glucose Sensation Can Increase the Fitness of Saccharomyces cerevisiae Lacking Mitochondrial DNA. PMID:26751567
Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures. PMID:26744270
The Saccharomyces Genome Database: A Tool for Discovery. PMID:26631132
N-Ethylmaleimide-Sensitive Factor b (nsfb) Is Required for Normal Pigmentation of the Zebrafish Retinal Pigment Epithelium. PMID:26618645
Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast. PMID:26615217
TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation in Saccharomyces cerevisiae. PMID:26582391
The Saccharomyces Genome Database Variant Viewer. PMID:26578556
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PMID:26539826
Targeted single molecule mutation detection with massively parallel sequencing. PMID:26384417
Tiling Assembly: a new tool for reference annotation-independent transcript assembly and novel gene identification by RNA-sequencing. PMID:26341416
Genome-wide replication landscape of Candida glabrata. PMID:26329162
The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts. PMID:26269586
Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress. PMID:26156140
Assembly of Slx4 signaling complexes behind DNA replication forks. PMID:26113155
Biocuration at the Saccharomyces genome database. PMID:25997651
Long-read, whole-genome shotgun sequence data for five model organisms. PMID:25977796
Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone. PMID:25977456
The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. PMID:25840857
PRIMED: PRIMEr database for deleting and tagging all fission and budding yeast genes developed using the open-source genome retrieval script (GRS). PMID:25643023
Macrotene chromosomes provide insights to a new mechanism of high-order gene amplification in eukaryotes. PMID:25635677
Heritable variation of mRNA decay rates in yeast. PMID:25258386
Structures of naturally evolved CUP1 tandem arrays in yeast indicate that these arrays are generated by unequal nonhomologous recombination. PMID:25236733
Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. PMID:25217194
Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage. PMID:24886553
YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit PubMed citations: 143.

143 articles citing: YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes. PMID:35766356
Humanized yeast to model human biology, disease and evolution. PMID:35661208
Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks. PMID:35495119
When Phosphatases Go Mad: The Molecular Basis for Toxicity of Yeast Ppz1. PMID:35457140
Adaptive Response of Saccharomyces Hosts to Totiviridae L-A dsRNA Viruses Is Achieved through Intrinsically Balanced Action of Targeted Transcription Factors. PMID:35448612
Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms. PMID:35314699
Rewiring phospholipid biosynthesis reveals resilience to membrane perturbations and uncovers regulators of lipid homeostasis. PMID:35188676
Fitness Effects of Mutations: An Assessment of PROVEAN Predictions Using Mutation Accumulation Data. PMID:35038732
Insights into cell robustness against lignocellulosic inhibitors and insoluble solids in bioethanol production processes. PMID:35017613
Forced association of SARS-CoV-2 proteins with the yeast proteome perturb vesicle trafficking. PMID:34909432
Ribo-Seq and RNA-Seq of TMA46 ( DFRP1) and GIR2 ( DFRP2) knockout yeast strains. PMID:34900236
The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. PMID:34830359
Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses. PMID:34740240
Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance. PMID:34566920
Transcriptional Profile of the Industrial Hybrid Saccharomyces pastorianus Reveals Temperature-Dependent Allele Expression Bias and Preferential Orthologous Protein Assemblies. PMID:34550394
Restoring fertility in yeast hybrids: Breeding and quantitative genetics of beneficial traits. PMID:34518218
Fur4-mediated uracil-scavenging to screen for surface protein regulators. PMID:34498791
Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci. PMID:34363476
Primordial super-enhancers: heat shock-induced chromatin organization in yeast. PMID:34001402
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PMID:33836000
Complete genome sequence and analysis of a Saccharomyces cerevisiae strain used for sugarcane spirit production. PMID:33835421
Trans-acting genetic variation affects the expression of adjacent genes. PMID:33789351
Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species. PMID:33772558
Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription. PMID:33689394
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63-branched ubiquitin chains. PMID:33576509
Inner-nuclear-membrane-associated degradation employs Dfm1-independent retrotranslocation and alleviates misfolded transmembrane-protein toxicity. PMID:33566711
Data-driven biological network alignment that uses topological, sequence, and functional information. PMID:33514304
Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network. PMID:33493158
In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. PMID:33491328
Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae. PMID:33462193
Complexity of the eukaryotic dolichol-linked oligosaccharide scramblase suggested by activity correlation profiling mass spectrometry. PMID:33446867
Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses. PMID:33318504
Minimum Description Length Codes Are Critical. PMID:33265844
Towards a unified open access dataset of molecular interactions. PMID:33262342
YQFC: a web tool to compare quantitative biological features between two yeast gene lists. PMID:33186464
Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. PMID:33093574
PartCrafter: find, generate and analyze BioParts. PMID:32995539
Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets. PMID:32973189
The effect of hybridization on transposable element accumulation in an undomesticated fungal species. PMID:32955438
Systematic analysis of bypass suppression of essential genes. PMID:32939983
Records of RNA locations in living yeast revealed through covalent marks. PMID:32907940
Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation. PMID:32811554
Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. PMID:32732306
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PMID:32421706
Combining data integration and molecular dynamics for target identification in α-Synuclein-aggregating neurodegenerative diseases: Structural insights on Synaptojanin-1 (Synj1). PMID:32419904
Proteomic analysis of the S. cerevisiae response to the anticancer ruthenium complex KP1019. PMID:32329475
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. PMID:32184324
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. PMID:32128557
Cross-Species Complementation of Nonessential Yeast Genes Establishes Platforms for Testing Inhibitors of Human Proteins. PMID:31937519
Autophagy is required for sulfur dioxide tolerance in Saccharomyces cerevisiae. PMID:31638329
The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown upon glucose availability. PMID:31604822
LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing. PMID:31486704
Screening the Saccharomyces cerevisiae Nonessential Gene Deletion Library Reveals Diverse Mechanisms of Action for Antifungal Plant Defensins. PMID:31451498
Insoluble solids at high concentrations repress yeast's response against stress and increase intracellular ROS levels. PMID:31439886
Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23. PMID:31371382
Leveraging genetic interactions for adverse drug-drug interaction prediction. PMID:31125330
The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae. PMID:31096715
The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. PMID:31092540
Hidden in plain sight: what remains to be discovered in the eukaryotic proteome? PMID:30938578
Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae. PMID:30816176
Inferring Gene Regulatory Networks from a Population of Yeast Segregants. PMID:30718595
Multi-study inference of regulatory networks for more accurate models of gene regulation. PMID:30677040
Perturbations of Transcription and Gene Expression-Associated Processes Alter Distribution of Cell Size Values in Saccharomyces cerevisiae. PMID:30463882
A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction. PMID:30319573
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Overlapping open reading frames strongly reduce human and yeast STN1 gene expression and affect telomere function. PMID:30067734
YARG: A repository for arsenic-related genes in yeast. PMID:30048518
Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts. PMID:29867869
Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK. PMID:29796388
High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. PMID:29786095
TelNet - a database for human and yeast genes involved in telomere maintenance. PMID:29776332
Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466
Updated regulation curation model at the Saccharomyces Genome Database. PMID:29688362
YAAM: Yeast Amino Acid Modifications Database. PMID:29688347
Exploiting mitochondrial and metabolic homeostasis as a vulnerability in NF1 deficient cells. PMID:29662612
JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846
Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. PMID:29620521
General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4. PMID:29432178
A systematic assessment of chemical, genetic, and epigenetic factors influencing the activity of anticancer drug KP1019 (FFC14A). PMID:29228701
Different Non-Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures. PMID:29163412
Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321
ComplexViewer: visualization of curated macromolecular complexes. PMID:29036573
Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PMID:28665995
Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PMID:28628618
Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs. PMID:28546148
Identifying pathogenicity of human variants via paralog-based yeast complementation. PMID:28542158
Functional mapping of yeast genomes by saturated transposition. PMID:28481201
A New Method, "Reverse Yeast Two-Hybrid Array" (RYTHA), Identifies Mutants that Dissociate the Physical Interaction Between Elg1 and Slx5. PMID:28476868
Curated protein information in the Saccharomyces genome database. PMID:28365727
Outreach and online training services at the Saccharomyces Genome Database. PMID:28365719
Coordinate responses to alkaline pH stress in budding yeast. PMID:28357292
Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii. PMID:28336969
Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer. PMID:28198375
Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response. PMID:28079179
Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. PMID:28057705
New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae. PMID:27733850
Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. PMID:27551064
A genome-wide imaging-based screening to identify genes involved in synphilin-1 inclusion formation in Saccharomyces cerevisiae. PMID:27440388
Principal component analysis based unsupervised feature extraction applied to budding yeast temporally periodic gene expression. PMID:27366210
Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant. PMID:27317780
Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PMID:27152522
Synthetic protein interactions reveal a functional map of the cell. PMID:27098839
Global translational impacts of the loss of the tRNA modification t6A in yeast. PMID:26798630
The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression. PMID:26740628
A Genome-Wide Screen with Nicotinamide to Identify Sirtuin-Dependent Pathways in Saccharomyces cerevisiae. PMID:26646153
The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining. PMID:26631124
Mouse genome database 2016. PMID:26578600
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PMID:26566239
Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast. PMID:26537787
Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds. PMID:26459777
Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655
Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response. PMID:26391581
RNA regulatory networks diversified through curvature of the PUF protein scaffold. PMID:26364903
Complementation of Yeast Genes with Human Genes as an Experimental Platform for Functional Testing of Human Genetic Variants. PMID:26354769
Rapid Identification of Chemoresistance Mechanisms Using Yeast DNA Mismatch Repair Mutants. PMID:26199284
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662
Cross-organism analysis using InterMine. PMID:26097192
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
A Genetic Screen for Saccharomyces cerevisiae Mutants That Fail to Enter Quiescence. PMID:26068574
Biocuration at the Saccharomyces genome database. PMID:25997651
Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes. PMID:25968466
Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation. PMID:25711830
Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/SWS1 protein family from Saccharomyces cerevisiae to Homo sapiens. PMID:25659377
The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast. PMID:25522035
Too much of a good thing: the unique and repeated paths toward copper adaptation. PMID:25519894
Araport: the Arabidopsis information portal. PMID:25414324
FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. PMID:25294921
TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids. PMID:25279700
esyN: network building, sharing and publishing. PMID:25181461
InterMine: extensive web services for modern biology. PMID:24753429
Predicting the dynamics of protein abundance. PMID:24532840
Saccharomyces genome database provides new regulation data. PMID:24265222
Saccharomyces cerevisiae genes involved in survival of heat shock. PMID:24142923
Genome-wide study of the adaptation of Saccharomyces cerevisiae to the early stages of wine fermentation. PMID:24040173
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057
Ptc6 is required for proper rapamycin-induced down-regulation of the genes coding for ribosomal and rRNA processing proteins in S. cerevisiae. PMID:23704987
Genome-scale studies of aging: challenges and opportunities. PMID:23633910
The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302
Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals. PMID:23183665
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. PMID:23023984

Gene Ontology annotations at SGD: new data sources and annotation methods PubMed citations: 138.

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms PubMed citations: 137.

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO) PubMed citations: 132.

Comparison of the complete protein sets of worm and yeast: orthology and divergence PubMed citations: 105.

Yeast as a model organism PubMed citations: 95.

Saccharomyces Genome Database provides mutant phenotype data PubMed citations: 82.

A guide to best practices for Gene Ontology (GO) manual annotation PubMed citations: 76.

Standardized description of scientific evidence using the Evidence Ontology (ECO) PubMed citations: 63.

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome PubMed citations: 59.

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis PubMed citations: 54.

Expanded protein information at SGD: new pages and proteome browser PubMed citations: 48.

Saccharomyces Genome Database PubMed citations: 43.

The complex portal--an encyclopaedia of macromolecular complexes PubMed citations: 43.

Saccharomyces genome database: underlying principles and organisation PubMed citations: 42.

Saccharomyces genome database provides new regulation data PubMed citations: 35.

Integrating functional genomic information into the Saccharomyces genome database PubMed citations: 34.

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins PubMed citations: 33.

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD) PubMed citations: 28.

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data PubMed citations: 27.

AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae PubMed citations: 24.

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure PubMed citations: 24.

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database PubMed citations: 21.

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns PubMed citations: 19.

New mutant phenotype data curation system in the Saccharomyces Genome Database PubMed citations: 17.

The Saccharomyces Genome Database: A Tool for Discovery PubMed citations: 15.

The Saccharomyces Genome Database Variant Viewer PubMed citations: 15.

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study PubMed citations: 10.

Molecular linguistics: extracting information from gene and protein sequences PubMed citations: 8.

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations PubMed citations: 7.

Biocuration at the Saccharomyces genome database PubMed citations: 7.

Genetic nomenclature guide. Saccharomyces cerevisiae PubMed citations: 7.

From one to many: expanding the Saccharomyces cerevisiae reference genome panel PubMed citations: 5.

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report PubMed citations: 4.

The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes PubMed citations: 4.

The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component PubMed citations: 4.

The YeastGenome app: the Saccharomyces Genome Database at your fingertips PubMed citations: 3.

Expanding yeast knowledge online PubMed citations: 3.

The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining PubMed citations: 2.

The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations PubMed citations: 1.

http://dx.doi.org/10.1002/9780470089941.et1104s01

http://dx.doi.org/10.1093/nar/gkt1158

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More detailed information about this field from each metasource.

autonomously replicating sequence
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

centromere
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

chromatin remodeling
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

citation
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

free text
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

gene array
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

gene model annotation
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

gene name
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

genetic strain
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

image
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

nucleotide
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

orthologous
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

plasmid
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

protein domain
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

pseudogene
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

reference genome
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

sequence feature
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

systematic name
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

transposable element
metasource: Fairsharing.org
version: FAIRsharing.org: SGD; Saccharomyces Genome Database; DOI: https://doi.org/10.25504/FAIRsharing.pzvw40; Last edited: Feb. 23, 2021, 3:53 p.m.; Last accessed: Jan 03 2022 7:08 p.m.

genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

fungal genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

genetics
metasource: re3data.org
version: re3data.org: Saccharomyces Genome Database; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N313 last accessed: 2022-11-04

pathway
metasource: re3data.org
version: re3data.org: Saccharomyces Genome Database; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N313 last accessed: 2022-11-04

predicted sequence
metasource: re3data.org
version: re3data.org: Saccharomyces Genome Database; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N313 last accessed: 2022-11-04

protein structure
metasource: re3data.org
version: re3data.org: Saccharomyces Genome Database; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N313 last accessed: 2022-11-04

yeast genome
metasource: re3data.org
version: re3data.org: Saccharomyces Genome Database; editing status 2021-09-03; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3N313 last accessed: 2022-11-04

genotype and phenotype
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

protein folds and structural domains
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:40.491505

autonomously replicating sequence centromere chromatin remodeling citation free text gene ontology enrichment gene array gene expression gene model annotation gene name genetic strain genome molecular interaction nucleotide orthology phenotype plasmid protein domain pseudogene reference genome sequence feature systematic name transposable element genomics fungal genome genetics pathway predicted sequence protein structure yeast genome genotype and phenotype model organisms mapping molecular interactions, pathways and networks protein folds and structural domains

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Yeast Searching for Transcriptional Regulators and Consensus Tracking

Yeast Intron Database

Candida Genome Database

TGD - Tetrahymena Genome Database

Comprehensive Yeast Genome Database

OriDB - The DNA Replication Origin Database

Biological General Repository for Interaction Datasets

YeastMine

UCSC Genome Browser database

SCPD - Saccharomyces cerevisiae promoter database

Aspergillus Genome Database

Gene Ontology

Mouse Genome Database - a Mouse Genome Informatics (MGI) Resource

PomBase

Yeast Phenotypes

YeastCyc

The Cell Map

Yeast Resource Center Public Data Repository

Bovine Genome Database

Pseudomonas Genome DB