YeastMine

Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.

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YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit
PMID: 22434830

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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http://dx.doi.org/10.1093/bioinformatics/bts577

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:21.860396

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• 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

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  HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040

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  DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes. PMID:35766356

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  Humanized yeast to model human biology, disease and evolution. PMID:35661208

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  Unveiling Forkhead-mediated regulation of yeast cell cycle and metabolic networks. PMID:35495119

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  When Phosphatases Go Mad: The Molecular Basis for Toxicity of Yeast Ppz1. PMID:35457140

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  Adaptive Response of Saccharomyces Hosts to Totiviridae L-A dsRNA Viruses Is Achieved through Intrinsically Balanced Action of Targeted Transcription Factors. PMID:35448612

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  Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms. PMID:35314699

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  Rewiring phospholipid biosynthesis reveals resilience to membrane perturbations and uncovers regulators of lipid homeostasis. PMID:35188676

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  Fitness Effects of Mutations: An Assessment of PROVEAN Predictions Using Mutation Accumulation Data. PMID:35038732

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  Insights into cell robustness against lignocellulosic inhibitors and insoluble solids in bioethanol production processes. PMID:35017613

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  Forced association of SARS-CoV-2 proteins with the yeast proteome perturb vesicle trafficking. PMID:34909432

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  Ribo-Seq and RNA-Seq of TMA46 ( DFRP1) and GIR2 ( DFRP2) knockout yeast strains. PMID:34900236

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  The Rpd3-Complex Regulates Expression of Multiple Cell Surface Recycling Factors in Yeast. PMID:34830359

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  Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses. PMID:34740240

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  Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance. PMID:34566920

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  Transcriptional Profile of the Industrial Hybrid Saccharomyces pastorianus Reveals Temperature-Dependent Allele Expression Bias and Preferential Orthologous Protein Assemblies. PMID:34550394

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  Restoring fertility in yeast hybrids: Breeding and quantitative genetics of beneficial traits. PMID:34518218

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  Fur4-mediated uracil-scavenging to screen for surface protein regulators. PMID:34498791

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  Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci. PMID:34363476

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  Primordial super-enhancers: heat shock-induced chromatin organization in yeast. PMID:34001402

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  A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PMID:33836000

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  Complete genome sequence and analysis of a Saccharomyces cerevisiae strain used for sugarcane spirit production. PMID:33835421

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  Trans-acting genetic variation affects the expression of adjacent genes. PMID:33789351

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  Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species. PMID:33772558

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  Increased numbers of nucleoli in a genome-wide RNAi screen reveal proteins that link the cell cycle to RNA polymerase I transcription. PMID:33689394

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  Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561

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  The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63-branched ubiquitin chains. PMID:33576509

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  Inner-nuclear-membrane-associated degradation employs Dfm1-independent retrotranslocation and alleviates misfolded transmembrane-protein toxicity. PMID:33566711

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  Data-driven biological network alignment that uses topological, sequence, and functional information. PMID:33514304

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  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

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  In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. PMID:33491328

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  Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae. PMID:33462193

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  Complexity of the eukaryotic dolichol-linked oligosaccharide scramblase suggested by activity correlation profiling mass spectrometry. PMID:33446867

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  Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses. PMID:33318504

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  Minimum Description Length Codes Are Critical. PMID:33265844

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  Towards a unified open access dataset of molecular interactions. PMID:33262342

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  YQFC: a web tool to compare quantitative biological features between two yeast gene lists. PMID:33186464

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  Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. PMID:33093574

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  PartCrafter: find, generate and analyze BioParts. PMID:32995539

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  Yeast Ppz1 protein phosphatase toxicity involves the alteration of multiple cellular targets. PMID:32973189

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  The effect of hybridization on transposable element accumulation in an undomesticated fungal species. PMID:32955438

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  Systematic analysis of bypass suppression of essential genes. PMID:32939983

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  Records of RNA locations in living yeast revealed through covalent marks. PMID:32907940

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  Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation. PMID:32811554

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  Genome-Wide Dynamic Evaluation of the UV-Induced DNA Damage Response. PMID:32732306

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  Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PMID:32421706

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  Combining data integration and molecular dynamics for target identification in α-Synuclein-aggregating neurodegenerative diseases: Structural insights on Synaptojanin-1 (Synj1). PMID:32419904

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  Proteomic analysis of the S. cerevisiae response to the anticancer ruthenium complex KP1019. PMID:32329475

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  Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. PMID:32184324

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  Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. PMID:32128557

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  Cross-Species Complementation of Nonessential Yeast Genes Establishes Platforms for Testing Inhibitors of Human Proteins. PMID:31937519

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  Autophagy is required for sulfur dioxide tolerance in Saccharomyces cerevisiae. PMID:31638329

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  The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown upon glucose availability. PMID:31604822

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  LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing. PMID:31486704

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  Screening the Saccharomyces cerevisiae Nonessential Gene Deletion Library Reveals Diverse Mechanisms of Action for Antifungal Plant Defensins. PMID:31451498

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  Insoluble solids at high concentrations repress yeast's response against stress and increase intracellular ROS levels. PMID:31439886

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  Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23. PMID:31371382

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  Leveraging genetic interactions for adverse drug-drug interaction prediction. PMID:31125330

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  The Reduced Level of Inorganic Polyphosphate Mobilizes Antioxidant and Manganese-Resistance Systems in Saccharomyces cerevisiae. PMID:31096715

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  The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae. PMID:31092540

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  Hidden in plain sight: what remains to be discovered in the eukaryotic proteome? PMID:30938578

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  Ribosome profiling analysis of eEF3-depleted Saccharomyces cerevisiae. PMID:30816176

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  Inferring Gene Regulatory Networks from a Population of Yeast Segregants. PMID:30718595

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  Multi-study inference of regulatory networks for more accurate models of gene regulation. PMID:30677040

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  Perturbations of Transcription and Gene Expression-Associated Processes Alter Distribution of Cell Size Values in Saccharomyces cerevisiae. PMID:30463882

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  A Unique Saccharomyces cerevisiae × Saccharomyces uvarum Hybrid Isolated From Norwegian Farmhouse Beer: Characterization and Reconstruction. PMID:30319573

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  AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679

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  Overlapping open reading frames strongly reduce human and yeast STN1 gene expression and affect telomere function. PMID:30067734

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  YARG: A repository for arsenic-related genes in yeast. PMID:30048518

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  Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts. PMID:29867869

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  Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK. PMID:29796388

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  High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. PMID:29786095

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  TelNet - a database for human and yeast genes involved in telomere maintenance. PMID:29776332

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  Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes. PMID:29761466

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  Updated regulation curation model at the Saccharomyces Genome Database. PMID:29688362

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  YAAM: Yeast Amino Acid Modifications Database. PMID:29688347

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  Exploiting mitochondrial and metabolic homeostasis as a vulnerability in NF1 deficient cells. PMID:29662612

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  JAMI: a Java library for molecular interactions and data interoperability. PMID:29642846

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  Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins. PMID:29620521

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  General amino acid control in fission yeast is regulated by a nonconserved transcription factor, with functions analogous to Gcn4/Atf4. PMID:29432178

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  A systematic assessment of chemical, genetic, and epigenetic factors influencing the activity of anticancer drug KP1019 (FFC14A). PMID:29228701

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  Different Non-Saccharomyces Yeast Species Stimulate Nutrient Consumption in S. cerevisiae Mixed Cultures. PMID:29163412

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  Confronting the catalytic dark matter encoded by sequenced genomes. PMID:29059321

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  ComplexViewer: visualization of curated macromolecular complexes. PMID:29036573

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  Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PMID:28665995

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  Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PMID:28628618

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  Translation initiation factor eIF4G1 preferentially binds yeast transcript leaders containing conserved oligo-uridine motifs. PMID:28546148

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  Identifying pathogenicity of human variants via paralog-based yeast complementation. PMID:28542158

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  Functional mapping of yeast genomes by saturated transposition. PMID:28481201

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  A New Method, "Reverse Yeast Two-Hybrid Array" (RYTHA), Identifies Mutants that Dissociate the Physical Interaction Between Elg1 and Slx5. PMID:28476868

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  Curated protein information in the Saccharomyces genome database. PMID:28365727

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  Outreach and online training services at the Saccharomyces Genome Database. PMID:28365719

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  Coordinate responses to alkaline pH stress in budding yeast. PMID:28357292

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  Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii. PMID:28336969

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  Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer. PMID:28198375

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  Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response. PMID:28079179

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  Translational control of lipogenic enzymes in the cell cycle of synchronous, growing yeast cells. PMID:28057705

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  New Genes Involved in Osmotic Stress Tolerance in Saccharomyces cerevisiae. PMID:27733850

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  Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer. PMID:27551064

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  A genome-wide imaging-based screening to identify genes involved in synphilin-1 inclusion formation in Saccharomyces cerevisiae. PMID:27440388

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  Principal component analysis based unsupervised feature extraction applied to budding yeast temporally periodic gene expression. PMID:27366210

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  Meiotic Interactors of a Mitotic Gene TAO3 Revealed by Functional Analysis of its Rare Variant. PMID:27317780

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  Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PMID:27152522

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  Synthetic protein interactions reveal a functional map of the cell. PMID:27098839

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  Global translational impacts of the loss of the tRNA modification t6A in yeast. PMID:26798630

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  The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression. PMID:26740628

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  A Genome-Wide Screen with Nicotinamide to Identify Sirtuin-Dependent Pathways in Saccharomyces cerevisiae. PMID:26646153

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  The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining. PMID:26631124

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  Mouse genome database 2016. PMID:26578600

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  Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564

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  Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PMID:26566239

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  Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast. PMID:26537787

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  Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds. PMID:26459777

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  Genome-Wide Detection and Analysis of Multifunctional Genes. PMID:26436655

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  Depletion of yeast PDK1 orthologs triggers a stress-like transcriptional response. PMID:26391581

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  RNA regulatory networks diversified through curvature of the PUF protein scaffold. PMID:26364903

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  Complementation of Yeast Genes with Human Genes as an Experimental Platform for Functional Testing of Human Genetic Variants. PMID:26354769

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  Rapid Identification of Chemoresistance Mechanisms Using Yeast DNA Mismatch Repair Mutants. PMID:26199284

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  toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. PMID:26130662

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  Cross-organism analysis using InterMine. PMID:26097192

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  ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180

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  A Genetic Screen for Saccharomyces cerevisiae Mutants That Fail to Enter Quiescence. PMID:26068574

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  Biocuration at the Saccharomyces genome database. PMID:25997651

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  Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes. PMID:25968466

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  Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation. PMID:25711830

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  Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/SWS1 protein family from Saccharomyces cerevisiae to Homo sapiens. PMID:25659377

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  The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast. PMID:25522035

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  Too much of a good thing: the unique and repeated paths toward copper adaptation. PMID:25519894

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  Araport: the Arabidopsis information portal. PMID:25414324

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  FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. PMID:25294921

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  TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids. PMID:25279700

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  esyN: network building, sharing and publishing. PMID:25181461

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  InterMine: extensive web services for modern biology. PMID:24753429

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  Predicting the dynamics of protein abundance. PMID:24532840

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  Saccharomyces genome database provides new regulation data. PMID:24265222

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  Saccharomyces cerevisiae genes involved in survival of heat shock. PMID:24142923

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  Genome-wide study of the adaptation of Saccharomyces cerevisiae to the early stages of wine fermentation. PMID:24040173

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  metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057

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  Ptc6 is required for proper rapamycin-induced down-regulation of the genes coding for ribosomal and rRNA processing proteins in S. cerevisiae. PMID:23704987

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  Genome-scale studies of aging: challenges and opportunities. PMID:23633910

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  The YeastGenome app: the Saccharomyces Genome Database at your fingertips. PMID:23396302

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  Evolutionary rate covariation in meiotic proteins results from fluctuating evolutionary pressure in yeasts and mammals. PMID:23183665

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  InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. PMID:23023984
• http://dx.doi.org/10.1093/bioinformatics/bts577

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More detailed information about this field from each metasource. ×

biological regulation

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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gene expression

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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homologous

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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molecular function

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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molecular interaction

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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orthologous

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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paralogous

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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protein

metasource: Fairsharing.org
version: FAIRsharing.org: YeastMine; YeastMine; DOI: https://doi.org/10.25504/FAIRsharing.KhTFtY; Last edited: Sept. 20, 2019, 11:51 a.m.; Last accessed: Jan 03 2022 7:06 p.m.

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data management

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:21.860396

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genomics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:21.860396

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proteomics

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:21.860396

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biological regulation gene expression homologous molecular function molecular interaction orthology paralogous protein data management genomics proteomics