The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Saccharomyces Genome Database: the genomics resource of budding yeast
Open accessAbstract
The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae. The SGD project provides the highest-quality manually curated information from peer-reviewed literature. The experimental results reported in the literature are extracted and integrated within a well-developed database. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine and rich genome browser. The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions and interactions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M., Dale, J. M., Lee, T. J., Kaipa, P., Gilham, F., Spaulding, A., Popescu, L., et al. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp043 · Cited by 694
Cited by
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets
Zhou, Y., Zhou, B., Pache, L., Chang, M., Khodabakhshi, A. H., Tanaseichuk, O., Benner, C., & Chanda, S. K. (2019) · Nature Communications · doi:10.1038/s41467-019-09234-6 · Cited by 14,611
Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A. L., Fang, T., Doncheva, N. T., Pyysalo, S., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1000 · Cited by 9,726
Szklarczyk, D., Gable, A. L., Nastou, K. C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N. T., Legeay, M., Fang, T., Bork, P., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa1074 · Cited by 8,056
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., Santos, A., Doncheva, N. T., Roth, A., Bork, P., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw937 · Cited by 6,980
Oughtred, R., Rust, J., Chang, C., Breitkreutz, B., Stark, C., Willems, A., Boucher, L., Leung, G., Kolas, N., Zhang, F., et al. (2021) · Protein Science · doi:10.1002/pro.3978 · Cited by 1,858
MycoCosm portal: gearing up for 1000 fungal genomes
Grigoriev, I. V., Nikitin, R., Haridas, S., Kuo, A., Ohm, R., Otillar, R., Riley, R., Salamov, A., Zhao, X., Korzeniewski, F., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1183 · Cited by 1,498
Spatial proteomics: a powerful discovery tool for cell biology
Lundberg, E., & Borner, G. H. H. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0094-y · Cited by 591
Hebert, A. S., Richards, A. L., Bailey, D. J., Ulbrich, A., Coughlin, E. E., Westphall, M. S., & Coon, J. J. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.034769 · Cited by 528
“Historically yeast, with its 6600 open reading frames, has been the preferred proteomic technology test-bed (8).”
BackgroundGrowing a circular economy with fungal biotechnology: a white paper
Meyer, V., Basenko, E. Y., Benz, J. P., Braus, G. H., Caddick, M. X., Csukai, M., de Vries, R. P., Endy, D., Frisvad, J. C., Gunde-Cimerman, N., et al. (2020) · Fungal Biology and Biotechnology · doi:10.1186/s40694-020-00095-z · Cited by 515
Rate-Limiting Steps in Yeast Protein Translation
Shah, P., Ding, Y., Niemczyk, M., Kudla, G., & Plotkin, J. B. (2013) · Cell · doi:10.1016/j.cell.2013.05.049 · Cited by 463
Schep, A. N., Buenrostro, J. D., Denny, S. K., Schwartz, K., Sherlock, G., & Greenleaf, W. J. (2015) · Genome Research · doi:10.1101/gr.192294.115 · Cited by 375
Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling
Williams, C. C., Jan, C. H., & Weissman, J. S. (2014) · Science · doi:10.1126/science.1257522 · Cited by 391
GeneMANIA Prediction Server 2013 Update
Zuberi, K., Franz, M., Rodriguez, H., Montojo, J., Lopes, C. T., Bader, G. D., & Morris, Q. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt533 · Cited by 396
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
de Boer, C. G., Vaishnav, E. D., Sadeh, R., Abeyta, E. L., Friedman, N., & Regev, A. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0315-8 · Cited by 283
Kemmeren, P., Sameith, K., van de Pasch, L. A. L., Benschop, J. J., Lenstra, T. L., Margaritis, T., O’Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C. W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.054 · Cited by 277
Integration site selection by retroviruses and transposable elements in eukaryotes
Sultana, T., Zamborlini, A., Cristofari, G., & Lesage, P. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.7 · Cited by 275
Lagging-strand replication shapes the mutational landscape of the genome
Reijns, M. A. M., Kemp, H., Ding, J., Marion de Procé, S., Jackson, A. P., & Taylor, M. S. (2015) · Nature · doi:10.1038/nature14183 · Cited by 241
Lahtvee, P.-J., Sánchez, B. J., Smialowska, A., Kasvandik, S., Elsemman, I. E., Gatto, F., & Nielsen, J. (2017) · Cell Systems · doi:10.1016/j.cels.2017.03.003 · Cited by 193
A gene ontology inferred from molecular networks
Dutkowski, J., Kramer, M., Surma, M. A., Balakrishnan, R., Cherry, J. M., Krogan, N. J., & Ideker, T. (2013) · Nature Biotechnology · doi:10.1038/nbt.2463 · Cited by 184
Csárdi, G., Franks, A., Choi, D. S., Airoldi, E. M., & Drummond, D. A. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005206 · Cited by 181
Functional Metabolomics Describes the Yeast Biosynthetic Regulome
Mülleder, M., Calvani, E., Alam, M. T., Wang, R. K., Eckerstorfer, F., Zelezniak, A., & Ralser, M. (2016) · Cell · doi:10.1016/j.cell.2016.09.007 · Cited by 178
Zrimec, J., Börlin, C. S., Buric, F., Muhammad, A. S., Chen, R., Siewers, V., Verendel, V., Nielsen, J., Töpel, M., & Zelezniak, A. (2020) · Nature Communications · doi:10.1038/s41467-020-19921-4 · Cited by 174
Gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure
Zrimec, J., Buric, F., Muhammad, A. S., Chen, R., Verendel, V., Töpel, M., & Zelezniak, A. (2019) · doi:10.1101/792531 · Cited by 173
Evolution at two levels of gene expression in yeast
Artieri, C. G., & Fraser, H. B. (2014) · Genome Research · doi:10.1101/gr.165522.113 · Cited by 138
Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
Steenwyk, J. L., Opulente, D. A., Kominek, J., Shen, X.-X., Zhou, X., Labella, A. L., Bradley, N. P., Eichman, B. F., Čadež, N., Libkind, D., et al. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000255 · Cited by 162
“Plotting gene presence and absence among pathways was done by examining depicted pathways available through the KEGG project [137] and the Saccharomyces Genome Database [131].”
MethodSegal, E. S., Gritsenko, V., Levitan, A., Yadav, B., Dror, N., Steenwyk, J. L., Silberberg, Y., Mielich, K., Rokas, A., Gow, N. A. R., et al. (2018) · mBio · doi:10.1128/mbio.02048-18 · Cited by 150
Mass spectrometry supported determination of protein complex structure
Walzthoeni, T., Leitner, A., Stengel, F., & Aebersold, R. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.02.008 · Cited by 146
Methods for causal inference from gene perturbation experiments and validation
Meinshausen, N., Hauser, A., Mooij, J. M., Peters, J., Versteeg, P., & Bühlmann, P. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510493113 · Cited by 140
Towards precision medicine: advances in computational approaches for the analysis of human variants
Peterson, T. A., Doughty, E., & Kann, M. G. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.08.008 · Cited by 123
Dhar, R., Sägesser, R., Weikert, C., & Wagner, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss253 · Cited by 126
Goldman, A., Roy, J., Bodenmiller, B., Wanka, S., Landry, C. R., Aebersold, R., & Cyert, M. S. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.012 · Cited by 109
Determinants and Regulation of Protein Turnover in Yeast
Martin-Perez, M., & Villén, J. (2017) · Cell Systems · doi:10.1016/j.cels.2017.08.008 · Cited by 99
Natural proteome diversity links aneuploidy tolerance to protein turnover
Muenzner, J., Trébulle, P., Agostini, F., Zauber, H., Messner, C. B., Steger, M., Kilian, C., Lau, K., Barthel, N., Lehmann, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07442-9 · Cited by 81
Genome scale models of yeast: towards standardized evaluation and consistent omic integration
Sánchez, B. J., & Nielsen, J. (2015) · Integrative Biology · doi:10.1039/c5ib00083a · Cited by 75
Sellam, A., van het Hoog, M., Tebbji, F., Beaurepaire, C., Whiteway, M., & Nantel, A. (2014) · Eukaryotic Cell · doi:10.1128/ec.00292-13 · Cited by 63
Dalal, C. K., Zuleta, I. A., Mitchell, K. F., Andes, D. R., El-Samad, H., & Johnson, A. D. (2016) · eLife · doi:10.7554/elife.18981 · Cited by 62
The economics of organellar gene loss and endosymbiotic gene transfer
Kelly, S. (2020) · doi:10.1101/2020.10.01.322487 · Cited by 62
The economics of organellar gene loss and endosymbiotic gene transfer
Kelly, S. (2021) · Genome Biology · doi:10.1186/s13059-021-02567-w · Cited by 62
Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR
Bhaduri, A., Ungewickell, A., Boxer, L. D., Lopez-Pajares, V., Zarnegar, B. J., & Khavari, P. A. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.10.023 · Cited by 60
Synergy of the antibiotic colistin with echinocandin antifungals in Candida species
Zeidler, U., Bougnoux, M.-E., Lupan, A., Helynck, O., Doyen, A., Garcia, Z., Sertour, N., Clavaud, C., Munier-Lehmann, H., Saveanu, C., et al. (2013) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dks538 · Cited by 58
O’Meara, T. R., O’Meara, M. J., Polvi, E. J., Pourhaghighi, M. R., Liston, S. D., Lin, Z.-Y., Veri, A. O., Emili, A., Gingras, A.-C., & Cowen, L. E. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000358 · Cited by 49
Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response
Bendjilali, N., MacLeon, S., Kalra, G., Willis, S. D., Hossian, A. K. M. N., Avery, E., Wojtowicz, O., & Hickman, M. J. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.034991 · Cited by 49
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection
Lu, H., Li, F., Yuan, L., Domenzain, I., Yu, R., Wang, H., Li, G., Chen, Y., Ji, B., Kerkhoven, E. J., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202110427 · Cited by 44
Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress
Yaakov, G., Lerner, D., Bentele, K., Steinberger, J., & Barkai, N. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-016-0016 · Cited by 45
Bojsen, R., Regenberg, B., Gresham, D., & Folkesson, A. (2016) · Scientific Reports · doi:10.1038/srep21874 · Cited by 42
Structural determinants of co-translational protein complex assembly
Mallik, S., Venezian, J., Lobov, A., Heidenreich, M., Garcia-Seisdedos, H., Yeates, T. O., Shiber, A., & Levy, E. D. (2025) · Cell · doi:10.1016/j.cell.2024.11.013 · Cited by 42
Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription
Villa, T., Barucco, M., Martin-Niclos, M.-J., Jacquier, A., & Libri, D. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107942 · Cited by 37
Sanchez-Casalongue, M. E., Lee, J., Diamond, A., Shuldiner, S., Moir, R. D., & Willis, I. M. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.626523 · Cited by 36
Yu, R., Vorontsov, E., Sihlbom, C., & Nielsen, J. (2021) · eLife · doi:10.7554/elife.65722 · Cited by 35
Pentland, D. R., Davis, J., Mühlschlegel, F. A., & Gourlay, C. W. (2021) · npj Biofilms and Microbiomes · doi:10.1038/s41522-021-00238-z · Cited by 28
Rojas, J., Hose, J., Dutcher, H. A., Place, M., Wolters, J. F., Hittinger, C. T., & Gasch, A. P. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100656 · Cited by 22
Calcineurin-dependent contributions to fitness in the opportunistic pathogen Candida glabrata
Pavesic, M. W., Gale, A. N., Nickels, T. J., Harrington, A. A., Bussey, M., & Cunningham, K. W. (2024) · mSphere · doi:10.1128/msphere.00554-23 · Cited by 22
Reusswig, K.-U., Bittmann, J., Peritore, M., Courtes, M., Pardo, B., Wierer, M., Mann, M., & Pfander, B. (2022) · Nature Communications · doi:10.1038/s41467-022-34379-2 · Cited by 18
Co-regulation of translation in protein complexes
Siwiak, M., & Zielenkiewicz, P. (2015) · Biology Direct · doi:10.1186/s13062-015-0048-7 · Cited by 8
Csárdi, G., Franks, A., Choi, D. S., Airoldi, E. M., & Drummond, D. A. (2014) · doi:10.1101/009472 · Cited by 8
Sterrett, M. C., Farchi, D., Strassler, S. E., Boise, L. H., Fasken, M. B., & Corbett, A. H. (2023) · G3: Genes, Genomes, Genetics · doi:10.1093/g3journal/jkad049 · Cited by 5
Redox control of the deubiquitinating enzyme Ubp2 regulates translation during stress
Santos, C. M., Cizubu, B. K., Okonkwo, D. A., Chen, C.-Y., Maske, N., Snyder, N. A., Simões, V., Washington, E. J., & Silva, G. M. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107870 · Cited by 5
Metadata
- Authors
- Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Karra, K., Krieger, C. J., Miyasato, S. R., Nash, R. S., Park, J., Skrzypek, M. S., Simison, M., Weng, S., & Wong, E. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-11-21
- Volume
- 40
- Issue
- D1
- Pages
- D700-D705
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2102221598
- Cited by
- 1,796
- References
- 1
- FWCI
- 41.26
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
