Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response
Open accessAbstract
Many cells experience hypoxia, or low oxygen, and respond by dramatically altering gene expression. In the yeast Saccharomyces cerevisiae, genes that respond are required for many oxygen-dependent cellular processes, such as respiration, biosynthesis, and redox regulation. To more fully characterize the global response to hypoxia, we exposed yeast to hypoxic conditions, extracted RNA at different times, and performed RNA sequencing (RNA-seq) analysis. Time-course statistical analysis revealed hundreds of genes that changed expression by up to 550-fold. The genes responded with varying kinetics suggesting that multiple regulatory pathways are involved. We identified most known oxygen-regulated genes and also uncovered new regulated genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis confirmed that the lysine methyltransferase EFM6 and the recombinase DMC1, both conserved in humans, are indeed oxygen-responsive. Looking more broadly, oxygen-regulated genes participate in expected processes like respiration and lipid metabolism, but also in unexpected processes like amino acid and vitamin metabolism. Using principle component analysis, we discovered that the hypoxic response largely occurs during the first 2 hr and then a new steady-state expression state is achieved. Moreover, we show that the oxygen-dependent genes are not part of the previously described environmental stress response (ESR) consisting of genes that respond to diverse types of stress. While hypoxia appears to cause a transient stress, the hypoxic response is mostly characterized by a transition to a new state of gene expression. In summary, our results reveal that hypoxia causes widespread and complex changes in gene expression to prepare the cell to function with little or no oxygen.
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
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Several genome-wide expression studies under low oxygen conditions have reflected that the pattern of expression differs among ERG genes, although some general trends can be extracted.
“Several genome-wide expression studies based on microarray and RNA-Seq analyses under low oxygen conditions have reflected that the pattern of expression differs among ERG genes, although some general trends can be extracted [94,96,98,100,101,102,103].”
From Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae (2020) · cites this paper as [100]
Conflicting results have been observed for the effect of Hap1 on the expression of ERG genes during anaerobic conditions.
“However, conflicting results have been observed for the effect of Hap1 on the expression of ERG genes during anaerobic conditions [75,96,99,100].”
From Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae (2020) · cites this paper as [100]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288 · see citing works
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013) · Genome Biology · doi:10.1186/gb-2013-14-4-r36 · Cited by 12,668 · see citing works
Cluster analysis and display of genome-wide expression patterns
Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.25.14863 · Cited by 12,617 · see citing works
Trapnell, C., Roberts, A., Goff, L. A., Pertea, G. M., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., & Pachter, L. S. (2012) · Nature Protocols · doi:10.1038/nprot.2012.016 · Cited by 11,930 · see citing works
How mitochondria produce reactive oxygen species
Murphy, M. P. (2009) · Biochemical Journal · doi:10.1042/bj20081386 · Cited by 8,207 · see citing works
Time Series Analysis: Forecasting and Control.
Anderson, O. D., Box, G. E. P., & Jenkins, G. M. (1978) · Journal of the Royal Statistical Society Series D (The Statistician) · doi:10.2307/2988198 · Cited by 5,368 · see citing works
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4241 · Cited by 4,815 · see citing works
Java Treeview—extensible visualization of microarray data
Saldanha, A. J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth349 · Cited by 2,991 · see citing works
Saccharomyces Genome Database: the genomics resource of budding yeast
Cherry, J., Hong, E., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K., Costanzo, M., Dwight, S., Engel, S., et al. (2011) · Nucleic Acids Res. · doi:10.1093/nar/gkr1029 · Cited by 1,886 · see citing works
Box, G. E. P., Jenkins, G. M., & Reinsel, G. C. (2008) · Wiley series in probability and statistics · doi:10.1002/9781118619193 · Cited by 1,507 · see citing works
Oxygen Sensing, Homeostasis, and Disease
Semenza, G. L. (2011) · New England Journal of Medicine · doi:10.1056/nejmra1011165 · Cited by 989 · see citing works
A Handbook of Statistical Analyses using R
Hothorn, T., & Everitt, B. J. (2014) · Chapman & Hall/CRC eBooks · doi:10.1201/b17081 · Cited by 585 · see citing works
Significance analysis of time course microarray experiments
Storey, J. D., Xiao, W., Leek, J. T., Tompkins, R. G., & Davis, R. W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504609102 · Cited by 567 · see citing works
Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast
Brauer, M. J., Huttenhower, C., Airoldi, E. M., Rosenstein, R., Matese, J. C., Gresham, D., Boer, V. M., Troyanskaya, O. G., & Botstein, D. (2008) · Molecular Biology of the Cell · doi:10.1091/mbc.e07-08-0779 · Cited by 558 · see citing works
Tkach, J. M., Yimit, A., Lee, A. Y., Riffle, M. E., Costanzo, M., Jaschob, D., Hendry, J. A., Ou, J., Moffat, J., Boone, C. M., et al. (2012) · Nature Cell Biology · doi:10.1038/ncb2549 · Cited by 476 · see citing works
SREBP pathway responds to sterols and functions as an oxygen sensor in fission yeast.
Hughes, A. L., Todd, B. L., & Espenshade, P. J. (2005) · Cell · doi:10.1016/j.cell.2005.01.012 · Cited by 320 · see citing works
Oxygen sensing and hypoxia signalling pathways in animals: The implications of physiology for cancer
Ratcliffe, P. J. (2013) · The Journal of Physiology · doi:10.1113/jphysiol.2013.251470 · Cited by 294 · see citing works
Linde, J. J. M. T., Liang, H., Davis, R. W., Steensma, H. Y., van Dijken, J. P., & Pronk, J. T. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.24.7409-7413.1999 · Cited by 268 · see citing works
Kwast, K. E., Lai, L., Menda, N. S., James, D. T., Aref, S., & Burke, P. V. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.1.250-265.2002 · Cited by 232 · see citing works
Li, Z., & Hach, A. (1999) · Cellular and Molecular Life Sciences · doi:10.1007/s000180050442 · Cited by 206 · see citing works
Abramova, N., Sertil, O., Mehta, S., & Lowry, C. V. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.9.2881-2887.2001 · Cited by 157 · see citing works
Rosenfeld, E., & Beauvoit, B. (2003) · Yeast · doi:10.1002/yea.1026 · Cited by 149 · see citing works
Hickman, M. J., & Winston, F. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00887-07 · Cited by 137 · see citing works
Self-citationBurke, P. V., Raitt, D. C., Allen, L. A., Kellogg, E. A., & Poyton, R. Ο. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.23.14705 · Cited by 134 · see citing works
Abramova, N. E., Cohen, B. D., Sertil, O., Kapoor, R., Davies, K. J. A., & Lowry, C. V. (2001) · Genetics · doi:10.1093/genetics/157.3.1169 · Cited by 128 · see citing works
A microarray‐assisted screen for potential Hap1 and Rox1 target genes in Saccharomyces cerevisiae
Linde, J. J. M. T., & Steensma, H. Y. (2002) · Yeast · doi:10.1002/yea.879 · Cited by 123 · see citing works
A Role for Sterol Levels in Oxygen Sensing in <i>Saccharomyces cerevisiae</i>
Davies, B. S. J., & Rine, J. (2006) · Genetics · doi:10.1534/genetics.106.059964 · Cited by 123 · see citing works
Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6
Rodríguez‐Navarro, S., Llorente, B., Rodríguez‐Manzaneque, M. T., Ramne, A., Uber, G., Marchesan, D., Dujon, B., Herrero, E., Sunnerhagen, P., & Pérez-Ortín, J. E. (2002) · Yeast · doi:10.1002/yea.916 · Cited by 101 · see citing works
Mitochondria and Hypoxic Signaling
Poyton, R. Ο., Castello, P. R., Ball, K. A., Woo, D. K., & Pan, N. (2009) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.2009.05046.x · Cited by 100 · see citing works
Chellappa, R., Kandasamy, P., Oh, C., Jiang, Y., Vemula, M., & Martin, C. E. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m107845200 · Cited by 100 · see citing works
Lai, L.-C., Kosorukoff, A. L., Burke, P. V., & Kwast, K. E. (2006) · Eukaryotic Cell · doi:10.1128/ec.00107-06 · Cited by 97 · see citing works
Ellahi, A., Thurtle-Schmidt, D. M., & Rine, J. (2015) · Genetics · doi:10.1534/genetics.115.175711 · Cited by 89 · see citing works
Synergistic repression of anaerobic genes by Mot3 and Rox1 in Saccharomyces cerevisiae
Sertil, O. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg792 · Cited by 88 · see citing works
Guzy, R. D., Mack, M. M., & Schumacker, P. T. (2007) · Antioxidants and Redox Signaling · doi:10.1089/ars.2007.1708 · Cited by 86 · see citing works
Becerra, M., Lombardía‐Ferreira, L. J., Hauser, N. C., Hoheisel, J. D., Tizon, B., & Cerdán, M. E. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02724.x · Cited by 85 · see citing works
Lai, L.-C., Kosorukoff, A. L., Burke, P. V., & Kwast, K. E. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.10.4075-4091.2005 · Cited by 84 · see citing works
Structure and mechanism of Escherichia coli pyridoxine 5′-phosphate oxidase
di Salvo, M. L., Safo, M. K., Musayev, F. N., Bossa, F., & Schirch, V. (2003) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/s1570-9639(03)00060-8 · Cited by 69 · see citing works
Hickman, M. J., Spatt, D., & Winston, F. (2011) · Genetics · doi:10.1534/genetics.111.128322 · Cited by 68 · see citing works
Self-citationShianna, K. V., Dotson, W. D., Tove, S. R., & Parks, L. W. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.3.830-834.2001 · Cited by 63 · see citing works
Jiang, Y., Vasconcelles, M. J., Wretzel, S., Light, A., Gilooly, L., McDaid, K., Oh, C., Martin, C. E., & Goldberg, M. A. (2002) · Eukaryotic Cell · doi:10.1128/ec.1.3.481-490.2002 · Cited by 52 · see citing works
Biotin synthase mechanism: an overview
Lotierzo, M., Bui, B. T. S., Florentin, D., Escalettes, F., & Marquet, A. (2005) · Biochemical Society Transactions · doi:10.1042/bst0330820 · Cited by 47 · see citing works
Llorente, B., Fairhead, C., & Dujon, B. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01412.x · Cited by 45 · see citing works
THIAMINE AND NICOTINIC ACID: ANAEROBIC GROWTH FACTORS FOR MUCOR ROUXII
Bartnicki-García, S., & Nickerson, W. J. (1961) · Journal of Bacteriology · doi:10.1128/jb.82.1.142-148.1961 · Cited by 44 · see citing works
Hypoxia and Gene Expression in Eukaryotic Microbes
Butler, G. (2013) · Annual Review of Microbiology · doi:10.1146/annurev-micro-092412-155658 · Cited by 44 · see citing works
Ramil, E., Agrimonti, C., Shechter, E., Gervais, M., & Guiard, B. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.02065.x · Cited by 38 · see citing works
Thiamine biosynthesis can be used to dissect metabolic integration
Koenigsknecht, M. J., & Downs, D. M. (2010) · Trends in Microbiology · doi:10.1016/j.tim.2010.03.003 · Cited by 30 · see citing works
Lai, L., Kissinger, M. T., Burke, P. V., & Kwast, K. E. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-627 · Cited by 27 · see citing works
Meurisse, J., Bacquin, A., Richet, N., Charbonnier, J., Ochsenbein, F., & Peyroche, A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1095 · Cited by 23 · see citing works
Thomas, K. C., Hynes, S. H., & Ingledew, W. M. (1998) · Journal of Industrial Microbiology & Biotechnology · doi:10.1038/sj.jim.2900584 · Cited by 17 · see citing works
Transcript analysis of 203 novel genes fromSaccharomyces cerevisiaeinhap1androx1mutant backgrounds
Lombardía, L., Cadahia, J. L., Freire-Picos, M. Á., González-Siso, M.-I., Rodríguez-Torres, A.-M., & Cerdán, M. E. (2000) · Genome · doi:10.1139/g00-049 · Cited by 10 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Regulation of Ergosterol Biosynthesis in Saccharomyces cerevisiae
Jordá, T., & Puig, S. (2020) · Genes · doi:10.3390/genes11070795 · Cited by 489 · see citing works
Methylation of Elongation Factor 1A: Where, Who, and Why?
Hamey, J. J., & Wilkins, M. R. (2018) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2018.01.004 · Cited by 69 · see citing works
Regulation of eukaryotic elongation factor 1 alpha (eEF1A) by dynamic lysine methylation
Jakobsson, M. E., Małecki, J., & Falnes, P. Ø. (2018) · RNA Biology · doi:10.1080/15476286.2018.1440875 · Cited by 59 · see citing works
Jakobsson, M. E., Małecki, J., Nilges, B. S., Moen, A. R., Leidel, S. A., & Falnes, P. Ø. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx432 · Cited by 58 · see citing works
Dense time-course gene expression profiling of the Drosophila melanogaster innate immune response
Schlamp, F., Delbare, S., Early, A. M., Wells, M. T., Basu, S., & Clark, A. G. (2021) · BMC Genomics · doi:10.1186/s12864-021-07593-3 · Cited by 54 · see citing works
Mattila, H., Mäkinen, M., & Lundell, T. (2020) · Biotechnology for Biofuels · doi:10.1186/s13068-020-01677-0 · Cited by 48 · see citing works
Enhanced Recombinant Protein Production Under Special Environmental Stress
Chen, X., Li, C., & Liu, H. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.630814 · Cited by 45 · see citing works
Serratore, N. D., Baker, K. M., Macadlo, L. A., Gress, A. R., Powers, B. L., Atallah, N., Westerhouse, K. M., Hall, M. C., Weake, V. M., & Briggs, S. D. (2018) · Genetics · doi:10.1534/genetics.117.300554 · Cited by 33 · see citing works
Rand, D. M., Mossman, J. A., Zhu, L., Biancani, L. M., & Ge, J. Y. (2018) · IUBMB Life · doi:10.1002/iub.1954 · Cited by 31 · see citing works
Sunyer-Figueres, M., Vázquez, J., Mas, A., Torija, M.-J., & Beltran, G. (2020) · Antioxidants · doi:10.3390/antiox9100947 · Cited by 24 · see citing works
Lukša, J., Ravoitytė, B., Konovalovas, A., Aitmanaitė, L., Butenko, A., Yurchenko, V., Serva, S., & Servienė, E. (2017) · Toxins · doi:10.3390/toxins9080233 · Cited by 23 · see citing works
Transcriptional responses of soybean aphids to sublethal insecticide exposure
Enders, L. S., Rault, L. C., Heng‐Moss, T., Siegfried, B. D., & Miller, N. J. (2019) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2019.103285 · Cited by 21 · see citing works
The transcriptomic response of a wine strain of Lachancea thermotolerans to oxygen deprivation
Shekhawat, K., Bauer, F. F., & Setati, M. E. (2020) · FEMS Yeast Research · doi:10.1093/femsyr/foaa054 · Cited by 18 · see citing works
Set4 regulates stress response genes and coordinates histone deacetylases within yeast subtelomeres
Jethmalani, Y., Tran, K., Jaiswal, D., Jezek, M., Ramos, M., Amos, S., Garcia, E. J., Negesse, M. Y., Sun, W., Park, D., et al. (2021) · Life Science Alliance · doi:10.26508/lsa.202101126 · Cited by 15 · see citing works
Tondini, F., Onetto, C. A., & Jiranek, V. (2020) · Food Microbiology · doi:10.1016/j.fm.2020.103463 · Cited by 15 · see citing works
Time-course effects and mechanisms of hypobaric hypoxia on nervous system in mice
Zhang, H., Zhang, X., Liu, Z., Mei, Y., Liu, Y., Xue, W., Xiao, C., Gao, Y., & Ma, Z. (2023) · Neuroscience Letters · doi:10.1016/j.neulet.2023.137163 · Cited by 12 · see citing works
Vandeputte, P., de Bernonville, T. D., Govic, Y. L., Gal, S. L., Nevez, G., Papon, N., & Bouchara, J. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.10.034 · Cited by 12 · see citing works
Bui, T. T., Lee, D. D., & Selvarajoo, K. (2020) · Scientific Reports · doi:10.1038/s41598-020-74564-1 · Cited by 10 · see citing works
ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Yutong, Z., Bui, T. T., & Selvarajoo, K. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00499 · Cited by 9 · see citing works
Shiel, B. P., Cooke, I., Hall, N. E., Robinson, N. A., & Strugnell, J. M. (2020) · Aquaculture · doi:10.1016/j.aquaculture.2020.735317 · Cited by 9 · see citing works
Cheng, F., Dennis, A. B., Baumann, O., Kirschbaum, F., Abdelilah‐Seyfried, S., & Tiedemann, R. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae021 · Cited by 7 · see citing works
Liu, T., & Zhong, J. (2021) · Process Biochemistry · doi:10.1016/j.procbio.2021.04.011 · Cited by 7 · see citing works
Metabolic Plasticity and Transcriptomic Reprogramming Orchestrate Hypoxia Adaptation in Yak
Huang, C., Liao, Y., Peng, W., Xiang, H., Wang, H., Ma, J., Chai, Z., Wu, Z., Yue, B., Cai, X. M., et al. (2025) · Animals · doi:10.3390/ani15142084 · Cited by 5 · see citing works
The ATP-dependent chromatin remodelling enzyme Uls1 prevents Topoisomerase II poisoning
Swanston, A., Zábrady, K., & Ferreira, H. C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz362 · Cited by 5 · see citing works
Contreras, E. J., Nagarajan, A., Bromberg, B. H., Villegas, M. P., & Kaplan, D. L. (2026) · Food Research International · doi:10.1016/j.foodres.2026.118368 · Cited by 3 · see citing works
First insight into the development of a new transcriptomic tool in French Corsica harbors
Pillet, M., Evensen, K. G., Marengo, M., Lejeune, P., Poynton, H. C., & Thomas, H. (2022) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2022.114173 · Cited by 3 · see citing works
Yang, T.-H., Hsu, C., Wang, Y., Yu, C., Rathod, J., Tseng, Y. Y., & Wu, W.-S. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.106314 · Cited by 3 · see citing works
Bidiuk, V. A., Agaphonov, M. O., & Alexandrov, A. I. (2020) · Yeast · doi:10.1002/yea.3543 · Cited by 3 · see citing works
Global characterization of Dictyostelium discoideum gene expression changes under hypoxic conditionsPreprint
Hesnard, J., Gas‐Pascual, E., van der Wel, H., Cochet‐Escartin, O., Joly, S., Rieu, J.-P., West, C. M., & Anjard, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.02.646759 · Cited by 3 · see citing works
Hesnard, J., Gas‐Pascual, E., van der Wel, H., Cochet‐Escartin, O., Joly, S., Rieu, J.-P., West, C. M., & Anjard, C. (2025) · BMC Genomics · doi:10.1186/s12864-025-12328-9 · Cited by 2 · see citing works
Multi-Omics Analysis of Stress Responses for Industrial Yeast During Beer Post-Fermentation
Fan, Y., Hou, X., Chang, Z., Ding, J., Li, J., Zhao, X., & He, Y. (2026) · Fermentation · doi:10.3390/fermentation12020070 · Cited by 2 · see citing works
Fu, W., Wang, S., Ouyang, Q., & Luo, C. (2024) · Integrative Biology · doi:10.1093/intbio/zyae011 · Cited by 2 · see citing works
Martin, V., Monique, D., & Laurence, V. (2021) · Journal of Probiotics & Health · doi:10.35248/2329-8901.21.9.233 · Cited by 1 · see citing works
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response
Willis, S. D., Hossian, A. K. M. N., Evans, N. J., & Hickman, M. J. (2017) · Journal of Visualized Experiments · doi:10.3791/56226 · Cited by 2 · see citing works
Self-citationReiter, T. E., Montpetit, R., Runnebaum, R. C., Brown, C. T., & Montpetit, B. (2021) · mBio · doi:10.1128/mbio.02345-21 · Cited by 2 · see citing works
Stair, E. R., Flinn, B. B., Grimmett, A., Balboa, S. J., Burr, A. J., Siebold, J. A., Baca, A. G., Daughtridge, M. H., Kolling, D. R. J., & Hicks, L. M. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00222 · Cited by 1 · see citing works
INFLUENCE OF OBESITY ON VASCULAR DYSFUNCTION AFTER TRAUMATIC HEMORRHAGE
Walker, A. E., Cole, J. A., Kumaran, S. K., Kato, J. I., Zhuang, X., Wolf, J. R., Henson, G. D., & McCully, B. H. (2022) · Shock · doi:10.1097/shk.0000000000001991 · Cited by 1 · see citing works
Gene function contributes to gene expression levels in S. cerevisiaePreprint
Hickman, M. J., Jackson, A., Smith, A. J., Thornton, J. M., & Tursi, A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/330365 · Cited by 1 · see citing works
Self-citationImpact of high sugar content on metabolism and physiology of indigenous yeasts
Tondini, F. (2018) · Adelaide Research & Scholarship (AR&S) (University of Adelaide)
Jethmalani, Y., Tran, K., Jaiswal, D., Jezek, M., Ramos, M., Amos, S., Garcia, E. J., Negesse, M. Y., Sun, W., Park, D., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.11.443697
Ishiya, K., & Taniguchi, T. (2023) · AIP conference proceedings · doi:10.1063/5.0163319
Alarie, H., Côté, N., Gaudreau, L. R., Houde, M., & Segura, P. A. (2023) · Environmental Science and Pollution Research · doi:10.1007/s11356-023-31087-2
Akbudak, M. A., Cirik, N., Erdeğer, Ş. N., Filiz, E., Doğu, S., & Bor, M. (2024) · Plant Biology · doi:10.1111/plb.13658
Schlamp, F., Delbare, S., Early, A. M., Wells, M. T., Basu, S., & Clark, A. G. (2021) · Figshare · doi:10.6084/m9.figshare.14489854
Schlamp, F., Delbare, S., Early, A. M., Wells, M. T., Basu, S., & Clark, A. G. (2021) · Figshare · doi:10.6084/m9.figshare.14489848
Raven, R. M., Williams, J., Whelan, C., White, J., Morris, K. W., Geen, J., & James, P. E. (2026) · Journal of Cerebral Blood Flow & Metabolism · doi:10.1177/0271678x261417191
Analysis of Short-Term Responses to Hypoxia During Stirred-Tank Fermentation in Aspergillus oryzae
Araki, S., Susukida, S., Miyazawa, K., Kumagai, T., Tokashiki, J., & Abe, K. (2026) · Journal of Fungi · doi:10.3390/jof12050347
Jibrin, M. O., Najar, F. Z., Liu, Q., Yu, F., Bello, U. R., Fomba, J. A., Zhang, Y., Jones, J. B., & Zhang, S. (2026) · Research Square · doi:10.21203/rs.3.rs-10083928/v1
- Authors
- Bendjilali, N., MacLeon, S., Kalra, G., Willis, S. D., Hossian, A. K. M. N., Avery, E., Wojtowicz, O., & Hickman, M. J.
- Affiliations
- Rowan University (US)
- Corresponding author
- Hickman, Mark J
- ORCID
- Venue
- G3 Genes Genomes Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-01-01
- Volume
- 7
- Issue
- 1
- Pages
- 221-231
- ISSN
- 2160-1836 (ISSN-L)
- PMC
- PMC5217111
- OpenAlex
- W2559018305
- Cited by
- 49
- References
- 54
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 3 · 2023: 4 · 2022: 3 · 2021: 9 · 2020: 9 · 2019: 3 · 2018: 5 · 2017: 4
- FWCI
- 2.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- G3 Genes Genomes Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Rowan Digitals Works (Rowan University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Princeton University
- Rowan University
- National Institute of General Medical Sciences (R15GM113187)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer, Hypoxia, and Metabolism
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Redox biology and oxidative stress
- Keywords
- hypoxia, Saccharomyces cerevisiae, gene expression, oxygen regulation, time-course transcriptome, DMC1, lysine methyltransferase, recombinases, respiration, lipid metabolism, amino acid metabolism, vitamin metabolism, environmental stress response, principal component analysis, redox regulation
- MeSH terms
- DNA-Binding Proteins, Humans, Methyltransferases, Oxygen, RNA, Messenger, Saccharomyces cerevisiae, Transcription Factors, Cell Hypoxia, Gene Expression Regulation, Fungal, Sequence Analysis, RNA, Cell Cycle Proteins, Oligonucleotide Array Sequence Analysis, Saccharomyces cerevisiae Proteins, Gene-Environment Interaction
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
