Candida albicans exhibits heterogeneous and adaptive cytoprotective responses to antifungal compounds

R: A Language and Environment for Statistical Computing

R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,706 · see citing works

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

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works

Cutadapt removes adapter sequences from high-throughput sequencing reads

Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · see citing works

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works

SCANPY: large-scale single-cell gene expression data analysis

Wolf, F. A., Angerer, P., & Theis, F. J. (2018) · Genome Biology · doi:10.1186/s13059-017-1382-0 · Cited by 8,881 · see citing works

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110 · see citing works

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

McInnes, L., Healy, J., & Melville, J. (2018) · arXiv · doi:10.48550/arxiv.1802.03426 · Cited by 7,101 · see citing works

From Louvain to Leiden: guaranteeing well-connected communities

Traag, V. A., Waltman, L., & van Eck, N. J. (2019) · Scientific Reports · doi:10.1038/s41598-019-41695-z · Cited by 5,635 · see citing works

Exploring the metabolic and genetic control of gene expression on a genomic scale.

Derisi, J., Iyer, V., & Brown, P. (1997) · Science · doi:10.1126/science.278.5338.680 · Cited by 4,832 · 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

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

Street, K., Risso, D., Fletcher, R. B., Das, D., Ngai, J., Yosef, N., Purdom, E., & Dudoit, S. (2018) · BMC Genomics · doi:10.1186/s12864-018-4772-0 · Cited by 3,159 · see citing works

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

Liao, Y., Smyth, G. K., & Shi, W. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz114 · Cited by 2,965 · see citing works

Deep generative modeling for single-cell transcriptomics

Lopez, R., Regier, J., Cole, M. B., Jordan, M. I., & Yosef, N. (2018) · Nature Methods · doi:10.1038/s41592-018-0229-2 · Cited by 2,530 · see citing works

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

Alexa, A., Rahnenführer, J., & Lengauer, T. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl140 · Cited by 2,194 · see citing works

Targets for Cell Cycle Arrest by the Immunosuppressant Rapamycin in Yeast

Heitman, J., Movva, N. R., & Hall, M. N. (1991) · Science · doi:10.1126/science.1715094 · Cited by 2,010 · see citing works

TOR, a Central Controller of Cell Growth

Schmelzle, T., & Hall, M. N. (2000) · Cell · doi:10.1016/s0092-8674(00)00117-3 · Cited by 1,914 · see citing works

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

van Dijk, D., Sharma, R., Nainys, J., Yim, K., Kathail, P., Carr, A. J., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.061 · Cited by 1,829 · see citing works

Invasive candidiasis

Pappas, P. G., Lionakis, M. S., Arendrup, M. C., Ostrosky-Zeichner, L., & Kullberg, B. J. (2018) · Nature Reviews Disease Primers · doi:10.1038/nrdp.2018.26 · Cited by 1,636 · see citing works

Distinguishing between resistance, tolerance and persistence to antibiotic treatment

Brauner, A., Fridman, O., Gefen, O., & Balaban, N. Q. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.34 · Cited by 1,612 · see citing works

Invasive candidiasis

Kullberg, B. J., & Arendrup, M. C. (2015) · New England Journal of Medicine · doi:10.1056/nejmra1315399 · Cited by 1,315 · see citing works

TRANSLATIONAL REGULATION OFGCN4AND THE GENERAL AMINO ACID CONTROL OF YEAST

Hinnebusch, A. G. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.031805.133833 · Cited by 1,258 · see citing works

Cellular Heterogeneity: Do Differences Make a Difference?

Altschuler, S. J., & Wu, L. F. (2010) · Cell · doi:10.1016/j.cell.2010.04.033 · Cited by 1,214 · see citing works

Antifungal agents: mechanisms of action

Odds, F. C., Brown, A. J. P., & Gow, N. A. R. (2003) · Trends in Microbiology · doi:10.1016/s0966-842x(03)00117-3 · Cited by 1,202 · see citing works

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Lun, A. T. L., Riesenfeld, S. J., Andrews, T. S., Dao, T. P., Gomes, T., Jamboree, P. I. T. 1. H. C. A., & Marioni, J. C. (2019) · Genome biology · doi:10.1186/s13059-019-1662-y · Cited by 1,044 · see citing works

Confronting false discoveries in single-cell differential expression

Squair, J. W., Gautier, M., Kathe, C., Anderson, M. A., James, N. D., Hutson, T. H., Hudelle, R., Qaiser, T., Matson, K. J. E., Barraud, Q., et al. (2021) · doi:10.1101/2021.03.12.435024 · Cited by 1,017 · see citing works

Orchestrating single-cell analysis with Bioconductor

Amezquita, R. A., Lun, A. T. L., Becht, E., Carey, V. J., Carpp, L. N., Geistlinger, L., Marini, F., Rue-Albrecht, K., Risso, D., Soneson, C., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0654-x · Cited by 945 · see citing works

A functional perspective on phenotypic heterogeneity in microorganisms

Ackermann, M. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3491 · Cited by 922 · see citing works

Twenty Years of the SENTRY Antifungal Surveillance Program: Results for Candida Species From 1997–2016

Pfaller, M. A., Diekema, D. J., Turnidge, J. D., Castanheira, M., & Jones, R. N. (2019) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofy358 · Cited by 825 · see citing works

A Python library for probabilistic analysis of single-cell omics data

Gayoso, A., Lopez, R., Xing, G., Boyeau, P., Valiollah Pour Amiri, V., Hong, J., Wu, K., Jayasuriya, M., Mehlman, E., Langevin, M., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01206-w · Cited by 789 · see citing works

Transcriptional Profiling Shows that Gcn4p Is a Master Regulator of Gene Expression during Amino Acid Starvation in Yeast

Natarajan, K., Meyer, M. R., Jackson, B. M., Slade, D., Roberts, C., Hinnebusch, A. G., & Marton, M. J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.13.4347-4368.2001 · Cited by 749 · see citing works

Resistance of Candida to azoles and echinocandins worldwide

Pristov, K. E., & Ghannoum, M. A. (2019) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2019.03.028 · Cited by 706 · see citing works

Hsp90 Potentiates the Rapid Evolution of New Traits: Drug Resistance in Diverse Fungi

Cowen, L. E., & Lindquist, S. (2005) · Science · doi:10.1126/science.1118370 · Cited by 698 · see citing works

Drug resistance and tolerance in fungi.

Berman, J., & Krysan, D. J. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0322-2 · Cited by 654 · 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

Regulation of ribosome biogenesis by the rapamycin-sensitive TOR-signaling pathway in Saccharomyces cerevisiae.

Powers, T., & Walter, P. (1999) · Molecular Biology of the Cell · doi:10.1091/mbc.10.4.987 · Cited by 540 · see citing works

mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding

Delarue, M., Brittingham, G. P., Pfeffer, S., Surovtsev, I. V., Pinglay, S., Kennedy, K. J., Schaffer, M., Gutierrez, J. I., Sang, D., Poterewicz, G., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.042 · Cited by 526 · see citing works

Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins

Hardwick, J. S., Kuruvilla, F. G., Tong, J. K., Shamji, A. F., & Schreiber, S. L. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.26.14866 · Cited by 523 · see citing works

Mechanisms and clinical relevance of bacterial heteroresistance

Andersson, D. I., Nicoloff, H., & Hjort, K. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0218-1 · Cited by 513 · see citing works

Estimation of Direct Healthcare Costs of Fungal Diseases in the United States

Benedict, K., Jackson, B. R., Chiller, T., & Beer, K. D. (2019) · Clinical Infectious Diseases · doi:10.1093/cid/ciy776 · Cited by 438 · see citing works

Genome-Wide Analysis of the Biology of Stress Responses through Heat Shock Transcription Factor

Hahn, J., Hu, Z., Thiele, D. J., & Iyer, V. R. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.12.5249-5256.2004 · Cited by 430 · see citing works

Emerging Threats in Antifungal-Resistant Fungal Pathogens

Sanglard, D. (2016) · Frontiers in Medicine · doi:10.3389/fmed.2016.00011 · Cited by 420 · see citing works

<i>Candida albicans</i> Mutations in the Ergosterol Biosynthetic Pathway and Resistance to Several Antifungal Agents

Sanglard, D., Ischer, F., Parkinson, T., Falconer, D., & Bille, J. (2003) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.47.8.2404-2412.2003 · Cited by 398 · see citing works

Role of the Hog1 Stress-activated Protein Kinase in the Global Transcriptional Response to Stress in the Fungal Pathogen<i>Candida albicans</i>

Enjalbert, B., Smith, D. A., Cornell, M. J., Alam, I., Nicholls, S., Brown, A. J. P., & Quinn, J. (2006) · Molecular Biology of the Cell · doi:10.1091/mbc.e05-06-0501 · Cited by 381 · see citing works

Neonatal Candidiasis: Epidemiology, Risk Factors, and Clinical Judgment

Benjamin, D. K., Stoll, B. J., Gantz, M. G., Walsh, M. C., Sánchez, P. J., Das, A., Shankaran, S., Higgins, R. D., Auten, K. J., Miller, N. A., et al. (2010) · PEDIATRICS · doi:10.1542/peds.2009-3412 · Cited by 380 · see citing works

Transcription Profiling of <i>Candida albicans</i> Cells Undergoing the Yeast-to-Hyphal Transition

Nantel, A., Dignard, D., Bachewich, C., Harcus, D., Marcil, A., Bouin, A.-P., Sensen, C. W., Hogues, H., van het Hoog, M., Gordon, P., et al. (2002) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-05-0272 · Cited by 378 · see citing works

Echinocandin resistance in Candida.

Perlin, D. S. (2015) · Clinical Infectious Diseases · doi:10.1093/cid/civ791 · Cited by 374 · see citing works

Hsp90 Governs Echinocandin Resistance in the Pathogenic Yeast Candida albicans via Calcineurin

Singh, S. D., Robbins, N., Zaas, A. K., Schell, W. A., Perfect, J. R., & Cowen, L. E. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000532 · Cited by 362 · see citing works

Droplet scRNA-seq is not zero-inflated

Svensson, V. (2019) · doi:10.1101/582064 · Cited by 356 · see citing works

Calcineurin A of <i>Candida albicans</i>: involvement in antifungal tolerance, cell morphogenesis and virulence

Sanglard, D., Ischer, F., Marchetti, O., Entenza, J., & Bille, J. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03495.x · Cited by 350 · see citing works

The evolution of drug resistance in clinical isolates of Candida albicans.

Ford, C. B., Funt, J. M., Abbey, D., Issi, L., Guiducci, C., Martinez, D. A., Delorey, T., Li, B. Y., White, T. C., Cuomo, C., et al. (2015) · eLife · doi:10.7554/elife.00662 · Cited by 348 · see citing works

Acquisition of Aneuploidy Provides Increased Fitness during the Evolution of Antifungal Drug Resistance

Selmecki, A. M., Dulmage, K., Cowen, L. E., Anderson, J. B., & Berman, J. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000705 · Cited by 319 · see citing works

Stress adaptation in a pathogenic fungus

Brown, A. J. P., Budge, S., Kaloriti, D., Tillmann, A., Jacobsen, M. D., Yin, Z., Ene, I. V., Bohovych, I., Sandai, D., Kastora, S., et al. (2014) · Journal of Experimental Biology · doi:10.1242/jeb.088930 · Cited by 299 · see citing works

YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

Balakrishnan, R., Park, J., Karra, K., Hitz, B. C., Binkley, G., Hong, E. L., Sullivan, J. M., Micklem, G., & Cherry, J. M. (2012) · Database · doi:10.1093/database/bar062 · Cited by 280 · see citing works

Stress-induced Gene Expression inCandida albicans: Absence of a General Stress Response

Enjalbert, B., Nantel, A., & Whiteway, M. S. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-08-0546 · Cited by 277 · see citing works

Antifungal tolerance is a subpopulation effect distinct from resistance and is associated with persistent candidemia

Rosenberg, A., Ene, I. V., Bibi, M., Zakin, S., Segal, E. S., Ziv, N., Dahan, A. M., Colombo, A. L., Bennett, R. J., & Berman, J. (2018) · Nature Communications · doi:10.1038/s41467-018-04926-x · Cited by 270 · see citing works

Candida albicans biofilm–induced vesicles confer drug resistance through matrix biogenesis

Zarnowski, R., Sanchez, H., Covelli, A. S., Dominguez, E., Jaromin, A., Bernhardt, J., Mitchell, K. F., Heiss, C., Azadi, P., Mitchell, A., et al. (2018) · PLOS Biology · doi:10.1371/journal.pbio.2006872 · Cited by 260 · see citing works

Functional interpretation of single cell similarity maps

DeTomaso, D., Jones, M. G., Subramaniam, M., Ashuach, T., Ye, C., & Yosef, N. (2019) · Nature Communications · doi:10.1038/s41467-019-12235-0 · Cited by 251 · see citing works

Candida albicans Gene Deletion with a Transient CRISPR-Cas9 System

Min, K., Ichikawa, Y., Woolford, C. A., & Mitchell, A. P. (2016) · mSphere · doi:10.1128/msphere.00130-16 · Cited by 246 · see citing works

Morphogenesis and cell cycle progression in Candida albicans

Berman, J. (2006) · Current Opinion in Microbiology · doi:10.1016/j.mib.2006.10.007 · Cited by 237 · see citing works

Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

Regenberg, B., Grotkjær, T., Winther, O., Fausbøll, A., Åkesson, M., Bro, C., Hansen, L. K., Brunak, S., & Nielsen, J. (2006) · Genome biology · doi:10.1186/gb-2006-7-11-r107 · Cited by 233 · see citing works

The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes

Wade, J. T., Hall, D. B., & Struhl, K. (2004) · Nature · doi:10.1038/nature03175 · Cited by 232 · see citing works

<i>CRZ1</i> , a target of the calcineurin pathway in <i>Candida albicans</i>

Karababa, M., Valentino, E., Pardini, G., Coste, A. T., Bille, J., & Sanglard, D. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.05037.x · Cited by 231 · see citing works

Paradoxical Effect of Caspofungin: Reduced Activity against Candida albicans at High Drug Concentrations

Stevens, D. A., Espiritu, M., & Parmar, R. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.9.3407-3411.2004 · Cited by 218 · see citing works

Comparative genomics of the environmental stress response in ascomycete fungi

Gasch, A. P. (2007) · Yeast · doi:10.1002/yea.1512 · Cited by 210 · see citing works

The Echinocandins

Cappelletty, D., & Eiselstein‐McKitrick, K. (2007) · Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy · doi:10.1592/phco.27.3.369 · Cited by 205 · see citing works

Gcn4 co‐ordinates morphogenetic and metabolic responses to amino acid starvation in Candida albicans

Tripathi, G., Wiltshire, C. J., Macaskill, S., Tournu, H., Budge, S., & Brown, A. J. P. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf507 · Cited by 204 · see citing works

A ribosome assembly stress response regulates transcription to maintain proteome homeostasis

Albert, B., Kos‐Braun, I. C., Henras, A. K., Dez, C., Rueda-Mejia, M. P., Zhang, X., Gadal, O., Koš, M., & Shore, D. (2019) · eLife · doi:10.7554/elife.45002 · Cited by 180 · see citing works

A Tetraploid Intermediate Precedes Aneuploid Formation in Yeasts Exposed to Fluconazole

Harrison, B. D., Hashemi, J., Bibi, M., Pulver, R., Bavli, D., Nahmias, Y., Wellington, M., Sapiro, G., & Berman, J. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001815 · Cited by 174 · see citing works

Components of the Calcium-Calcineurin Signaling Pathway in Fungal Cells and Their Potential as Antifungal Targets

Liu, S., Hou, Y., Liu, W., Lu, C., Wang, W., & Sun, S. (2015) · Eukaryotic Cell · doi:10.1128/ec.00271-14 · Cited by 174 · see citing works

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

Jackson, C. A., Castro, D. M., Saldi, G.-A., Bonneau, R., & Gresham, D. (2020) · eLife · doi:10.7554/elife.51254 · Cited by 174 · see citing works

Rapamycin (AY-22,989), a new antifungal antibiotic. III. In vitro and in vivo evaluation.

BAKER, H., SIDOROWICZ, A., Sehgal, S. N., & Vézina, C. (1978) · The Journal of Antibiotics · doi:10.7164/antibiotics.31.539 · Cited by 168 · see citing works

Rapamycin and Less Immunosuppressive Analogs Are Toxic to <i>Candida albicans</i> and <i>Cryptococcus neoformans</i> via FKBP12-Dependent Inhibition of TOR

Cruz, M. C., Goldstein, A. L., Blankenship, J., Del Poeta, M., Perfect, J. R., McCusker, J. H., Bennani, Y. L., Cardenas, M. E., & Heitman, J. (2001) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.45.11.3162-3170.2001 · Cited by 159 · see citing works

Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress

Gasch, A. P., Yu, F. B., Hose, J., Escalante, L. E., Place, M., Bacher, R. L., Kanbar, J. N., Ciobanu, D., Sandor, L., Grigoriev, I. V., et al. (2017) · PLoS Biology · doi:10.1371/journal.pbio.2004050 · Cited by 159 · see citing works

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

Brionne, A., Juanchich, A., & Hennequet‐Antier, C. (2019) · BioData Mining · doi:10.1186/s13040-019-0204-1 · Cited by 156 · see citing works

Global analysis of mutations driving microevolution of a heterozygous diploid fungal pathogen

Ene, I. V., Farrer, R. A., Hirakawa, M. P., Agwamba, K., Cuomo, C. A., & Bennett, R. J. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1806002115 · Cited by 155 · see citing works

The Protein Kinase Tor1 Regulates Adhesin Gene Expression in Candida albicans

Bastidas, R. J., Heitman, J., & Cardenas, M. E. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000294 · Cited by 154 · see citing works

Expandable and reversible copy number amplification drives rapid adaptation to antifungal drugs

Todd, R. T., & Selmecki, A. (2020) · eLife · doi:10.7554/elife.58349 · Cited by 138 · see citing works

Fungal persister cells: The basis for recalcitrant infections?

Wuyts, J., Van Dijck, P., & Holtappels, M. (2018) · PLOS Pathogens · doi:10.1371/journal.ppat.1007301 · Cited by 136 · see citing works

Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness

Tye, B., Commins, N., Ryazanova, L. V., Wühr, M., Springer, M., Pincus, D., & Churchman, L. S. (2019) · eLife · doi:10.7554/elife.43002 · Cited by 134 · see citing works

Evolutionary Tinkering with Conserved Components of a Transcriptional Regulatory Network

Lavoie, H., Hogues, H., Mallick, J., Sellam, A., Nantel, A., & Whiteway, M. S. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000329 · Cited by 133 · see citing works

Hsp90 Orchestrates Transcriptional Regulation by Hsf1 and Cell Wall Remodelling by MAPK Signalling during Thermal Adaptation in a Pathogenic Yeast

Leach, M. D., Budge, S., Walker, L. A., Munro, C. A., Cowen, L. E., & Brown, A. J. P. (2012) · PLoS Pathogens · doi:10.1371/journal.ppat.1003069 · Cited by 133 · see citing works

Caspofungin

McCormack, P. L., & Perry, C. M. (2005) · Drugs · doi:10.2165/00003495-200565140-00009 · Cited by 122 · see citing works

Defining the frontiers between antifungal resistance, tolerance and the concept of persistence

Delarze, E., & Sanglard, D. (2015) · Drug Resistance Updates · doi:10.1016/j.drup.2015.10.001 · Cited by 118 · see citing works

Determining sequencing depth in a single-cell RNA-seq experiment

Zhang, M. J., Ntranos, V., & Tse, D. (2020) · Nature Communications · doi:10.1038/s41467-020-14482-y · Cited by 112 · see citing works

Cell cycle population effects in perturbation studies

O’Duibhir, E., Lijnzaad, P., Benschop, J. J., Lenstra, T. L., van Leenen, D., Koerkamp, M. J. A. G., Margaritis, T., Brok, M. O., Kemmeren, P., & Holstege, F. C. P. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145172 · Cited by 109 · see citing works

Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data

He, D., Zakeri, M., Sarkar, H., Soneson, C., Srivastava, A., & Patro, R. (2022) · Nature Methods · doi:10.1038/s41592-022-01408-3 · Cited by 106 · see citing works

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing dataPreprint

Lun, A., Riesenfeld, S. J., Andrews, T., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/234872 · Cited by 104 · see citing works

Hypo-osmotic-like stress underlies general cellular defects of aneuploidy

Tsai, H.-J., Nelliat, A. R., Choudhury, M. I., Kucharavy, A., Bradford, W. D., Cook, M. E., Kim, J., Mair, D. B., Sun, S. X., Schatz, M. C., et al. (2019) · Nature · doi:10.1038/s41586-019-1187-2 · Cited by 103 · see citing works

Hsf1 and Hsp90 orchestrate temperature-dependent global transcriptional remodelling and chromatin architecture in Candida albicans

Leach, M. D., Farrer, R. A., Tan, K., Miao, Z., Walker, L. A., Cuomo, C. A., Wheeler, R. T., Brown, A. J. P., Wong, K. H., & Cowen, L. E. (2016) · Nature Communications · doi:10.1038/ncomms11704 · Cited by 100 · see citing works

Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations

Nadal‐Ribelles, M., Islam, S., Wu, W., Latorre, P., Nguyen, M., de Nadal, E., Posas, F., & Steinmetz, L. M. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0346-9 · Cited by 95 · see citing works

Multicenter Study of Method-Dependent Epidemiological Cutoff Values for Detection of Resistance in Candida spp. and Aspergillus spp. to Amphotericin B and Echinocandins for the Etest Agar Diffusion Method

Espinel‐Ingroff, A., Arendrup, M. C., Cantón, R., Córdoba, S. B., Dannaoui, É., García‐Rodríguez, J., González, G. M., Govender, N. P., Martín‐Mazuelos, E., Lackner, M., et al. (2016) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01792-16 · Cited by 90 · see citing works

The Krebs cycle meets the cell cycle: Mitochondria and the G 1 –S transition

Finkel, T., & Hwang, P. M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906430106 · Cited by 87 · see citing works

Tolerance to Caspofungin in Candida albicans Is Associated with at Least Three Distinctive Mechanisms That Govern Expression of <i>FKS</i> Genes and Cell Wall Remodeling

Yang, F., Zhang, L., Wakabayashi, H., Myers, J., Jiang, Y., Cao, Y., Jimenez-Ortigosa, C., Perlin, D. S., & Rustchenko, E. (2017) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00071-17 · Cited by 81 · see citing works

Cytocidal amino acid starvation of Saccharomyces cerevisiae and Candida albicans acetolactate synthase (ilv2Δ) mutants is influenced by the carbon source and rapamycin

Kingsbury, J. M., & McCusker, J. H. (2009) · Microbiology · doi:10.1099/mic.0.034348-0 · Cited by 74 · see citing works

Transcriptional Analysis of the <i>Candida albicans</i> Cell Cycle

Côte, P., Hogues, H., & Whiteway, M. (2009) · Molecular Biology of the Cell · doi:10.1091/mbc.e09-03-0210 · Cited by 72 · see citing works

Principles of open source bioinstrumentation applied to the poseidon syringe pump system

Booeshaghi, A. S., Beltrame, E. D. V., Bannon, D., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-48815-9 · Cited by 72 · see citing works

Filamentation Involves Two Overlapping, but Distinct, Programs of Filamentation in the Pathogenic Fungus Candida albicans

Azadmanesh, J., Gowen, A. M., Creger, P. E., Brandquist, N. D., & Blankenship, J. R. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.117.300224 · Cited by 69 · see citing works

A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast

Jariani, A., Vermeersch, L., Cerulus, B., Perez-Samper, G., Voordeckers, K., Brussel, T. V., Thienpont, B., Lambrechts, D., & Verstrepen, K. J. (2020) · eLife · doi:10.7554/elife.55320 · Cited by 69 · see citing works

Cdc28 provides a molecular link between Hsp90, morphogenesis, and cell cycle progression in<i>Candida albicans</i>

Senn, H., Shapiro, R. S., & Cowen, L. E. (2012) · Molecular Biology of the Cell · doi:10.1091/mbc.e11-08-0729 · Cited by 67 · see citing works

scvi-tools: a library for deep probabilistic analysis of single-cell omics dataPreprint

Gayoso, A., Lopez, R., Xing, G. K., et al. (2021) · bioRxiv · doi:10.1101/2021.04.28.441833 · Cited by 66 · see citing works

diskImageR: quantification of resistance and tolerance to antimicrobial drugs using disk diffusion assays

Gerstein, A. C., Rosenberg, A., Hecht, I., & Berman, J. (2016) · Microbiology · doi:10.1099/mic.0.000295 · Cited by 63 · see citing works

Ploidy dynamics and evolvability in fungi

Wertheimer, N. B., Stone, N. R. H., & Berman, J. G. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0461 · Cited by 63 · see citing works

The rewiring of transcription circuits in evolution

Johnson, A. D. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.09.004 · Cited by 59 · see citing works

A Fungal-Selective Cytochrome bc1 Inhibitor Impairs Virulence and Prevents the Evolution of Drug Resistance

Vincent, B. M., Langlois, J.-B., Srinivas, R., Lancaster, A. K., Scherz-Shouval, R., Whitesell, L., Tidor, B., Buchwald, S. L., & Lindquist, S. (2016) · Cell Chemical Biology · doi:10.1016/j.chembiol.2016.06.016 · Cited by 58 · see citing works

Tuning Hsf1 levels drives distinct fungal morphogenetic programs with depletion impairing Hsp90 function and overexpression expanding the target space

Veri, A. O., Miao, Z., Shapiro, R. S., Tebbji, F., O’Meara, T. R., Kim, S. H., Colazo, J., Tan, K., Vyas, V. K., Whiteway, M., et al. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007270 · Cited by 51 · see citing works

Impact of tolerance to fluconazole on treatment response in <i>Candida albicans</i> bloodstream infection

Levinson, T., Dahan, A., Novikov, A., Paran, Y., Berman, J., & Ben‐Ami, R. (2021) · Mycoses · doi:10.1111/myc.13191 · Cited by 50 · see citing works

Implications of the EUCAST Trailing Phenomenon in Candida tropicalis for the In Vivo Susceptibility in Invertebrate and Murine Models

Astvad, K. M. T., Sanglard, D., Delarze, E., Hare, R. K., & Arendrup, M. C. (2018) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01624-18 · Cited by 43 · see citing works

Candida albicans Genetic Background Influences Mean and Heterogeneity of Drug Responses and Genome Stability during Evolution in Fluconazole

Gerstein, A. C., & Berman, J. G. (2020) · mSphere · doi:10.1128/msphere.00480-20 · Cited by 42 · see citing works

A common mechanism involving the TORC1 pathway can lead to amphotericin B-persistence in biofilm and planktonic Saccharomyces cerevisiae populations

Bojsen, R., Regenberg, B., Gresham, D., & Folkesson, A. (2016) · Scientific Reports · doi:10.1038/srep21874 · Cited by 42 · see citing works

The Rim pathway mediates antifungal tolerance in Candida albicans through newly identified Rim101 transcriptional targets, including Hsp90 and Ipt1

Garnaud, C., García-Oliver, E., Wang, Y., Maubon, D., Bailly, S., Despinasse, Q., Champleboux, M., Govin, J., & Cornet, M. (2018) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01785-17 · Cited by 41 · see citing works

Cell Cycle Sensing of Oxidative Stress in Saccharomyces cerevisiae by Oxidation of a Specific Cysteine Residue in the Transcription Factor Swi6p

Chiu, J., Tactacan, C. M., Tan, S., Lin, R. C. Y., Wouters, M. A., & Dawes, I. W. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.172973 · Cited by 38 · see citing works

Exciting Developments in the Immunology of Fungal Infections

Brown, G. D., & Netea, M. G. (2012) · Cell Host & Microbe · doi:10.1016/j.chom.2012.04.010 · Cited by 35 · see citing works

Novel fluconazole derivatives with promising antifungal activity

Chandrika, N. T., Shrestha, S. K., Ngo, H., Howard, K. C., & Garneau‐Tsodikova, S. (2017) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2017.12.018 · Cited by 35 · see citing works

Functional connections between cell cycle and proteostasis in the regulation of Candida albicans morphogenesis

Hossain, S., Lash, E., Veri, A. O., & Cowen, L. E. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108781 · Cited by 31 · see citing works

mDrop-Seq: Massively Parallel Single-Cell RNA-Seq of Saccharomyces cerevisiae and Candida albicans

Dohn, R., Xie, B., Back, R., Selewa, A., Eckart, H., Rao, R. P., & Basu, A. (2021) · Vaccines · doi:10.3390/vaccines10010030 · Cited by 26 · see citing works

Hsp21 Potentiates Antifungal Drug Tolerance in Candida albicans

Mayer, F. L., Wilson, D., & Hube, B. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060417 · Cited by 25 · see citing works

Identification and characterization of mediators of fluconazole tolerance in Candida albicans

Delarze, E., Brandt, L., Trachsel, E., Patxot, M., Pralong, C., Maranzano, F., Chauvel, M., Legrand, M., Znaidi, S., Bougnoux, M.-E., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.591140 · Cited by 25 · see citing works

Candida albicans Msi3p, a homolog of the Saccharomyces cerevisiae Sse1p of the Hsp70 family, is involved in cell growth and fluconazole tolerance

Nagao, J.-I., Cho, T., Uno, J., Ueno, K., Imayoshi, R., Nakayama, H., Chibana, H., & Kaminishi, H. (2012) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2012.00822.x · Cited by 25 · see citing works

Effects of fluconazole on the metabolomic profile of Candida albicans

Katragkou, A., Alexander, E. L., Eoh, H., Raheem, S., Roilides, E., & Walsh, T. J. (2015) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkv381 · Cited by 21 · see citing works

Hyper-Synergistic Antifungal Activity of Rapamycin and Peptide-Like Compounds against Candida albicans Orthogonally via Tor1 Kinase

Tong, Y., Zhang, J., Wang, L., Wang, Q., Huang, H., Chen, X., Zhang, Q., Li, H., Sun, N., Liu, G., et al. (2021) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.1c00448 · Cited by 21 · see citing works

Genome-Wide Response to Drugs and Stress in the Pathogenic Yeast Candida glabrata

Pais, P., Galocha, M., & Teixeira, M. C. (2019) · Progress in molecular and subcellular biology · doi:10.1007/978-3-030-13035-0_7 · Cited by 16 · see citing works

Genome Sequence for Candida albicans Clinical Oral Isolate 529L

Cuomo, C. A., Fanning, S., Gujja, S., et al. (2019) · Microbiology Resource Announcements · doi:10.1128/mra.00554-19 · Cited by 13 · see citing works

Alevin-fry unlocks rapid, accurate, and memory-frugal quantification of single-cell RNA-seq dataPreprint

He, D., Zakeri, M., Sarkar, H., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.29.450377 · Cited by 13 · see citing works

Candida albicans exhibits distinct cytoprotective responses to anti-fungal drugs that facilitate the evolution of drug resistancePreprint

Bettauer, V., Massahi, S., Khurdia, S. S., Costa, A., Omran, R., Khosravi, N., Simpson, S., Harb, M., Dumeaux, V., Whiteway, M. S., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.21.914549 · Cited by 4 · see citing works

Yeast Single-cell RNA-seq, Cell by Cell and Step by Step

Nadal‐Ribelles, M., Islam, S., Wei, W., Latorre, P., Nguyen, M., de Nadal, E., Posas, F., & Steinmetz, L. M. (2019) · BIO-PROTOCOL · doi:10.21769/bioprotoc.3359 · Cited by 3 · see citing works

Author Correction: A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels

Urbonaite, G., Lee, J. T. H., Liu, P., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02420-7 · Cited by 1 · see citing works

The Dynamic Fungal Genome: Polyploidy, Aneuploidy and Copy Number Variation in Response to Stress

Vande Zande, P., Zhou, X., & Selmecki, A. (2023) · Annual Review of Microbiology · doi:10.1146/annurev-micro-041320-112443 · Cited by 70 · see citing works

Understanding fluconazole tolerance in Candida albicans: implications for effective treatment of candidiasis and combating invasive fungal infections

Feng, Y., Lu, H., Whiteway, M., & Jiang, Y. (2023) · Journal of Global Antimicrobial Resistance · doi:10.1016/j.jgar.2023.10.019 · Cited by 40 · see citing works

Insight into the Mechanisms and Clinical Relevance of Antifungal Heteroresistance

Su, Y., Li, Y., Yi, Q., Xu, Y., Sun, T., & Li, Y. (2025) · Journal of Fungi · doi:10.3390/jof11020143 · Cited by 18 · see citing works

Are there proteins between the ribosomal subunits?

Yusupov, M., & Spirin, A. S. (1986) · FEBS Letters · doi:10.1016/0014-5793(86)80332-5 · Cited by 27 · see citing works

Proteins of ribosomes formed from “relaxed particles”

Nakada, D. (1967) · Journal of Molecular Biology · doi:10.1016/0022-2836(67)90113-1 · Cited by 10 · see citing works

Analysis of kethoxal bound to ribosomal proteins from Escherichia coli 70S reacted ribosomes

Benkov, K. J., & Delihas, N. (1974) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(74)90400-8 · Cited by 8 · see citing works

Present conceptions on the peptidyltransferase centre of animal ribosomes.

Stahl, J., & BIELKA, H. (1983) · PubMed · Cited by 2 · see citing works

Heterogeneity of pea ribosomes with regard to protein synthesis

Webster, G. C., Whitman, S. L., & Heintz, R. L. (1962) · Experimental Cell Research · doi:10.1016/0014-4827(62)90166-0 · Cited by 13 · see citing works