GGCN Lab Publications

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2021

Mer, A. S. et al. Biological and therapeutic implications of a unique subtype of NPM1 mutated AML. Nat. Commun. 12, 1054 (2021).

 

Gaikani, H., Smith, A. M., Lee, A. Y., Giaever, G. & Nislow, C. Combining chemogenomic and gene-dose assays to investigate drug synergy. bioRxiv 1–20 (2021).

Fekadu, A. et al. Understanding the key processes of excellence as a prerequisite to establishing academic centres of excellence in Africa. BMC Med. Educ. 21, 36 (2021).

Breaux, S., Desrosiers, F. A. D., Neira, M., Sinha, S. & Nislow, C. Pharmacogenomics at the Point of Care: A Community Pharmacy Project in British  Columbia. J. Pers. Med. 11, (2020).

2020

Rajashekara, I., Acuna, Ulyana Munoz & Nislow, C. Novel Small Molecule Antimicrobials. US Pat. App. 16/083,811 (2020).

Hammond, T. G. et al. Moonshot: Affordable, Simple, Flight Hardware for the Artemis-1 Mission and Beyond. Front. Sp. Technol. 1, 5 (2020).

Edouarzin, E. et al. Broad-spectrum antifungal activities and mechanism of drimane sesquiterpenoids. Microb. Cell 7, 146–159 (2020).

Black, H. F. et al. A competence-regulated toxin-antitoxin system in Haemophilus influenzae. PLoS One 15, (2020).

 

Coutin, N. P. J., Giaever, G. & Nislow, C. Interactively AUDIT Your Growth Curves with a Suite of R Packages. G3. 10, 933–943 (2020).

2019

Tigchelaar, S. et al. MicroRNA Biomarkers in Cerebrospinal Fluid and Serum Reflect Injury Severity in Human Acute Traumatic Spinal Cord Injury. J. Neurotrauma 36, 2358–2371 (2019).

 

Ellison, M. A. et al. The paf1 complex broadly impacts the transcriptome of Saccharomyces cerevisiae. Genetics 212, 711–728 (2019).

 

Tarailo-Graovac, M. et al. De novo pathogenic DNM1L variant in a patient diagnosed with atypical hereditary sensory and autonomic neuropathy. Mol. Genet. Genomic Med. 7, (2019

 

Zea, L. et al. Experiment design for a genome-wide yeast fitness profiling experiment on board Orion’s ARTEMIS 1 mission. in Proceedings of the International Astronautical Congress, IAC 2019-October, (2019).

 

Filho, F. S. L. et al. Sputum microbiome is associated with 1-year mortality after chronic obstructive pulmonary disease hospitalizations. Am. J. Respir. Crit. Care Med. 199, 1205–1213 (2019).

 

Nawrotek, A. et al. PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling. Nat. Chem. Biol. 15, 358–366 (2019).

 

Nawrotek, A. et al. Publisher Correction: PH-domain-binding inhibitors of nucleotide exchange factor BRAG2 disrupt Arf GTPase signaling (Nature Chemical Biology, (2019), 15, 4, (358-366), 10.1038/s41589-019-0228-3). Nat. Chem. Biol. 15, 549 (2019).

 

Giaever, G., Lissina, E. & Nislow, C. Network dynamics of the yeast methyltransferome. Microb. Cell 6, 356–369 (2019).

 

Hippman, C. & Nislow, C. Pharmacogenomic testing: Clinical evidence and implementation challenges. J. Pers. Med. 9, (2019).

 

Thiombane, N. K. et al. Single-cell analysis for drug development using convex lens-induced confinement imaging. Biotechniques 67, 210–217 (2019).

 

2018

Page, M. M. et al. Reducing insulin via conditional partial gene ablation in adults reverses diet-induced weight gain. FASEB J. 32, 1196–1206 (2018).

 

Xu, S. et al. Decreased microbiome diversity in the HIV small airway epithelium. Respir. Res. 19, (2018).

 

Tiefenbach, J. et al. Idebenone and coenzyme Q10 are novel PPARα/γ ligands, with potential for treatment of fatty liver diseases. DMM Dis. Model. Mech. 11, (2018).

 

Mor, V. et al. Erratum for Mor et al., ‘Identification of a New Class of Antifungals Targeting the Synthesis of Fungal Sphingolipids’. MBio 9, (2018).

 

Hammond, T. G. et al. Physical Forces Modulate Oxidative Status and Stress Defense Meditated Metabolic Adaptation of Yeast Colonies: Spaceflight and Microgravity Simulations. Microgravity Sci. Technol. 30, 195–208 (2018).

 

2017

Cho, G. et al. Caryolan-1-ol, an antifungal volatile produced by Streptomyces spp., inhibits the endomembrane system of fungi. Open Biol. 7, (2017).

 

Templeman, N. M. et al. Reduced Circulating Insulin Enhances Insulin Sensitivity in Old Mice and Extends Lifespan. Cell Rep. 20, 451–463 (2017).

 

Zhang, D. et al. Heparanase overexpression induces glucagon resistance and protects animals from chemically induced diabetes. Diabetes 66, 45–57 (2017).

 

Tigchelaar, S. et al. Serum MicroRNAs Reflect Injury Severity in a Large Animal Model of Thoracic Spinal Cord Injury. Sci. Rep. 7, (2017).

 

Acton, E. et al. Comparative functional genomic screens of three yeast deletion collections reveal unexpected effects of genotype in response to diverse stress. Open Biol. 7, (2017).

 

Sinha, S. et al. Insight into the recent genome duplication of the halophilic yeast Hortaea werneckii: Combining an improved genome with gene expression and chromatin structure. G3 Genes, Genomes, Genet. 7, 2015–2022 (2017).

 

Wong, L. H. et al. Genome-wide screen reveals sec21 mutants of Saccharomyces cerevisiae are methotrexate-resistant. G3 Genes, Genomes, Genet. 7, 1251–1257 (2017).

 

Lee, A. H.-Y. et al. Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-Term chronic infection of cystic fibrosis lungs. Genome Res. 27, 650–662 (2017).

2016

 

Kwon, Y. et al. Lichen-forming fungus Caloplaca flavoruscens inhibits transcription factors and chromatin remodeling system in fungi. FEMS Microbiol. Lett. 363, 1–6 (2016).

 

Shekhar-Guturja, T. et al. Dual action antifungal small molecule modulates multidrug efflux and TOR signaling. Nat. Chem. Biol. 12, 867–875 (2016).

 

Kumar, A. et al. Novel anti-campylobacter compounds identified using high throughput screening of a pre-selected enriched small molecules library. Front. Microbiol. 7, (2016).

 

Szabat, M. et al. Reduced Insulin Production Relieves Endoplasmic Reticulum Stress and Induces β Cell Proliferation. Cell Metab. 23, 179–193 (2016).

 

Mell, J. C. et al. Transformed Recombinant Enrichment Profiling Rapidly Identifies HMW1 as an Intracellular Invasion Locus in Haemophilus influenza. PLoS Pathog. 12, (2016).

 

Nislow, C., Wong, L. H., Lee, A. H.-Y. & Giaever, G. Functional profiling using the Saccharomyces genome deletion project collections. Cold Spring Harb. Protoc. 2016, 802–808 (2016).

 

Kwon, Y. et al. Signaling pathways coordinating the alkaline pH response confer resistance to the hevein-type plant antimicrobial peptide Pn-AMP1 in Saccharomyces cerevisiae. Planta 244, 1229–1240 (2016).

 

Kennedy, M. A. et al. A Signaling Lipid Associated with Alzheimer’s Disease Promotes Mitochondrial Dysfunction. Sci. Rep. 6, (2016).

 

Jeyaraju, D. V et al. A novel isoflavone, ME-344, targets the cytoskeleton in acute myeloid leukemia. Oncotarget 7, 49777–49785 (2016).

 

Kwon, Y. et al. A chemogenomic approach to understand the antifungal action of Lichen-derived vulpinic acid. J. Appl. Microbiol. 121, 1580–1591 (2016).

 

Suresh, S. et al. Identification of chemical–genetic interactions via parallel analysis of barcoded yeast strains. Cold Spring Harb. Protoc. 2016, 812–820 (2016).

 

Williamson, A. E. et al. Open source drug discovery: Highly potent antimalarial compounds derived from the tres cantos arylpyrroles. ACS Cent. Sci. 2, 687–701 (2016).

 

Nislow, C., Wong, L. H., Lee, A. H.-Y. & Giaever, G. Functional genomics using the Saccharomyces cerevisiae yeast deletion collections. Cold Spring Harb. Protoc. 2016, 751–756 (2016).

 

Suresh, S. et al. Systematic mapping of chemical–genetic interactions in Saccharomyces cerevisiae. Cold Spring Harb. Protoc. 2016, 757–761 (2016).

 

Cha, J.-Y. et al. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. 10, 119–129 (2016).

 

Simoneau, A. et al. Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress. Nucleic Acids Res. 44, 2706–2726 (2016).

 

Mathew, M. D. et al. Using C. elegans Forward and Reverse Genetics to Identify New Compounds with Anthelmintic Activity. PLoS Negl. Trop. Dis. 10, (2016).

 

Wong, L. H. et al. Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions. PLoS Genet. 12, (2016).

 

Sze, M. A. et al. The bronchial epithelial cell bacterial microbiome and host response in patients infected with human immunodeficiency virus. BMC Pulm. Med. 16, (2016).

 

2015

Chandrashekhar, K. et al. Transcriptome analysis of Campylobacter jejuni polyphosphate kinase (ppk1 and ppk2) mutants. Virulence 6, 814–818 (2015).

 

Lim, G. E. et al. 14-3-3ζ coordinates adipogenesis of visceral fat. Nat. Commun. 6, (2015).

 

Kim, S. H. et al. Global Analysis of the Fungal Microbiome in Cystic Fibrosis Patients Reveals Loss of Function of the Transcriptional Repressor Nrg1 as a Mechanism of Pathogen Adaptation. PLoS Pathog. 11, (2015).

 

Larriba, E., Jaime, M. D. L. A., Nislow, C., Martín-Nieto, J. & Lopez-Llorca, L. V. Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response. J. Plant Res. 128, 665–678 (2015).

 

Xu, X. et al. Discovery of novel small molecule modulators of Clavibacter michiganensis subsp. michiganensis. Front. Microbiol. 6, (2015).

 

Burns, A. R. et al. Caenorhabditis elegans is a useful model for anthelmintic discovery. Nat. Commun. 6, (2015).

 

Mor, V. et al. Identification of a new class of antifungals targeting the synthesis of fungal sphingolipids. MBio 6, (2015).

 

Kofoed, M. et al. An updated collection of sequence barcoded temperature-sensitive alleles of yeast essential genes. G3 Genes, Genomes, Genet. 5, 1879–1887 (2015).

 

Hamza, A. et al. Complementation of yeast genes with human genes as an experimental platform for functional testing of human genetic variants. Genetics 201, 1263–1274 (2015).

 

Bernard, D. et al. Select microtubule inhibitors increase lysosome acidity and promote lysosomal disruption in acute myeloid leukemia (AML) cells. Apoptosis 20, 948–959 (2015).

 

Pandyra, A. A. et al. Genome-wide RNAi analysis reveals that simultaneous inhibition of specific mevalonate pathway genes potentiates tumor cell death. Oncotarget 6, 26909–26921 (2015).

 

Nislow, C. et al. Genes required for survival in microgravity revealed by genome-wide yeast deletion collections cultured during spaceflight. Biomed Res. Int. 2015, (2015).

 

Bose, R. N. et al. Absence of Activation of DNA Repair Genes and Excellent Efficacy of Phosphaplatins against Human Ovarian Cancers: Implications To Treat Resistant Cancers. J. Med. Chem. 58, 8387–8401 (2015).

 

2014

Liachko, I. et al. GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris. PLoS Genet. 10, (2014).

 

De Boer, C. G. et al. A unified model for yeast transcript definition. Genome Res. 24, 154–166 (2014).

 

Kittanakom, S. et al. CHIP-MYTH: A Novel Interactive Proteomics Method for the Assessment of Agonist-Dependent Interactions of the Human β₂-adrenergic Receptor. Biochem. Biophys. Res. Commun. 445, 746–756 (2014).

 

VanderSluis, B. et al. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. Genome Biol. 15, (2014).

 

Mell, J. C. et al. Complete genome sequence of Haemophilus influenzae strain 375 from the middle ear of a pediatric patient with otitis media. Genome Announc. 2, (2014).

 

Lee, A. Y. et al. Erratum for the report: ‘Mapping the cellular response to small molecules using chemogenomic fitness signatures’. Science (80-. ). 344, (2014).

 

Nile, A. H. et al. PITPs as targets for selectively interfering with phosphoinositide signaling in cells. Nat. Chem. Biol. 10, 76–84 (2014).

 

Cokol, M. et al. Large-scale identification and analysis of suppressive drug interactions. Chem. Biol. 21, 541–551 (2014).

 

Lee, A. Y. et al. Mapping the cellular response to small molecules using chemogenomic fitness signatures. Science (80-. ). 344, 208–211 (2014).

 

Giaever, G. & Nislow, C. The yeast deletion collection: A decade of functional genomics. Genetics 197, 451–465 (2014).

 

Arnoldo, A. et al. A genome scale overexpression screen to reveal drug activity in human cells. Genome Med. 6, (2014).

 

Larriba, E. et al. Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia. Fungal Genet. Biol. 65, 69–80 (2014).

 

2013

Warnecke, T., Becker, E. A., Facciotti, M. T., Nislow, C. & Lehner, B. Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution. PLoS Comput. Biol. 9, (2013).

 

Lenassi, M. et al. Whole Genome Duplication and Enrichment of Metal Cation Transporters Revealed by De Novo Genome Sequencing of Extremely Halotolerant Black Yeast Hortaea werneckii. PLoS One 8, (2013).

 

Wan, L. C. K. et al. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic Acids Res. 41, 6332–6346 (2013).

 

Hill, J. A., Ammar, R., Torti, D., Nislow, C. & Cowen, L. E. Genetic and Genomic Architecture of the Evolution of Resistance to Antifungal Drug Combinations. PLoS Genet. 9, (2013).

 

Lis, M. et al. Chemical genomic screening of a saccharomyces cerevisiae genomewide mutant collection reveals genes required for defense against four antimicrobial peptides derived from proteins found in human saliva. Antimicrob. Agents Chemother. 57, 840–847 (2013).

 

Tomson, B. N. et al. Effects of the Paf1 Complex and Histone Modifications on snoRNA 3′-End Formation Reveal Broad and Locus-Specific Regulation. Mol. Cell. Biol. 33, 170–182 (2013).

 

Srikumar, T. et al. Global analysis of SUMO chain function reveals multiple roles in chromatin regulation. J. Cell Biol. 201, 145–163 (2013).

 

Sukhai, M. A. et al. Lysosomal disruption preferentially targets acute myeloid leukemia cells and progenitors. J. Clin. Invest. 123, 315–328 (2013).

 

Lee, A. Y., Bader, G. D., Nislow, C. & Giaever, G. Chemogenomic Profiling: Understanding the Cellular Response to Drug. Handbook of Systems Biology (2013). doi:10.1016/B978-0-12-385944-0.00008-3

 

Lissina, E. et al. A novel small molecule methyltransferase is important for virulence in candida albicans. ACS Chem. Biol. 8, 2785–2793 (2013).

 

Cheung-Ong, K., Giaever, G. & Nislow, C. DNA-damaging agents in cancer chemotherapy: Serendipity and chemical biology. Chem. Biol. 20, 648–659 (2013).

 

Kittanakom, S. et al. Miniature short hairpin rna screens to characterize antiproliferative drugs. G3 Genes, Genomes, Genet. 3, 1375–1387 (2013).

 

van Bakel, H. et al. A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription. PLoS Genet. 9, (2013).

 

Torres, N. P., Lee, A. Y., Giaever, G., Nislow, C. & Brown, G. W. A high-throughput yeast assay identifies synergistic drug combinations. Assay Drug Dev. Technol. 11, 299–307 (2013).

 

2012

Chan, J. N. Y. et al. Target identification by chromatographic co-elution: Monitoring of drug-protein interactions without immobilization or chemical derivatization. Mol. Cell. Proteomics 11, (2012).

 

Tkach, J. M. et al. Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat. Cell Biol. 14, 966–976 (2012).

 

Onodera, N. T. et al. Genome sequence of shigella flexneri serotype 5a strain M90T Sm. J. Bacteriol. 194, 3022 (2012).

 

Klionsky, D. J. et al. Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8, 445–544 (2012).

 

Xu, M. et al. Timing of Transcriptional Quiescence during Gametogenesis Is Controlled by Global Histone H3K4 Demethylation. Dev. Cell 23, 1059–1071 (2012).

 

Singh-Babak, S. D. et al. A novel calcineurin-independent activity of cyclosporin A in Saccharomyces cerevisiae. Mol. Biosyst. 8, 2575–2584 (2012).

 

Orij, R. et al. Genome-wide analysis of intracellular pH reveals quantitative control of cell division rate by pH(c) in Saccharomyces cerevisiae. Genome Biol. 13, (2012).

 

Luciani, G. M. et al. Correction: Corrigendum: Dafadine inhibits DAF-9 to promote dauer formation and longevity of Caenorhabditis elegans. Nat. Chem. Biol. 8, 318 (2012).

 

Alfred, S. E. et al. A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis. Genome Biol. 13, R105 (2012).

 

Ryan, O. et al. Global gene deletion analysis exploring yeast filamentous growth. Science (80-. ). 337, 1352–1356 (2012).

 

Roemer, T., Davies, J., Giaever, G. & Nislow, C. Bugs, drugs and chemical genomics. Nat. Chem. Biol. 8, 46–56 (2012).

 

Cheung-Ong, K. et al. Comparative chemogenomics to examine the mechanism of action of DNA-targeted platinum-acridine anticancer agents. ACS Chem. Biol. 7, 1892–1901 (2012).

 

Douglas, A. C. et al. Functional analysis with a barcoder yeast gene overexpression system. G3 Genes, Genomes, Genet. 2, 1279–1289 (2012).

 

Smith, A. M., Durbic, T., Kittanakom, S., Giaever, G. & Nislow, C. Barcode sequencing for understanding drug-gene interactions. Methods Mol. Biol. 910, 55–69 (2012).

 

Ammar, R. et al. Chromatin is an ancient innovation conserved between Archaea and Eukarya. Elife 2012, (2012).

 

Jaime, M. D. L. A. et al. Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. BMC Genomics 13, (2012).

 

Tsui, K., Durbic, T., Gebbia, M. & Nislow, C. Genomic approaches for determining nucleosome occupancy in yeast. Methods Mol. Biol. 833, 389–411 (2012).

Shabtai, D., Giaever, G. & Nislow, C. An algorithm for chemical genomic profiling that minimizes batch effects: Bucket evaluations. BMC Bioinformatics 13, (2012).

 

Blackman, R. K. et al. Mitochondrial electron transport is the cellular target of the oncology drug Elesclomol. PLoS One 7, (2012).

 

2011

Ganapathi, M. et al. Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast. Nucleic Acids Res. 39, 2032–2044 (2011).

 

Gkikopoulos, T. et al. The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4. EMBO J. 30, 1919–1927 (2011).

 

Kurat, C. F. et al. Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein. Genes Dev. 25, 2489–2501 (2011).

 

van Bakel, H., Nislow, C., Blencowe, B. J. & Hughes, T. R. Response to ‘The reality of pervasive transcription’. PLoS Biol. 9, (2011).

 

Bendaha, H. et al. New azole antifungal agents with novel modes of action: Synthesis and biological studies of new tridentate ligands based on pyrazole and triazole. Eur. J. Med. Chem. 46, 4117–4124 (2011).

 

Tamble, C. M. et al. The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae. Mol. Biosyst. 7, 2019–2030 (2011).

 

Luciani, G. M. et al. Dafadine inhibits DAF-9 to promote dauer formation and longevity of Caenorhabditis elegans. Nat. Chem. Biol. 7, 891–893 (2011).

 

Berry, D. B. et al. Multiple means to the same end: The genetic basis of acquired stress resistance in yeast. PLoS Genet. 7, (2011).

 

Cokol, M. et al. Systematic exploration of synergistic drug pairs. Mol. Syst. Biol. 7, (2011).

 

Škrtić, M. et al. Inhibition of Mitochondrial Translation as a Therapeutic Strategy for Human Acute Myeloid Leukemia. Cancer Cell 20, 674–688 (2011).

 

Minear, S. et al. Curcumin inhibits growth of saccharomyces cerevisiae through iron chelation. Eukaryot. Cell 10, 1574–1581 (2011).

 

Klein, M. et al. Design, synthesis and characterization of a highly effective inhibitor for analog-sensitive (as) kinases. PLoS One 6, (2011).

 

Li, Z. et al. Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat. Biotechnol. 29, 361–367 (2011).

 

Wallace, I. M. et al. Compound prioritization methods increase rates of chemical probe discovery in model organisms. Chem. Biol. 18, 1273–1283 (2011).

 

Dinér, P. et al. Design, synthesis, and characterization of a highly effective Hog1 inhibitor: A powerful tool for analyzing map kinase signaling in yeast. PLoS One 6, (2011).

 

Suzuki, Y. et al. Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nat. Methods 8, 159–164 (2011).

 

Magtanong, L. et al. Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell. Nat. Biotechnol. 29, 505–511 (2011).

 

Ketela, T. et al. A comprehensive platform for highly multiplexed mammalian functional genetic screens. BMC Genomics 12, (2011).

 

Guan, Y. et al. Nucleosome-coupled expression differences in closely-related species. BMC Genomics 12, (2011).

 

Oh, J. & Nislow, C. Signature-tagged mutagenesis to characterize genes through competitive selection of bar-coded genome libraries. Methods Mol. Biol. 765, 225–252 (2011).

 

Lissina, E. et al. A systems biology approach reveals the role of a novel methyltransferase in response to chemical stress and lipid homeostasis. PLoS Genet. 7, (2011).

 

Tsui, K. et al. Evolution of nucleosome occupancy: Conservation of global properties and divergence of gene-specific patterns. Mol. Cell. Biol. 31, 4348–4355 (2011).

 

Hoon, S. et al. A global perspective of the genetic basis for carbonyl stress resistance. G3 Genes, Genomes, Genet. 1, 219–231 (2011).

 

Wallace, I. M., Bader, G. D., Giaever, G. & Nislow, C. Displaying chemical information on a biological network using cytoscape. Methods Mol. Biol. 781, 363–376 (2011).

 

Proctor, M. et al. The automated cell: Compound and environment screening system (ACCESS) for chemogenomic screening. Methods Mol. Biol. 759, 239–269 (2011).

 

Smith, A. M. et al. Competitive genomic screens of barcoded yeast libraries. J. Vis. Exp. (2011).

 

2010

Longo, V. D., Nislow, C. & Fabrizio, P. Endosomal protein sorting and autophagy genes contribute to the regulation of yeast life span. Autophagy 6, 1227–1228 (2010).

 

Vizeacoumar, F. J. et al. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J. Cell Biol. 188, 69–81 (2010).

 

Chan, J. N. Y., Nislow, C. & Emili, A. Recent advances and method development for drug target identification. Trends Pharmacol. Sci. 31, 82–88 (2010).

 

van Bakel, H., Nislow, C., Blencowe, B. J. & Hughes, T. R. Most ‘dark matter’ transcripts are associated with known genes. PLoS Biol. 8, (2010).

 

Smith, A. M., Ammar, R., Nislow, C. & Giaever, G. A survey of yeast genomic assays for drug and target discovery. Pharmacol. Ther. 127, 156–164 (2010).

 

Ericson, E., Hoon, S., St Onge, R. P., Giaever, G. & Nislow, C. Exploring gene function and drug action using chemogenomic dosage assays. Methods Enzymol. 470, 233–255 (2010).

 

Burns, A. R. et al. A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans. Nat. Chem. Biol. 6, 549–557 (2010).

 

Dowell, R. D. et al. Genotype to phenotype: A Complex problem. Science (80-. ). 328, 469 (2010).

 

Costanzo, M. et al. The genetic landscape of a cell. Science (80-. ). 327, 425–431 (2010).

 

Smith, A. M. et al. Highly-multiplexed barcode sequencing: An efficient method for parallel analysis of pooled samples. Nucleic Acids Res. 38, e142–e142 (2010).

 

Berbenetz, N. M., Nislow, C. & Brown, G. W. Diversity of Eukaryotic DNA replication origins revealed by Genome-wide analysis of chromatin structure. PLoS Genet. 6, (2010).

 

Fabrizio, P. et al. Genome-wide screen in Saccharomyces cerevisiae identifies vacuolar protein sorting, autophagy, biosynthetic, and tRNA methylation genes involved in life span regulation. PLoS Genet. 6, 1–14 (2010).

 

Hillenmeyer, M. E. et al. Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action. Genome Biol. 11, (2010).

 

Oh, J. et al. Gene annotation and drug target discovery in candida albicans with a tagged transposon mutant collection. PLoS Pathog. 6, (2010).

 

Oh, J. et al. A universal tagmodule collection for parallel genetic analysis of microorganisms. Nucleic Acids Res. 38, e146–e146 (2010).

 

2009

Costanzo, M., Baryshnikova, A., Nislow, C., Andrews, B. & Boone, C. You too can play with an edge. Nat. Methods 6, 797–798 (2009).

 

Fillingham, J. et al. Two-Color Cell Array Screen Reveals Interdependent Roles for Histone Chaperones and a Chromatin Boundary Regulator in Histone Gene Repression. Mol. Cell 35, 340–351 (2009).

 

Juneau, K., Nislow, C. & Davis, R. W. Alternative splicing of PTC7 in Saccharomyces cerevisiae determines protein localization. Genetics 183, 185–194 (2009).

 

Ho, C. H. et al. A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds. Nat. Biotechnol. 27, 369–377 (2009).

 

Hess, D. C. et al. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet. 5, (2009).

 

Pierce, S. E., Davis, R. W., Nislow, C. & Giaever, G. Chemogenomic approaches to elucidation of gene function and genetic pathways. Methods Mol. Biol. 548, 115–143 (2009).

 

Jo, W. J. et al. Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae. BMC Genomics 10, (2009).

 

Smith, A. M. et al. Quantitative phenotyping via deep barcode sequencing. Genome Res. 19, 1836–1842 (2009).

 

Kemmer, D. et al. Combining chemical genomics screens in yeast to reveal spectrum of effects of chemical inhibition of sphingolipid biosynthesis. BMC Microbiol. 9, (2009).

 

Ammar, R., Smith, A. M., Heisler, L. E., Giaever, G. & Nislow, C. A comparative analysis of DNA barcode microarray feature size. BMC Genomics 10, 471 (2009).

 

Yan, Z., Berbenetz, N. M., Giaever, G. & Nislow, C. Precise gene-dose alleles for chemical genetics. Genetics 182, 623–626 (2009).

 

Giaever, G. & Nislow, C. Knocking sense into regulatory pathways. Nat. Biotechnol. 27, 149–150 (2009).

 

Nislow, C. Self-reporting cells. Biotechniques 46, 356–357 (2009).

 

2008

Badis, G. et al. A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters. Mol. Cell 32, 878–887 (2008).

 

Jo, W. J. et al. Identification of genes involved in the toxic response of saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants. Toxicol. Sci. 101, 140–151 (2008).

 

Yan, Z. et al. Yeast Barcoders: A chemogenomic application of a universal donor-strain collection carrying bar-code identifiers. Nat. Methods 5, 719–725 (2008).

 

Hillenmeyer, M. E. et al. The chemical genomic portrait of yeast: Uncovering a phenotype for all genes. Science (80-. ). 320, 362–365 (2008).

 

Mani, R., St. Onge, R. P., Hartman IV, J. L., Giaever, G. & Roth, F. P. Defining genetic interaction. Proc. Natl. Acad. Sci. U. S. A. 105, 3461–3466 (2008).

 

Dueck, D. et al. Constructing treatment portfolios using affinity propagation. Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics) 4955 LNBI, 360–371 (2008).

 

Musso, G. et al. The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res. 18, 1092–1099 (2008).

 

Lopez, A., Parsons, A. B., Nislow, C., Giaever, G. & Boone, C. Chemical-genetic approaches for exploring the mode of action of natural products. Prog. Drug Res. 66, 237–271 (2008).

 

Arnoldo, A. et al. Identification of small molecule inhibitors of Pseudomonas aeruginosa exoenzyme S using a yeast phenotypic screen. PLoS Genet. 4, (2008).

 

Hoon, S., St.Onge, R. P., Giaever, G. & Nislow, C. Yeast chemical genomics and drug discovery: an update. Trends Pharmacol. Sci. 29, 499–504 (2008).

 

Lehár, J., Stockwell, B. R., Giaever, G. & Nislow, C. Combination chemical genetics. Nat. Chem. Biol. 4, 674–681 (2008).

 

Yu, L. et al. Chemical-genetic profiling of imidazo[1,2-a]pyridines and -pyrimidines reveals target pathways conserved between yeast and human cells. PLoS Genet. 4, (2008).

 

Ericson, E. et al. Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet. 4, (2008).

 

Hoon, S. et al. An integrated platform of genomic assays reveals small-molecule bioactivities. Nat. Chem. Biol. 4, 498–506 (2008).

 

2007

Suter, B. et al. Examining protein-protein interactions using endogenously tagged yeast arrays: The Cross-and-Capture system. Genome Res. 17, 1774–1782 (2007).

 

Doostzadeh, J., Davis, R. W., Giaever, G. N., Nislow, C. & Langston, J. W. Chemical genomic profiling for identifying intracellular targets of toxicants producing parkinson’s disease. Toxicol. Sci. 95, 182–187 (2007).

 

Nislow, C. & Giaever, G. 17 Chemical Genomic Tools for Understanding Gene Function and Drug Action. Methods Microbiol. 36, 387-"414,708-709" (2007).

 

Pierce, S. E., Davis, R. W., Nislow, C. & Giaever, G. Genome-wide analysis of barcoded saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat. Protoc. 2, 2958–2974 (2007).

 

Gassner, N. C. et al. Accelerating the discovery of biologically active small molecules using a high-throughput yeast halo assay. J. Nat. Prod. 70, 383–390 (2007).

 

Onge, R. P. S. et al. Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nat. Genet. 39, 199–206 (2007).

 

Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat. Genet. 39, 1235–1244 (2007).

 

2006

Juneau, K., Miranda, M., Hillenmeyer, M. E., Nislow, C. & Davis, R. W. Introns regulate RNA and protein abundance in yeast. Genetics 174, 511–518 (2006).

 

Wall, D. P. et al. Erratum: Functional genomic analysis of the rates of protein evolution. Proc. Natl. Acad. Sci. U. S. A. 103, 7935 (2006).

 

Costanzo, M., Giaever, G., Nislow, C. & Andrews, B. Experimental approaches to identify genetic networks. Curr. Opin. Biotechnol. 17, 472–480 (2006).

 

Pierce, S. E. et al. A unique and universal molecular barcode array. Nat. Methods 3, 601–603 (2006).

 

2005

Wall, D. P. et al. Functional genomic analysis of the rates of protein evolution. Proc. Natl. Acad. Sci. U. S. A. 102, 5483–5488 (2005).

 

Deutschbauer, A. M. et al. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169, 1915–1925 (2005).

 

Lee, W. et al. Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet. 1, 235–246 (2005).

 

Flaherty, P., Giaever, G., Kumm, J., Jordan, M. I. & Arkin, A. P. A latent variable model for chemogenomic profiling. Bioinformatics 21, 3286–3293 (2005).

 

2004

Giaever, G. et al. Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast. Proc. Natl. Acad. Sci. U. S. A. 101, 793–798 (2004).

 

Fraser, H. B., Hirsh, A. E., Giaever, G., Kumm, J. & Eisen, M. B. Noise minimization in eukaryotic gene expression. PLoS Biol. 2, (2004).

 

2003

Giaever, G. A chemical genomics approach to understanding drug action. Trends Pharmacol. Sci. 24, 444–446 (2003).

 

Nislow, C. & Giaever, G. ‘Chemogenomics: Tools for protein families’ and ‘chemical genomics: Chemical and biological integration’. Pharmacogenomics 4, 15–18 (2003).

 

2002

Birrell, G. W. et al. Transcriptional response of saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc. Natl. Acad. Sci. U. S. A. 99, 8778–8783 (2002).

 

Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).

 

Steinmetz, L. M. et al. Systematic screen for human disease genes in yeast. Nat. Genet. 31, 400–404 (2002).

 

2001

Birrell, G. W., Giaever, G., Chu, A. M., Davis, R. W. & Brown, J. M. A genome-wide screen in Saccharomyces cerevisiae for genes affecting UV radiation sensitivity. Proc. Natl. Acad. Sci. U. S. A. 98, 12608–12613 (2001).

 

1999

Giaever, G. et al. Genomic profiling of drug sensitivities via induced haploinsufficiency. Nat. Genet. 21, 278–283 (1999).

 

Male, T., Feder, J., Giaever, G. N. & Giaever, I. Oscillations in yeast observed electrically. Biol. Rhythm Res. 30, 361–370 (1999).

 

Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (80-. ). 285, 901–906 (1999).

 

1997

Nislow, C., Ray, E. & Pillus, L. SET1, a yeast member of the Trithorax family, functions in transcriptional silencing and diverse cellular processes. Mol. Biol. Cell 8, 2421–2436 (1997).

 

Laible, G. et al. Mammalian homologues of the Polycomb-group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at S. cerevisiae telomeres. EMBO J. 16, 3219–3232 (1997).

 

1995

Lombillo, V. A., Nislow, C., Yen, T. J., Gelfand, V. I. & McIntosh, J. R. Antibodies to the kinesin motor domain and CENP-E inhibit microtubule depolymerization-dependent motion of chromosomes in vitro. J. Cell Biol. 128, 107–115 (1995).

 

1992

Nislow, C., Lombillo, V. A., Kuriyama, R. & McIntosh, J. R. A plus-end-directed motor enzyme that moves antiparallel microtubules in vitro localizes to the interzone of mitotic spindles. Nature 359, 543–547 (1992).

 

Kuriyama, R. & Nislow, C. Molecular components of the mitotic spindle. BioEssays 14, 81–88 (1992).

 

1991

Klymkowsky, M. W., Maynell, L. A. & Nislow, C. Cytokeratin phosphorylation, cytokeratin filament severing and the solubilization of the maternal mRNA Vg1. J. Cell Biol. 114, 787–797 (1991).

 

1988

Urben, S., Nislow, C. & Spiegel, M. The origin of skeleton forming cells in the sea urchin embryo. Roux’s Arch. Dev. Biol. 197, 447–456 (1988).

 

NISLOW, C. & MORRILL, J. B. Regionalized Cell Division during Sea Urchin Gastrulation Contributes to Archenteron Formation and Is Correlated with the Establishment of Larval Symmetry. Dev. Growth & Differ. 30, 483–499 (1988).

 

Giaever, G. N., Snyder, L. & Wang, J. C. DNA supercoiling in vivo. Biophys. Chem. 29, 7–15 (1988).

 

Giaever, G. N. & Wang, J. C. Supercoiling of intracellular DNA can occur in eukaryotic cells. Cell 55, 849–856 (1988).

 

Wang, J. C. & Giaever, G. N. Action at a distance along a DNA. Science (80-. ). 240, 300–304 (1988).

 

1986

Lynn, R., Giaever, G., Swanberg, S. L. & Wang, J. C. Tandem regions of yeast DNA topoisomerase II share homology with different subunits of bacterial gyrase. Science (80-. ). 233, 647–649 (1986).

 

Giaever, G., Lynn, R., Goto, T. & Wang, J. C. The complete nucleotide sequence of the structural gene TOP2 of yeast DNA topoisomerase II. J. Biol. Chem. 261, 12448–12454 (1986).