Regulatory Networks Revealed by Transcriptional Profiling of Damaged Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with Proteasomes

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

DNA Repair and Mutagenesis

Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. (2005) · doi:10.1128/9781555816704 · Cited by 5,683 · 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

Comprehensive Identification of Cell Cycle–regulated Genes of the YeastSaccharomyces cerevisiaeby Microarray Hybridization

Spellman, P. T., Sherlock, G. J., Zhang, M. Q., Iyer, V. R., Anders, K. R., Eisen, M. B., Brown, P. O., Botstein, D., & Futcher, B. (1998) · Molecular Biology of the Cell · doi:10.1091/mbc.9.12.3273 · Cited by 4,724 · see citing works

Checkpoints: Controls That Ensure the Order of Cell Cycle Events

Hartwell, L. H., & Weinert, T. A. (1989) · Science · doi:10.1126/science.2683079 · Cited by 3,053 · see citing works

Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation

Tamayo, P., Slonim, D. K., Mesirov, J. P., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S., & Golub, T. R. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.6.2907 · Cited by 2,924 · see citing works

Systematic determination of genetic network architecture

Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J., & Church, G. M. (1999) · Nature Genetics · doi:10.1038/10343 · Cited by 2,509 · see citing works

DNA repair and mutagenesis

Bootsma, D., & Hoeijmakers, J. H. J. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)81408-9 · Cited by 2,286 · see citing works

Cell Cycle Checkpoints: Preventing an Identity Crisis

Elledge, S. J. (1996) · Science · doi:10.1126/science.274.5293.1664 · Cited by 2,047 · see citing works

A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle

Cho, R. J., Campbell, M. J., Winzeler, E. A., Steinmetz, L. M., Conway, A. R., Wodicka, L. M., Wolfsberg, T. G., Gabrielian, A. E., Landsman, D., Lockhart, D. J., et al. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80114-8 · Cited by 2,024 · see citing works

The Transcriptional Program of Sporulation in Budding Yeast

Chu, S., DeRisi, J. L., Eisen, M. B., Mulholland, J., Botstein, D., Brown, P. O., & Herskowitz, I. (1998) · Science · doi:10.1126/science.282.5389.699 · Cited by 1,860 · see citing works

DNA Damage Produced by Ionizing Radiation in Mammalian Cells: Identities, Mechanisms of Formation, and Reparability

Ward, J. F. (1988) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60611-x · Cited by 1,499 · see citing works

The RAD9 Gene Controls the Cell Cycle Response to DNA Damage in Saccharomyces cerevisiae

Weinert, T. A., & Hartwell, L. H. (1988) · Science · doi:10.1126/science.3291120 · Cited by 1,171 · see citing works

Genome-wide expression monitoring in Saccharomyces cerevisiae

Wodicka, L. M., Dong, H., Mittmann, M., Ho, M.-H., & Lockhart, D. J. (1997) · Nature Biotechnology · doi:10.1038/nbt1297-1359 · Cited by 973 · see citing works

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

Roth, F. P., Hughes, J. D., Estep, P. W., & Church, G. M. (1998) · Nature Biotechnology · doi:10.1038/nbt1098-939 · Cited by 939 · see citing works

Heat shock factors and the control of the stress response

SANTORO, M. G. (2000) · Biochemical Pharmacology · doi:10.1016/s0006-2952(99)00299-3 · Cited by 581 · see citing works

The Regulatory Particle of the Saccharomyces cerevisiae Proteasome

Glickman, M. H., Rubin, D. M., Fried, V. A., & Finley, D. J. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.6.3149 · Cited by 484 · see citing works

Rad23 links DNA repair to the ubiquitin/proteasome pathway

Schauber, C., Chen, L., Tongaonkar, P., Vega, I. E., Lambertson, D., Potts, W., & Madura, K. (1998) · Nature · doi:10.1038/35661 · Cited by 457 · see citing works

Global response of <i>Saccharomyces cerevisiae</i> to an alkylating agent

Jelinsky, S. A., & Samson, L. D. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.4.1486 · Cited by 419 · see citing works

Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast

Mannhaupt, G., Schnall, R., Карпов, В. Л., Vetter, I., & Feldmann, H. (1999) · FEBS Letters · doi:10.1016/s0014-5793(99)00467-6 · Cited by 322 · see citing works

Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding.Preprint

McNabb, D., Xing, Y., & Guarente, L. (1995) · Genes & Development · doi:10.1101/gad.9.1.47 · Cited by 290 · see citing works

A transcriptional switch in the expression of yeast tricarboxylic acid cycle genes in response to a reduction or loss of respiratory function

Liu, Z., & Butow, R. A. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.10.6720 · Cited by 290 · see citing works

The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information

Costanzo, M. C. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.73 · Cited by 288 · see citing works

Endogenous DNA adducts: Potential and paradox

Marnett, L. J., & Burcham, P. C. (1993) · Chemical Research in Toxicology · doi:10.1021/tx00036a005 · Cited by 281 · see citing works

Sensing and responding to DNA damage

Lowndes, N. F., & Murguía, J. R. (2000) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(99)00050-7 · Cited by 269 · see citing works

Genome-Wide Transcriptional Analysis of Aerobic and Anaerobic Chemostat Cultures of Saccharomyces cerevisiae

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

Cell Cycle Control, Checkpoint Mechanisms, and Genotoxic Stress

Shackelford, R. E., Kaufmann, W. K., & Paules, R. S. (1999) · Environmental Health Perspectives · doi:10.1289/ehp.99107s15 · Cited by 261 · see citing works

Reconstitution of Yeast Nucleotide Excision Repair with Purified Rad Proteins, Replication Protein A, and Transcription Factor TFIIH

Guzder, S. N., Habraken, Y., Sung, P., Prakash, L., & Prakash, S. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.22.12973 · Cited by 241 · see citing works

The 19S Regulatory Complex of the Proteasome Functions Independently of Proteolysis in Nucleotide Excision Repair

Russell, S. J., Reed, S. H., Huang, W., Friedberg, E. C., & Johnston, S. A. (1999) · Molecular Cell · doi:10.1016/s1097-2765(01)80001-0 · Cited by 197 · see citing works

Saccharomyces cerevisiae 3‐methyladenine DNA glycosylase has homology to the AlkA glycosylase of E. coli and is induced in response to DNA alkylation damage.

Chen, J., Derfler, B. H., & Samson, L. D. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07910.x · Cited by 144 · see citing works

Transcriptional Elements Involved in the Repression of Ribosomal Protein Synthesis

Li, B., Nierras, C. R., & Warner, J. R. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.8.5393 · Cited by 117 · see citing works

The ABF1 factor is the transcriptional activator of the L2 ribosomal protein genes in Saccharomyces cerevisiae.

Seta, F. D., Ciafrè, S. A., Marck, C., Santoro, B., Presutti, C., Sentenac, A., & Bozzoni, I. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.5.2437 · Cited by 113 · see citing works

RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III)

Déquard-Chablat, M., Riva, M., Carles, C., & Sentenac, A. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)98616-3 · Cited by 111 · see citing works

DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences.

Lascaris, R., Mager, W. H., & Planta, R. J. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.4.267 · Cited by 100 · see citing works

Integrating functional genomic information into the Saccharomyces Genome Database

Ball, C. A. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.77 · Cited by 100 · see citing works

Coupling of cell identity to signal response in yeast: interaction between the alpha 1 and STE12 proteins.Preprint

Yuan, Y. O., Stroke, I. L., & Fields, S. (1993) · Genes & Development · doi:10.1101/gad.7.8.1584 · Cited by 78 · see citing works

Replication protein A binds to regulatory elements in yeast DNA repair and DNA metabolism genes.

Singh, K. K., & Samson, L. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.11.4907 · Cited by 60 · see citing works

Son1p is a component of the 26S proteasome of the yeast Saccharomyces cerevisiae

Fujimuro, M., Tanaka, K., Yokosawa, H., & Toh‐e, A. (1998) · FEBS Letters · doi:10.1016/s0014-5793(98)00084-2 · Cited by 58 · see citing works

A common element involved in transcriptional regulation of two DNA alkylation repair genes (MAG and MGT1) of Saccharomyces cerevisiae.

Xiao, W., Singh, K. K., Chen, B., & Samson, L. D. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.12.7213 · Cited by 53 · see citing works

Induction ofS.cerevisiae MAG3-methyladenine DNA glycosylase transcript levels in response to DNA damage

Chen, J., & Samson, L. D. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.23.6427 · Cited by 45 · see citing works

Promoter elements of the PHR1 gene of Saccharomyces cerevisiae and their roles in the response to DNA damage

Sancar, G. B., Ferris, R. G., Smith, F. W., & Berg, B. J. V. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.21.4320 · Cited by 19 · see citing works

A Common Element Involved in Transcriptional Regulation of Two DNA Alkylation Repair Genes ( MAG and MGT1 ) of Saccharomyces cerevisiae

Xiao, W., Singh, K. K., Chen, B., & Samson, L. D. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.12.7213-7221.1993 · Cited by 14 · see citing works

The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction

Glickman, M. H., & Ciechanover, A. J. (2002) · Physiological Reviews · doi:10.1152/physrev.00027.2001 · Cited by 4,216 · see citing works

ATM and related protein kinases: safeguarding genome integrity

Shiloh, Y. (2003) · Nature Reviews Cancer · doi:10.1038/nrc1011 · Cited by 2,577 · see citing works

"Stemness": Transcriptional Profiling of Embryonic and Adult Stem Cells

Ramalho‐Santos, M., Yoon, S., Matsuzaki, Y., Mulligan, R. C., & Melton, D. A. (2002) · Science · doi:10.1126/science.1072530 · Cited by 1,711 · see citing works

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

Cliften, P. F., Sudarsanam, P., Desikan, A., Fulton, L. A., Fulton, B., Majors, J. E., Waterston, R., Cohen, B. A., & Johnston, M. (2003) · Science · doi:10.1126/science.1084337 · Cited by 805 · 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

Identifying regulatory networks by combinatorial analysis of promoter elements

Pilpel, Y., Sudarsanam, P., & Church, G. M. (2001) · Nature Genetics · doi:10.1038/ng724 · Cited by 653 · see citing works

“Sleeping Beauty”: Quiescence in Saccharomyces cerevisiae

Gray, J. V., Petsko, G. A., Johnston, G. C., Ringe, D., Singer, R. A., & Werner‐Washburne, M. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.2.187-206.2004 · Cited by 573 · see citing works

Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae

Ge, H., Liu, Z., Church, G. M., & Vidal, M. (2001) · Nature Genetics · doi:10.1038/ng776 · Cited by 575 · see citing works

Genomic Expression Responses to DNA-damaging Agents and the Regulatory Role of the Yeast ATR Homolog Mec1p

Gasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J., & Brown, P. O. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.10.2987 · Cited by 542 · see citing works

Regulation of proteasome activity in health and disease

Schmidt, M., & Finley, D. J. (2013) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2013.08.012 · Cited by 461 · see citing works

The genomics of yeast responses to environmental stress and starvation

Gasch, A. P., & Werner‐Washburne, M. (2002) · Functional & Integrative Genomics · doi:10.1007/s10142-002-0058-2 · Cited by 448 · see citing works

RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: A negative feedback circuit

Xie, Y., & Varshavsky, A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.071022298 · Cited by 436 · see citing works

Toxicology and genetic toxicology in the new era of “toxicogenomics”: impact of “-omics” technologies

Aardema, M. J., & MacGregor, J. T. (2002) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/s0027-5107(01)00292-5 · Cited by 390 · see citing works

Gcn4p, a Master Regulator of Gene Expression, Is Controlled at Multiple Levels by Diverse Signals of Starvation and Stress

Hinnebusch, A. G., & Natarajan, K. (2002) · Eukaryotic Cell · doi:10.1128/ec.01.1.22-32.2002 · Cited by 383 · see citing works

CLICK and EXPANDER: a system for clustering and visualizing gene expression data

Sharan, R., Maron‐Katz, A., & Ron Shamir, A. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg232 · Cited by 369 · see citing works

Genes required for ionizing radiation resistance in yeast

Bennett, C. B., Lewis, L. K., Karthikeyan, G., Lobachev, K. S., Jin, Y. H., Sterling, J. F., Snipe, J. R., & Resnick, M. A. (2001) · Nature Genetics · doi:10.1038/ng778 · Cited by 328 · see citing works

Trm9-Catalyzed tRNA Modifications Link Translation to the DNA Damage Response

Begley, U., Dyavaiah, M., Patil, A., Rooney, J. P., DiRenzo, D. M., Young, C. M., Conklin, D. S., Zitomer, R. S., & Begley, T. J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.021 · Cited by 325 · see citing works

PA200, a nuclear proteasome activator involved in DNA repair

Ustrell, V., Hoffman, L., Pratt, G., & Rechsteiner, M. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf333 · Cited by 325 · see citing works

Elucidating mechanisms of drug-induced toxicity

Liebler, D. C., & Guengerich, F. P. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1720 · Cited by 324 · see citing works

Transitive functional annotation by shortest-path analysis of gene expression data

Zhou, X. J., Kao, M. J., & Wong, W. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.192159399 · Cited by 323 · see citing works

Judging the Quality of Gene Expression-Based Clustering Methods Using Gene AnnotationPreprint

Gibbons, F. D., & Roth, F. P. (2002) · Genome Research · doi:10.1101/gr.397002 · Cited by 322 · see citing works

A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age

Close, T. J., Wanamaker, S. I., Caldo, R. A., Turner, S. M., Ashlock, D., Dickerson, J. A., Wing, R. A., Muehlbauer, G. J., Kleinhofs, A., & Wise, R. P. (2004) · PLANT PHYSIOLOGY · doi:10.1104/pp.103.034462 · Cited by 312 · see citing works

Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human CellsPreprint

Elkon, R., Linhart, C., Sharan, R., Ron Shamir, A., & Shiloh, Y. (2003) · Genome Research · doi:10.1101/gr.947203 · Cited by 297 · see citing works

Degradation-Mediated Protein Quality Control in the Nucleus

Gardner, R. G., Nelson, Z. W., & Gottschling, D. E. (2005) · Cell · doi:10.1016/j.cell.2005.01.016 · Cited by 280 · see citing works

Stt4 PI 4-Kinase Localizes to the Plasma Membrane and Functions in the Pkc1-Mediated MAP Kinase Cascade

Audhya, A., & Emr, S. D. (2002) · Developmental Cell · doi:10.1016/s1534-5807(02)00168-5 · Cited by 277 · see citing works

A Systems Approach to Mapping DNA Damage Response Pathways

Workman, C. T., Mak, H. C., McCuine, S., Tagne, J., Agarwal, M., Ozier, O. W., Begley, T. J., Samson, L. D., & Ideker, T. E. (2006) · Science · doi:10.1126/science.1122088 · Cited by 268 · see citing works

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiaePreprint

Horak, C. E., Luscombe, N. M., Qian, J. X., Bertone, P., Piccirillo, S., Gerstein, M., & Snyder, M. P. (2002) · Genes & Development · doi:10.1101/gad.1039602 · Cited by 259 · see citing works

Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents

Birrell, G. W., Brown, J. A. L., Wu, H. I., Giaever, G. N., Chu, A. M., Davis, R. W., & Brown, J. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.132275199 · Cited by 255 · see citing works

Sulfur Sparing in the Yeast Proteome in Response to Sulfur Demand

Fauchon, M., Lagniel, G., Aude, J.-C., Lombardía, L., Soularue, P., Petat, C., Marguerie, G. A., Sentenac, A., Werner, M., & Labarre, J. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00500-2 · Cited by 249 · see citing works

Elevated Proteasome Capacity Extends Replicative Lifespan in Saccharomyces cerevisiae

Krügel, U., Robison, B., Dange, T., Kahlert, G., Delaney, J. R., Kotireddy, S., Tsuchiya, M., Tsuchiyama, S. K., Murakami, C. J., Schleit, J., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002253 · Cited by 243 · see citing works

Protein Damage by Reactive Electrophiles: Targets and Consequences

Liebler, D. C. (2007) · Chemical Research in Toxicology · doi:10.1021/tx700235t · Cited by 235 · see citing works

Functional Division of Substrate Processing Cofactors of the Ubiquitin-Selective Cdc48 Chaperone

Rumpf, S., & Jentsch, S. (2006) · Molecular Cell · doi:10.1016/j.molcel.2005.12.014 · Cited by 236 · see citing works

Reproducibility of Oligonucleotide Microarray Transcriptome Analyses

Piper, M. D. W., Daran-Lapujade, P. A. S., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J., & Pronk, J. T. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m204490200 · Cited by 236 · see citing works

Over 1000 genes are involved in the DNA damage response of Escherichia coli

Khil, P. P., & Camerini‐Otero, R. D. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02878.x · Cited by 234 · see citing works

A Rad26–Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage

Woudstra, E. C., Gilbert, C., Fellows, J., Jansen, L. E. T., Brouwer, J., Erdjument‐Bromage, H., Tempst, P., & Svejstrup, J. Q. (2002) · Nature · doi:10.1038/415929a · Cited by 234 · see citing works

Transcriptional Regulation in Yeast during Diauxic Shift and Stationary Phase

Galdieri, L. C., Mehrotra, S., Yu, S., & Vančura, A. (2010) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2010.0069 · Cited by 227 · see citing works

Genomic and proteomic profiling of responses to toxic metals in human lung cells.

Andrew, A. S., Warren, A. J., Barchowsky, A., Temple, K. A., Klei, L. R., Soucy, N. V., O’Hara, K. A., & Hamilton, J. W. (2003) · Environmental Health Perspectives · doi:10.1289/ehp.111-1241504 · Cited by 222 · see citing works

Normal hemostasis but defective hematopoietic response to growth factors in mice deficient in phospholipid scramblase 1

Zhou, Q., Zhao, J., Wiedmer, T., & Sims, P. J. (2002) · Blood · doi:10.1182/blood-2001-12-0271 · Cited by 219 · see citing works

Evaluation of genotoxic risk and oxidative DNA damage in mammalian cells exposed to mycotoxins, patulin and citrinin

Liu, B.-H., Yu, F., Wu, T., Li, S., Su, M., Wang, M.-C., & Shih, S.-M. (2003) · Toxicology and Applied Pharmacology · doi:10.1016/s0041-008x(03)00254-0 · Cited by 200 · see citing works

Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341

Fleming, J., Lightcap, E. S., Sadis, S., Thoroddsen, V., Bulawa, C., & Blackman, R. K. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032516399 · Cited by 198 · see citing works

Enzymology of the repair of free radicals-induced DNA damage

Gros, L., Saparbaev, M. K., & Laval, J. (2002) · Oncogene · doi:10.1038/sj.onc.1206005 · Cited by 196 · see citing works

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation

Shalem, O., Dahan, O., Levo, M., Martínez, M. R., Furman, I., Segal, E., & Pilpel, Y. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.59 · Cited by 194 · see citing works

ORMDL proteins are a conserved new family of endoplasmic reticulum membrane proteins

Hjelmqvist, L., Tuson, M., Marfany, G., Herrero, E., Balcells, S., & Gonzàlez‐Duarte, R. (2002) · Genome biology · doi:10.1186/gb-2002-3-6-research0027 · Cited by 192 · see citing works

Aft1p and Aft2p Mediate Iron-responsive Gene Expression in Yeast through Related Promoter Elements

Rutherford, J. C., Jaron, S., & Winge, D. R. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m300076200 · Cited by 192 · see citing works

Integrating phenotypic and expression profiles to map arsenic-response networks

Haugen, A. C., Kelley, R., Collins, J. B., Tucker, C. J., Deng, C., Afshari, C. A., Brown, J. M., Ideker, T. E., & Houten, B. V. (2004) · Genome biology · doi:10.1186/gb-2004-5-12-r95 · Cited by 186 · see citing works

Endogenous DNA damage and mutation

Marnett, L. J. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02239-9 · Cited by 183 · see citing works

Deciphering gene expression regulatory networks

Wyrick, J. J., & Young, R. A. (2002) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(02)00277-0 · Cited by 179 · see citing works

Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activationPreprint

白髭, 克., Doksani, Y., Capra, T., Katou, Y.-M., Tanaka, H., Shirahige, K., & Foiani, M. (2007) · Genes & Development · doi:10.1101/gad.432107 · Cited by 178 · see citing works

A proteasome for all occasions

Hanna, J. W., & Finley, D. J. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.03.053 · Cited by 178 · see citing works

Proteasome-associated proteins: regulation of a proteolytic machine

Schmidt, M., Hanna, J. W., Elsasser, S., & Finley, D. J. (2005) · Biological Chemistry · doi:10.1515/bc.2005.085 · Cited by 171 · see citing works

Characterization of a Six-Subunit Holo-Elongator Complex Required for the Regulated Expression of a Group of Genes in Saccharomyces cerevisiae

Krogan, N. J., & Greenblatt, J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.23.8203-8212.2001 · Cited by 170 · see citing works

Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping.

Begley, T. J., Rosenbach, A., Ideker, T. E., & Samson, L. D. (2002) · PubMed · Cited by 163 · see citing works

A second iron-regulatory system in yeast independent of Aft1p

Rutherford, J. C., Jaron, S., Ray, E., Brown, P. O., & Winge, D. R. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.261381198 · Cited by 153 · see citing works

General Statistics of Stochastic Process of Gene Expression in Eukaryotic Cells

Kuznetsov, V. A., Knott, G. D., & Bonner, R. F. (2002) · Genetics · doi:10.1093/genetics/161.3.1321 · Cited by 151 · see citing works

The ubiquitin receptor Rad23: At the crossroads of nucleotide excision repair and proteasomal degradation

Dantuma, N. P., Heinen, C., & Hoogstraten, D. (2009) · DNA repair · doi:10.1016/j.dnarep.2009.01.005 · Cited by 141 · see citing works

The role of the ubiquitin/proteasome system in cellular responses to radiation

McBride, W. H., Iwamoto, K. S., Syljuåsen, R. G., Pervan, M., & Pajonk, F. (2003) · Oncogene · doi:10.1038/sj.onc.1206676 · Cited by 140 · see citing works

Genome‐wide transcriptional plasticity underlies cellular adaptation to novel challenge

Stern, S., Dror, T. W., Stolovicki, E., Brenner, N., & Braun, E. (2007) · Molecular Systems Biology · doi:10.1038/msb4100147 · Cited by 136 · see citing works

Stress-specific signatures: expression profiling of p53 wild-type and -null human cells

Amundson, S. A., Do, K. T., Vinikoor, L. C., Koch-Paiz, C. A., Bittner, M. L., Trent, J. M., Meltzer, P. S., & Fornace, A. J. (2005) · Oncogene · doi:10.1038/sj.onc.1208653 · Cited by 135 · see citing works

Regulation of Subtelomeric Silencing during Stress Response

Ai, W., Bertram, P. G., Tsang, C. K., Chan, T., & Zheng, X. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00695-0 · Cited by 131 · see citing works

Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae

Said, M. R., Begley, T. J., Oppenheim, A. V., Lauffenburger, D. A., & Samson, L. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405996101 · Cited by 121 · see citing works

The environmental stress response: a common yeast response to diverse environmental stresses

Gasch, A. P. (2007) · Springer eBooks · doi:10.1007/3-540-45611-2_2 · Cited by 125 · see citing works

A stress regulatory network for co‐ordinated activation of proteasome expression mediated by yeast heat shock transcription factor

Hahn, J., Neef, D. W., & Thiele, D. J. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05097.x · Cited by 123 · see citing works

The Transcriptome of Prematurely Aging Yeast Cells Is Similar to That of Telomerase-deficient Cells

Lesur, I., & Campbell, J. L. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-10-0742 · Cited by 123 · see citing works

The proteasome: a macromolecular assembly designed for controlled proteolysis

Zwickl, P., Voges, D., & Baumeister, W. P. (1999) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.1999.0494 · Cited by 122 · see citing works

The Sphingolipid Long-chain Base-Pkh1/2-Ypk1/2 Signaling Pathway Regulates Eisosome Assembly and Turnover

Luo, G., Gruhler, A., Liu, Y., Jensen, O. N., & Dickson, R. C. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m709972200 · Cited by 119 · 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

The utility of DNA microarrays for characterizing genotoxicity.

Newton, R. K., Aardema, M. J., & Aubrecht, J. (2004) · Environmental Health Perspectives · doi:10.1289/ehp.6709 · Cited by 109 · see citing works

Identifying functional modules using expression profiles and confidence-scored protein interactions

Ulitsky, I., & Ron Shamir, A. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp118 · Cited by 108 · see citing works

Control of 26S proteasome expression by transcription factors regulating multidrug resistance in Saccharomyces cerevisiae

Owsianik, G., Balzi, L., & Ghislain, M. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02823.x · Cited by 106 · see citing works

Pil1p and Lsp1p Negatively Regulate the 3-Phosphoinositide-dependent Protein Kinase-like Kinase Pkh1p and Downstream Signaling Pathways Pkc1p and Ypk1p

Zhang, X., Lester, R. L., & Dickson, R. C. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m400299200 · Cited by 104 · see citing works

From co-expression to co-regulation: how many microarray experiments do we need?

Yeung, K. Y., Medvedovic, M., & Bumgarner, R. E. (2004) · Genome biology · doi:10.1186/gb-2004-5-7-r48 · Cited by 104 · see citing works

The fate of the messenger is pre-determined: A new model for regulation of gene expression

Haimovich, G., Choder, M., Singer, R. H., & Trcek, T. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2013.01.004 · Cited by 103 · see citing works

Hot Spots for Modulating Toxicity Identified by Genomic Phenotyping and Localization Mapping

Begley, T. J., Rosenbach, A., Ideker, T. E., & Samson, L. D. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.09.005 · Cited by 101 · see citing works

Toxicogenomics: a pivotal piece in the puzzle of toxicological research

Gatzidou, E. T., Zira, A. N., & Theocharis, S. E. (2007) · Journal of Applied Toxicology · doi:10.1002/jat.1248 · Cited by 102 · see citing works

Repair of 8-oxoguanine in Saccharomyces cerevisiae: interplay of DNA repair and replication mechanisms2,3 2Guest Editor: Miral Dizdaroglu 3This article is part of a series of reviews on “Oxidative DNA Damage and Repair.” The full list of papers may be found on the homepage of the journal.

Boiteux, S., Gellon, L., & Guibourt, N. (2002) · Free Radical Biology and Medicine · doi:10.1016/s0891-5849(02)00822-5 · Cited by 101 · see citing works

The DNA Damage-Inducible UbL-UbA Protein Ddi1 Participates in Mec1-Mediated Degradation of Ho Endonuclease

Kaplun, L., Tzirkin, R., Bakhrat, A., Shabek, N., Ivantsiv, Y., & Raveh, D. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.13.5355-5362.2005 · Cited by 101 · see citing works

Emerging technologies in yeast genomics

Kumar, A., & Snyder, M. P. (2001) · Nature Reviews Genetics · doi:10.1038/35066084 · Cited by 100 · see citing works

MFS transporters required for multidrug/multixenobiotic (MD/MX) resistance in the model yeast: understanding their physiological function through post-genomic approaches

dos Santos, S. C., Teixeira, M. C., Dias, P. J., & Sá‐Correia, I. (2014) · Frontiers in Physiology · doi:10.3389/fphys.2014.00180 · Cited by 97 · see citing works

Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level ConservationPreprint

Pritsker, M., Liu, Y.-C., Beer, M., & Tavazoie, S. (2003) · Genome Research · doi:10.1101/gr.1739204 · Cited by 99 · see citing works

The genome-wide expression response to telomerase deletion in <i>Saccharomyces</i> <i>cerevisiae</i>

Nautiyal, S., DeRisi, J. L., & Blackburn, E. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.142162499 · Cited by 96 · see citing works

Apoptotic Signaling in Response to a Single Type of DNA Lesion, O6-Methylguanine

Hickman, M. J., & Samson, L. D. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00162-5 · Cited by 91 · see citing works

GENOME-WIDE RESPONSES TO DNA-DAMAGING AGENTS

Fry, R. C., Begley, T. J., & Samson, L. D. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.031805.133658 · Cited by 95 · see citing works

Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes

Chan, C. T. Y., Deng, W., Li, F., DeMott, M. S., Babu, I. R., Begley, T. J., & Dedon, P. C. (2015) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.5b00004 · Cited by 91 · see citing works

Sequestration of Highly Expressed mRNAs in Cytoplasmic Granules, P-Bodies, and Stress Granules Enhances Cell Viability

Lavut, A., & Raveh, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002527 · Cited by 90 · see citing works

Relationships between genomic, cell cycle, and mutagenic responses of TK6 cells exposed to DNA damaging chemicals

Islaih, M., Halstead, B. W., Kadura, I. A., Li, B., Reid‐Hubbard, J. L., Flick, L. M., Altizer, J. L., Deahl, J. T., Monteith, D., Newton, R. K., et al. (2005) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2005.04.012 · Cited by 89 · see citing works

Ubiquitin-independent Mechanisms of Mouse Ornithine Decarboxylase Degradation Are Conserved between Mammalian and Fungal Cells

Hoyt, M. A., Zhang, M., & Coffino, P. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211802200 · Cited by 89 · see citing works

Identification of a gene expression profile that discriminates indirect-acting genotoxins from direct-acting genotoxins

Hu, T., Gibson, D. P., Carr, G. J., Torontali, S. M., Tiesman, J. P., Chaney, J. G., & Aardema, M. J. (2004) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/j.mrfmmm.2003.11.012 · Cited by 88 · see citing works

Genome-wide Co-occurrence of Promoter Elements Reveals a cis-Regulatory Cassette of rRNA Transcription Motifs in Saccharomyces cerevisiaePreprint

Sudarsanam, P., Pilpel, Y., & Church, G. M. (2002) · Genome Research · doi:10.1101/gr.301202 · Cited by 87 · see citing works

Perspectives on the DNA damage and replication checkpoint responses in Saccharomyces cerevisiae

Putnam, C. D., Jaehnig, E. J., & Kolodner, R. D. (2009) · DNA Repair · doi:10.1016/j.dnarep.2009.04.021 · Cited by 83 · see citing works

Identifying the conserved network of cis-regulatory sites of a eukaryotic genome

Wang, T., & Stormo, G. D. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0505147102 · Cited by 84 · see citing works

The Proteasome and Its Network: Engineering for AdaptabilityPreprint

Finley, D. J., & Prado, M. A. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a033985 · Cited by 84 · see citing works

Regulatory mechanisms controlling biogenesis of ubiquitin and the proteasome

London, M. K., Keck, B., Ramos, P. C., & Dohmen, R. J. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.04.078 · Cited by 82 · see citing works

Sugar metabolism, redox balance and oxidative stress response in the respiratory yeast Kluyveromyces lactis

González-Siso, M.-I., García-Leiro, A., Tarrío, N., & Cerdán, M. E. (2009) · Microbial Cell Factories · doi:10.1186/1475-2859-8-46 · Cited by 81 · see citing works

Proteolysis of a nucleotide excision repair protein by the 26S proteasome

Lommel, L., Ortolan, T. G., Chen, L., Madura, K., & Sweder, K. (2002) · Current Genetics · doi:10.1007/s00294-002-0332-9 · Cited by 80 · see citing works

Treasures and traps in genome-wide data sets: case examples from yeast

Grünenfelder, B., & Winzeler, E. A. (2002) · Nature Reviews Genetics · doi:10.1038/nrg886 · Cited by 78 · see citing works

ATP-dependent Proteases Differ Substantially in Their Ability to Unfold Globular Proteins

Koodathingal, P., Jaffe, N. E., Kraut, D. A., Prakash, S., Fishbain, S., Herman, C., & Matouschek, A. T. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m900783200 · Cited by 77 · see citing works

Homeostatic regulation of the proteasome via an Rpn4-dependent feedback circuit

Ju, D., Wang, L., Mao, X., & Xie, Y. (2004) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2004.06.105 · Cited by 77 · see citing works

Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue

Rashi‐Elkeles, S., Elkon, R., Weizman, N., Linhart, C., Amariglio, N., Sternberg, G., Rechavi, G., Barzilai, A., Ron Shamir, A., & Shiloh, Y. (2005) · Oncogene · doi:10.1038/sj.onc.1209189 · Cited by 75 · see citing works

Handling very large numbers of association rules in the analysis of microarray data

Tuzhilin, A., & Adomavičius, G. (2002) · ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) · doi:10.1145/775047.775104 · Cited by 74 · see citing works

DNA damage regulation and its role in drug-related phenotypes in the malaria parasites

Gupta, D. K., Patra, A. T., Zhu, L., Gupta, A. P., & Bozdech, Z. (2016) · Scientific Reports · doi:10.1038/srep23603 · Cited by 71 · see citing works

Escherichia coli Dam-methylase as a molecular tool for mapping binding sites of the yeast transcription factor Rpn4

Spasskaya, D. S., Karpov, D. S., & Карпов, В. Л. (2011) · Molecular Biology · doi:10.1134/s0026893311030186 · Cited by 11 · see citing works

The transcription activation domain of Rpn4 is separate from its degrons

Ju, D., Xu, H., Wang, X., & Xie, Y. (2009) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2009.11.003 · Cited by 6 · see citing works

Yeast Rpn4 Links the Proteasome and DNA Repair via RAD52 Regulation

Spasskaya, D. S., Nadolinskaia, N. I., Tutyaeva, V. V., Lysov, Y. P., Карпов, В. Л., & Karpov, D. S. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218097 · Cited by 8 · see citing works

Rpn4p without the DNA-Binding Domain Provides Saccharomyces cerevisiae Resistance to Oxidative Stress and Cycloheximide

Karpov, D. S., Spasskaya, D. S., Tutyaeva, V. V., & Карпов, В. Л. (2022) · Molecular Biology · doi:10.1134/s0026893322040057

Transcriptional Networks in S. cerevisiae Linked to an Accumulation of Base Excision Repair Intermediates

¤a, I. R., Fry, R. C., Begley, T. J., Klapacz, J., Svensson, J. P., ¤c, M. A., & Samson, L. D. (2013)