| Year |
Citation |
Score |
| 2023 |
Smerdon MJ, Wyrick JJ, Delaney S. A HALF CENTURY OF EXPLORING DNA EXCISION REPAIR IN CHROMATIN. The Journal of Biological Chemistry. 105118. PMID 37527775 DOI: 10.1016/j.jbc.2023.105118 |
0.379 |
|
| 2023 |
Bohm KA, Morledge-Hampton B, Stevison S, Mao P, Roberts SA, Wyrick JJ. Genome-wide maps of rare and atypical UV photoproducts reveal distinct patterns of damage formation and mutagenesis in yeast chromatin. Proceedings of the National Academy of Sciences of the United States of America. 120: e2216907120. PMID 36853943 DOI: 10.1073/pnas.2216907120 |
0.384 |
|
| 2022 |
Stark B, Poon GMK, Wyrick JJ. Molecular mechanism of UV damage modulation in nucleosomes. Computational and Structural Biotechnology Journal. 20: 5393-5400. PMID 36212527 DOI: 10.1016/j.csbj.2022.08.071 |
0.345 |
|
| 2022 |
Selvam K, Plummer DA, Mao P, Wyrick JJ. Set2 histone methyltransferase regulates transcription coupled-nucleotide excision repair in yeast. Plos Genetics. 18: e1010085. PMID 35263330 DOI: 10.1371/journal.pgen.1010085 |
0.453 |
|
| 2021 |
Geijer ME, Zhou D, Selvam K, Steurer B, Mukherjee C, Evers B, Cugusi S, van Toorn M, van der Woude M, Janssens RC, Kok YP, Gong W, Raams A, Lo CSY, Lebbink JHG, ... ... Wyrick JJ, et al. Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nature Cell Biology. 23: 608-619. PMID 34108662 DOI: 10.1038/s41556-021-00692-z |
0.359 |
|
| 2021 |
Bohm KA, Hodges AJ, Czaja W, Selvam K, Smerdon MJ, Mao P, Wyrick JJ. Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair. Genome Research. PMID 34001524 DOI: 10.1101/gr.274373.120 |
0.389 |
|
| 2020 |
Duan M, Selvam K, Wyrick JJ, Mao P. Genome-wide role of Rad26 in promoting transcription-coupled nucleotide excision repair in yeast chromatin. Proceedings of the National Academy of Sciences of the United States of America. PMID 32690696 DOI: 10.1073/Pnas.2003868117 |
0.527 |
|
| 2020 |
Mao P, Wyrick JJ. Genome-Wide Mapping of UV-Induced DNA Damage with CPD-Seq. Methods in Molecular Biology (Clifton, N.J.). 2175: 79-94. PMID 32681485 DOI: 10.1007/978-1-0716-0763-3_7 |
0.357 |
|
| 2019 |
Mao P, Smerdon MJ, Roberts SA, Wyrick JJ. Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer. Genome Research. PMID 31871068 DOI: 10.1101/Gr.253146.119 |
0.419 |
|
| 2019 |
Meas R, Wyrick JJ, Smerdon MJ. Nucleosomes Regulate Base Excision Repair in Chromatin. Mutation Research. 780: 29-36. PMID 31388331 DOI: 10.1016/J.Mrrev.2017.10.002 |
0.497 |
|
| 2019 |
Mao P, Wyrick JJ. Organization of DNA damage, excision repair, and mutagenesis in chromatin: A genomic perspective. Dna Repair. 102645. PMID 31307926 DOI: 10.1016/J.Dnarep.2019.102645 |
0.42 |
|
| 2019 |
Hodges AJ, Roberts SA, Wyrick JJ. Using Yeast as a Model Organism to Study the Functional Roles of Histone Acetylation in DNA Excision Repair. Methods in Molecular Biology (Clifton, N.J.). 1983: 175-190. PMID 31087298 DOI: 10.1007/978-1-4939-9434-2_10 |
0.522 |
|
| 2019 |
Roberts SA, Brown AJ, Wyrick JJ. Recurrent Noncoding Mutations in Skin Cancers: UV Damage Susceptibility or Repair Inhibition as Primary Driver? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 41: e1800152. PMID 30801747 DOI: 10.1002/Bies.201800152 |
0.377 |
|
| 2018 |
Laughery MF, Mayes HC, Pedroza IK, Wyrick JJ. R-loop formation by dCas9 is mutagenic in Saccharomyces cerevisiae. Nucleic Acids Research. PMID 30590793 DOI: 10.1093/Nar/Gky1278 |
0.334 |
|
| 2018 |
Brown AJ, Mao P, Smerdon MJ, Wyrick JJ, Roberts SA. Nucleosome positions establish an extended mutation signature in melanoma. Plos Genetics. 14: e1007823. PMID 30485262 DOI: 10.1371/Journal.Pgen.1007823 |
0.443 |
|
| 2018 |
Hodges AJ, Plummer DA, Wyrick JJ. NuA4 acetyltransferase is required for efficient nucleotide excision repair in yeast. Dna Repair. PMID 30473425 DOI: 10.1016/J.Dnarep.2018.11.006 |
0.527 |
|
| 2018 |
Mao P, Brown AJ, Esaki S, Lockwood S, Poon GMK, Smerdon MJ, Roberts SA, Wyrick JJ. ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma. Nature Communications. 9: 2626. PMID 29980679 DOI: 10.1038/S41467-018-05064-0 |
0.381 |
|
| 2018 |
Rodriguez Y, Duan M, Wyrick JJ, Smerdon MJ. A cassette of basic amino acids in histone H2B regulates nucleosome dynamics and access to DNA damage. The Journal of Biological Chemistry. PMID 29588367 DOI: 10.1074/Jbc.Ra117.000358 |
0.548 |
|
| 2017 |
Choi JA, Wyrick JJ. RegulatorDB: a resource for the analysis of yeast transcriptional regulation. Database : the Journal of Biological Databases and Curation. 2017. PMID 29220449 DOI: 10.1093/Database/Bax058 |
0.448 |
|
| 2017 |
Mao P, Brown AJ, Malc EP, Mieczkowski PA, Smerdon MJ, Roberts SA, Wyrick JJ. Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity. Genome Research. PMID 28912372 DOI: 10.1101/Gr.225771.117 |
0.45 |
|
| 2017 |
Hodges AJ, Gloss LM, Wyrick JJ. Residues in the Nucleosome Acidic Patch Regulate Histone Occupancy and Are Important for FACT Binding in Saccharomyces cerevisiae. Genetics. PMID 28468903 DOI: 10.1534/Genetics.117.201939 |
0.541 |
|
| 2016 |
Hinz JM, Laughery MF, Wyrick JJ. Nucleosomes Selectively Inhibit Cas9 Off-Target Activity at a Site Located at the Nucleosome Edge. The Journal of Biological Chemistry. PMID 27756838 DOI: 10.1074/Jbc.C116.758706 |
0.364 |
|
| 2016 |
Mao P, Wyrick JJ. Emerging roles for histone modifications in DNA excision repair. Fems Yeast Research. PMID 27737893 DOI: 10.1093/Femsyr/Fow090 |
0.437 |
|
| 2016 |
Kong M, Liu L, Chen X, Driscoll KI, Mao P, Böhm S, Kad NM, Watkins SC, Bernstein KA, Wyrick JJ, Min JH, Van Houten B. Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process. Molecular Cell. PMID 27720644 DOI: 10.1016/J.Molcel.2016.09.005 |
0.344 |
|
| 2016 |
Mao P, Wyrick JJ, Roberts SA, Smerdon MJ. UV-Induced DNA Damage and Mutagenesis in Chromatin. Photochemistry and Photobiology. PMID 27716995 DOI: 10.1111/Php.12646 |
0.458 |
|
| 2016 |
Mao P, Smerdon MJ, Roberts SA, Wyrick JJ. Chromosomal landscape of UV damage formation and repair at single-nucleotide resolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 27457959 DOI: 10.1073/Pnas.1606667113 |
0.429 |
|
| 2016 |
Mao P, Kyriss MN, Hodges AJ, Duan M, Morris RT, Lavine MD, Topping TB, Gloss LM, Wyrick JJ. A basic domain in the histone H2B N-terminal tail is important for nucleosome assembly by FACT. Nucleic Acids Research. PMID 27369377 DOI: 10.1093/Nar/Gkw588 |
0.787 |
|
| 2016 |
Rodriguez Y, Hinz JM, Laughery MF, Wyrick JJ, Smerdon MJ. Site-specific Acetylation of Histone H3 Decreases Polymerase β Activity on Nucleosome Core Particles in vitro. The Journal of Biological Chemistry. PMID 27033702 DOI: 10.1074/Jbc.M116.725788 |
0.496 |
|
| 2015 |
Hinz JM, Laughery MF, Wyrick JJ. Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro. Biochemistry. 54: 7063-6. PMID 26579937 DOI: 10.1021/Acs.Biochem.5B01108 |
0.432 |
|
| 2015 |
Wyrick JJ, Roberts SA. Genomic approaches to DNA repair and mutagenesis. Dna Repair. PMID 26411877 DOI: 10.1016/J.Dnarep.2015.09.018 |
0.359 |
|
| 2015 |
Laughery MF, Hunter T, Brown A, Hoopes J, Ostbye T, Shumaker T, Wyrick JJ. New vectors for simple and streamlined CRISPR-Cas9 genome editing in Saccharomyces cerevisiae. Yeast (Chichester, England). PMID 26305040 DOI: 10.1002/Yea.3098 |
0.329 |
|
| 2015 |
Hodges AJ, Gallegos IJ, Laughery MF, Meas R, Tran L, Wyrick JJ. Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability in Saccharomyces cerevisiae. Genetics. 200: 795-806. PMID 25971662 DOI: 10.1534/Genetics.115.175885 |
0.525 |
|
| 2015 |
Meas R, Smerdon MJ, Wyrick JJ. The amino-terminal tails of histones H2A and H3 coordinate efficient base excision repair, DNA damage signaling and postreplication repair in Saccharomyces cerevisiae. Nucleic Acids Research. 43: 4990-5001. PMID 25897129 DOI: 10.1093/Nar/Gkv372 |
0.467 |
|
| 2014 |
Zavala AG, Morris RT, Wyrick JJ, Smerdon MJ. High-resolution characterization of CPD hotspot formation in human fibroblasts. Nucleic Acids Research. 42: 893-905. PMID 24137003 DOI: 10.1093/Nar/Gkt912 |
0.458 |
|
| 2012 |
Doroshenk KA, Crofts AJ, Morris RT, Wyrick JJ, Okita TW. RiceRBP: A Resource for Experimentally Identified RNA Binding Proteins in Oryza sativa. Frontiers in Plant Science. 3: 90. PMID 22645600 DOI: 10.3389/Fpls.2012.00090 |
0.343 |
|
| 2012 |
Wyrick JJ, Kyriss MN, Davis WB. Ascending the nucleosome face: recognition and function of structured domains in the histone H2A-H2B dimer. Biochimica Et Biophysica Acta. 1819: 892-901. PMID 22521324 DOI: 10.1016/J.Bbagrm.2012.04.001 |
0.776 |
|
| 2012 |
Wyrick JJ. Computational analysis of promoter elements and chromatin features in yeast. Methods in Molecular Biology (Clifton, N.J.). 809: 217-35. PMID 22113279 DOI: 10.1007/978-1-61779-376-9_15 |
0.51 |
|
| 2010 |
Zheng S, Wyrick JJ, Reese JC. Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N terminus of histone H2A. Molecular and Cellular Biology. 30: 3635-45. PMID 20498280 DOI: 10.1128/Mcb.00324-10 |
0.577 |
|
| 2010 |
Kyriss MN, Jin Y, Gallegos IJ, Sanford JA, Wyrick JJ. Novel functional residues in the core domain of histone H2B regulate yeast gene expression and silencing and affect the response to DNA damage. Molecular and Cellular Biology. 30: 3503-18. PMID 20479120 DOI: 10.1128/Mcb.00290-10 |
0.784 |
|
| 2010 |
Nag R, Kyriss M, Smerdon JW, Wyrick JJ, Smerdon MJ. A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi/Snf binding in UV irradiated yeast. Nucleic Acids Research. 38: 1450-60. PMID 20007597 DOI: 10.1093/Nar/Gkp1074 |
0.773 |
|
| 2010 |
Morris RT, O'Connor TR, Wyrick JJ. Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae. Bioinformatics (Oxford, England). 26: 168-74. PMID 19959498 DOI: 10.1093/Bioinformatics/Btp657 |
0.429 |
|
| 2010 |
Doroshenk KA, Crofts AJ, Washida H, Satoh-Cruz M, Crofts N, Sugino A, Okita TW, Morris RT, Wyrick JJ, Fukuda M, Kumamaru T, Satoh H. Characterization of the rice glup4 mutant suggests a role for the small GTPase Rab5 in the biosynthesis of carbon and nitrogen storage reserves in developing endosperm Breeding Science. 60: 556-567. DOI: 10.1270/Jsbbs.60.556 |
0.327 |
|
| 2009 |
Chaudhuri S, Wyrick JJ, Smerdon MJ. Histone H3 Lys79 methylation is required for efficient nucleotide excision repair in a silenced locus of Saccharomyces cerevisiae. Nucleic Acids Research. 37: 1690-700. PMID 19155276 DOI: 10.1093/Nar/Gkp003 |
0.551 |
|
| 2009 |
Jin Y, Rodriguez AM, Wyrick JJ. Genetic and genomewide analysis of simultaneous mutations in acetylated and methylated lysine residues in histone H3 in Saccharomyces cerevisiae. Genetics. 181: 461-72. PMID 19087956 DOI: 10.1534/Genetics.108.098897 |
0.523 |
|
| 2009 |
Wyrick JJ, Parra MA. The role of histone H2A and H2B post-translational modifications in transcription: a genomic perspective. Biochimica Et Biophysica Acta. 1789: 37-44. PMID 18675384 DOI: 10.1016/J.Bbagrm.2008.07.001 |
0.744 |
|
| 2009 |
Wyrick JJ. Genomic tools for analyzing transcriptional regulatory networks Bioinformatics For Systems Biology. 119-136. DOI: 10.1007/978-1-59745-440-7_7 |
0.338 |
|
| 2008 |
Morris RT, O'Connor TR, Wyrick JJ. Osiris: an integrated promoter database for Oryza sativa L. Bioinformatics (Oxford, England). 24: 2915-7. PMID 18922805 DOI: 10.1093/Bioinformatics/Btn537 |
0.409 |
|
| 2007 |
Parra MA, Wyrick JJ. Regulation of gene transcription by the histone H2A N-terminal domain. Molecular and Cellular Biology. 27: 7641-8. PMID 17724083 DOI: 10.1128/Mcb.00742-07 |
0.763 |
|
| 2007 |
Jin Y, Rodriguez AM, Stanton JD, Kitazono AA, Wyrick JJ. Simultaneous mutation of methylated lysine residues in histone H3 causes enhanced gene silencing, cell cycle defects, and cell lethality in Saccharomyces cerevisiae. Molecular and Cellular Biology. 27: 6832-41. PMID 17664279 DOI: 10.1128/Mcb.00745-07 |
0.542 |
|
| 2007 |
O'Connor TR, Wyrick JJ. ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae. Bioinformatics (Oxford, England). 23: 1828-30. PMID 17485428 DOI: 10.1093/Bioinformatics/Btm236 |
0.534 |
|
| 2007 |
Wood A, Shukla A, Schneider J, Lee JS, Stanton JD, Dzuiba T, Swanson SK, Florens L, Washburn MP, Wyrick J, Bhaumik SR, Shilatifard A. Ctk complex-mediated regulation of histone methylation by COMPASS. Molecular and Cellular Biology. 27: 709-20. PMID 17088385 DOI: 10.1128/Mcb.01627-06 |
0.512 |
|
| 2006 |
Parra MA, Kerr D, Fahy D, Pouchnik DJ, Wyrick JJ. Deciphering the roles of the histone H2B N-terminal domain in genome-wide transcription. Molecular and Cellular Biology. 26: 3842-52. PMID 16648479 DOI: 10.1128/Mcb.26.10.3842-3852.2006 |
0.742 |
|
| 2005 |
O'Connor TR, Dyreson C, Wyrick JJ. Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics (Oxford, England). 21: 4411-3. PMID 16223790 DOI: 10.1093/Bioinformatics/Bti714 |
0.342 |
|
| 2004 |
Martin AM, Pouchnik DJ, Walker JL, Wyrick JJ. Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae. Genetics. 167: 1123-32. PMID 15280228 DOI: 10.1534/Genetics.104.026674 |
0.544 |
|
| 2002 |
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, ... Wyrick JJ, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (New York, N.Y.). 298: 799-804. PMID 12399584 DOI: 10.1126/Science.1075090 |
0.613 |
|
| 2002 |
Wyrick JJ, Young RA. Deciphering gene expression regulatory networks. Current Opinion in Genetics & Development. 12: 130-6. PMID 11893484 DOI: 10.1016/S0959-437X(02)00277-0 |
0.567 |
|
| 2001 |
Wyrick JJ, Aparicio JG, Chen T, Barnett JD, Jennings EG, Young RA, Bell SP, Aparicio OM. Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science (New York, N.Y.). 294: 2357-60. PMID 11743203 DOI: 10.1126/Science.1066101 |
0.502 |
|
| 2001 |
Simon I, Barnett J, Hannett N, Harbison CT, Rinaldi NJ, Volkert TL, Wyrick JJ, Zeitlinger J, Gifford DK, Jaakkola TS, Young RA. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 106: 697-708. PMID 11572776 DOI: 10.1016/S0092-8674(01)00494-9 |
0.599 |
|
| 2000 |
Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA. Genome-wide location and function of DNA binding proteins. Science (New York, N.Y.). 290: 2306-9. PMID 11125145 DOI: 10.1126/science.290.5500.2306 |
0.623 |
|
| 1999 |
Wyrick JJ, Holstege FC, Jennings EG, Causton HC, Shore D, Grunstein M, Lander ES, Young RA. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature. 402: 418-21. PMID 10586882 DOI: 10.1038/46567 |
0.638 |
|
| 1999 |
Jennings EG, Holstege FC, Wyrick JJ, Young RA. Combinatorial negative regulation of glucose-responsive genes in yeast Nature Genetics. 23: 53-53. DOI: 10.1038/14333 |
0.561 |
|
| 1998 |
Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 95: 717-28. PMID 9845373 DOI: 10.1016/S0092-8674(00)81641-4 |
0.604 |
|
| 1998 |
Lee TI, Wyrick JJ, Koh SS, Jennings EG, Gadbois EL, Young RA. Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme. Molecular and Cellular Biology. 18: 4455-62. PMID 9671455 DOI: 10.1128/Mcb.18.8.4455 |
0.571 |
|
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