| Year |
Citation |
Score |
| 2023 |
Chen H, Yan C, Dhasarathy A, Kladde M, Bai L. Investigating pioneer factor activity and its coordination with chromatin remodelers using integrated synthetic oligo assay. Star Protocols. 4: 102279. PMID 37289591 DOI: 10.1016/j.xpro.2023.102279 |
0.716 |
|
| 2022 |
Murray KO, Brant JO, Kladde MP, Clanton TL. Long-term epigenetic and metabolomic changes in the mouse ventricular myocardium after exertional heat stroke. Physiological Genomics. PMID 36215393 DOI: 10.1152/physiolgenomics.00147.2021 |
0.383 |
|
| 2022 |
Chen H, Kharerin H, Dhasarathy A, Kladde M, Bai L. Partitioned usage of chromatin remodelers by nucleosome-displacing factors. Cell Reports. 40: 111250. PMID 36001970 DOI: 10.1016/j.celrep.2022.111250 |
0.723 |
|
| 2021 |
Knight P, Gauthier ML, Pardo CE, Darst RP, Kapadia K, Browder H, Morton E, Riva A, Kladde MP, Bacher R. Methylscaper: an R/shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data. Bioinformatics (Oxford, England). PMID 34125875 DOI: 10.1093/bioinformatics/btab438 |
0.494 |
|
| 2019 |
Hollen MK, Stortz JA, Darden D, Dirain ML, Nacionales DC, Hawkins RB, Cox MC, Lopez MC, Rincon JC, Ungaro R, Wang Z, Wu Q, Brumback B, Gauthier ML, Kladde M, et al. Myeloid-derived suppressor cell function and epigenetic expression evolves over time after surgical sepsis. Critical Care (London, England). 23: 355. PMID 31722736 DOI: 10.1186/S13054-019-2628-X |
0.337 |
|
| 2017 |
Riva A, Poudyal R, Ianov L, Gu T, Kladde M, Foster T. A high-performance pipeline for differential methylation analysis F1000research. 6. DOI: 10.7490/F1000Research.1114663.1 |
0.393 |
|
| 2015 |
Stees JR, Hossain MA, Sunose T, Kudo Y, Pardo CE, Nabilsi NH, Darst RP, Poudyal R, Igarashi K, Huang S, Kladde MP, Bungert J. High Fractional Occupancy of a Tandem MARE and its Role in Long-Range β-globin Gene Regulation. Molecular and Cellular Biology. PMID 26503787 DOI: 10.1128/Mcb.00723-15 |
0.453 |
|
| 2015 |
Pardo CE, Nabilsi NH, Darst RP, Kladde MP. Integrated DNA methylation and chromatin structural analysis at single-molecule resolution. Methods in Molecular Biology (Clifton, N.J.). 1288: 123-41. PMID 25827879 DOI: 10.1007/978-1-4939-2474-5_9 |
0.517 |
|
| 2015 |
Lu Z, Lieber MR, Tsai AG, Pardo CE, Müschen M, Kladde MP, Hsieh CL. Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin. Molecular and Cellular Biology. 35: 1209-22. PMID 25624348 DOI: 10.1128/Mcb.01085-14 |
0.353 |
|
| 2014 |
Nabilsi NH, Deleyrolle LP, Darst RP, Riva A, Reynolds BA, Kladde MP. Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma. Genome Research. 24: 329-39. PMID 24105770 DOI: 10.1101/Gr.161737.113 |
0.521 |
|
| 2013 |
Nabilsi NH, Ryder DJ, Peraza-Penton AC, Poudyal R, Loose DS, Kladde MP. Local depletion of DNA methylation identifies a repressive p53 regulatory region in the NEK2 promoter Journal of Biological Chemistry. 288: 35940-35951. PMID 24163369 DOI: 10.1074/Jbc.M113.523837 |
0.521 |
|
| 2013 |
Darst RP, Haecker I, Pardo CE, Renne R, Kladde MP. Epigenetic diversity of Kaposi's sarcoma-associated herpesvirus. Nucleic Acids Research. 41: 2993-3009. PMID 23361465 DOI: 10.1093/Nar/Gkt033 |
0.462 |
|
| 2012 |
Darst RP, Nabilsi NH, Pardo CE, Riva A, Kladde MP. DNA methyltransferase accessibility protocol for individual templates by deep sequencing. Methods in Enzymology. 513: 185-204. PMID 22929770 DOI: 10.1016/B978-0-12-391938-0.00008-2 |
0.469 |
|
| 2012 |
Santostefano KE, Hamazaki T, Pardo CE, Kladde MP, Terada N. Fibroblast growth factor receptor 2 homodimerization rapidly reduces transcription of the pluripotency gene Nanog without dissociation of activating transcription factors. The Journal of Biological Chemistry. 287: 30507-17. PMID 22787153 DOI: 10.1074/Jbc.M112.388181 |
0.441 |
|
| 2012 |
Darst RP, Pardo CE, Pondugula S, Gangaraju VK, Nabilsi NH, Bartholomew B, Kladde MP. Simultaneous single-molecule detection of endogenous C-5 DNA methylation and chromatin accessibility using MAPit. Methods in Molecular Biology (Clifton, N.J.). 833: 125-41. PMID 22183592 DOI: 10.1007/978-1-61779-477-3_9 |
0.493 |
|
| 2011 |
Delmas AL, Riggs BM, Pardo CE, Dyer LM, Darst RP, Izumchenko EG, Monroe M, Hakam A, Kladde MP, Siegel EM, Brown KD. WIF1 is a frequent target for epigenetic silencing in squamous cell carcinoma of the cervix. Carcinogenesis. 32: 1625-33. PMID 21873353 DOI: 10.1093/Carcin/Bgr193 |
0.388 |
|
| 2011 |
Pardo CE, Darst RP, Nabilsi NH, Delmas AL, Kladde MP. Simultaneous single-molecule mapping of protein-DNA interactions and DNA methylation by MAPit. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 21.22. PMID 21732317 DOI: 10.1002/0471142727.Mb2122S95 |
0.494 |
|
| 2011 |
Pardo CE, Carr IM, Hoffman CJ, Darst RP, Markham AF, Bonthron DT, Kladde MP. MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects. Nucleic Acids Research. 39: e5. PMID 20959287 DOI: 10.1093/Nar/Gkq716 |
0.47 |
|
| 2010 |
Darst RP, Pardo CE, Ai L, Brown KD, Kladde MP. Bisulfite sequencing of DNA. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 7.9.1-17. PMID 20583099 DOI: 10.1002/0471142727.Mb0709S91 |
0.387 |
|
| 2010 |
Dechassa ML, Sabri A, Pondugula S, Kassabov SR, Chatterjee N, Kladde MP, Bartholomew B. SWI/SNF has intrinsic nucleosome disassembly activity that is dependent on adjacent nucleosomes. Molecular Cell. 38: 590-602. PMID 20513433 DOI: 10.1016/J.Molcel.2010.02.040 |
0.438 |
|
| 2009 |
Pondugula S, Neef DW, Voth WP, Darst RP, Dhasarathy A, Reynolds MM, Takahata S, Stillman DJ, Kladde MP. Coupling phosphate homeostasis to cell cycle-specific transcription: mitotic activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead proteins. Molecular and Cellular Biology. 29: 4891-905. PMID 19596791 DOI: 10.1128/Mcb.00222-09 |
0.752 |
|
| 2009 |
Pardo C, Hoose SA, Pondugula S, Kladde MP. DNA methyltransferase probing of chromatin structure within populations and on single molecules. Methods in Molecular Biology (Clifton, N.J.). 523: 41-65. PMID 19381922 DOI: 10.1007/978-1-59745-190-1_4 |
0.534 |
|
| 2008 |
Pondugula S, Kladde MP. Single-molecule analysis of chromatin: changing the view of genomes one molecule at a time. Journal of Cellular Biochemistry. 105: 330-7. PMID 18615586 DOI: 10.1002/jcb.21849 |
0.496 |
|
| 2007 |
Kilgore JA, Hoose SA, Gustafson TL, Porter W, Kladde MP. Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods (San Diego, Calif.). 41: 320-32. PMID 17309843 DOI: 10.1016/J.Ymeth.2006.08.008 |
0.409 |
|
| 2006 |
Hoose SA, Kladde MP. DNA methyltransferase probing of DNA-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 338: 225-44. PMID 16888362 DOI: 10.1385/1-59745-097-9:225 |
0.468 |
|
| 2006 |
Jessen WJ, Hoose SA, Kilgore JA, Kladde MP. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nature Structural & Molecular Biology. 13: 256-63. PMID 16491089 DOI: 10.1038/Nsmb1062 |
0.794 |
|
| 2005 |
Dhasarathy A, Kladde MP. Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements. Molecular and Cellular Biology. 25: 2698-707. PMID 15767675 DOI: 10.1128/Mcb.25.7.2698-2707.2005 |
0.772 |
|
| 2004 |
Norwood LE, Grade SK, Cryderman DE, Hines KA, Furiasse N, Toro R, Li Y, Dhasarathy A, Kladde MP, Hendrix MJ, Kirschmann DA, Wallrath LL. Conserved properties of HP1(Hsalpha). Gene. 336: 37-46. PMID 15225874 DOI: 10.1016/J.Gene.2004.04.003 |
0.716 |
|
| 2004 |
Carvin CD, Kladde MP. Effectors of lysine 4 methylation of histone H3 in Saccharomyces cerevisiae are negative regulators of PHO5 and GAL1-10. The Journal of Biological Chemistry. 279: 33057-62. PMID 15180994 DOI: 10.1074/Jbc.M405033200 |
0.764 |
|
| 2004 |
Jessen WJ, Dhasarathy A, Hoose SA, Carvin CD, Risinger AL, Kladde MP. Mapping chromatin structure in vivo using DNA methyltransferases. Methods (San Diego, Calif.). 33: 68-80. PMID 15039089 DOI: 10.1016/J.Ymeth.2003.10.025 |
0.7 |
|
| 2003 |
Carvin CD, Parr RD, Kladde MP. Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins. Nucleic Acids Research. 31: 6493-501. PMID 14602907 DOI: 10.1093/Nar/Gkg853 |
0.788 |
|
| 2003 |
Carvin CD, Dhasarathy A, Friesenhahn LB, Jessen WJ, Kladde MP. Targeted cytosine methylation for in vivo detection of protein-DNA interactions. Proceedings of the National Academy of Sciences of the United States of America. 100: 7743-8. PMID 12808133 DOI: 10.1073/Pnas.1332672100 |
0.707 |
|
| 2003 |
Neef DW, Kladde MP. Polyphosphate loss promotes SNF/SWI- and Gcn5-dependent mitotic induction of PHO5. Molecular and Cellular Biology. 23: 3788-97. PMID 12748282 DOI: 10.1128/Mcb.23.11.3788-3797.2003 |
0.771 |
|
| 2001 |
Samudio I, Vyhlidal C, Wang F, Stoner M, Chen I, Kladde M, Barhoumi R, Burghardt R, Safe S. Transcriptional Activation of Deoxyribonucleic Acid Polymerase α Gene Expression in MCF-7 Cells by 17β-Estradiol. Endocrinology. 142: 1000-1008. PMID 28201425 DOI: 10.1210/Endo.142.3.8022 |
0.478 |
|
| 2000 |
Gavin IM, Kladde MP, Simpson RT. Tup1p represses Mcm1p transcriptional activation and chromatin remodeling of an a-cell-specific gene. The Embo Journal. 19: 5875-83. PMID 11060038 DOI: 10.1093/Emboj/19.21.5875 |
0.451 |
|
| 2000 |
Vyhlidal C, Samudio I, Kladde MP, Safe S. Transcriptional activation of transforming growth factor alpha by estradiol: requirement for both a GC-rich site and an estrogen response element half-site. Journal of Molecular Endocrinology. 24: 329-38. PMID 10828826 DOI: 10.1677/Jme.0.0240329 |
0.449 |
|
| 1999 |
Kladde MP, Xu M, Simpson RT. DNA methyltransferases as probes for chromatin structure in yeast. Methods in Molecular Biology (Clifton, N.J.). 119: 395-416. PMID 10804528 DOI: 10.1385/1-59259-681-9:395 |
0.413 |
|
| 1999 |
Duan R, Porter W, Samudio I, Vyhlidal C, Kladde M, Safe S. Transcriptional activation of c-fos protooncogene by 17beta-estradiol: mechanism of aryl hydrocarbon receptor-mediated inhibition. Molecular Endocrinology (Baltimore, Md.). 13: 1511-21. PMID 10478842 DOI: 10.1210/Mend.13.9.0338 |
0.378 |
|
| 1999 |
Kladde MP, Xu M, Simpson RT. DNA methyltransferases as probes of chromatin structure in vivo. Methods in Enzymology. 304: 431-47. PMID 10372375 DOI: 10.1016/S0076-6879(99)04026-4 |
0.514 |
|
| 1998 |
Xu M, Kladde MP, Van Etten JL, Simpson RT. Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC. Nucleic Acids Research. 26: 3961-6. PMID 9705505 DOI: 10.1093/Nar/26.17.3961 |
0.357 |
|
| 1998 |
Xu M, Simpson RT, Kladde MP. Gal4p-mediated chromatin remodeling depends on binding site position in nucleosomes but does not require DNA replication. Molecular and Cellular Biology. 18: 1201-12. PMID 9488435 DOI: 10.1128/Mcb.18.3.1201 |
0.543 |
|
| 1998 |
Kladde MP, Simpson RT. Rapid detection of functional expression of C-5-DNA methyltransferases in yeast. Nucleic Acids Research. 26: 1354-5. PMID 9469849 DOI: 10.1093/Nar/26.5.1354 |
0.413 |
|
| 1997 |
Wechser MA, Kladde MP, Alfieri JA, Peterson CL. Effects of Sin- versions of histone H4 on yeast chromatin structure and function. The Embo Journal. 16: 2086-95. PMID 9155034 DOI: 10.1093/Emboj/16.8.2086 |
0.432 |
|
| 1996 |
Kladde MP, Xu M, Simpson RT. Direct study of DNA-protein interactions in repressed and active chromatin in living cells. The Embo Journal. 15: 6290-300. PMID 8947052 DOI: 10.1002/J.1460-2075.1996.Tb01019.X |
0.443 |
|
| 1996 |
Kladde MP, Simpson RT. Chromatin structure mapping in vivo using methyltransferases. Methods in Enzymology. 274: 214-33. PMID 8902807 DOI: 10.1016/S0076-6879(96)74019-3 |
0.496 |
|
| 1994 |
Kladde MP, Simpson RT. Positioned nucleosomes inhibit Dam methylation in vivo. Proceedings of the National Academy of Sciences of the United States of America. 91: 1361-5. PMID 8108416 DOI: 10.1073/Pnas.91.4.1361 |
0.571 |
|
| 1993 |
Cullen KE, Kladde MP, Seyfred MA. Interaction between transcription regulatory regions of prolactin chromatin. Science (New York, N.Y.). 261: 203-6. PMID 8327891 DOI: 10.1126/science.8327891 |
0.42 |
|
| 1993 |
Simpson RT, Roth SY, Morse RH, Patterton HG, Cooper JP, Murphy M, Kladde MP, Shimizu M. Nucleosome positioning and transcription. Cold Spring Harbor Symposia On Quantitative Biology. 58: 237-45. PMID 7956034 DOI: 10.1101/Sqb.1993.058.01.028 |
0.33 |
|
| 1989 |
Seyfred MA, Kladde MP, Gorski J. Transcriptional regulation by estrogen of episomal prolactin gene regulatory elements. Molecular Endocrinology (Baltimore, Md.). 3: 305-14. PMID 2540428 DOI: 10.1210/Mend-3-2-305 |
0.332 |
|
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