| Year |
Citation |
Score |
| 2024 |
Moyung K, Li Y, Hartemink AJ, MacAlpine DM. Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation. Biorxiv : the Preprint Server For Biology. PMID 38826400 DOI: 10.1101/2024.05.24.595391 |
0.423 |
|
| 2023 |
Chen B, MacAlpine HK, Hartemink AJ, MacAlpine DM. Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. Genome Research. PMID 38081658 DOI: 10.1101/gr.278273.123 |
0.414 |
|
| 2023 |
Chen B, MacAlpine HK, Hartemink AJ, MacAlpine DM. Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase. Biorxiv : the Preprint Server For Biology. PMID 37292814 DOI: 10.1101/2023.05.25.541209 |
0.415 |
|
| 2021 |
Li Y, Hartemink AJ, MacAlpine DM. Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins. Genes. 12. PMID 34946946 DOI: 10.3390/genes12121998 |
0.504 |
|
| 2021 |
Hoffman RA, MacAlpine HK, MacAlpine DM. Disruption of origin chromatin structure by helicase activation in the absence of DNA replication. Genes & Development. 35: 1339-1355. PMID 34556529 DOI: 10.1101/gad.348517.121 |
0.489 |
|
| 2021 |
MacAlpine DM. Stochastic initiation of DNA replication across the human genome. Molecular Cell. 81: 2873-2874. PMID 34270943 DOI: 10.1016/j.molcel.2021.06.022 |
0.345 |
|
| 2021 |
Mitra S, Zhong J, Tran TQ, MacAlpine DM, Hartemink AJ. RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Nucleic Acids Research. PMID 34255854 DOI: 10.1093/nar/gkab553 |
0.456 |
|
| 2021 |
Tran TQ, MacAlpine HK, Tripuraneni V, Mitra S, MacAlpine DM, Hartemink AJ. Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Research. PMID 33893157 DOI: 10.1101/gr.267237.120 |
0.436 |
|
| 2021 |
Tripuraneni V, Memisoglu G, MacAlpine HK, Tran TQ, Zhu W, Hartemink AJ, Haber JE, MacAlpine DM. Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair. Genome Research. PMID 33811083 DOI: 10.1101/gr.271155.120 |
0.405 |
|
| 2020 |
Mitra S, Zhong J, MacAlpine DM, Hartemink AJ. RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 12074: 136-151. PMID 34386808 DOI: 10.1007/978-3-030-45257-5_9 |
0.439 |
|
| 2019 |
Gutiérrez MP, MacAlpine HK, MacAlpine DM. Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork. Genome Research. PMID 31217252 DOI: 10.1101/Gr.243386.118 |
0.621 |
|
| 2019 |
Foss EJ, Gatbonton-Schwager T, Thiesen AH, Taylor E, Soriano R, Lao U, MacAlpine DM, Bedalov A. Sir2 suppresses transcription-mediated displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats. Plos Genetics. 15: e1008138. PMID 31083663 DOI: 10.1371/Journal.Pgen.1008138 |
0.518 |
|
| 2019 |
Lee H, McManus CJ, Cho DY, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, ... ... MacAlpine D, et al. Correction to: DNA copy number evolution in Drosophila cell lines. Genome Biology. 20: 53. PMID 30857560 DOI: 10.1186/S13059-019-1668-5 |
0.643 |
|
| 2018 |
Armstrong RL, Penke TJR, Strahl BD, Matera AG, McKay DJ, MacAlpine DM, Duronio RJ. Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila. Genome Research. PMID 30279224 DOI: 10.1101/Gr.239913.118 |
0.615 |
|
| 2017 |
Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP. Nucleosomes influence multiple steps during replication initiation. Elife. 6. PMID 28322723 DOI: 10.7554/Elife.22512 |
0.562 |
|
| 2017 |
Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP. Author response: Nucleosomes influence multiple steps during replication initiation Elife. DOI: 10.7554/Elife.22512.030 |
0.379 |
|
| 2016 |
Wang Y, Khan A, Marks AB, Smith OK, Giri S, Lin YC, Creager R, MacAlpine DM, Prasanth KV, Aladjem MI, Prasanth SG. Temporal association of ORCA/LRWD1 to late-firing origins during G1 dictates heterochromatin replication and organization. Nucleic Acids Research. PMID 27924004 DOI: 10.1093/Nar/Gkw1211 |
0.569 |
|
| 2016 |
Prioleau MN, MacAlpine DM. DNA replication origins-where do we begin? Genes & Development. 30: 1683-97. PMID 27542827 DOI: 10.1101/Gad.285114.116 |
0.603 |
|
| 2016 |
MacAlpine DM. ORChestrating the human DNA replication program. Proceedings of the National Academy of Sciences of the United States of America. PMID 27496327 DOI: 10.1073/Pnas.1610336113 |
0.591 |
|
| 2016 |
Feng J, Gan H, Eaton ML, Zhou H, Li S, Belsky JA, MacAlpine DM, Zhang Z, Li Q. Non-coding transcription is a driving force for nucleosome instability in spt16 mutant cells. Molecular and Cellular Biology. PMID 27141053 DOI: 10.1128/Mcb.00152-16 |
0.664 |
|
| 2016 |
Li Y, Armstrong RL, Duronio RJ, MacAlpine DM. Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila. Nucleic Acids Research. PMID 27131378 DOI: 10.1093/Nar/Gkw333 |
0.599 |
|
| 2015 |
Tsai FL, Vijayraghavan S, Prinz J, MacAlpine HK, MacAlpine DM, Schwacha A. Mcm2-7 Is an Active Player in the DNA Replication Checkpoint Signaling Cascade via Proposed Modulation of Its DNA Gate. Molecular and Cellular Biology. 35: 2131-43. PMID 25870112 DOI: 10.1128/Mcb.01357-14 |
0.49 |
|
| 2015 |
Creager RL, Li Y, MacAlpine DM. SnapShot: Origins of DNA replication. Cell. 161: 418-418.e1. PMID 25860614 DOI: 10.1016/J.Cell.2015.03.043 |
0.538 |
|
| 2015 |
Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM. Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly. Genes & Development. 29: 212-24. PMID 25593310 DOI: 10.1101/Gad.247924.114 |
0.542 |
|
| 2015 |
Powell SK, MacAlpine HK, Prinz JA, Li Y, Belsky JA, MacAlpine DM. Dynamic loading and redistribution of the Mcm2-7 helicase complex through the cell cycle. The Embo Journal. 34: 531-43. PMID 25555795 DOI: 10.15252/Embj.201488307 |
0.425 |
|
| 2014 |
Lee H, McManus CJ, Cho DY, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, ... ... MacAlpine D, et al. DNA copy number evolution in Drosophila cell lines. Genome Biology. 15: R70. PMID 25262759 DOI: 10.1186/Gb-2014-15-8-R70 |
0.657 |
|
| 2014 |
Lujan SA, Clausen AR, Clark AB, MacAlpine HK, MacAlpine DM, Malc EP, Mieczkowski PA, Burkholder AB, Fargo DC, Gordenin DA, Kunkel TA. Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition. Genome Research. 24: 1751-64. PMID 25217194 DOI: 10.1101/Gr.178335.114 |
0.449 |
|
| 2014 |
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... MacAlpine DM, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415 |
0.556 |
|
| 2014 |
Lubelsky Y, Prinz JA, DeNapoli L, Li Y, Belsky JA, MacAlpine DM. DNA replication and transcription programs respond to the same chromatin cues. Genome Research. 24: 1102-14. PMID 24985913 DOI: 10.1101/Gr.160010.113 |
0.662 |
|
| 2013 |
MacAlpine DM, Almouzni G. Chromatin and DNA replication. Cold Spring Harbor Perspectives in Biology. 5: a010207. PMID 23751185 DOI: 10.1101/Cshperspect.A010207 |
0.571 |
|
| 2013 |
Lampson BL, Pershing NL, Prinz JA, Lacsina JR, Marzluff WF, Nicchitta CV, MacAlpine DM, Counter CM. Rare codons regulate KRas oncogenesis. Current Biology : Cb. 23: 70-5. PMID 23246410 DOI: 10.1016/J.Cub.2012.11.031 |
0.339 |
|
| 2012 |
Herr A, Longworth M, Ji JY, Korenjak M, Macalpine DM, Dyson NJ. Identification of E2F target genes that are rate limiting for dE2F1-dependent cell proliferation. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 241: 1695-707. PMID 22972499 DOI: 10.1002/Dvdy.23857 |
0.398 |
|
| 2012 |
Lubelsky Y, MacAlpine HK, MacAlpine DM. Genome-wide localization of replication factors. Methods (San Diego, Calif.). 57: 187-95. PMID 22465279 DOI: 10.1016/J.Ymeth.2012.03.022 |
0.596 |
|
| 2012 |
Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Research. 22: 64-75. PMID 22090375 DOI: 10.1101/Gr.126003.111 |
0.767 |
|
| 2011 |
Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proceedings of the National Academy of Sciences of the United States of America. 108: 18318-23. PMID 22025700 DOI: 10.1073/Pnas.1110731108 |
0.45 |
|
| 2011 |
Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, MacAlpine DM, Orr-Weaver TL. Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes & Development. 25: 1384-98. PMID 21724831 DOI: 10.1101/Gad.2043111 |
0.56 |
|
| 2011 |
Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, ... ... MacAlpine DM, et al. A cis-regulatory map of the Drosophila genome. Nature. 471: 527-31. PMID 21430782 DOI: 10.1038/Nature09990 |
0.698 |
|
| 2011 |
Ding Q, MacAlpine DM. Defining the replication program through the chromatin landscape. Critical Reviews in Biochemistry and Molecular Biology. 46: 165-79. PMID 21417598 DOI: 10.3109/10409238.2011.560139 |
0.751 |
|
| 2011 |
Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, ... ... MacAlpine DM, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 471: 480-5. PMID 21179089 DOI: 10.1038/Nature09725 |
0.559 |
|
| 2011 |
Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM. Chromatin signatures of the Drosophila replication program. Genome Research. 21: 164-74. PMID 21177973 DOI: 10.1101/Gr.116038.110 |
0.767 |
|
| 2011 |
Nordman J, Li S, Eng T, Macalpine D, Orr-Weaver TL. Developmental control of the DNA replication and transcription programs. Genome Research. 21: 175-81. PMID 21177957 DOI: 10.1101/Gr.114611.110 |
0.547 |
|
| 2010 |
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, ... ... MacAlpine DM, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.). 330: 1787-97. PMID 21177974 DOI: 10.1126/Science.1198374 |
0.718 |
|
| 2010 |
Ding Q, MacAlpine DM. Preferential re-replication of Drosophila heterochromatin in the absence of geminin. Plos Genetics. 6: e1001112. PMID 20838463 DOI: 10.1371/Journal.Pgen.1001112 |
0.703 |
|
| 2010 |
Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, Weinreich M, Eaton ML, MacAlpine DM, Fox CA. The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin Genes and Development. 24: 1418-1433. PMID 20595233 DOI: 10.1101/Gad.1906410 |
0.735 |
|
| 2010 |
Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM. Conserved nucleosome positioning defines replication origins Genes and Development. 24: 748-753. PMID 20351051 DOI: 10.1101/Gad.1913210 |
0.691 |
|
| 2010 |
Zhang Y, Malone JH, Powell SK, Periwal V, Spana E, Macalpine DM, Oliver B. Expression in aneuploid Drosophila S2 cells. Plos Biology. 8: e1000320. PMID 20186269 DOI: 10.1371/Journal.Pbio.1000320 |
0.413 |
|
| 2010 |
Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD. Co-orientation of replication and transcription preserves genome integrity. Plos Genetics. 6: e1000810. PMID 20090829 DOI: 10.1371/Journal.Pgen.1000810 |
0.569 |
|
| 2010 |
MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Research. 20: 201-11. PMID 19996087 DOI: 10.1101/Gr.097873.109 |
0.52 |
|
| 2009 |
Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, et al. Unlocking the secrets of the genome. Nature. 459: 927-30. PMID 19536255 DOI: 10.1038/459927A |
0.403 |
|
| 2007 |
Bell O, Wirbelauer C, Hild M, Scharf AN, Schwaiger M, MacAlpine DM, Zilbermann F, van Leeuwen F, Bell SP, Imhof A, Garza D, Peters AH, Schübeler D. Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. The Embo Journal. 26: 4974-84. PMID 18007591 DOI: 10.1038/Sj.Emboj.7601926 |
0.417 |
|
| 2007 |
Georlette D, Ahn S, MacAlpine DM, Cheung E, Lewis PW, Beall EL, Bell SP, Speed T, Manak JR, Botchan MR. Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells. Genes & Development. 21: 2880-96. PMID 17978103 DOI: 10.1101/Gad.1600107 |
0.555 |
|
| 2007 |
Park EA, Macalpine DM, Orr-Weaver TL. Drosophila follicle cell amplicons as models for metazoan DNA replication: a cyclinE mutant exhibits increased replication fork elongation. Proceedings of the National Academy of Sciences of the United States of America. 104: 16739-46. PMID 17940024 DOI: 10.1073/Pnas.0707804104 |
0.548 |
|
| 2006 |
Tanny RE, MacAlpine DM, Blitzblau HG, Bell SP. Genome-wide analysis of re-replication reveals inhibitory controls that target multiple stages of replication initiation Molecular Biology of the Cell. 17: 2415-2423. PMID 16525018 DOI: 10.1091/Mbc.E05-11-1037 |
0.573 |
|
| 2005 |
MacAlpine DM, Bell SP. A genomic view of eukaryotic DNA replication. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. 13: 309-326. PMID 15868424 DOI: 10.1007/S10577-005-1508-1 |
0.605 |
|
| 2005 |
Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. Temporal profile of replication of human chromosomes. Proceedings of the National Academy of Sciences of the United States of America. 102: 6419-24. PMID 15845769 DOI: 10.1073/Pnas.0405088102 |
0.481 |
|
| 2004 |
MacAlpine DM, Rodríguez HK, Bell SP. Coordination of replication and transcription along a Drosophila chromosome Genes and Development. 18: 3094-3105. PMID 15601823 DOI: 10.1101/Gad.1246404 |
0.566 |
|
| 2004 |
Schübeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O'Neill LP, Turner BM, Delrow J, Bell SP, Groudine M. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes & Development. 18: 1263-71. PMID 15175259 DOI: 10.1101/Gad.1198204 |
0.454 |
|
| 2002 |
Claycomb JM, MacAlpine DM, Evans JG, Bell SP, Orr-Weaver TL. Visualization of replication initiation and elongation in Drosophila. The Journal of Cell Biology. 159: 225-36. PMID 12403810 DOI: 10.1083/Jcb.200207046 |
0.535 |
|
| 2001 |
Macalpine DM, Kolesar J, Okamoto K, Butow RA, Perlman PS. Replication and preferential inheritance of hypersuppressive petite mitochondrial DNA Embo Journal. 20: 1807-1817. PMID 11285243 DOI: 10.1093/Emboj/20.7.1807 |
0.467 |
|
| 2000 |
MacAlpine DM, Perlman PS, Butow RA. The numbers of individual mitochondrial DNA molecules and mitochondrial DNA nucleoids in yeast are co-regulated by the general amino acid control pathway Embo Journal. 19: 767-775. PMID 10675346 DOI: 10.1093/Emboj/19.4.767 |
0.32 |
|
| 1998 |
Macalpine DM, Perlman PS, Butow RA. The high mobility group protein Abf2p influences the level of yeast mitochondrial DNA recombination intermediates in vivo Proceedings of the National Academy of Sciences of the United States of America. 95: 6739-6743. PMID 9618482 DOI: 10.1073/Pnas.95.12.6739 |
0.351 |
|
| 1997 |
Zhang Z, Macalpine DM, Kapler GM. Developmental regulation of DNA replication: Replication fork barriers and programmed gene amplification in Tetrahymena thermophila Molecular and Cellular Biology. 17: 6147-6156. PMID 9315675 DOI: 10.1128/Mcb.17.10.6147 |
0.552 |
|
| 1997 |
MacAlpine DM, Zhang Z, Kapler GM. Type I elements mediate replication fork pausing at conserved upstream sites in the Tetrahymena thermophila ribosomal DNA minichromosome Molecular and Cellular Biology. 17: 4517-4525. PMID 9234709 DOI: 10.1128/Mcb.17.8.4517 |
0.537 |
|
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