David M. MacAlpine - Publications

Affiliations: 
Computational Biology and Bioinformatics Duke University, Durham, NC 
Area:
Bioinformatics, Molecular Biology, Computer Science, Genetics

40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.44
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  1
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  1
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  1
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  1
2015 Pershing NL, Lampson BL, Belsky JA, Kaltenbrun E, MacAlpine DM, Counter CM. Rare codons capacitate Kras-driven de novo tumorigenesis. The Journal of Clinical Investigation. 125: 222-33. PMID 25437878 DOI: 10.1172/JCI77627  1
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  1
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  1
2013 MacAlpine DM, Almouzni G. Chromatin and DNA replication. Cold Spring Harbor Perspectives in Biology. 5: a010207. PMID 23751185 DOI: 10.1101/cshperspect.a010207  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
1994 Andrews DL, MacAlpine DM, Johnson JR, Kelley PM, Cobb BG, Drew MC. Differential induction of mRNAs for the glycolytic and ethanolic fermentative pathways by hypoxia and anoxia in maize seedlings Plant Physiology. 106: 1575-1582. PMID 7846162  1
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