Charles G Danko - Publications

Biological Statistics and Computational Biology Cornell University, Ithaca, NY, United States 

58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2021 Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A. Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics (Oxford, England). PMID 34382072 DOI: 10.1093/bioinformatics/btab582  1
2021 Cicconardi F, Lewis JJ, Martin SH, Reed RD, Danko CG, Montgomery SH. Chromosome fusion affects genetic diversity and evolutionary turnover of functional loci, but consistently depends on chromosome size. Molecular Biology and Evolution. PMID 34146107 DOI: 10.1093/molbev/msab185  1
2021 Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH. The Dryas iulia genome supports multiple gains of a W chromosome from a B chromosome in butterflies. Genome Biology and Evolution. PMID 34117762 DOI: 10.1093/gbe/evab128  1
2021 Wang MFZ, Mantri M, Chou SP, Scuderi GJ, McKellar DW, Butcher JT, Danko CG, De Vlaminck I. Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis. Nature Communications. 12: 2158. PMID 33846360 DOI: 10.1038/s41467-021-22496-3  0.01
2021 Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. Bmc Biology. 19: 30. PMID 33588838 DOI: 10.1186/s12915-021-00949-x  1
2021 Saikia M, Holter MM, Donahue LR, Lee IS, Zheng QC, Wise JL, Todero JE, Phuong DJ, Garibay D, Coch R, Sloop KW, Garcia-Ocana A, Danko CG, Cummings BP. GLP-1 receptor signaling increases PCSK1 and β cell features in human α cells. Jci Insight. 6. PMID 33554958 DOI: 10.1172/jci.insight.141851  0.04
2020 Lewis JJ, Van Belleghem SM, Papa R, Danko CG, Reed RD. Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone. Science Advances. 6. PMID 32978147 DOI: 10.1126/sciadv.abb8617  1
2020 Wan YCE, Liu J, Zhu L, Kang TZE, Zhu X, Lis J, Ishibashi T, Danko CG, Wang X, Chan KM. The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in pancreatic ductal adenocarcinoma. Signal Transduction and Targeted Therapy. 5: 106. PMID 32606294 DOI: 10.1038/S41392-020-00219-2  0.01
2020 Mukai C, Choi E, Sams KL, Klampen EZ, Anguish L, Marks BA, Rice EJ, Wang Z, Choate LA, Chou SP, Kato Y, Miller AD, Danko CG, Coonrod SA. Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis. Bmc Veterinary Research. 16: 206. PMID 32571313 DOI: 10.1186/s12917-020-02395-3  1
2020 Dinh TA, Sritharan R, Smith FD, Francisco AB, Ma RK, Bunaciu RP, Kanke M, Danko CG, Massa AP, Scott JD, Sethupathy P. Hotspots of Aberrant Enhancer Activity in Fibrolamellar Carcinoma Reveal Candidate Oncogenic Pathways and Therapeutic Vulnerabilities. Cell Reports. 31: 107509. PMID 32294439 DOI: 10.1016/J.Celrep.2020.03.073  0.01
2020 Früh SP, Saikia M, Eule J, Mazulis CA, Miller JE, Cowulich JM, Oyesola OO, Webb LM, Peng SA, Cubitt RL, Danko CG, Miller WH, Tait Wojno ED. Elevated circulating Th2 but not group 2 innate lymphoid cell responses characterize canine atopic dermatitis. Veterinary Immunology and Immunopathology. 221: 110015. PMID 32058160 DOI: 10.1016/J.Vetimm.2020.110015  0.04
2020 Saikia M, Holter MM, Garibay D, Garcia-Ocana A, Danko CG, Cummings B. 1784-P: Liraglutide Treatment Stimulates Alpha Cells to Produce Glucagon-Like Peptide-1 via Expression of Prohormone Convertase 1/3 in Mice and Human Diabetes. 69. DOI: 10.2337/Db20-1784-P  0.01
2019 Lewis JJ, Geltman RC, Pollak PC, Rondem KE, Van Belleghem SM, Hubisz MJ, Munn PR, Zhang L, Benson C, Mazo-Vargas A, Danko CG, Counterman BA, Papa R, Reed RD. Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry. Proceedings of the National Academy of Sciences of the United States of America. PMID 31712408 DOI: 10.1073/Pnas.1907068116  1
2019 Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT. Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock. Proceedings of the National Academy of Sciences of the United States of America. PMID 31506350 DOI: 10.1073/Pnas.1901244116  1
2019 Lu YC, Chu T, Hall MS, Fu DJ, Shi Q, Chiu A, An D, Wang LH, Pardo Y, Southard T, Danko CG, Liphardt J, Nikitin AY, Wu M, Fischbach C, et al. Physical confinement induces malignant transformation in mammary epithelial cells. Biomaterials. 217: 119307. PMID 31271857 DOI: 10.1016/J.Biomaterials.2019.119307  1
2019 van der Burg KRL, Lewis JJ, Martin A, Nijhout HF, Danko CG, Reed RD. Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis. Cell Reports. 27: 1027-1038.e3. PMID 31018121 DOI: 10.1016/J.Celrep.2019.03.092  1
2019 Webb LM, Oyesola OO, Früh SP, Kamynina E, Still KM, Patel RK, Peng SA, Cubitt RL, Grimson A, Grenier JK, Harris TH, Danko CG, Tait Wojno ED. The Notch signaling pathway promotes basophil responses during helminth-induced type 2 inflammation. The Journal of Experimental Medicine. PMID 30975892 DOI: 10.1084/Jem.20180131  1
2019 Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D. Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Genome Research. 29: 710.1. PMID 30936176 DOI: 10.1101/gr.248971.119  1
2019 Chou SP, Danko CG. AlleleHMM: a data-driven method to identify allele specific differences in distributed functional genomic marks. Nucleic Acids Research. PMID 30918970 DOI: 10.1093/nar/gkz176  0.08
2018 Wang Z, Christie MA, Abeysinghe E, Chu T, Marru S, Pierce M, Danko CG. Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata. Practice and Experience in Advanced Research Computing 2018 : Seamless Creativity : July 22-26 2017, Pittsburgh, Pennsylvania. Practice and Experience in Advanced Research Computing (Conference) (2018 : Pittsburgh, Pa.). 2018. PMID 31598610 DOI: 10.1145/3219104.3219141  1
2018 Chu T, Wang Z, Chou SP, Danko CG. Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway. Current Protocols in Bioinformatics. e70. PMID 30589513 DOI: 10.1002/cpbi.70  1
2018 Wang Z, Chu T, Choate LA, Danko CG. Identification of regulatory elements from nascent transcription using dREG. Genome Research. PMID 30573452 DOI: 10.1101/gr.238279.118  1
2018 Saikia M, Burnham P, Keshavjee SH, Wang MFZ, Heyang M, Moral-Lopez P, Hinchman MM, Danko CG, Parker JSL, De Vlaminck I. Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells. Nature Methods. PMID 30559431 DOI: 10.1038/S41592-018-0259-9  0.01
2018 Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, Lis JT, Kwak H, Danko CG. Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme. Nature Genetics. PMID 30349114 DOI: 10.1038/S41588-018-0244-3  1
2018 Blumberg A, Danko CG, Kundaje A, Mishmar D. A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization. Genome Research. 28: 1158-1168. PMID 30002158 DOI: 10.1101/Gr.230409.117  1
2018 Horibata S, Rice EJ, Zheng H, Mukai C, Chu T, Marks BA, Coonrod SA, Danko CG. A bi-stable feedback loop between GDNF, EGR1, and ERα contribute to endocrine resistant breast cancer. Plos One. 13: e0194522. PMID 29614078 DOI: 10.1371/journal.pone.0194522  1
2018 Horibata S, Rice EJ, Mukai C, Marks BA, Sams K, Zheng H, Anguish LJ, Coonrod SA, Danko CG. ER-positive breast cancer cells are poised for RET-mediated endocrine resistance. Plos One. 13: e0194023. PMID 29608602 DOI: 10.1371/journal.pone.0194023  1
2018 Birkenheuer CH, Danko CG, Baines JD. Herpes Simplex Virus 1 Dramatically Alters Loading and Positioning of RNA Polymerase II on Host Genes Early in Infection. Journal of Virology. PMID 29437966 DOI: 10.1128/JVI.02184-17  0.01
2018 Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait Wojno ED, Lis JT, Kraus WL, Siepel A. Dynamic evolution of regulatory element ensembles in primate CD4+ T cells. Nature Ecology & Evolution. PMID 29379187 DOI: 10.1038/S41559-017-0447-5  1
2017 Meyers-Wallen VN, Boyko AR, Danko CG, Grenier JK, Mezey JG, Hayward JJ, Shannon LM, Gao C, Shafquat A, Rice EJ, Pujar S, Eggers S, Ohnesorg T, Sinclair AH. XX Disorder of Sex Development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris). Plos One. 12: e0186331. PMID 29053721 DOI: 10.1371/Journal.Pone.0186331  1
2017 Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A. Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Research. PMID 29025894 DOI: 10.1101/Gr.222935.117  1
2017 Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L. Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Nature Communications. 8: 255. PMID 28811569 DOI: 10.1038/S41467-017-00151-0  1
2017 Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D. Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Genome Research. 27: 362-373. PMID 28049628 DOI: 10.1101/Gr.209924.116  1
2016 Choate LA, Danko CG. Poised for development. Nature Genetics. 48: 822-3. PMID 27463395 DOI: 10.1038/ng.3628  0.28
2016 Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols. 11: 1455-1476. PMID 27442863 DOI: 10.1038/Nprot.2016.086  1
2016 Wang Z, Martins AL, Danko CG. RTFBSDB: an integrated framework for transcription factor binding site analysis. Bioinformatics (Oxford, England). PMID 27288497 DOI: 10.1093/bioinformatics/btw338  1
2016 Mahat DB, Salamanca HH, Duarte FM, Danko CG, Lis JT. Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation. Molecular Cell. 62: 63-78. PMID 27052732 DOI: 10.1016/j.molcel.2016.02.025  1
2016 Lis JT, Danko C, Duarte F, Mahat DB. Abstract IA05: Genome-wide views into the mechanisms of transcription regulation Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-Ia05  1
2015 Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA. Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality. Cell Reports. PMID 26411685 DOI: 10.1016/J.Celrep.2015.08.075  1
2015 Chae M, Danko CG, Kraus WL. groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. Bmc Bioinformatics. 16: 222. PMID 26173492 DOI: 10.1186/s12859-015-0656-3  1
2015 Andersson R, Sandelin A, Danko CG. A unified architecture of transcriptional regulatory elements. Trends in Genetics : Tig. 31: 426-33. PMID 26073855 DOI: 10.1016/j.tig.2015.05.007  0.01
2015 Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. Plos Genetics. 11: e1005108. PMID 25815464 DOI: 10.1371/Journal.Pgen.1005108  1
2015 Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. Identification of active transcriptional regulatory elements from GRO-seq data. Nature Methods. 12: 433-8. PMID 25799441 DOI: 10.1038/Nmeth.3329  1
2015 Chae M, Danko CG, Kraus WL. groHMM: A computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data Bmc Bioinformatics. DOI: 10.1186/s12859-015-0656-3  1
2014 Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nature Genetics. 46: 1311-20. PMID 25383968 DOI: 10.1038/Ng.3142  1
2014 Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL. Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses. Bmc Genomics. 15: 155. PMID 24564208 DOI: 10.1186/1471-2164-15-155  1
2014 Oxford EM, Danko CG, Fox PR, Kornreich BG, Moïse NS. Change in β-catenin localization suggests involvement of the canonical Wnt pathway in Boxer dogs with arrhythmogenic right ventricular cardiomyopathy. Journal of Veterinary Internal Medicine / American College of Veterinary Internal Medicine. 28: 92-101. PMID 24428316 DOI: 10.1111/Jvim.12238  1
2013 Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. Enhancer transcripts mark active estrogen receptor binding sites. Genome Research. 23: 1210-23. PMID 23636943 DOI: 10.1101/gr.152306.112  1
2013 Zeng L, Choi SC, Danko CG, Siepel A, Stanhope MJ, Burne RA. Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. Plos One. 8: e60465. PMID 23555977 DOI: 10.1371/Journal.Pone.0060465  1
2013 Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Molecular Cell. 50: 212-22. PMID 23523369 DOI: 10.1016/J.Molcel.2013.05.025  1
2011 Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences Nature Genetics. 43: 1031-1034. PMID 21926973 DOI: 10.1038/Ng.937  1
2011 Oxford EM, Danko CG, Kornreich BG, Maass K, Hemsley SA, Raskolnikov D, Fox PR, Delmar M, Moïse NS. Ultrastructural changes in cardiac myocytes from Boxer dogs with arrhythmogenic right ventricular cardiomyopathy. Journal of Veterinary Cardiology : the Official Journal of the European Society of Veterinary Cardiology. 13: 101-13. PMID 21636338 DOI: 10.1016/J.Jvc.2011.03.002  1
2011 Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 145: 622-34. PMID 21549415 DOI: 10.1016/J.Cell.2011.03.042  1
2011 Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. Erratum: A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells (Cell (2011) 145 (622-634)) Cell. 145. DOI: 10.1016/J.Cell.2011.06.003  1
2010 Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, ... ... Danko CG, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463: 943-7. PMID 20164927 DOI: 10.1038/Nature08795  1
2009 Danko CG, Pertsov AM. Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. Bmc Medical Genomics. 2: 31. PMID 19476647 DOI: 10.1186/1755-8794-2-31  0.01
2007 Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM. Bioinformatic identification of novel putative photoreceptor specific cis-elements. Bmc Bioinformatics. 8: 407. PMID 17953763 DOI: 10.1186/1471-2105-8-407  0.01
2003 Jarrar MH, Danko CG, Reddy S, Lee YJ, Bibat G, Kaufmann WE. MeCP2 expression in human cerebral cortex and lymphoid cells: immunochemical characterization of a novel higher-molecular-weight form. Journal of Child Neurology. 18: 675-82. PMID 14649548 DOI: 10.1177/08830738030180101001  1
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