Publications (* denotes equal contribution)(Danko lab members underlined.) [Pubmed][Google Scholar]

  • Preprints
    Genetic Dissection of the RNA Polymerase II Transcription Cycle.
    Chou SP, Alexander AK, Rice EJ, Choate LA, Cohen PE, Danko CG.
    Preprint: bioRxiv.

    Multiple stages of evolutionary change in anthrax toxin receptor expression in humans.
    Choate LA, Barshad G, McMahon PW, Said I, Rice EJ, Munn PR, Lewis JJ, Danko CG.
    Preprint: bioRxiv.

    A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq).
    Judd J, Wojenski LA, Wainman LM, Tippens ND, Rice EJ, Dziubek A, Villafano GJ, Wissink EW, Versluis P, Bagepalli L, Shah SR, Mahat DB, Tome JM, Danko CG, Lis JT, Core LJ.
    Preprint: bioRxiv.

    Accurate imputation of histone modifications using transcription.
    Wang Z, Chivu AG, Choate LA, Rice EJ, Miller DC, Chu T, Chou S, Kingsley NB, Petersen JL, Finno CJ, Bellone RR, Antczak DF, Danko CG.
    Preprint: bioRxiv.

    Bayesian Inference of Cell Composition and Gene Expression Reveals Tumor-Microenvironment Interactions.
    Chu T, Danko CG.
    Preprint: bioRxiv.

  • 2021
    Identification and prediction of developmental enhancers in sea urchin embryos.
    Arenas-Mena C, Miljovska S, Rice EJ, Gurges J, Shashikant T, Ercan S, Danko CG.
    BMC Genomics. Preprint: bioRxiv.

    Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells.
    Zhao Y, Dukler N, Barshad G, Toneyan S, Danko CG, Siepel A.
    Bioinformatics. Preprint: bioRxiv.

    Chromosome fusion affects genetic diversity and evolutionary turnover of functional loci, but consistently depends on chromosome size.
    Cicconardi F, Lewis JJ, Martin SH, Reed RD, Danko CG, Montgomery SH.
    Molecular Biology and Evolution.

    The Dryas iulia genome supports multiple gains of a W chromosome from a B chromosome in butterflies.
    Lewis JJ, Cicconardi F, Martin SH, Reed RD, Danko CG, Montgomery SH.
    Genome Biology and Evolution.

    Uncovering Transcriptional Dark Matter via Gene Annotation Independent Single-Cell RNA Sequencing Analysis.
    Wang MFZ, Mantri M, Chou SP, Scuderi GJ, McKellar D, Butcher JT, Danko CG, De Vlaminck I.
    Nature Communications. Preprint: bioRxiv.

    Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data.
    Blumberg A, Zhao Y, Huang YF, Dukler N, Rice EJ, Chivu AG, Krumholz K, Danko CG, Siepel A.
    BMC Biology. Preprint: bioRxiv.

    GLP-1 receptor signaling increases PCSK1 and β cell features in human α cells.
    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.
    JCI Insight.
  • 2020
    Many functionally connected loci foster adaptive diversification along a neotropical hybrid zone.
    Lewis JJ, Van Belleghem SM, Papa R, Danko CG, Reed RD.
    Science Advances.

    The H2BG53D oncohistone directly upregulates ANXA3 transcription and enhances cell migration in Pancreatic Ductal Adenocarcinoma.
    Wan YCE, Liu J, Zhu L, Kang TZE, Zhu X, Ramakrishnan S, Tai SK, Yang D, Chan SY, Chan LL, Li Q, Lis J, Ishibashi T, Han J, Danko CG, Wang X, Chan KM.
    Signal Transduction and Targeted Therapy.

    Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance.
    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.
    BMC Veterinary Research.

    Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance.
    Dinh TA, Sritharan R, Smith FD, Francisco AB, Ma RK, Bunaciu RP, Kanke M, Danko CG, Massa AP, Scott JD, Sethupathy P.
    Cell Reports. Preprint: bioRxiv.

    Elevated circulating Th2 but not group 2 innate lymphoid cell responses characterize canine atopic dermatitis.
    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.
    Vet Immunol Immunopathol.
  • 2019
    Parallel evolution of ancient, pleiotropic enhancers underlies butterfly wing pattern mimicry.
    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.
    Proc Natl Acad Sci U S A.

    Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.
    Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT.
    Proc Natl Acad Sci U S A. Preprint: bioRxiv.

    Physical confinement induces malignant transformation in mammary epithelial cells.
    Lu YC, Chu T, Hall MS, Fu DJ, Shi Q, Chiu A, An D, Wang L, Pardo Y, Southard T, Danko CG, Liphardt J, Nikitin AY, Wu M, Fischbach C, Coonrod S, Ma M.

    Contrasting Roles of Transcription Factors Spineless and EcR in the Highly Dynamic Chromatin Landscape of Butterfly Wing Metamorphosis.
    van der Burg KRL, Lewis JJ, Martin A, Nijhout HF, Danko CG, Reed RD.
    Cell Reports.

    The Notch signaling pathway promotes basophil responses during helminth-induced type 2 inflammation.
    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.
    J Exp Med.

    AlleleHMM: a data-driven method to identify allele-specific differences in distributed functional genomic marks.
    Chou S, Danko CG.
    Nucleic Acids Research. Preprint: bioRxiv.

    Identification of regulatory elements from nascent transcription using dREG.
    Wang Z, Chu T, Choate LA, Danko CG.
    Genome Research. Preprint: bioRxiv.

    Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells.
    Saikia M, Burnham P, Keshavjee SH, Wang MFZ, Moral-Lopez P, Hinchman MM, Danko CG, Parker JSL, De Vlaminck I
    Nature Methods. Preprint: bioRxiv. Featured in preLights.
  • 2018 Discovering Transcriptional Regulatory Elements From Run‐On and Sequencing Data Using the Web-Based dREG Gateway.
    Chu T, Wang Z, Chou S, Danko CG.
    Current Protocols in Bioinformatics.

    Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme.
    Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, List JT, Kwak H, Danko CG.
    Nature Genetics. Preprint: bioRxiv.

    Building a Science Gateway for processing and modeling sequencing data via Apache Airavata.
    Wang Z, Christie M, Abeysinghe E, Chu T, Marru S, Pierce M, Danko CG.
    Proceedings of the Practice and Experience on Advanced Research Computing Article No. 39.

    A common pattern of DNase-I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization.
    Blumberg A, Danko CG, Kundaje A, Mishmar D.
    Genome Research. Preprint: bioRxiv.

    A bi-stable feedback loop between GDNF, EGR1, and ERα contribute to endocrine resistant breast cancer.
    Horibata S, Rice EJ, Zheng H, Mukai C, Chu T, Marks BA, Coonrod SA, Danko CG.
    PLoS One.

    ER-positive breast cancer cells are poised for RET-mediated endocrine resistance.
    Horibata S, Rice EJ, Mukai C, Marks BA, Sams K, Zheng H, Anguish LJ, Coonrod SA, Danko CG.
    PLoS One.

    Herpes Simplex Virus 1 Dramatically Alters Loading and Positioning of RNA Polymerase II on Host Genes Early in Infection.
    Birkenheuer CH, Danko CG, Baines JD.
    J Virology.

    Dynamic evolution of regulatory element ensembles in primate CD4+ T cells.
    Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait-Wojno E, List JT, Kraus WL, Siepel A.
    Nature Ecology & Evolution. Preprint: bioRxiv. Featured in a perspective piece.
  • 2017 XX Disorder of Sex Development is associated with an insertion on chromosome 9 and downregulation of RSPO1 in dogs (Canis lupus familiaris).
    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.
    PLoS One.

    Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.
    Dukler N, Booth GT, Huang YF, Tippens N, Danko CG, Lis JT, Siepel A.
    Genome Research. Preprint: bioRxiv.

    Transcriptional response to stress is pre-wired by promoter and enhancer architecture.
    Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L.
    Nature Communications.

    Initiation of mtDNA transcription is followed by pausing, and diverge across human cell types and during evolution.
    Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D.
    Genome Research. Preprint: bioRxiv.

    Rgtsvm: Support Vector Machines on a GPU in R.
    Wang Z, Chu T, Choate LA, Danko CG.
    Preprint: arXiv.
  • 2016 Poised for development.
    Choate LA, Danko CG.
    Nature Genetics. Our News and Views article on: Lesch et. al. (2016). Nature Genetics.

    Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq).
    Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT.
    Nature Protocols.

    RTFBSDB: an integrated framework for transcription factor binding site analysis.
    Wang Z, Martins AL, Danko CG.
    Bioinformatics. Preprint: bioRxiv. Software: Github.

    Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation.
    Mahat DB, Salamanca H, Duarte FM, Danko CG, Lis JT.
    Molecular Cell.
  • 2015 Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality.
    Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA.
    Cell Reports. Cover Article.

    groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data.
    Chae M, Danko CG, Kraus WL.
    BMC Bioinformatics. Highly accessed.

    A unified architecture of transcriptional regulatory elements.
    Andersson R, Sandelin A, Danko CG.
    Trends in Genetics. Preprint: bioRxiv.

    GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters.
    Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT.
    PLoS Genetics.

    Identification of active transcriptional regulatory elements from GRO-seq data.
    Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, and Siepel A.
    Nature Methods. Preprint: bioRxiv. Software: Github. Data: UCSC Track hub.
  • 2014 Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.
    Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT.
    Nature Genetics. Featured in NG News and Views.

    Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFalpha signaling revealed by integrated genomic analyses.
    Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL.
    BMC Genomics.

    Change in ß-Catenin Localization Suggests Involvement of the Canonical Wnt Pathway in Boxer Dogs with Arrhythmogenic Right Ventricular Cardiomyopathy.
    Oxford EM, Danko CG, Fox PR, Kornreich BG, Moïse NS.
    Journal of Veterinary Internal Medicine.
  • 2013 Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites.
    Hah N, Murakami S, Nagari A, Danko CG, Kraus WL.
    Genome Research.

    Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans.
    Zeng L, Sang Chul C, Danko CG, Siepel A, Stanhope MJ, Burne RA.
    PLoS ONE.

    Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells.
    Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL.
    Molecular Cell. Featured in a perspective piece. Cover Article. Recommended by F1000.
  • 2011 Bayesian inference of ancient human demography from individual genome sequences.
    Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A.
    Nature Genetics.

    Ultrastructural changes in cardiac myocytes from Boxer dogs with arrhythmogenic right ventricular cardiomyopathy.
    Oxford EM, Danko CG, Kornreich BG, Maass K, Hemsley SA, Raskolnikov D, Fox PR, Delmar M, Moïse NS.
    Journal of Veterinary Cardiology. Cover Article.

    A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.
    Hah N*, Danko CG*, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL.
    Cell. Featured in a perspective piece.
  • 2010- Complete Khoisan and Bantu genomes from southern Africa.
    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, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM.
    Nature. Cover Article.

    Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease.
    Danko CG, Pertsov AM.
    BMC Medical Genomics.

    Bioinformatic identification of novel putative photoreceptor specific cis-elements.
    Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.
    BMC Bioinformatics.

    MeCP2 expression in human cerebral cortex and lymphoid cells: immunochemical characterization of a novel higher-molecular-weight form.
    Jarrar MH, Danko CG, Reddy S, Lee YJ, Bibat G, Kaufmann WE.
    Journal of Child Neurology.