Publications

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

  • Preprints
    Chromatin run-on reveals nascent RNAs that differentiate normal and malignant brain tissue.
    Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, List JT, Kwak H, Danko CG.
    Preprint: bioRxiv.

    Natural Selection has Shaped Coding and Non-coding Transcription 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.
    Preprint: bioRxiv.

    Rgtsvm: Support Vector Machines on a GPU in R.
    Wang Z, Chu T, Choate LA, Danko CG.
    Preprint: arXiv.

    RET Ligands Mediate Endocrine Sensitivity via a Bi-stable Feedback Loop with ERα.
    Horibata S, Rice EJ, Zheng H, Anguish LJ, Mukai C, Marks BA, Chu T, Coonrod S, Danko CG.
    Preprint: bioRxiv.

  • 2017 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.
    In Press @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.
  • 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.