Tools and software

  • Grüning B*, Dale RK*, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J, Bioconda Team (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods 15, 475-476. external link
  • Dale RK, Matzat LH, Lei EP (2014). metaseq: a Python package for integrative genome-wide analysis reveals relationships between chromatin insulators and associated nuclear mRNA. Nucleic Acids Res 42, 9158-70. external link
  • Dale RK, Pedersen BS, Quinlan AR (2011). Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 27, 3423-4. external link


(BSPC members in bold).

  • Chang E, Fu C, Coon SL, Alon S, Bozinoski M, Breymaier M, Bustos DM, Clokie SJ, Gothilf Y, Esnault C, Michael Iuvone P, Mason CE, Ochocinska MJ, Tovin A, Wang C, Xu P, Zhu J, Dale R, Klein DC (2020) Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. J Pineal Res, in press (e-pub ahead of print) external link
  • Kang H, Jha S, Ivovic A, Fratzl-Zelman N, Deng Z, Mitra A, Cabral WA, Hanson EP, Lange E, Cowen EW, Katz J, Roschger P, Klaushofer K, Dale RK, Siegel RM, Bhattacharyya T, Marini JC (2020). Somatic SMAD3-activating mutations cause melorheostosis by up-regulating the TGF-β/SMAD pathway. J Exp Med 217. external link
  • Lee SY, Hung S, Esnault C, Pathak R, Johnson KR, Bankole O, Yamashita A, Zhang H, Levin HL (2020). Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation. Cell Rep 30, 2686-2698.e8. external link
  • Li L, Mitra A, Cui K, Zhao B, Choi S, Lee JY, Stamos DB, El-Khoury D, Warzecha C, Pfeifer K, Hardwick J, Zhao K, Venters B, Davé UP, Love PE (2020). Ldb1 is required for Lmo2 oncogene-induced thymocyte self-renewal and T-cell acute lymphoblastic leukemia. Blood 135, 2252-2265. external link
  • Martin KB, Williams IM, Cluzeau CV, Cougnoux A, Dale RK, Iben JR, Cawley NX, Wassif CA, Porter FD (2020). Identification of Novel Pathways Associated with Patterned Cerebellar Purkinje Neuron Degeneration in Niemann-Pick Disease, Type C1. Int J Mol Sci 21. external link
  • Matson CA, Choi S, Livak F, Zhao B, Mitra A, Love PE, Singh NJ (2020). CD5 dynamically calibrates basal NF-κB signaling in T cells during thymic development and peripheral activation. Proc Natl Acad Sci U S A 117, 14342-14353. external link
  • Tanizaki Y, Shibata Y, Zhang H, Shi YB (2020) Analysis of Thyroid Hormone Receptor α-Knockout Tadpoles Reveals That the Activation of Cell Cycle Program Is Involved in Thyroid Hormone-Induced Larval Epithelial Cell Death and Adult Intestinal Stem Cell Development During Xenopus tropicalis Metamorphosis. Thyroid, in press (e-pub ahead of print) external link
  • Zhou F, Zhang H, Kulkarni SD, Lorsch JR, Hinnebusch AG (2020). eIF1 discriminates against suboptimal initiation sites to prevent excessive uORF translation genome-wide. RNA 26, 419-438. external link
  • Kulkarni SD, Zhou F, Sen ND, Zhang H, Hinnebusch AG, Lorsch JR (2019). Temperature-dependent regulation of upstream open reading frame translation in S. cerevisiae. BMC Biol 17, 101. external link
  • Melamed S, Adams PP, Zhang A, Zhang H, Storz G (2019). RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles. Mol Cell 77, 411-425.e7. external link
  • Nakajima K, Tanizaki Y, Luu N, Zhang H, Shi YB (2019). Comprehensive RNA-Seq analysis of notochord-enriched genes induced during Xenopus tropicalis tail resorption. Gen Comp Endocrinol 287, 113349. external link
  • Chen D, Dale RK, Lei EP (2018). Shep regulates neuronal remodeling by controlling transcription of its chromatin targets. Development 145. external link
  • Nazer E, Dale RK, Chinen M, Radmanesh B, Lei EP (2018). Argonaute2 and LaminB modulate gene expression by controlling chromatin topology. PLoS Genet 14, e1007276. external link
  • Lee J, Krivega I, Dale RK, Dean A (2017). The LDB1 complex co-opts CTCF for erythroid lineage-specific long-range enhancer interactions. Cell Rep 19, 2490-2502. external link
  • Clough E, Jimenez E, Kim Y, Whitworth C, Neville MC, Hempel LU, Pavlou HJ, Chen Z, Sturgill D, Dale RK, Smith HE, Przytycka TM, Goodwin SF, Van Doren M, Oliver B (2014). Sex- and tissue-specific functions of Drosophila Doublesex transcription factor target genes. Dev Cell 31, 761-773. external link
  • King MR, Matzat LH, Dale RK, Lim SJ, Lei EP (2014). The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner. J Cell Sci 127, 2956-66. external link
  • Krivega I, Dale RK, Dean A (2014) Role of LDB1 in the transition from chromatin looping to transcription activation. Genes Dev 28:1278-90
  • Li L, Freudenberg J, Cui K, Dale R, Song SH, Dean A, Zhao K, Jothi R, Love PE (2013). Ldb1-nucleated transcription complexes function as primary mediators of global erythroid gene activation. Blood 121, 4575-85.
  • Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP (2013). Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic Acids Res 41, 2963-80.
  • Matzat LH, Dale RK, Lei EP (2013). Messenger RNA is a functional component of a chromatin insulator complex. EMBO Rep 14, 916-22. external link
  • Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, et al. [10 more authors] (2013). A compendium of RNA-binding motifs for decoding gene regulation. Nature 499, 172-7. external link
  • Junier I, Dale RK, Hou C, Képès F, Dean A (2012). CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the beta-globin locus. Nucleic Acids Res 40, 7718-27. external link
  • Malone JH, Cho DY, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, Smith HE, McDaniel J, Munro S, Salit M, Andrews J, Przytycka TM, Oliver B (2012). Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biol 13, r28. external link
  • Matzat LH, Dale RR, Moshkovich N, Lei EP (2012) Tissue-specific regulation of chromatin insulator function. PLoS Genet 8:e1003069
  • Song SH, Kim A, Dale R, Dean A (2012) Ldb1 regulates carbonic anhydrase 1 during erythroid differentiation. Biochim Biophys Acta 1819:885-91
  • Kiefer CM, Lee J, Hou C, Dale RK, Lee YT, Meier ER, Miller JL, Dean A (2011) Distinct Ldb1/NLI complexes orchestrate -globin repression and reactivation through ETO2 in human adult erythroid cells. Blood 118:6200-8.
  • Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, Lei EP (2011) RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev 25:1686-701.
  • Hou C, Dale R, Dean A (2010) Cell type specificity of chromatin organization mediated by CTCF and cohesin. Proc Natl Acad Sci U S A 107:3651-6.
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