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Items: 43

1.

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. 2019 Nov 26;116(48):24174-24183. doi: 10.1073/pnas.1907068116. Epub 2019 Nov 11.

PMID:
31712408
2.

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. 2019 Sep 24;116(39):19431-19439. doi: 10.1073/pnas.1901244116. Epub 2019 Sep 10.

PMID:
31506350
3.

Physical confinement induces malignant transformation in mammary epithelial cells.

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, Coonrod S, Ma M.

Biomaterials. 2019 Oct;217:119307. doi: 10.1016/j.biomaterials.2019.119307. Epub 2019 Jun 26.

PMID:
31271857
4.

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 Rep. 2019 Apr 23;27(4):1027-1038.e3. doi: 10.1016/j.celrep.2019.03.092.

5.

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. 2019 Jun 3;216(6):1268-1279. doi: 10.1084/jem.20180131. Epub 2019 Apr 11.

6.

Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution.

Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D.

Genome Res. 2019 Apr;29(4):710.1. doi: 10.1101/gr.248971.119. No abstract available.

7.

AlleleHMM: a data-driven method to identify allele specific differences in distributed functional genomic marks.

Chou SP, Danko CG.

Nucleic Acids Res. 2019 Jun 20;47(11):e64. doi: 10.1093/nar/gkz176.

8.

Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway.

Chu T, Wang Z, Chou SP, Danko CG.

Curr Protoc Bioinformatics. 2019 Jun;66(1):e70. doi: 10.1002/cpbi.70. Epub 2018 Dec 27.

PMID:
30589513
9.

Identification of regulatory elements from nascent transcription using dREG.

Wang Z, Chu T, Choate LA, Danko CG.

Genome Res. 2019 Feb;29(2):293-303. doi: 10.1101/gr.238279.118. Epub 2018 Dec 20.

10.

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells.

Saikia M, Burnham P, Keshavjee SH, Wang MFZ, Heyang M, Moral-Lopez P, Hinchman MM, Danko CG, Parker JSL, De Vlaminck I.

Nat Methods. 2019 Jan;16(1):59-62. doi: 10.1038/s41592-018-0259-9. Epub 2018 Dec 17.

11.

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, Lis JT, Kwak H, Danko CG.

Nat Genet. 2018 Nov;50(11):1553-1564. doi: 10.1038/s41588-018-0244-3. Epub 2018 Oct 22.

12.

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 Res. 2018 Aug;28(8):1158-1168. doi: 10.1101/gr.230409.117. Epub 2018 Jul 12.

13.

Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata.

Wang Z, Christie MA, Abeysinghe E, Chu T, Marru S, Pierce M, Danko CG.

Pract Exp Adv Res Comput 2018 (2018). 2018 Jul;2018. pii: 39. doi: 10.1145/3219104.3219141.

14.

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. 2018 Apr 3;13(4):e0194522. doi: 10.1371/journal.pone.0194522. eCollection 2018.

15.

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. 2018 Apr 2;13(4):e0194023. doi: 10.1371/journal.pone.0194023. eCollection 2018.

16.

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 Virol. 2018 Mar 28;92(8). pii: e02184-17. doi: 10.1128/JVI.02184-17. Print 2018 Apr 15.

17.

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 ED, Lis JT, Kraus WL, Siepel A.

Nat Ecol Evol. 2018 Mar;2(3):537-548. doi: 10.1038/s41559-017-0447-5. Epub 2018 Jan 29.

18.

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. 2017 Oct 20;12(10):e0186331. doi: 10.1371/journal.pone.0186331. eCollection 2017.

19.

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, Waters CT, Danko CG, Lis JT, Siepel A.

Genome Res. 2017 Nov;27(11):1816-1829. doi: 10.1101/gr.222935.117. Epub 2017 Oct 12.

20.

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.

Nat Commun. 2017 Aug 15;8(1):255. doi: 10.1038/s41467-017-00151-0.

21.

Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution.

Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D.

Genome Res. 2017 Mar;27(3):362-373. doi: 10.1101/gr.209924.116. Epub 2017 Jan 3. Erratum in: Genome Res. 2019 Apr;29(4):710.1.

22.

Poised for development.

Choate LA, Danko CG.

Nat Genet. 2016 Jul 27;48(8):822-3. doi: 10.1038/ng.3628.

PMID:
27463395
23.

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.

Nat Protoc. 2016 Aug;11(8):1455-76. doi: 10.1038/nprot.2016.086. Epub 2016 Jul 21.

24.

RTFBSDB: an integrated framework for transcription factor binding site analysis.

Wang Z, Martins AL, Danko CG.

Bioinformatics. 2016 Oct 1;32(19):3024-6. doi: 10.1093/bioinformatics/btw338. Epub 2016 Jun 10.

25.

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation.

Mahat DB, Salamanca HH, Duarte FM, Danko CG, Lis JT.

Mol Cell. 2016 Apr 7;62(1):63-78. doi: 10.1016/j.molcel.2016.02.025. Epub 2016 Mar 24.

26.

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 Rep. 2015 Oct 13;13(2):337-49. doi: 10.1016/j.celrep.2015.08.075. Epub 2015 Sep 24.

27.

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. 2015 Jul 16;16:222. doi: 10.1186/s12859-015-0656-3.

28.

A unified architecture of transcriptional regulatory elements.

Andersson R, Sandelin A, Danko CG.

Trends Genet. 2015 Aug;31(8):426-33. doi: 10.1016/j.tig.2015.05.007. Epub 2015 Jun 11. Review.

PMID:
26073855
29.

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 Genet. 2015 Mar 27;11(3):e1005108. doi: 10.1371/journal.pgen.1005108. eCollection 2015 Mar.

30.

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, Siepel A.

Nat Methods. 2015 May;12(5):433-8. doi: 10.1038/nmeth.3329. Epub 2015 Mar 23.

31.

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.

Nat Genet. 2014 Dec;46(12):1311-20. doi: 10.1038/ng.3142. Epub 2014 Nov 10.

32.

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses.

Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL.

BMC Genomics. 2014 Feb 24;15:155. doi: 10.1186/1471-2164-15-155.

33.

Change in β-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.

J Vet Intern Med. 2014 Jan-Feb;28(1):92-101. doi: 10.1111/jvim.12238. Epub 2013 Nov 8.

34.

Enhancer transcripts mark active estrogen receptor binding sites.

Hah N, Murakami S, Nagari A, Danko CG, Kraus WL.

Genome Res. 2013 Aug;23(8):1210-23. doi: 10.1101/gr.152306.112. Epub 2013 May 1.

35.

Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans.

Zeng L, Choi SC, Danko CG, Siepel A, Stanhope MJ, Burne RA.

PLoS One. 2013;8(3):e60465. doi: 10.1371/journal.pone.0060465. Epub 2013 Mar 28.

36.

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.

Mol Cell. 2013 Apr 25;50(2):212-22. doi: 10.1016/j.molcel.2013.02.015. Epub 2013 Mar 21. Erratum in: Mol Cell. 2013 Jun 6;50(5):778.

37.

Bayesian inference of ancient human demography from individual genome sequences.

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A.

Nat Genet. 2011 Sep 18;43(10):1031-4. doi: 10.1038/ng.937.

38.

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.

J Vet Cardiol. 2011 Jun;13(2):101-13. doi: 10.1016/j.jvc.2011.03.002. Epub 2011 Jun 1.

39.

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. 2011 May 13;145(4):622-34. doi: 10.1016/j.cell.2011.03.042. Epub 2011 May 5. Erratum in: Cell. 2011 Jun 24;145(7):1156.

40.

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. 2010 Feb 18;463(7283):943-7. doi: 10.1038/nature08795.

41.

Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease.

Danko CG, Pertsov AM.

BMC Med Genomics. 2009 May 28;2:31. doi: 10.1186/1755-8794-2-31.

42.

Bioinformatic identification of novel putative photoreceptor specific cis-elements.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM.

BMC Bioinformatics. 2007 Oct 22;8:407.

43.

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.

J Child Neurol. 2003 Oct;18(10):675-82.

PMID:
14649548

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