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Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology.

Chu T, Wang Z, Pe'er D, Danko CG. Chu T, et al. Among authors: danko cg, wang z. Nat Cancer. 2022 Apr;3(4):505-517. doi: 10.1038/s43018-022-00356-3. Epub 2022 Apr 25. Nat Cancer. 2022. PMID: 35469013 Free PMC article.

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Prediction of histone post-translational modification patterns based on nascent transcription data.

Wang Z, Chivu AG, Choate LA, Rice EJ, Miller DC, Chu T, Chou SP, Kingsley NB, Petersen JL, Finno CJ, Bellone RR, Antczak DF, Lis JT, Danko CG. Wang Z, et al. Among authors: danko cg. Nat Genet. 2022 Mar;54(3):295-305. doi: 10.1038/s41588-022-01026-x. Epub 2022 Mar 10. Nat Genet. 2022. PMID: 35273399

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Identification and prediction of developmental enhancers in sea urchin embryos.

Arenas-Mena C, Miljovska S, Rice EJ, Gurges J, Shashikant T, Wang Z, Ercan S, Danko CG. Arenas-Mena C, et al. Among authors: danko cg, wang z. BMC Genomics. 2021 Oct 19;22(1):751. doi: 10.1186/s12864-021-07936-0. BMC Genomics. 2021. PMID: 34666684 Free PMC article.

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Chromatin run-on sequencing analysis finds that ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis.

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. Mukai C, et al. Among authors: danko cg, wang z. BMC Vet Res. 2020 Jun 22;16(1):206. doi: 10.1186/s12917-020-02395-3. BMC Vet Res. 2020. PMID: 32571313 Free PMC article.

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

Chu T, Wang Z, Chou SP, Danko CG. Chu T, et al. Among authors: danko cg, wang z. Curr Protoc Bioinformatics. 2019 Jun;66(1):e70. doi: 10.1002/cpbi.70. Epub 2018 Dec 27. Curr Protoc Bioinformatics. 2019. PMID: 30589513 Free PMC article.

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Identification of regulatory elements from nascent transcription using dREG.

Wang Z, Chu T, Choate LA, Danko CG. Wang Z, et al. Among authors: danko cg. Genome Res. 2019 Feb;29(2):293-303. doi: 10.1101/gr.238279.118. Epub 2018 Dec 20. Genome Res. 2019. PMID: 30573452 Free PMC article.

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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. Chu T, et al. Among authors: danko cg, wang z. Nat Genet. 2018 Nov;50(11):1553-1564. doi: 10.1038/s41588-018-0244-3. Epub 2018 Oct 22. Nat Genet. 2018. PMID: 30349114 Free PMC article.

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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. Wang Z, et al. Among authors: danko cg. Pract Exp Adv Res Comput 2018 (2018). 2018 Jul;2018:39. doi: 10.1145/3219104.3219141. Pract Exp Adv Res Comput 2018 (2018). 2018. PMID: 31598610 Free PMC article.

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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. Danko CG, et al. Among authors: wang z. Nat Ecol Evol. 2018 Mar;2(3):537-548. doi: 10.1038/s41559-017-0447-5. Epub 2018 Jan 29. Nat Ecol Evol. 2018. PMID: 29379187 Free PMC article.

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

Wang Z, Martins AL, Danko CG. Wang Z, et al. Among authors: danko cg. Bioinformatics. 2016 Oct 1;32(19):3024-6. doi: 10.1093/bioinformatics/btw338. Epub 2016 Jun 10. Bioinformatics. 2016. PMID: 27288497 Free PMC article.

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