Bioinformatic identification of novel putative photoreceptor specific cis-elements. - Charles G. Danko; Vera A. McIlvain; Maochun Qin; Barry E. Knox; Arkady M. Pertsov (BMC Bioinform., 2007)

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data. - Minho Chae; Charles G. Danko; W. Kraus (BMC Bioinform., 2015)

RTFBSDB: an integrated framework for transcription factor binding site analysis. - Zhong Wang 001; André L. Martins; Charles G. Danko (Bioinform., 2016)

Rgtsvm: Support Vector Machines on a GPU in R. - Zhong Wang 001; Tinyi Chu; Lauren A. Choate; Charles G. Danko (CoRR, 2017)

Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata. - Zhong Wang 001; Marcus A. Christie; Eroma Abeysinghe; Tinyi Chu; Suresh Marru; Marlon E. Pierce; Charles G. Danko (PEARC, 2018)

Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. - Yixin Zhao; Noah Dukler; Gilad Barshad; Shushan Toneyan; Charles G. Danko; Adam C. Siepel (Bioinform., 2021)

dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility. - Wen Wen; Jiaxin Zhong; Zhaoxi Zhang; Lijuan Jia; Tinyi Chu; Nating Wang; Charles G. Danko; Zhong Wang 001 (Briefings Bioinform., 2024)