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Biorxiv : the Preprint Server for Biology|July 16, 2025
QCatch: A framework for quality control assessment and analysis of single-cell sequencing dataYuan Gao, Dongze He, Rob PatroBioinformatics (Oxford, England)|April 16, 2026
QCatch: A framework for quality control assessment and analysis of single-cell sequencing dataYuan Gao, Dongze He, Rob PatroBioinformatics (Oxford, England)|October 6, 2023
simpleaf: a simple, flexible, and scalable framework for single-cell data processing using alevin-fryDongze He, Rob PatroBiorxiv : the Preprint Server for Biology|April 10, 2023
simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fryDongze He, Rob PatroBiorxiv : the Preprint Server for Biology|February 19, 2024
Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq readsDongze He, Yuan Gao, Spencer Skylar Chan, et al.Bioinformatics (Oxford, England)|June 28, 2024
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq readsDongze He, Yuan Gao, Spencer Skylar Chan, et al.Biorxiv : the Preprint Server for Biology|January 30, 2023
Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencingDongze He, Charlotte Soneson, Rob PatroBiorxiv : the Preprint Server for Biology|February 14, 2024
scCensus: Off-target scRNA-seq reads reveal meaningful biologyDongze He, Stephen M Mount, Rob PatroBioinformatics (Oxford, England)|October 26, 2024
Collapsible tree: interactive web app to present collapsible hierarchiesYuan Gao, Rob Patro, Peng JiangNature Methods|March 12, 2022
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq dataDongze He, Mohsen Zakeri, Hirak Sarkar, et al.Pageof 509