By Dr Hani Kim

Preprints

Cao Y; Tran A; Kim H; Robertson N; Lin Y; Torkel M; Yang P; Patrick E; Ghazanfar S; Yang J, 2023, Thinking process templates for constructing data stories with SCDNEY, http://dx.doi.org/10.12688/f1000research.130623.2

Kim HJ; Kim T; Hoffman NJ; Xiao D; James DE; Humphrey SJ; Yang P, 2020, PhosR Enables Processing and Functional Analysis of Phosphoproteomic Data, http://dx.doi.org/10.2139/ssrn.3628295

Kim HJ; Wang K; Chen C; Lin Y; Tam PP; Lin DM; Yang JY; Yang P, Cepo uncovers cell identity through differential stability, http://dx.doi.org/10.1101/2021.01.10.426138

Masamsetti VP; Salehin N; Kim HJ; Santucci N; Weatherstone M; Knowles H; Sun J; McMahon R; Studdert JB; Aryamanesh N; Wang R; Jing N; Yang P; Osteil P; Tam PPL, Characterization of the mesendoderm progenitors in the gastrulating mouse embryo, http://dx.doi.org/10.1101/2024.04.28.591221

Kim HJ; Lin Y; Geddes TA; Yang J; Yang P, CiteFuse enables multi-modal analysis of CITE-seq data, http://dx.doi.org/10.1101/854299

Kim HJ; O’Hara-Wright M; Kim D; Loi TH; Lim BY; Jamieson RV; Gonzalez-Cordero A; Yang P, Comprehensive Characterisation of Fetal and Mature Retinal Cell Identity to Assess the Fidelity of Retinal Organoids, http://dx.doi.org/10.1101/2022.06.13.495996

Fernando M; Lee S; Wark JR; Xiao D; Kim HJ; Smith GC; Wong T; Teber ET; Ali RR; Yang P; Graham ME; Gonzalez-Cordero A, Differentiation of cortical brain organoids and optic nerve-like structures from retinal confluent cultures of pluripotent stem cells, http://dx.doi.org/10.1101/2021.05.16.444356

Chen C; Kim HJ; Yang P, Evaluating spatially variable gene detection methods for spatial transcriptomics data, http://dx.doi.org/10.1101/2022.11.23.517747

Kim HJ; Kim T; Oldfield AJ; Yang P, Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Associates with RNA Polymerase II Pausing, http://dx.doi.org/10.1101/2020.10.13.338103

Liu C; Ding S; Kim HJ; Long S; Xiao D; Ghazanfar S; Yang P, Multi-task benchmarking of single-cell multimodal omics integration methods, http://dx.doi.org/10.1101/2024.09.15.613149

Kim HJ; Kim T; Hoffman NJ; Xiao D; James DE; Humphrey SJ; Yang P, PhosR enables processing and functional analysis of phosphoproteomic data, http://dx.doi.org/10.1101/2020.08.31.276329

Xiao D; Sahadevan S; Mangala MM; Kim HJ; Fredericks A; Huang H; Jothi R; Tam P; Gonzalez-Cordero A; Zyner KG; Yang P, Refate identifies chemical compounds to target trans-regulatory networks for cellular conversion, http://dx.doi.org/10.1101/2025.07.09.664003

Lin Y; Cao Y; Kim HJ; Salim A; Speed TP; Lin D; Yang P; Yang JYH, scClassify: hierarchical classification of cells, http://dx.doi.org/10.1101/776948

Kim HJ; Salehin N; Huang H; Zhang X; Jothi R; Yang P, Systematic evaluation of blastoid models of early human development, http://dx.doi.org/10.1101/2024.07.11.603073

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