By Dr Hani Kim

Journal articles

Chen C; Kim HJ; Yang P, 2024, 'Evaluating spatially variable gene detection methods for spatial transcriptomics data', Genome Biology, 25, http://dx.doi.org/10.1186/s13059-023-03145-y

Robertson H; Kim HJ; Li J; Robertson N; Robertson P; Jimenez-Vera E; Ameen F; Tran A; Trinh K; O’Connell PJ; Yang JYH; Rogers NM; Patrick E, 2024, 'Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas', Nature Medicine, http://dx.doi.org/10.1038/s41591-024-03030-6

Kim D; Tran A; Kim HJ; Lin Y; Yang JYH; Yang P, 2023, 'Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data', npj Systems Biology and Applications, 9, http://dx.doi.org/10.1038/s41540-023-00312-6

Ting KK; Coleman P; Kim HJ; Zhao Y; Mulangala J; Cheng NC; Li W; Gunatilake D; Johnstone DM; Loo L; Neely GG; Yang P; Götz J; Vadas MA; Gamble JR, 2023, 'Vascular senescence and leak are features of the early breakdown of the blood–brain barrier in Alzheimer’s disease models', GeroScience, 45, pp. 3307 - 3331, http://dx.doi.org/10.1007/s11357-023-00927-x

Kim T; Kim HJ; Oldfield AJ; Yang P, 2023, 'PAD2: interactive exploration of transcription factor genomic colocalization using ChIP-seq data', STAR Protocols, 4, http://dx.doi.org/10.1016/j.xpro.2023.102203

Kim HJ; O'Hara-Wright M; Kim D; Loi TH; Lim BY; Jamieson RV; Gonzalez-Cordero A; Yang P, 2023, 'Comprehensive characterization of fetal and mature retinal cell identity to assess the fidelity of retinal organoids', Stem Cell Reports, 18, pp. 175 - 189, http://dx.doi.org/10.1016/j.stemcr.2022.12.002

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', F1000Research, 12, http://dx.doi.org/10.12688/f1000research.130623.2

Kim HJ; Li P; Kim T; Oldfield AJ; Zheng X; Yang P, 2022, 'Integrative analysis reveals histone demethylase LSD1 promotes RNA polymerase II pausing', iScience, 25, http://dx.doi.org/10.1016/j.isci.2022.105049

Xiao D; Caldow M; Kim HJ; Blazev R; Koopman R; Manandi D; Parker BL; Yang P, 2022, 'Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis', iScience, 25, http://dx.doi.org/10.1016/j.isci.2022.104489

Fernando M; Lee S; Wark JR; Xiao D; Lim BY; O'Hara-Wright M; Kim HJ; Smith GC; Wong T; Teber ET; Ali RR; Yang P; Graham ME; Gonzalez-Cordero A, 2022, 'Differentiation of brain and retinal organoids from confluent cultures of pluripotent stem cells connected by nerve-like axonal projections of optic origin', Stem Cell Reports, 17, pp. 1476 - 1492, http://dx.doi.org/10.1016/j.stemcr.2022.04.003

Xiao D; Kim HJ; Pang I; Yang P, 2022, 'Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities', Bioinformatics, 38, pp. 1956 - 1963, http://dx.doi.org/10.1093/bioinformatics/btac015

Kim HJ; Tam PPL; Yang P, 2021, 'Defining cell identity beyond the premise of differential gene expression', Cell Regeneration, 10, http://dx.doi.org/10.1186/s13619-021-00083-7

Kim HJ; Wang K; Chen C; Lin Y; Tam PPL; Lin DM; Yang JYH; Yang P, 2021, 'Uncovering cell identity through differential stability with Cepo', Nature Computational Science, 1, pp. 784 - 790, http://dx.doi.org/10.1038/s43588-021-00172-2

Robertson H; Li J; Kim HJ; Rhodes JW; Harman AN; Patrick E; Rogers NM, 2021, 'Transcriptomic Analysis Identifies A Tolerogenic Dendritic Cell Signature', Frontiers in Immunology, 12, http://dx.doi.org/10.3389/fimmu.2021.733231

Kim HJ; Kim T; Xiao D; Yang P, 2021, 'Protocol for the processing and downstream analysis of phosphoproteomic data with PhosR', STAR Protocols, 2, http://dx.doi.org/10.1016/j.xpro.2021.100585

Kim HJ; Kim T; Hoffman NJ; Xiao D; James DE; Humphrey SJ; Yang P, 2021, 'PhosR enables processing and functional analysis of phosphoproteomic data', Cell Reports, 34, http://dx.doi.org/10.1016/j.celrep.2021.108771

Norris D; Yang P; Shin SY; Kearney AL; Kim HJ; Geddes T; Senior AM; Fazakerley DJ; Nguyen LK; James DE; Burchfield JG, 2021, 'Signaling Heterogeneity is Defined by Pathway Architecture and Intercellular Variability in Protein Expression', iScience, 24, http://dx.doi.org/10.1016/j.isci.2021.102118

Kim HJ; Lin Y; Geddes TA; Yang JYH; Yang P, 2020, 'CiteFuse enables multi-modal analysis of CITE-seq data', Bioinformatics, 36, pp. 4137 - 4143, http://dx.doi.org/10.1093/bioinformatics/btaa282

Lin Y; Cao Y; Kim HJ; Salim A; Speed TP; Lin DM; Yang P; Yang JYH, 2020, 'scClassify: sample size estimation and multiscale classification of cells using single and multiple reference', Molecular Systems Biology, 16, http://dx.doi.org/10.15252/msb.20199389

Kim HJ; Osteil P; Humphrey SJ; Cinghu S; Oldfield AJ; Patrick E; Wilkie EE; Peng G; Suo S; Jothi R; Tam PPL; Yang P, 2020, 'Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning', Nucleic Acids Research, 48, pp. 1828 - 1842, http://dx.doi.org/10.1093/nar/gkz1179

Kim T; Lo K; Geddes TA; Kim HJ; Yang JYH; Yang P, 2019, 'ScReClassify: Post hoc cell type classification of single-cell RNA-seq data', BMC Genomics, 20, http://dx.doi.org/10.1186/s12864-019-6305-x

Preprints

Masamsetti P; Salehin N; Kim HJ; Santucci N; Weatherstone M; Knowles H; Sun J; McMahon R; Studdert J; Aryamanesh N; Wang R; Jing N; Yang P; Osteil P; Tam PPL, 2024, Characterization of the mesendoderm progenitors in the gastrulating mouse embryo, http://dx.doi.org/10.1101/2024.04.28.591221

Liu C; Ding S; Kim HJ; Long S; Xiao D; Ghazanfar S; Yang P, 2024, Multi-task benchmarking of single-cell multimodal omics integration methods, http://dx.doi.org/10.1101/2024.09.15.613149

Kim HJ; Salehin N; Huang H; Zhang X; Jothi R; Yang P, 2024, Systematic evaluation of blastoid models of early human development, http://dx.doi.org/10.1101/2024.07.11.603073

Kim HJ; O’Hara-Wright M; Kim D; Loi TH; Lim B; Jamieson R; Gonzalez-Cordero A; Yang P, 2022, 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

Chen C; Kim HJ; Yang P, 2022, Evaluating spatially variable gene detection methods for spatial transcriptomics data, http://dx.doi.org/10.1101/2022.11.23.517747

Kim HJ; Wang K; Chen C; Lin Y; Tam PPL; Lin D; Yang JYH; Yang P, 2021, Cepo uncovers cell identity through differential stability, http://dx.doi.org/10.1101/2021.01.10.426138

Fernando M; Lee S; Wark J; Xiao D; Kim H; Smith G; Wong T; Teber E; Ali R; Yang P; Graham M; Gonzalez-Cordero A, 2021, 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

Kim HJ; Kim T; Oldfield A; Yang P, 2020, Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Associates with RNA Polymerase II Pausing, http://dx.doi.org/10.1101/2020.10.13.338103

Kim HJ; Kim T; Hoffman N; Xiao D; James D; Humphrey S; Yang P, 2020, PhosR enables processing and functional analysis of phosphoproteomic data, http://dx.doi.org/10.1101/2020.08.31.276329

Kim HJ; Lin Y; Geddes T; Yang J; Yang P, 2019, CiteFuse enables multi-modal analysis of CITE-seq data, http://dx.doi.org/10.1101/854299

Lin Y; Cao Y; Kim H; Salim A; Speed T; Lin D; Yang P; Yang JYH, 2019, scClassify: hierarchical classification of cells, http://dx.doi.org/10.1101/776948

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/10.2139/ssrn.3628295

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