By Dr Hani Kim

Journal articles

Dutt M; Liao L; Kim HJ; Blazev R; Chan A; Kore H; Bezawork-Geleta A; Dong L; Rivera IS; Wee NKY; Molendijk J; Wong JPH; Haynes VR; Uribe V; Lynch GS; Smith KA; Montgomery MK; Watt MJ; Yang P; Dodd GT; Vervoort SJ; Sims NA; Parker BL, 2026, 'Phosphoproteomics of aged insulin-resistant bone identifies P70S6K phosphorylation of AFF4 as a gene-specific transcriptional regulator', Nature Communications, 17, http://dx.doi.org/10.1038/s41467-025-68106-4

Apostolov E; Roden DL; Holliday H; Cazet A; Harvey K; Zhang H; Wu SZ; van der Leij S; Jieun Kim H; Selth LA; Bartonicek N; Al-Eryani G; Reeves JL; He M; Lundeberg J; Potter AJ; Kench JG; Stricker PD; Joshua AM; Horvath LG; Swarbrick A, 2026, 'Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy-Naïve Localized Prostate Cancer', Cancer Research, 86, pp. 1836 - 1853, http://dx.doi.org/10.1158/0008-5472.CAN-25-1202

Loi TH; Cheng A; Kim HJ; Fernando M; Nash BM; Aryamanesh N; Grigg JR; Yang P; Gonzalez-Cordero A; Jamieson RV, 2025, 'Connecting cilium, stress response, and proteostasis abnormalities inform variant and therapy assessment in RPGRIP1 retinal organoids', Stem Cell Reports, 20, http://dx.doi.org/10.1016/j.stemcr.2025.102717

Liu C; Ding S; Kim HJ; Long S; Xiao D; Ghazanfar S; Yang P, 2025, 'Multitask benchmarking of single-cell multimodal omics integration methods', Nature Methods, 22, pp. 2449 - 2460, http://dx.doi.org/10.1038/s41592-025-02856-3

Masamsetti VP; Salehin N; Kim HJ; Santucci N; Weatherstone M; McMahon R; Marshall LL; Knowles H; Sun J; Studdert JB; Aryamanesh N; Wang R; Jing N; Yang P; Osteil P; Tam PPL, 2025, 'Lineage contribution of the mesendoderm progenitors in the gastrulating mouse embryo', Developmental Cell, 60, pp. 1991 - 2006.e9, http://dx.doi.org/10.1016/j.devcel.2025.02.015

Kim HJ; Ruan T; Swarbrick A, 2025, 'Pan-Cancer Spatial Profiling Reveals Conserved Subtypes and Niches of Cancer-Associated Fibroblasts', Cancer Research, 85, pp. 2555 - 2557, http://dx.doi.org/10.1158/0008-5472.CAN-25-2181

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, 30, pp. 3748 - 3757, http://dx.doi.org/10.1038/s41591-024-03030-6

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

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

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, pp. 261 - 261, http://dx.doi.org/10.12688/f1000research.130623.1

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

Jung SJ; Kim JEH; Junne T; Spiess M; Kim H, 2021, 'Cotranslational Targeting and Posttranslational Translocation can Cooperate in Spc3 Topogenesis', Journal of Molecular Biology, 433, http://dx.doi.org/10.1016/j.jmb.2021.167109

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

Yim C; Jung SJ; Kim JEH; Jung Y; Jeong SD; Kim H, 2018, 'Profiling of signal sequence characteristics and requirement of different translocation components', Biochimica Et Biophysica Acta Molecular Cell Research, 1865, pp. 1640 - 1648, http://dx.doi.org/10.1016/j.bbamcr.2018.08.018

Jung SJ; Kim JEH; Reithinger JH; Kim H, 2014, 'The Sec62-Sec63 translocon facilitates translocation of the C-terminus of membrane proteins', Journal of Cell Science, 127, pp. 4270 - 4278, http://dx.doi.org/10.1242/jcs.153650

Reithinger JH; Kim JEH; Kim H, 2013, 'Sec62 Protein mediates membrane insertion and orientation of moderately hydrophobic signal anchor proteins in the endoplasmic reticulum (ER)', Journal of Biological Chemistry, 288, pp. 18058 - 18067, http://dx.doi.org/10.1074/jbc.M113.473009

Conference Abstracts

Kim HJ; Kiedik B; Harvey K; Kanwal S; Douglas J; Reeves J; Lobanov A; Roden DL; Van Der Leij S; Hui MN; Al’Khafaji A; Lim E; Grimmond SM; Lundeberg J; Perou CM; Swarbrick A, 2026, 'A comprehensive multiomics atlas of treatment-naïve breast cancer uncovers co-occurring tumor-immune ecosystems driving immune hot and cold phenotypes', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, CA, San Diego, Vol. 86, presented at AACR Annual Meeting, CA, San Diego, 17 April 2026 - 22 April 2026, http://dx.doi.org/10.1158/1538-7445.AM2026-7282

Lobanov AV; Kim HJ; Kanwal S; Harvey K; Reeves J; Batten M; Kiedik B; Roden DL; Hui MN; Stewart KP; Hofmann O; O’Toole S; Lim E; Grimmond SM; Swarbrick A; Perou CM, 2026, 'scSubtype2.0: Predictor of breast cancer molecular subtypes at single cell resolution.', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, CA, San Diego, Vol. 86, presented at AACR Annual Meeting, CA, San Diego, 17 April 2026 - 22 April 2026, http://dx.doi.org/10.1158/1538-7445.AM2026-44

Preprints

Xiao D; Sahadevan S; Mangala MM; Kim HJ; Fredericks A; Huang H; Jothi R; Tam P; Gonzalez-Cordero A; Zyner KG; Yang P, 2025, Refate identifies chemical compounds to target trans-regulatory networks for cellular conversion., http://dx.doi.org/10.1101/2025.07.09.664003

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

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; 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

Other

Apostolov E; Roden DL; Holliday H; Cazet A; Harvey K; Zhang H; Wu SZ; van der Leij S; Jieun Kim H; Selth LA; Bartonicek N; Al-Eryani G; Reeves JL; He M; Lundeberg J; Potter AJ; Kench JG; Stricker PD; Joshua AM; Horvath LG; Swarbrick A, 2026, Data from Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy–Naïve Localized Prostate Cancer, http://dx.doi.org/10.1158/0008-5472.c.8542546

Apostolov E; Roden DL; Holliday H; Cazet A; Harvey K; Zhang H; Wu SZ; van der Leij S; Jieun Kim H; Selth LA; Bartonicek N; Al-Eryani G; Reeves JL; He M; Lundeberg J; Potter AJ; Kench JG; Stricker PD; Joshua AM; Horvath LG; Swarbrick A, 2026, Supp Fig S1 from Single-Cell and Spatial Transcriptomic Profiling Reveals Epithelial Functional States and Fibroblast Phenotypes in Hormone Therapy–Naïve Localized Prostate Cancer, http://dx.doi.org/10.1158/0008-5472.32711665

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