Dr Hani Kim

Dr Hani Kim

Conjoint Lecturer

PhD in Computational Biology, School of Mathematics and Statistics, Australia (Supervision: A/Prof Pengyi Yang)

The University of Sydney

MSc in Biological Sciences, School of Biological Sciences, South Korea

Seoul National University

BSc, Biomedical Sciences, School of Biomedical Sciences, UK

Imperial College London

 

Medicine & Health
School of Clinical Medicine

Hani is a Senior Research Officer at the Swarbrick Lab and a conjoint lecturer at UNSW. She completed her undergraduate and graduate training at Imperial College London (UK) and Seoul National University (South Korea), followed by a PhD in Computational Biology at The University of Sydney. Her current research focuses on the development of state-of-the-art computational tools and analytics framework for the integration of high-dimensional single-cell and spatial multi-omics that propels discovery of new biological insight and clinically relevant solutions for breast cancer. She has developed a wide range of bespoke computational software including CiteFuse, Cepo, PhosR, and Maxima.

Location
384 Victoria Street, Darlinghurst NSW 2010
  • Journal articles | 2024
    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
    Journal articles | 2024
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2022
    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
    Journal articles | 2022
    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
    Journal articles | 2022
    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
    Journal articles | 2022
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2020
    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
    Journal articles | 2019
    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 | 2024
    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
    Preprints | 2024
    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
    Preprints | 2024
    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
    Preprints | 2022
    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
    Preprints | 2022
    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
    Preprints | 2021
    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
    Preprints | 2021
    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
    Preprints | 2020
    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
    Preprints | 2020
    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
    Preprints | 2019
    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
    Preprints | 2019
    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
    Preprints |
    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

01/07/2024-06/12/2024

Australian Academy of Science: Theo Murphy Initiatives Amplify Activities ($14,800 AUD) (CIA: Hani Jieun Kim)

01/02/2023-31/01/2025

MRFF Stem Cell Therapies Mission: Purification and cryopreservation of an allogeneic stem cell-derived photoreceptor cell product. ($515,340 AUD) (CID: Hani Jieun Kim)

 

2023

ABACBS Outstanding PhD Thesis Award from the Australian Bioinformatics And Computational Biology Society (ABACBS)

2023

Best Oral Presentation Award at the Sydney Bioinformatics Research Symposium

2023

CMRI Travel Award ($2000) from the Children’s Medical Research Institute

2018 – 2022

Postgraduate Research Scholarship in Computational Biology from The University of Sydney, Australia

2019 – 2022

CMRI PhD Top-up Scholarship from the Children’s Medical Research Institute

2022

Best Oral Presentation Award at the Sydney Bioinformatics Research Symposium

2021

Best Student Poster Presentation Award ($250) at the Oz Single Cell Conference

2021

Winter School Scholarship Recipient ($190) from the Australian Mathematical Sciences Institute (AMSI)

2021

2nd Best Student Oral Presentation Award ($150) at the Australasian Society for Stem Cell Research Symposium (ASSCR)

2020

2020

USYD Postgraduate Research Support Scheme ($500)

Student Oral Presentation Award ($250) at the 25th Annual Lorne Proteomics Symposium

2019

2nd Best Oral Presentation Award ($120) at the Australian Computational Biology and Bioinformatics (COMBINE) Student Society Symposium

2019

Winning Team of Oz Single Cell Challenge 2019 ($1000) at Oz Single Cell Conference

2019

Travel Award for EMBL Australia PhD Course at the University of Tasmania, Hobart

2018

2nd Best Poster Presentation Award ($120) at the COMBINE Symposium

Presentations

2024

Melbourne Integrative Genomics (MIG) Seminar Series, invited oral presentation

2024

UNSW BioMedical Machine Learning Laboratory, invited oral presentation

2023

Korea University (South Korea), invited oral presentation

2023

Seoul National University (South Korea), invited oral presentation

2023

The Australian Bioinformatics And Computational Biology Society (ABACBS), selected oral presentatio

2023

The Australasian Society for Stem Cell Research (ASSCR) Symposium, selected poster presentation

2023

Westmead Research and Innovation Conference Symposium, selected oral presentation

2023

Sydney Bioinformatics Research Symposium (SBRS), selected oral presentation

2023

International Society for Stem Cell Research (ISSCR) (Boston), selected poster presentation

2022

The Australian Bioinformatics And Computational Biology Society (ABACBS), selected poster presentation

2022

Australian Society of Immunology (ASI) Hackathon, selected participant

2022

OzSingleCell 2022 conference, selected poster presentation

2022

Sydney Bioinformatics Research Symposium (SBRS), selected oral presentation

2021

OzSingleCell 2021 conference (virtual), selected poster presentation

2021

AMSI Winter School on Statistical Data Science (virtual), selected oral presentation

2021

International Society for Stem Cell Research (ISSCR) (virtual), selected oral presentation

2021

Charles Perkins Centre (CPC) BioDomain Seminar, invited oral presentation

2021

The Australasian Society for Stem Cell Research (ASSCR) Symposium, selected oral presentation

2021

Keystone Symposia (KS) “Single Cell Biology” (virtual), selected e-poster presentation

2020

The Australian Bioinformatics And Computational Biology Society (ABACBS) (virtual), selected poster presentation

2020

Charles Perkins Centre (CPC) EMCR Symposium (virtual), selected poster presentation

2020

A/Prof Hagen Tigner Laboratory at Weill Cornell Medicine, New York, USA (virtual), invited oral presentation

2020

OzSingleCell 2020 Episode on New technologies: Exploring the complexities of genetic regulation in single cells (virtual), invited oral presentation

2020

Cold Spring Harbor Laboratory (CSHL) “Epigenetics & Chromatin” (virtual), selected poster presentation

2020

2020

28th Conference on Intelligent Systems for Molecular Biology (ISMB) (virtual), selected poster presentation

25th Annual Lorne Proteomics Symposium in Lorne, Australia, selected oral presentation

2019

The Australian Bioinformatics And Computational Biology Society (ABACBS) in Sydney, Australia, selected poster presentation

2019

COMBINE Symposium in Sydney, Australia, selected oral presentation

2019

10x Genomics User Guide Meeting in Sydney, Australia, invited oral presentation

2019

EMBL Australia PhD Course in Tasmania, Australia, selected poster presentation

2018

COMBINE Symposium in Melbourne, Australia, selected poster presentation

2018

Garvan Signalling Symposium in Sydney, Australia, selected poster presentation

 

Professional services

2024 Co-chair and committee member of the 2024 ABACBS EMCR Hackathon.
2024 Postdoctoral co-representative and committee member of the 2024 ABACBS Conference.
2022-current Committee member of the ABACBS Postdoc Sub-committee.
2022,2023 Co-chair of sessions at ABACBS National Conference.
2022-2023 Co-chair of sessions at ABACBS National Conference in 2022, 2023.Co-chair of the ABACBS National Seminar Series and Sydney Precision Data Science Statistical Seminar Series.
2022 Co-chair of the Early Career Research Committee of the Sydney Precision Data Science centre.
2021 Committee member of 2021 COMBINE Symposium, a student-run Australian organisation for researchers in computational biology and bioinformatics.

 

My Research Supervision

  • 2021 - current: Carissa Chen PhD Candidate (co-supervision)