Publications

For the full list of publications from my lab, please visit my Google Scholar Page.

Notable publications

* : Co-first authors † : Coresponding authors

BrainSTEM: A single-cell multiresolution fetal brain atlas reveals transcriptomic fidelity of human midbrain cultures

HSY Toh*, L Xu*, C Chen, P Yang, AX Sun†, JF Ouyang† Science Advances 11, eadu7944 (2025) Link

ShinyCell2: An extended library for simple and sharable visualisation of spatial, peak-based and multi-omic single-cell data

BJ Chen, YY Lim, X Yang, L Wang, OJL Rackham†, JF Ouyang† biorxiv Link

scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets

Y Xie, J Yang, JF Ouyang†, E Petretto† Briefings in bioinformatics 25, bbae482 (2024) Link

Systems level identification of a matrisome-associated macrophage polarisation state in multi-organ fibrosis

JF Ouyang*, K Mishra*, Y Xie, H Park, KY Huang, E Petretto†, J Behmoaras† eLife 25, e85530 (2023) Link

Transient naive reprogramming corrects hiPS cells functionally and epigenetically

S Buckberry, X Liu, D Poppe, JP Tan, G Sun, J Chen, TV Nguyen, A Mendoza, J Pflueger, T Frazer, DB Vargas-Landin, JM Paynter, N Smits, N Liu, JF Ouyang, FJ Rossello, HS Chy, OJL Rackham, AL Laslett, J Breen, GJ Faulkner, CM Nefzger, JM Polo†, R Lister† Nature 620, 863-872 (2023) Link

ShinyCell: simple and sharable visualization of single-cell gene expression data

JF Ouyang, US Kamaraj, EY Cao, OJL Rackham† Bioinformatics 19, 3374–3376 (2021) Link

Modelling human blastocysts by reprogramming fibroblasts into iBlastoids

X Liu*, JP Tan*, J Schröder, A Aberkane, JF Ouyang, M Mohenska, SM Lim, YBY Sun, J Chen, G Sun, Y Zhou, D Poppe, R Lister, AT Clark, OJL Rackham, J Zenker, JM Polo† Nature 591, 627–632 (2021) Link

Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments

XY Choo, YM Lim, K Katwadi, L Yap, K Tryggvason, AX Sun, S Li, L Handoko, JF Ouyang†, OJL Rackham† ACS Synthetic Biology 10, 640–645 (2021) Link

Reprogramming roadmap reveals route to human induced trophoblast stem cells

X Liu*, JF Ouyang*, FJ Rossello*, JP Tan, KC Davidson, DS Valdes, J Schröder, YBY Sun, J Chen, AS Knaupp, G Sun, HS Chy, Z Huang, J Pflueger, J Firas, V Tano, S Buckberry, JM Paynter, MR Larcombe, D Poppe, XY Choo, CM O’Brien, WA Pastor, D Chen, AL Leichter, H Naeem, P Tripathi, PP Das, A Grubman, DR Powell, AL Laslett, L David, SK Nilsson, AT Clark, R Lister, CM Nefzger, LG Martelotto, OJL Rackham†, JM Polo† Nature 586, 101–107 (2020) link

A single-cell atlas of entorhinal cortex from individuals with Alzheimer’s disease reveals cell-type-specific gene expression regulation

A Grubman*, G Chew*, JF Ouyang*, G Sun, XY Choo, C McLean, RK Simmons, S Buckberry, DB Vargas-Landin, D Poppe, J Pflueger, R Lister, OJL Rackham†, E Petretto†, JM Polo† Nature Neuroscience 22, 2087–2097 (2019) link