Shuzhen Kuang

Jan 12, 2025 | biorxiv.org | Zoë Grant |Shuzhen Kuang |Shu Zhang |Abraham Horrillo

AbstractDosage-sensitive transcription factors (TFs) underlie altered gene regulation in human developmental disorders, and cell-type specific gene regulation is linked to the reorganization of 3D chromatin during cellular differentiation. Here, we show dose-dependent regulation of chromatin organization by the congenital heart disease (CHD)-linked, lineage-restricted TF TBX5 in human cardiomyocyte differentiation.

Jul 28, 2024 | nature.com | Shuzhen Kuang |Katherine S. Pollard

AbstractRecent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells.

Jul 28, 2024 | flipboard.com | Shuzhen Kuang |Katherine S. Pollard

The Brain2 hours agoNeurologist diagnosed with dementia in his 60s reveals his 'first clue' - and it was 'smelly'gbnews.com - Adam Chapman • 2hA neurologist diagnosed with dementia in his 60s has revealed his first symptom.

Oct 26, 2023 | biorxiv.org | Colin M Brand |Shuzhen Kuang |Erin N Gilbertson |Evonne McArthur

AbstractPhenotypic divergence between closely related species, including bonobos and chimpanzees (genus Pan), is largely driven by variation in gene regulation. The 3D structure of the genome mediates gene expression; however, genome folding differences in Pan are not well understood. Here, we apply machine learning to predict genome-wide 3D genome contact maps from DNA sequence for 56 bonobos and chimpanzees, encompassing all five extant lineages.

Oct 24, 2023 | biorxiv.org | Shuzhen Kuang |Katherine S. Pollard |Chan Zuckerberg Biohub

AbstractRecent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells.