Data‐and theory‐driven approaches for understanding paths of epithelial–mesenchymal transition

T Hong, J **ng - genesis, 2024 - Wiley Online Library
Reversible transitions between epithelial and mesenchymal cell states are a crucial form of
epithelial plasticity for development and disease progression. Recent experimental data and …

SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers environmental cues of epithelial-mesenchymal plasticity in breast cancer

E Withnell, M Secrier - Genome Biology, 2024 - Springer
Spatial transcriptomics is revolutionizing the exploration of intratissue heterogeneity in
cancer, yet capturing cellular niches and their spatial relationships remains challenging. We …

Soluble guanylate cyclase dysfunction and nitric oxide pathway in chronic rhinosinusitis with nasal polyps: predictive markers for postoperative recurrence

S Jiang, MD, C Zhang, MD… - American Journal of …, 2025 - journals.sagepub.com
Background Elevated nitric oxide (NO) levels have been linked to a heightened risk of
recurrence in patients with chronic rhinosinusitis with nasal polyps (CRSwNP). However, the …

WENDY: Covariance dynamics based gene regulatory network inference

Y Wang, P Zheng, YC Cheng, Z Wang… - Mathematical …, 2024 - Elsevier
Determining gene regulatory network (GRN) structure is a central problem in biology, with a
variety of inference methods available for different types of data. For a widely prevalent and …

SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers new environmental cues of epithelial-mesenchymal plasticity in cancer

E Withnell, M Secrier - bioRxiv, 2023 - biorxiv.org
Spatial transcriptomics is revolutionising our ability to explore intratissue heterogeneity in
cancer, but methods that can effectively capture cancer cell niches and explore their …

TRENDY: Gene Regulatory Network Inference Enhanced by Transformer

X Tian, Y Patel, Y Wang - bioRxiv, 2024 - biorxiv.org
Gene regulatory networks (GRNs) play a crucial role in the control of cellular functions.
Numerous methods have been developed to infer GRNs from gene expression data …

WENDY: Gene Regulatory Network Inference with Covariance Dynamics

Y Wang, P Zheng, YC Cheng, Z Wang, A Aravkin - bioRxiv, 2024 - biorxiv.org
Determining the structure of gene regulatory networks (GRNs) is a central problem in
biology, with a variety of inference methods available for different types of data. However, for …