Y.-A. Chen

Cross-institutional HER2 assessment via a computer-aided system using federated learning and stain composition augmentation

This paper develops a HER2 assessment system using federated learning and stain composition augmentation, achieving over 90% accuracy across two institutions with improved generalizability.

RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4

This study identifies RPL22 as a tumor suppressor in MSI-H cancers that regulates MDM4 splicing and reveals its role in oncogenic pathways.

Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers

This study creates a multimodal tumor atlas to analyze how metastatic HR+ breast cancers adapt to CDK4/6 inhibitors, revealing mechanisms like mTORC1 activation and immune microenvironment changes.

Anaplerotic nutrient stress drives synergy of angiogenesis inhibitors with therapeutics targeting tumor metabolism

This study shows that angiogenesis inhibitors enhance the effectiveness of metabolic therapies in gliomas by inducing anaplerotic nutrient stress.

Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section

The paper develops a multi-modal imaging platform combining H&E and high-plex immunofluorescence for colorectal cancer diagnosis, showing improved predictive models for progression-free survival.

Massively Parallel Selection of NanoCluster Beacons

The paper develops a high-throughput method to screen and design multicolor NanoCluster Beacons using NGS chips and machine learning.

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution

The paper uses spatial techniques to study immune evasion and immunoediting in primary melanoma, finding localized immunosuppressive environments and coexistence of invasion and regression.

Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer

This study uses multiplexed 3D imaging and machine learning to analyze colorectal cancer morphology and immune interactions, revealing molecular gradients and cell state transitions.

Micro-region transcriptomics of fixed human tissue using Pick-Seq

Pick-Seq enables deep spatial transcriptomic profiling of fixed human tissue, revealing transcriptional differences in tumor invasion, proliferation, and immuno-editing.

Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung

The paper uses multiplexed proteomics and imaging to compare inflammatory and thrombotic responses in resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans.

Online narrative guides for illuminating tissue atlas data and digital pathology images

The paper discusses the need for interactive guides to help interpret complex tissue atlas data and digital pathology images, using Minerva software as an example.

Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer

The paper describes a dataset of multiplexed immunofluorescence images and single-cell immune marker data from human tonsil and lung cancer tissues, along with analysis methods and tools.