Fan Zhang

OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

OTTER improves bisulfite deconvolution in tumor xenograft sequencing by restoring recall to 52%-54% while preserving transcriptomic accuracy.

AMPK-dependent brain-wide norepinephrine release promotes recovery from metabolic coma in mice

This study identifies an AMPK-dependent brainstem circuit that promotes recovery from metabolic coma in mice through widespread norepinephrine release.

Accurate and scalable decontamination of imaging-based spatial transcriptomics via optimal transport

CellDot improves spatial transcriptomics by accurately decontaminating transcript assignments using optimal transport, enhancing biological interpretation and spatial pattern recovery.

A hybrid framework integrating structural machine learning and 3D liver-on-chip assay for drug-induced liver injury prediction

Oakuloid combines a structural machine learning model with a 3D liver-on-chip assay to predict drug-induced liver injury, achieving high AUROC on external benchmarks and offering orthogonal confirmation signals.

CAD rewires nucleotide metabolism to drive oxidative stress in myocardial ischemia/reperfusion injury

This study identifies CAD as a key regulator of myocardial ischemia/reperfusion injury by linking nucleotide metabolism to oxidative stress through dual-compartment ROS signaling.

STAT: A multi-agent framework for integrated and interactive spatial transcriptomics analysis

STAT is a multi-agent framework that improves spatial transcriptomics analysis by enabling interactive, transparent, and efficient multi-task analysis across different data resolutions.

Expanding the genetic code with diverse backbone structures across diverse sequence contexts

This paper expands the genetic code by incorporating non-canonical monomers into proteins using evolved tRNAs and orthogonal synthetases, enabling broader sequence context compatibility.

DrugPlayGround: Benchmarking Large Language Models and Embeddings for Drug Discovery

DrugPlayGround benchmarks large language models for drug discovery tasks like drug characteristics and interactions, assessing their performance against traditional methods.

A green fluorescent protein for live imaging in hyperthermophiles

The paper develops a thermostable green fluorescent protein, Matcha, for live imaging in hyperthermophiles and uses it to study division ring dynamics in Sulfolobus.

DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation

DBSCAN-SWA rapidly detects and annotates prophages in bacterial genomes with high recall and user-friendly visualizations.