Biology subjects

Zha, C.

Publications and source records attributed to Zha, C..

3 recordsLinked to original sources

bioRxiv2026

BioMINTREL expands biological problem solving through cross-disciplinary representations

Biological research agents often rely on familiar analytical methods, limiting the questions explored in existing data. We introduce BioMINTREL, an AI agent that finds methods from other disciplines and connects them to biological measurements. It can draw on relationships among datasets and complementary ideas from several methods to develop new questions and analyses. We evaluate it on BioMDC-Bench, which assesses 228 possible applications of computational methods to biological tasks. Compared with GPT-5.4 mini and Qwen3.6-35B, BioMINTREL improves F1 agreement with human experts by up to 45.3 percentage points and increases coverage of applications supported by studies published in subsequent years by up to 58.8 percentage points. Four case studies on real data go beyond previous analyses to reveal dose-specific variant effects, constraints on spatial cell communication and routes through perturbation-response states, and identify the sampling needed to test whether rare high-state cells predict later lineage size. These results highlight BioMINTREL's potential to expand questions in existing data and suggest directions for subsequent research.

bioinformatics↗

bioRxiv2026

ProteinMCP: An Agentic AI Framework for Autonomous Protein Engineering

Computational protein design is often constrained by slow, complex, inaccessible, and highly sophiscated and expert-dependent workflows that hinder its transferrability and generalization power for broader applications. We present ProteinMCP, an agentic AI framework designed to accelerate and democratize protein engineering. ProteinMCP automates end-to-end scientific tasks, delivering dramatic gains in efficiency; for instance, a comprehensive protein fitness modeling workflow was completed in just 11 minutes. This performance is achieved by an AI agent that intelligently orchestrates a unified ecosystem of 38 specialized tools, made accessible through a Model-Context-Protocol (MCP). A cornerstone of the framework is an automated pipeline that converts existing software into MCP-compliant servers, ensuring the platform is both powerful and perpetually extensible. We further demonstrate its capabilities through the successful autonomous design and selection of high-affinity de novo binders and therapeutic nanobodies. By removing technical barriers, ProteinMCP has the potential to shorten the design-build-test cycle and make advanced computational protein design accessible to the broader scientific community.

bioinformatics↗

bioRxiv2019

Disruption of Capn15 in mice leads to brain and eye deficits

The Small Optic Lobe (SOL) family of calpains are intracellular cysteine proteases that are expressed in the nervous system and play an important role in neuronal development in both Drosophila, where loss of this calpain leads to the eponymous small optic lobes, and in mouse and human, where loss of this calpain leads to eye anomalies. Some human individuals with biallelic variants in CAPN15 also have developmental delay and autism. However, neither the specific effect of the loss of the Capn15 protein on brain development nor the brain regions where this calpain is expressed in the adult is known. Here we show using small animal MRI that mice with the complete loss of Capn15 have smaller brains overall with larger decreases in the thalamus and subregions of the hippocampus. These losses are not seen in Capn15 conditional KO mice where Capn15 is knocked out only in excitatory neurons in the adult. Based on {beta}-galactosidase expression in an insert strain where lacZ is expressed under the control of the Capn15 promoter, we show that Capn15 is expressed in adult mice, particularly in neurons involved in plasticity such as the hippocampus, lateral amygdala and Purkinje neurons, and partially in other non-characterized cell types. The regions of the brain in the adult where Capn15 is expressed do not correspond well to the regions of the brain most affected by the complete knockout suggesting distinct roles of Capn15 in brain development and adult brain function.

neuroscience↗