Author

Hong Zhang

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#software testing Open access Sep 2026

MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics.

Since the original publication of Model-based Analysis for ChIP-Seq (MACS), the software has been widely used to identify enriched genomic regions in ChIP-seq, ATAC-seq, CUT&RUN, DNase-seq, and related regulatory genomics assays. Over the years, MACS has evolved substantially, with MACS version 3 (MACS3) now serving as...

Philippa Doherty, Qiang Hu, Zi-Han Zhuang et al. · Genomics, Proteomics & Bioin... · 0 citations

Open access Aug 2026

Coala: a standard-based framework for converting CWL-described command-line tools into agentic toolsets

Command-line LLM-agent Adapter (Coala), a standard-based framework that bridges the Model Context Protocol (MCP) and the Common Workflow Language (CWL), which turns CWL tool descriptions into MCP-compatible, LLM-accessible schemas, treating tool definitions as data rather than code.

Qiang Hu, Qian-Qian Zhu, Hong Zhang et al. · Bioinformatics · 0 citations