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Nicholas Piccaro

dblp:440/7325 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2026
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 67% Computational science and engineering · 33%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › biological database
biological database curation
1.012026
CistromeMeta: a large language model powered tool for automated ChIP-seq metadata extraction · Bioinform. 2026
Bioinformatics and computational biology › epigenomics
ChIP-seq analysis
1.012026
CistromeMeta: a large language model powered tool for automated ChIP-seq metadata extraction · Bioinform. 2026
Computational science and engineering › data infrastructure
metadata standardization
1.012026
CistromeMeta: a large language model powered tool for automated ChIP-seq metadata extraction · Bioinform. 2026

Methods — techniques the papers use, named apart from their topics

ontology mapping · 1.0large language model · 1.0few-shot learning · 1.0
YearPublicationVenuePosition
2026 CistromeMeta: a large language model powered tool for automated ChIP-seq metadata extraction
abstract
SUMMARY: Public repositories such as NCBI's Gene Expression Omnibus (GEO) contain large numbers of ChIP-seq experiments, but their reuse is limited by heterogeneous free-text metadata describing target proteins, histone marks, cell lines, tissues, and disease states. We introduce CistromeMeta, a Python-based command-line tool that leverages large language models (LLMs) in a few-shot setting to automatically extract and standardize ChIP-seq metadata from GEO XML records without custom model training. The tool validates extracted terms against authoritative biological databases, including NCBI Gene, Harmonizome 3.0, AnimalTFDB 4.0, Cellosaurus, Experimental Factor Ontology, and Uberon, producing standardized outputs with official gene symbols and ontology identifiers for scalable metadata curation. AVAILABILITY AND IMPLEMENTATION: The Python source code is freely available at https://github.com/nickpiccaro/CistromeMetaX. An archived version of the software is available through Zenodo at DOI: 10.5281/zenodo.20244834. The tool requires Python 3.6+ and an OpenAI API key.
Nicholas Piccaro, Myles Brown, Clifford A. Meyer
Bioinform.1