Burak Ogan Mancarci

Detailed curation of biological samples and experimental designs for genomics using LLM-supported agentic workflows

The paper describes a software tool using LLMs to automate data curation for genomics, achieving performance near human curators with lower cost and higher speed.

Application of large language models to the annotation of cell lines and mouse strains in genomics data

This paper evaluates using GPT-4o to annotate mouse strains and cell lines in genomics data, achieving 77% and 59% accuracy, and identifies manual curation errors.

Curation of over 10,000 transcriptomic studies to enable data reuse

The paper curates over 10,000 transcriptomic datasets to improve data reuse by standardizing metadata, processing, and annotations.

A critical assessment of single-cell transcriptomes sampled following patch-clamp electrophysiology

This study assesses patch-seq, showing technical artifacts in single-cell transcriptomes and proposing a marker gene-based approach to improve gene expression-electrophysiological feature alignment.

Cross-laboratory analysis of brain cell type transcriptomes with applications to interpretation of bulk tissue data

The paper compiles a database of mouse brain cell type-specific gene expression profiles, identifies novel marker genes, and demonstrates their use in analyzing bulk tissue data.

Transcriptomic Correlates Of Neuron Electrophysiological Diversity

The paper identifies 420 genes whose expression correlates with electrophysiological parameters in neurons, suggesting general principles linking gene expression to functional diversity.