Marni Torkel

TRACE: a framework for traceable biomedical resource construction demonstrated through single-cell glaucoma data

TRACE provides a framework for creating traceable biomedical resources, demonstrated with a single-cell glaucoma dataset, enabling reproducible analyses and resource reuse.

BenchHub enables an inclusive and transparent ecosystem for community-focused benchmarking in computational biology

BenchHub provides a modular ecosystem for community-focused benchmarking in computational biology by linking datasets, metrics, and ground truth to improve reproducibility and sustainability.

The current landscape and emerging challenges of benchmarking single-cell methods

This paper benchmarks single-cell methods by analyzing 282 papers, highlighting challenges in combining benchmarking studies and preventing fatigue.

Multi-view gene panel characterization for spatially resolved omics

The paper develops a framework to characterize and design gene panels for spatially resolved omics, showing that both computational and manually curated panels have strengths in capturing cell types and reducing redundancy.

A Message Passing Framework for Precise Cell State Identification with scClassify2

scClassify2 is a message-passing neural network for cell state identification, outperforming existing methods in annotating adjacent cell states and applicable to multiple data types.

Multi-task benchmarking of spatially resolved gene expression simulation models

The paper benchmarks spatially resolved gene expression simulation models using a framework that evaluates 13 methods across 10 datasets and 35 metrics, highlighting performance differences and factors affecting model accuracy.