Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
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Trimmomatic: a decade of feature-rich, high-performance NGS read preprocessing.
PMID 42178219 · PMC13242794 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 4 setups
A high-performance multithreading architecture allows batches of read pairs to be processed independently by a pool of worker threads, scaling efficiently with available hardware.
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rMAP 2.0: a modular, reproducible, and scalable WDL-Cromwell-Docker workflow for genomic analysis of ESKAPEE pathogens.
PMID 41782684 · PMC12955837 · Bioinformatics advances · 2026 · 8 claims · 8 setups
rMAP 2.0 standardizes end-to-end bacterial WGS analysis (QC, trimming, assembly, annotation, AMR/virulence/mobile-element profiling, sequence typing, pangenome inference, phylogenetics) via containerized WDL/Cromwell execution
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Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.
PMID 41631412 · PMC12885427 · mAbs · 2026 · 8 claims · 8 setups
alpseq is an open-source, end-to-end workflow combining a PCR-free sequencing library prep protocol with a Nextflow pre-processing pipeline and an R-based analysis/reporting module for nanobody NGS data.
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Has reproduction · 50
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.
PMID 36451166 · PMC9710047 · Genome biology · 2022 · 8 claims · 6 setups
MoDLE is a high-performance stochastic model/software for simulating DNA-DNA contacts generated by loop extrusion genome-wide