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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FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.
PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups
FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells
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Lift&Add-rapid and robust addition of new species to alignments of conserved non-coding sequences.
PMID 42203687 · PMC13224966 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 5 setups
Lift&Add, a Snakemake/bash workflow combining UCSC liftOver, Liftoff, and MAFFT, enables rapid addition of new genome sequences to existing multi-species alignments of conserved elements without requiring new whole-genome alignments.
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Has reproduction · 63
hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer.
PMID 36498841 · PMC9738810 · International journal of molecular sciences · 2022 · 8 claims · 8 setups
hgtseq is a fully automated, portable, and scalable Nextflow/nf-core pipeline for detecting horizontal gene transfer signatures from unmapped sequencing reads.
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Tissue compartment analysis for biomarker discovery by gene expression profiling.
PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups
TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures