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).
-
Has reproduction · 75
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries.
PMID 27756200 · PMC5069797 · BMC bioinformatics · 2016 · 8 claims · 5 setups
Roar, a method using PRE/POST read counts around annotated APA sites to compute an m/M ratio and a ratio-of-ratios (roar) statistic, detects differential 3'UTR shortening/lengthening from standard RNA-seq libraries.
-
Has reproduction · 59
WASP: a versatile, web-accessible single cell RNA-Seq processing platform.
PMID 33736596 · PMC7977290 · BMC genomics · 2021 · 7 claims · 7 setups
WASP is a software platform for processing Drop-Seq-based scRNA-seq data generated with ddSEQ or 10x protocols, combining a Snakemake pre-processing pipeline with an R Shiny post-processing application.
-
Has reproduction · 90
CONSULT: accurate contamination removal using locality-sensitive hashing.
PMID 34377979 · PMC8340999 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups
CONSULT uses locality-sensitive hashing to test whether query k-mers fall within a user-defined Hamming distance of a reference k-mer database, allowing inexact matching against tens of thousands of microbial species.
-
Has reproduction · 86
The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.
PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups
Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.
-
Full-text index only
High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.
PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups
A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development
-
Has reproduction · 90
Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.
PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.
-
Has reproduction · 53
Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.
PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups
Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)
-
Has reproduction · 67
Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.
PMID 37994351 · PMC10663991 · F1000Research · 2023 · 7 claims · 7 setups
A reproducible R-based workflow combines Seurat (QC, clustering, integration), monocle3 (trajectory inference), and edgeR (pseudo-bulk time course analysis) to perform single-cell pseudotemporal time course analysis.
-
Has reproduction · 61
Multi-omics analyses identify mannose phosphate isomerase-centered hypoxia-induced angiogenesis signature in colorectal cancer.
PMID 41204349 · PMC12595641 · Journal of translational medicine · 2025 · 8 claims · 8 setups
Twelve HIA-related genes were identified that are transcriptionally activated by HIFs and functionally implicated in angiogenesis in CRC.
-
Has reproduction · 69
Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).
PMID 41490125 · PMC12768360 · PloS one · 2026 · 7 claims · 7 setups
Manual curation of RNA-seq-derived de novo transcripts increased the number of functional genes in the NWR annotation by 81% (from 8,701 to 15,738).
-
Has reproduction · 98
Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.
PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups
Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing
-
Has reproduction · 50
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.
PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups
330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.
-
Has reproduction · 52
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.
PMID 35178872 · PMC9311447 · Molecular ecology resources · 2022 · 8 claims · 8 setups
epiGBS2 provides a laboratory protocol and revised bioinformatics pipeline for de novo cytosine methylation and SNP calling in species with or without a reference genome