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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Has reproduction · 95
OptiType: precision HLA typing from next-generation sequencing data.
PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups
OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.
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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.
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Has reproduction · 43
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.
PMID 34089405 · PMC8179884 · Rice (New York, N.Y.) · 2021 · 8 claims · 7 setups
N22 performs better under dual (low N + low water) stress owing to better root architecture, chlorophyll/porphyrin synthesis and oxidative stress management
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Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity
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Has reproduction · 90
Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits.
PMID 33461502 · PMC7812657 · Genetics, selection, evolution : GSE · 2021 · 7 claims · 6 setups
Many significant cis-eQTL (geQTL, eeQTL, sQTL) were detected in sheep liver and muscle at FDR < 0.01.
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Has reproduction · 74
Toward a Consensus in the Repertoire of Hemocytes Identified in Drosophila.
PMID 33748138 · PMC7969988 · Frontiers in cell and developmental biology · 2021 · 8 claims · 8 setups
Comparative analysis of three scRNAseq studies identifies eight common, robust hemocyte subgroups associated with distinct functions (proliferation, immune response, phagocytosis, secretion)
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Has reproduction · 65
SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses.
PMID 33932985 · PMC8088074 · BMC bioinformatics · 2021 · 8 claims · 5 setups
SPEAQeasy is a portable, easy-to-install, Nextflow-powered RNA-seq processing pipeline that lowers the computational entry barrier for biologists/clinicians
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Has reproduction · 89
HTSQualC is a flexible and one-step quality control software for high-throughput sequencing data analysis.
PMID 34548573 · PMC8455540 · Scientific reports · 2021 · 8 claims · 5 setups
HTSQualC is a standalone, one-step QC software that performs filtering and trimming of raw HTS data in a single run
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Has reproduction · 49
Neuronal Small RNAs Control Behavior Transgenerationally.
PMID 31178120 · PMC6579485 · Cell · 2019 · 8 claims · 8 setups
Neuron-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous siRNAs and germline gene expression for multiple generations
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Has reproduction · 67
GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.
PMID 35501696 · PMC9063052 · BMC bioinformatics · 2022 · 6 claims · 3 setups
GEMmaker, an nf-core compliant Nextflow workflow, can quantify gene expression from small to massive RNA-seq datasets while remaining reproducible via versioned containerized software.
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Has reproduction · 100
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.
PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups
NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.
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Has reproduction · 71
Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.
PMID 40211845 · PMC12229932 · Animal bioscience · 2025 · 7 claims · 5 setups
311 SNPs and 73 candidate genes (e.g., IGF2BP1, BMP3, ACSL5) are significantly associated with carcass traits in Sanhuang chickens
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Has reproduction · 50
The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.
PMID 35371105 · PMC8964954 · Frontiers in immunology · 2022 · 8 claims · 8 setups
HCV E1E2 glycoproteins, and more so E2, down-modulate HIV-1 LTR activation in 293T, TZM-bl and Huh7 cells
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Has reproduction · 85
Ensembl 2013.
PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups
Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.