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 · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
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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.
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Has reproduction · 84
Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.
PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups
Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.
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Has reproduction · 41
Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.
PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups
A CPAN-index prognostic model built from 11 PANoptosis-related differentially expressed genes (CPAN_DEGs) stratifies CRC patients into high-risk and low-risk groups with distinct survival and immunophenotypes.
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Has reproduction · 97
Determination of complete chromosomal haplotypes by bulk DNA sequencing.
PMID 33957932 · PMC8101039 · Genome biology · 2021 · 8 claims · 8 setups
A hierarchical computational strategy that first builds high-confidence local haplotype blocks from long-range/linked-read linkage and then concatenates them into whole-chromosome haplotypes using Hi-C contacts
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Has reproduction · 90
Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts.
PMID 39959292 · PMC11825298 · Bio-protocol · 2025 · 7 claims · 6 setups
Mapping adapter-trimmed reads first to the pathogen genome recovers more pathogen reads than the traditional host-first mapping approach.
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Has reproduction · 44
Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.
PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups
DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection
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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).
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Has reproduction · 87
De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.
PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups
A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).
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Has reproduction · 64
Blood Transcriptome Analysis of Septic Patients Reveals a Long Non-Coding Alu-RNA in the Complement C5a Receptor 1 Gene.
PMID 35447887 · PMC9027897 · Non-coding RNA · 2022 · 6 claims · 7 setups
A computational pipeline intersecting immune gene coordinates with Alu element coordinates can identify candidate Alu-lncRNAs
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Has reproduction · 75
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.
PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups
RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.
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Has reproduction · 67
Optimal scaling of digital transcriptomes.
PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups
Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.
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Has reproduction · 38
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups
A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).
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Has reproduction · 74
Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.
PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups
RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).
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Has reproduction · 58
The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).
PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups
The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.
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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 · 61
lncEvo: automated identification and conservation study of long noncoding RNAs.
PMID 33563213 · PMC7871587 · BMC bioinformatics · 2021 · 8 claims · 5 setups
lncEvo is an integrated Nextflow/Docker pipeline combining transcriptome assembly, lncRNA identification, and cross-species conservation analysis into a single workflow.
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Has reproduction · 97
Easy and efficient ensemble gene set testing with EGSEA.
PMID 29333246 · PMC5747338 · F1000Research · 2017 · 8 claims · 2 setups
EGSEA combines results from up to 12 prominent gene set testing algorithms to obtain a consensus ranking of biologically relevant gene sets.
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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 · 71
Comprehensive comparison of gene expression diversity among a variety of human stem cells.
PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 6 claims · 7 setups
iPSC gene expression is more strongly influenced by tissue origin than other stem cell types, whereas ESCs and somatic stem cells (MSCs, HSCs) are more strongly impacted by culture condition.