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 · 88
AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.
PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 4 setups
Sample-sample correlation of transcript abundances is trivially high regardless of condition and gives misleading estimates of the replicability of conditional (differential) variation in expression.
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Has reproduction · 85
Exploring microproteins from various model organisms using the mip-mining database.
PMID 37919660 · PMC10623795 · BMC genomics · 2023 · 5 claims · 4 setups
Mip-mining is a database of 336 curated RNA-seq datasets from 8626 samples across nine species, built specifically to explore microprotein functions under stress and disease conditions
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Has reproduction · 56
Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.
PMID 41909810 · PMC13022592 · Frontiers in bioinformatics · 2026 · 8 claims · 4 setups
ChickpeaOmicsR is the first comprehensive/specialized R package integrating transcriptomic, genomic, and proteomic (RNA-seq, GWAS, PPI) data within a unified, reproducible framework and standardizing fragmented chickpea gene nomenclature.
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Has reproduction · 100
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.
PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups
Hsp90-dependent gene expression varies among different yeast strains
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Has reproduction
Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.
PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 6 setups
CD4 T cells and B cells independently mediate MS GWAS genetic signals through their open chromatin regions, beyond shared regulatory landscapes.
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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 · 59
Comparison between short-term stress and long-term adaptive responses reveal common paths to molecular adaptation.
PMID 35243257 · PMC8873613 · iScience · 2022 · 8 claims · 7 setups
Short-term stress and long-term adaptations share common metabolic pathways
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Has reproduction · 76
Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.
PMID 35806266 · PMC9267015 · International journal of molecular sciences · 2022 · 8 claims · 7 setups
mCCD cl1 cells mount a broad transcriptional response to 24 h hypoxia (0.2% O2), with 3086 genes differentially expressed
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Has reproduction · 81
Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.
PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups
SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains
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Has reproduction · 95
Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.
PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 8 claims · 7 setups
254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs) were detected in the P. ostreatus CCEF00389 genome assembly, the first genome-scale identification of sncRNAs for a basidiomycete.
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Has reproduction · 50
huSA: a comprehensive database for multi-dimensional resolution of bulk, single cell and spatial transcription profiles in skin diseases.
PMID 41719583 · PMC12923168 · Database : the journal of biological databases and curation · 2026 · 7 claims · 8 setups
huSA is a publicly accessible database integrating data from 17 skin diseases and 63 independent datasets, including 1434 scRNA-seq, 63 spatial transcriptomics, and 1502 bulk RNA-seq samples
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Has reproduction · 83
Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.
PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups
Mural cell-derived chemokines CCL2 and MIF preserve vascular macrophage survival and homeostatic function, generating a protective niche.
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Has reproduction · 87
Covalent binding of thioredoxin to TXNIP is required for diet-induced insulin resistance in the liver.
PMID 40345590 · PMC12180993 · The Journal of biological chemistry · 2025 · 8 claims · 9 setups
TXNIP Cysteine 247 is required for high-fat diet-induced hepatic and whole-body insulin resistance in mice
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Has reproduction · 91
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.
PMID 35348734 · PMC9756952 · Nucleic acids research · 2022 · 7 claims · 6 setups
A nascent intermediate central helix forms in the yxjA riboswitch that is mutually exclusive with both the aptamer's P1 helix and the expression platform's intrinsic terminator hairpin.
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Has reproduction · 98
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups
maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors
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Has reproduction · 85
Distinct sympathetic projections to brown fat regulate thermogenesis and glucose tolerance.
PMID 41559445 · PMC12945688 · Nature metabolism · 2026 · 8 claims · 8 setups
Distinct sympathetic neuron subpopulations in the stellate ganglion (SG) innervating iBAT parenchyma versus its vasculature mediate separable functions of the depot.
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Has reproduction · 96
Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.
PMID 31918046 · PMC6992905 · iScience · 2020 · 8 claims · 8 setups
Data-driven, high-dimensional ML approaches that learn multivariate signatures directly from genome-wide transcriptomic data (no prior gene selection) yield accurate and robust AML classifiers.