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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A distinct epigenetic signature at targets of a leukemia protein.
PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups
Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve
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Use of functional genomics to understand influenza-host interactions.
PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups
Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques
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Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.
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Has reproduction · 66
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups
RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.
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Has reproduction · 95
Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.
PMID 32111840 · PMC7048732 · Nature communications · 2020 · 8 claims · 8 setups
SuSr-D1 encodes Med15b.D, a subunit of the Mediator complex
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Has reproduction · 89
Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.
PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups
MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa
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System-based proteomic analysis of the interferon response in human liver cells.
PMID 15287976 · PMC507879 · Genome biology · 2004 · 7 claims · 4 setups
ICAT-based quantitative proteomics identified 1,364 proteins in Huh7 cells at <5% false-positive rate, with 54 induced and 24 repressed >2-fold by IFN treatment
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Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.
PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups
The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.
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Has reproduction · 50
Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.
PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups
BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes
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Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.
PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups
Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency
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Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.
PMID 18612418 · PMC2440534 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups
Developed a firefly luciferase (fLUC) reporter gene assay to test for the presence of a viable RNAi pathway in helminth parasites
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Has reproduction · 62
Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).
PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups
TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR
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Has reproduction · 54
A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans.
PMID 40629379 · PMC12239316 · BMC biology · 2025 · 8 claims · 7 setups
A 14-bp deletion in the KIT gene promoter region is associated with the all-white phenotype in yaks, identified via GWAS
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 90
Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.
PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups
Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)
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Has reproduction · 78
Purinergic adipocyte-macrophage crosstalk promotes degeneration of thermogenic brown adipose tissue.
PMID 41261284 · PMC12715258 · EMBO reports · 2025 · 8 claims · 8 setups
Imbalanced sympathetic/thermogenic activation (via UCP1 deficiency or pharmacological futile thermogenesis) causes BAT inflammation, fibrosis and degeneration
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Has reproduction · 62
Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury.
PMID 33021470 · PMC7538157 · eLife · 2020 · 8 claims · 8 setups
Plasma AHR ligands derived from heme metabolism (biliverdin, bilirubin) and tryptophan/kynurenine pathway metabolites increase during acute Pc malaria in mice and acute cerebral malaria in humans
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Has reproduction · 100
Betacoronavirus-specific alternate splicing.
PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups
Genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those in SARS-CoV and MERS, affecting a diverse set of genes and biological functions related to virus biology.
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Has reproduction
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.
PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups
The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells
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Has reproduction · 67
NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution.
PMID 31156037 · PMC6693550 · RNA biology · 2019 · 8 claims · 7 setups
NET-prism, an adapted NET-seq protocol using immunoprecipitation of Pol II-associated factors, enables strand-specific, nucleotide-resolution interrogation of transcription dynamics for any Pol II-interacting protein.