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 · 80
Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.
PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups
DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.
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Has reproduction · 77
Sequential structure probing of cotranscriptional RNA folding intermediates.
PMID 40450030 · PMC12126503 · Nature communications · 2025 · 8 claims · 6 setups
TECprobe-LM (linked-multipoint Transcription Elongation Complex RNA structure probing) directly measures cotranscriptional rearrangement of RNA structures by sequentially arresting RNAP at two or more template positions and chemically probing nascent RNA at each point
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Has reproduction
Genome scans of facial features in East Africans and cross-population comparisons reveal novel associations.
PMID 34411106 · PMC8375984 · PLoS genetics · 2021 · 8 claims · 3 setups
Genome scans of multivariate 3D facial shape phenotypes in Tanzanian children revealed significant associations at 20 loci (p < 2.5 × 10^-8).
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Has reproduction · 100
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.
PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 5 setups
A network-based approach integrating RNA-seq and cell-shape imaging data identifies data-derived signaling networks specific to cell-shape regulation in breast cancer.
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Has reproduction · 77
Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.
PMID 28398514 · PMC5499547 · Nucleic acids research · 2017 · 6 claims · 6 setups
A sequence-independent biotin–streptavidin (SAv) roadblocking strategy using randomly biotinylated DNA templates can stall TECs across all template positions for cotranscriptional SHAPE-Seq, simplifying template preparation and reducing cost.
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Has reproduction · 37
A Bayesian approach to accurate and robust signature detection on LINCS L1000 data.
PMID 32003771 · PMC7203754 · Bioinformatics (Oxford, England) · 2020 · 6 claims · 4 setups
A novel Bayesian-based peak deconvolution algorithm gives unbiased likelihood estimations for peak locations and characterizes peaks with probability-based z-scores.
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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 · 55
Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF.
PMID 35508485 · PMC9068813 · Nature communications · 2022 · 8 claims · 8 setups
eRNAs longer than 200 nucleotides that contain unpaired guanosines make multiple, allosteric contacts with NELF subunits -A and -E to trigger efficient NELF release
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Has reproduction · 88
Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo.
PMID 35707454 · PMC9178280 · F1000Research · 2021 · 8 claims · 6 setups
A.D.I.C.T. provides a robust, reproducible semi-automated imaging workflow for monitoring antibiotic stress response in bacteria in vivo
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Evolutionary distance estimation and fidelity of pair wise sequence alignment.
PMID 15840174 · PMC1087827 · BMC bioinformatics · 2005 · 8 claims · 8 setups
Evolutionary distance estimation is relatively unaffected by alignment error as long as 50% or more of homologous sites remain identical between sequences
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Improving melanoma classification by integrating genetic and morphologic features.
PMID 18532874 · PMC2408611 · PLoS medicine · 2008 · 7 claims · 5 setups
BRAF-mutant melanomas show distinct morphological features (upward migration and nesting of intraepidermal melanocytes, epidermal thickening, sharper lateral demarcation, larger/rounder/more pigmented tumor cells) compared to non-mutant melanomas
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Has reproduction · 38
Genomic capacities for Reactive Oxygen Species metabolism across marine phytoplankton.
PMID 37098087 · PMC10128935 · PloS one · 2023 · 8 claims · 3 setups
Genes encoding superoxide (O2•−) scavenging are ubiquitous across phytoplankton, but their fractional gene allocation decreases with increasing cell radius, consistent with a nearly fixed core gene set.
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Has reproduction · 94
Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials.
PMID 33558569 · PMC7870661 · Scientific data · 2021 · 7 claims · 7 setups
A unified collection of 101 manually curated and homogenized transcriptomics datasets covering human, mouse, and rat ENM exposures in vitro and in vivo was compiled.
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Has reproduction · 45
RNA structure maps across mammalian cellular compartments.
PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups
icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.
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Has reproduction · 80
Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.
PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups
WGCNA identified 214 key genes in the blue module most correlated with LUAD
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Detection of mutations in the dystrophin gene via automated DHPLC screening and direct sequencing.
PMID 11710958 · PMC59832 · BMC genetics · 2001 · 7 claims · 6 setups
DHPLC screening combined with direct sequencing detects likely disease-causative point mutations in the dystrophin gene missed by multiplexed PCR deletion/duplication testing
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CD155/PVR plays a key role in cell motility during tumor cell invasion and migration.
PMID 15471548 · PMC524493 · BMC cancer · 2004 · 8 claims · 8 setups
A FALI-coupled scFv antibody library screen identifies CD155 (poliovirus receptor) as a mediator of tumor cell invasion
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Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.
PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups
New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach
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Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails.
PMID 15799778 · PMC1080126 · BMC evolutionary biology · 2005 · 8 claims · 6 setups
Dart shooting introduces an allohormone that inhibits digestion of donated sperm, increasing the amount reaching the spermathecae and fertilizing eggs, thereby manipulating the mating partner's sperm storage.
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Detecting transcriptionally active regions using genomic tiling arrays.
PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups
A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.