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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Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics.
PMID 18783599 · PMC2559821 · Theoretical biology & medical modelling · 2008 · 8 claims · 2 setups
Probability landscapes permit systematic detection, analysis, and utilization of feature context-dependency in genomic data.
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Association between alcoholism and the genetic polymorphisms of the GABAA receptor genes on chromosome 5q33-34 in Korean population.
PMID 16778401 · PMC2729963 · Journal of Korean medical science · 2006 · 6 claims · 5 setups
Genetic polymorphisms of the GABA A α1 and α6 receptor genes are significantly associated with alcohol dependence, surviving Bonferroni correction.
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Comparing cellular proteomes by mass spectrometry.
PMID 19886975 · PMC2784314 · Genome biology · 2009 · 8 claims · 6 setups
MS-based proteomics combined with cryo-electron tomography (CET) enables determination of absolute and relative protein abundances and localization
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Expression profiling of drug response--from genes to pathways.
PMID 17117610 · PMC3181826 · Dialogues in clinical neuroscience · 2006 · 8 claims · 8 setups
Understanding individual response to a drug (efficacy/tolerability) is the major bottleneck in current drug development and clinical trials.
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CorGen--measuring and generating long-range correlations for DNA sequence analysis.
PMID 16845099 · PMC1538783 · Nucleic acids research · 2006 · 8 claims · 3 setups
CorGen is a web server that measures long-range correlations in DNA sequences and generates random sequences with the same (or user-specified) correlation and composition parameters
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Environmental genomics: an opportunity for the NIEHS.
PMID 16393638 · PMC1332673 · Environmental health perspectives · 2006 · 8 claims · 5 setups
Intrauterine exposure to endocrine-disrupting pesticides can produce transgenerational adverse effects on male fertility
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Quantitative phosphoproteomics by mass spectrometry: past, present, and future.
PMID 18846511 · PMC2701620 · Proteomics · 2008 · 8 claims · 6 setups
Selective enrichment of phosphopeptides (antiphosphotyrosine IP, IMAC, TiO2/MOAC, SCX, chemical tagging) is required to detect substoichiometric, transient phosphorylation events by MS
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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 · 50
BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.
PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups
BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length
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Has reproduction · 85
Single-Cell Differential Network Analysis with Sparse Bayesian Factor Models.
PMID 35186014 · PMC8855158 · Frontiers in genetics · 2021 · 8 claims · 2 setups
A hierarchical Bayesian factor model using treatment-dependent latent factor loadings can construct gene co-expression networks from scRNA-seq data and identify differences in network structure between two (or more) biological conditions.