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).

• Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome.

  PMID 16277660 · PMC1309615 · BMC evolutionary biology · 2005 · 8 claims · 5 setups

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  Ligands are not more closely linked (shorter physical distance) to their cognate receptors than expected by chance

  genome genomic chromosome randomization

• Needles in the haystack: identifying individuals present in pooled genomic data.

  PMID 19798441 · PMC2747273 · PLoS genetics · 2009 · 8 claims · 7 setups

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  The distribution of T for null samples (individuals not in F or G) deviates strongly from the assumed standard normal, in both location and width.

  cgems hapmap genetic-distance within-population snp-count

• BTW: a web server for Boltzmann time warping of gene expression time series.

  PMID 16845055 · PMC1538860 · Nucleic acids research · 2006 · 5 claims · 4 setups

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  Symmetric time warping distance is more flexible than Euclidean distance or correlation coefficient for identifying genes with similar temporal expression profiles, especially across sequences of different length.

  cerevisiae homologous yeast boltzmann histogram time

• Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM.

  PMID 18565236 · PMC2442058 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  The combined LD-PCR/DHPLC diagnostic strategy achieved a 100% mutation detection rate across 122 Taiwanese hemophilia A families.

  genomic pcr long-distance pcr sanger

• Development of animal models to test the fundamental basis of gene-environment interactions.

  PMID 19037209 · PMC2703424 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 8 setups

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  Selective breeding for low and high intrinsic aerobic treadmill running capacity produced divergent rat lines (LCR and HCR) that contrast in propensity for complex disease

  nih-derived lcr carotid treadmill body maximal

• Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

  PMID 8903171 · PMC2626880 · Emerging infectious diseases · 1995 · 7 claims · 4 setups

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  Romanian and Brazilian HIV-1 subtype F envelope C2-V3 sequences cluster into two related but distinct phylogenetic groups.

  hiv-1 same brazilian phylogenetic bootstrap pruning

• Clustering by neurocognition for fine mapping of the schizophrenia susceptibility loci on chromosome 6p.

  PMID 19694819 · PMC4286260 · Genes, brain, and behavior · 2009 · 6 claims · 6 setups

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  A family-based clustering strategy using neurocognitive test scores (CPT, WCST) can identify more homogeneous subgroups of schizophrenia families for genetic association analysis

  multiplex affected subjects cluster-specific family-based continuous wisconsin

• GABRG1 and GABRA2 as independent predictors for alcoholism in two populations.

  PMID 18818659 · PMC2656604 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 8 setups

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  GABRG1 SNPs and haplotypes are significantly associated with alcohol use disorder (AUD) in both Finnish Caucasians and Plains American Indians

  finnish plains population hapmap snp haplotype ancestry

• A computational screen for type I polyketide synthases in metagenomics shotgun data.

  PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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  Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

  predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds

• Investigating hookworm genomes by comparative analysis of two Ancylostoma species.

  PMID 15854223 · PMC1112591 · BMC genomics · 2005 · 8 claims · 8 setups

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  Nearly 20,000 ESTs from 7 cDNA libraries define nearly 7,000 hookworm genes across A. caninum and A. ceylanicum

  caninum ceylanicum est bioinformatic functional

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region.

  PMID 16998187 · PMC1636422 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The major BCL2 promoter G-quadruplex (bcl2Mid) is a well-defined, mixed parallel/antiparallel-stranded intramolecular structure with three G-tetrads, two lateral loops, one side loop, and four grooves of different widths

  synthetic bcl2mid bcl2pu39 nmr 31p site-specific

• Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

  PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments

  tcga-blca famc1-3 differentially gse32894 bulk consensus gene

• SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.

  PMID 42146899 · PMC13176606 · Computational and structural biotechnology journal · 2026 · 8 claims · 6 setups

  Has reproduction · 74

  SpaGene improves average PCC and SSIM and reduces RMSE compared to 6 baseline methods (SpaGE, gimVI, Tangram, VISTA, spRefine, stDiff) across 8 diverse ST-SC dataset pairs under gene-holdout evaluation.

  pairs nanostring st-sc osmfish_zeisel st-sc 5-fold spatially

• A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

  PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

  Has reproduction · 78

  METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• Long-term trends in evolution of indels in protein sequences.

  PMID 17298668 · PMC1805498 · BMC evolutionary biology · 2007 · 8 claims · 5 setups

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  More than one third of protein domains show a statistically significant tendency to increase or decrease in size over evolutionary distance.

  curated individual cdd linear pearson binomial

• Bases and spaces: resources on the web for accessing the draft human genome.

  PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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  By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

  bac whole-genome draft submitted bac radiation initio

• CONSULT: accurate contamination removal using locality-sensitive hashing.

  PMID 34377979 · PMC8340999 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 90

  CONSULT uses locality-sensitive hashing to test whether query k-mers fall within a user-defined Hamming distance of a reference k-mer database, allowing inexact matching against tens of thousands of microbial species.

  tree gtdb kraken-ii genome k-mer genome-skim organelle

• MMASS: an optimized array-based method for assessing CpG island methylation.

  PMID 17041235 · PMC1635254 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  MMASS-v2 (optimized AciI/HinP1I/HpyCH4IV/HpaII enzyme combination with McrBC digestion) offers improved sensitivity and statistical power for microarray-based CpG island methylation detection compared to MMASS-v1, MMASS-sub and the Nouzova method

  hct116 sssi-methylated hcgi12k methylation spike-in cobra

• Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

  PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

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  Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

  bxd simulated subset populations genome-wide simulation genotype-phenotype