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).

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.

  tcga gse72056 gse40419 gse103322 bulk single-cell rna-seq

• The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

  PMID 17712414 · PMC1942082 · PloS one · 2007 · 8 claims · 5 setups

  Full-text index only

  P-POD is the first comparative genomics database to combine results from multiple computational ortholog/homolog prediction methods with manually curated literature-derived experimental evidence of functional conservation.

  sequences orthomcl yeast orthomcl jaccard phylogenetic

• InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

  PMID 19892828 · PMC2808972 · Nucleic acids research · 2010 · 8 claims · 7 setups

  Full-text index only

  InParanoid 7 expands the database by an order of magnitude to 100 species, 1.3 million proteins, and 42.7 million pairwise ortholog groups.

  eukaryotic homo sequence species pairwise algorithm low-complexity

• Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

  PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups

  Full-text index only

  ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.

  blood baseline-corrected 953-dimensional training seldi-tof wavelet ant

• A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

  PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

  Full-text index only

  Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

  simulated same mcmc-based direct original

• High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

  PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

  Full-text index only

  WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

  genomic whole-genome same call snp technical genotype

• spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.

  PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups

  Has reproduction · 77

  spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.

  coli simulated net-seq ribosome stochastic

• Genetic polyploid phasing from low-depth progeny samples.

  PMID 35692633 · PMC9184567 · iScience · 2022 · 8 claims · 7 setups

  Has reproduction · 73

  WH-PPG phases polyploid parental samples by scoring informative variant pairs with a Bayesian log-likelihood model of progeny allele depths, clustering alleles by co-occurrence likelihood, and assigning clusters to haplotypes via interval scheduling

  solanum illumina pacbio wh-ppg

• CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

  PMID 15796777 · PMC1274267 · BMC bioinformatics · 2005 · 8 claims · 2 setups

  Full-text index only

  CGMIM is a Perl program that text-mines OMIM entries to identify cancer-gene associations and genetically-related cancer type pairs.

  omim automated manual

• The human phylome.

  PMID 17567924 · PMC2394744 · Genome biology · 2007 · 6 claims · 5 setups

  Full-text index only

  Reconstruction of the human phylome: evolutionary trees for all human proteins and their homologs among 39 fully sequenced eukaryotic genomes, using a pipeline combining alignment trimming, NJ, ML (PhyML) and Bayesian (MrBayes) methods.

  proteome proteins neighbor-joining maximum bayesian

• Sequence analysis of p53 response-elements suggests multiple binding modes of the p53 tetramer to DNA targets.

  PMID 17439973 · PMC1888811 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  p53REs are not simple direct repeats of half-sites; the two half-sites couple to form a higher-order 20-bp full-site palindrome

  compiled genome artificial sequence computational simulated

• Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

  PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

  Full-text index only

  AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

  entorhinal subjects expression differentially microarray significance principal

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

  Full-text index only

  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation

• Shotgun haplotyping: a novel method for surveying allelic sequence variation.

  PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

  Full-text index only

  A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

  genomic long pcr ampicillin-resistant long cloning short

• Predictive genomics of cardioembolic stroke.

  PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

  Full-text index only

  A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

  blood-derived gasros same custom bayesian roc

• Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

  PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups

  Full-text index only

  Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.

  paired lung tissue-pair pooled hiv-1 maximum statistical

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript