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).

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 8 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign is the first RNA sequence/structure pairwise alignment algorithm based on incremental ensemble mountain distance, running in O(n^3) time and O(n^2) space for two sequences of length n.

  sequences sequence trna target pairwise global single

• Designating eukaryotic orthology via processed transcription units.

  PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

  ortholog blat exon-intron blast-based

• Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

  PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups

  Has reproduction · 89

  MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa

  eukdetect simulated zymobiomics read holdout mutation-rate

• A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

  PMID 37247570 · PMC10878300 · Ticks and tick-borne diseases · 2023 · 7 claims · 3 setups

  Full-text index only

  The MPAS pipeline is a portable, reproducible Nextflow-based bioinformatics pipeline that identifies and summarizes amplicon sequences produced by the MPAS assay.

  host-seeking mpas same targeted mpas clc

• Computational verification of protein-protein interactions by orthologous co-expression.

  PMID 15740634 · PMC555590 · BMC bioinformatics · 2005 · 7 claims · 8 setups

  Full-text index only

  Co-expression of orthologous protein pairs across multiple species can verify/predict S. cerevisiae PPIs with better performance than S. cerevisiae co-expression alone.

  cerevisiae orthologs cdc28 yeast co-expression ortholog orthologous

• 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

• oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

  PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

  Has reproduction · 49

  oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

  PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups

  Has reproduction · 69

  TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.

  ppm1d-transgenic genome genome read touchdown-pcr

• SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.

  PMID 15927052 · PMC1156871 · BMC bioinformatics · 2005 · 8 claims · 6 setups

  Full-text index only

  SeqDoC generates a subtracted difference trace between a reference and test chromatogram that highlights single base changes

  melanocortin same paired test chromatogram tracediff weak

• Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

  PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

  Full-text index only

  Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

  peripheral mhc2ta pcr sanger bisulfite cpg

• Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

  PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

  Full-text index only

  Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

  plasma ppp reference identification quantitative specimen

• Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

  PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes

  melanogaster dgrp drosophila genes bulk locomotor gene

• Rho GTPases in human breast tumours: expression and mutation analyses and correlation with clinical parameters.

  PMID 12237774 · PMC2364248 · British journal of cancer · 2002 · 8 claims · 8 setups

  Full-text index only

  RhoA, RhoB, Rac1 and Cdc42 protein levels are markedly overexpressed in breast tumours compared to matched normal tissue from the same patient

  breast western c3-mediated 32p-gtp

• Benchmarking ortholog identification methods using functional genomics data.

  PMID 16613613 · PMC1557999 · Genome biology · 2006 · 8 claims · 7 setups

  Full-text index only

  InParanoid is the best overall ortholog identification method for identifying functionally equivalent proteins when sensitivity and selectivity are combined into an overall score.

  known human-mouse expression interpro co-expression

• PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

  PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

  Full-text index only

  The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

  individually reference equimolar independently snp reference pooled

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr

• Alcohol consumption and breast tumor mitochondrial DNA mutations.

  PMID 19847642 · PMC4403627 · Breast cancer research and treatment · 2010 · 8 claims · 6 setups

  Full-text index only

  Somatic mtDNA mutations are a frequent occurrence in breast tumors

  breast paraffin-embedded blood study ttge sequencing immunohistochemistry

• Accurate sequence variant genotyping in cattle using variation-aware genome graphs.

  PMID 31092189 · PMC6521551 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 7 setups

  Has reproduction · 45

  Graphtyper outperformed GATK and SAMtools in genotype concordance, non-reference sensitivity, and non-reference discrepancy compared to microarray genotypes

  original sire-son whole-genome multi-sample graph-based

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 4 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is trivially high regardless of condition and gives misleading estimates of the replicability of conditional (differential) variation in expression.

  encode liver bulk rna-seq meta-analysis

• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

  PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

  Has reproduction

  Transposable elements make up nearly 45% of the human genome, vastly exceeding the ~1.5% that is protein-coding.

  genome normal drosophila long short-read whole-genome synthetic