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).

• Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

  PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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  Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

  human-mouse adjacent est genome splice

• A whole-genome assembly of St. Augustinegrass and visualizing diversity within the species.

  PMID 41873115 · PMC13009705 · The plant genome · 2026 · 7 claims · 7 setups

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  First chromosome-scale, phased haplotype genome assemblies of Stenotaphrum secundatum (cultivar Raleigh) were produced, anchored on nine chromosomes each

  stenotaphrum secundatum diploid long-read short-read hi-c

• Ontological visualization of protein-protein interactions.

  PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

  gene interacting interaction annotation yeast co-immunoprecipitation

• Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

  PMID 16925841 · PMC1810556 · Genome biology · 2006 · 8 claims · 5 setups

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  Exogean is a framework using directed acyclic coloured multigraphs (DACMs) to represent biological objects (mRNA, ESTs, protein alignments, exons) and iteratively combine them into complex protein-coding transcript models.

  genome sequences automatic manual sequence

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Diversity of tRNA genes in eukaryotes.

  PMID 17088292 · PMC1693877 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  The number of tRNA genes having the same anticodon but different sequences elsewhere (isodecoder genes) varies significantly (10–246) across 11 eukaryotes despite isoacceptor numbers being similar (41–55)

  eukaryotic bacterial genome synthetic genome-wide sequence manual

• Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

  PMID 16757574 · PMC1475747 · Nucleic acids research · 2006 · 6 claims · 8 setups

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  Applying seven independent computational disease-gene prioritization methods in concert to 9556 positional candidate genes identifies a prioritized set of likely T2D and obesity candidate genes

  pubmed genes same randomly geneseeker evoc disease

• Large-scale trends in the evolution of gene structures within 11 animal genomes.

  PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

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  Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

  annotated animal unannotated comparative all-against-all neighbor-joining

• L1Base: from functional annotation to prediction of active LINE-1 elements.

  PMID 15608246 · PMC539998 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  L1Base is a database of putatively active LINE-1 insertions in human, mouse and rat genomes, containing FLI-L1s (intact in both ORFs), ORF2-L1s (intact ORF2, disrupted ORF1), and FLnI-L1s (full-length, >6000 bp, non-intact)

  sapiens orf1 orf fli-l1s genomic repeatmasker hmm-profile

• Distribution and effects of nonsense polymorphisms in human genes.

  PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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  Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

  genome genes nonsense snps genome-wide snp codon

• Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

  PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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  SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

  genome autosomal hapmap chromosome snp chromosomal minor

• Genome-wide identification of human functional DNA using a neutral indel model.

  PMID 16410828 · PMC1326222 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  A neutral indel model predicting a geometric distribution of intergap segment (IGS) lengths fits human-mouse ancestral repeat (AR) alignment data excellently

  chromosome human-mouse genome individual whole-genome probabilistic comparative

• Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

  PMID 18438408 · PMC2705838 · Nature genetics · 2008 · 8 claims · 8 setups

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  Massively parallel paired-end sequencing can characterize somatic and germline structural rearrangements to base-pair resolution across a whole cancer genome

  nci-h2171 nci-h1770 massively genomic rt-pcr

• Protein function assignment through mining cross-species protein-protein interactions.

  PMID 18253506 · PMC2216687 · PloS one · 2008 · 8 claims · 6 setups

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  CSIDOP predicts protein molecular function with 95.42% accuracy using 2,972 GO functional categories in H. sapiens

  sapiens cross-species majority simple

• CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.

  PMID 41481570 · PMC12758788 · PLoS computational biology · 2026 · 8 claims · 7 setups

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  CellPredX is a unified semi-supervised framework integrating domain adaptation and deep metric learning to align heterogeneous embeddings for cross-modality cell type annotation.

  pbmc fetal pancreas gse149683 matched unmatched cross-protocol

• A chromosome-level reference genome and pangenome for barn swallow population genomics.

  PMID 36662619 · PMC10044405 · Cell reports · 2023 · 8 claims · 8 setups

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  A chromosome-level, karyotype-validated reference genome (bHirRus1) was assembled using the VGP pipeline combining PacBio CLR, 10x Linked-Reads, Bionano optical maps, and Hi-C data

  single barn bhirrus1 rustica genome cytogenetic reference-free

• Assembly, Characterization and Comparative Analysis of the Complete Mitogenome of Small-Leaved Eriobotrya seguinii (Maleae, Rosaceae).

  PMID 41595526 · PMC12841229 · Genes · 2026 · 8 claims · 7 setups

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  The E. seguinii mitogenome is the smallest and has the highest GC content of any known Eriobotrya species

  seguinii protein-coding mitogenomes whole-genome mitogenome repeat

• PRDM1 Is Associated with Chemoradiotherapy-Associated Enrichment of Adaptive NK Cells in Cervical Cancer.

  PMID 42110212 · PMC13150072 · Computational and structural biotechnology journal · 2026 · 8 claims · 8 setups

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  CRT enriches adaptive NK (aNK) cells within the cervical cancer immune microenvironment, with enrichment apparent after the first fraction and persisting after the second

  cervical subclusters ank overlapping single-cell cluster differential

• More biology from the sequence.

  PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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  The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

  schizosaccharomyces chromosome genome cervical whole-genome sequence genome