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).

• Estimation of genetic parameters and genome-wide association study for carcass traits in native chickens.

  PMID 40211845 · PMC12229932 · Animal bioscience · 2025 · 8 claims · 7 setups

  Has reproduction · 71

  Carcass traits (SW, EW, ThW, and their percentages except SP) show moderate to high heritability (0.20-0.50), while SP has low heritability (0.08)

  sanhuang breast whole-genome genome-wide heritability

• A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.

  PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 7 claims · 6 setups

  Has reproduction · 78

  MERLIN-P-TFA network inference on 18 curated public RNA-seq datasets produced a genome-wide GRN resource for A. fumigatus called GRAsp.

  aspergillus fumigatus bulk computational chip-seq-based

• Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

  PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 80

  WGCNA identified 214 key genes in the blue module most correlated with LUAD

  tcga-luad merged tedc2-associated a549 wgcna differential machine

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions

  compendium ffpe simulated frna-seq statistical bulk integrity

• Metatranscriptomics-based investigation of bacterial community dynamics across a dissolved organic matter gradient in southern Lake Michigan.

  PMID 41860215 · PMC13101498 · Applied and environmental microbiology · 2026 · 7 claims · 6 setups

  Has reproduction · 81

  Offshore Lake Michigan bacterioplankton show higher expression of DOM, N, and P acquisition/transporter genes than nearshore bacterioplankton

  bacterioplankton lake metatranscriptomics metagenomic nutrient

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 45

  Eight distinct T cell populations can be identified from CRC tumor tissue by unsupervised clustering of scRNA-seq data

  tumor-infiltrating peripheral cd4+ tumor single-cell unsupervised pearson

• Contributions from molecular/biochemical approaches in epidemiology to cancer risk assessment and prevention.

  PMID 1486845 · PMC1519598 · Environmental health perspectives · 1992 · 8 claims · 8 setups

  Full-text index only

  Genotoxicity of chemicals is a continuous, graded property (agent score) rather than a simple dichotomy of mutagenic vs. nonmutagenic chemicals

  chemical drosophila normal uv-sensitive short-term drosophila excision

• Global distribution of rubella virus genotypes.

  PMID 14720390 · PMC3034328 · Emerging infectious diseases · 2003 · 8 claims · 6 setups

  Full-text index only

  Phylogenetic analysis of 103 E1 gene sequences from 17 countries confirms at least two rubella virus genotypes, RGI and RGII

  rubella same phylogenetic genetic virus

• GeneSeer: a sage for gene names and genomic resources.

  PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

  Full-text index only

  GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

  sofar clusters rnai gene blast sequence shrna

• Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different.

  PMID 16105176 · PMC1201154 · BMC structural biology · 2005 · 8 claims · 5 setups

  Full-text index only

  Interaction patterns across obligatory and non-obligatory interfaces are different, with obligatory contacts predominantly non-polar

  pdb obligatory same psi-blast solvent residue

• Characterization of the linkage disequilibrium structure and identification of tagging-SNPs in five DNA repair genes.

  PMID 16091150 · PMC1208870 · BMC cancer · 2005 · 7 claims · 5 setups

  Full-text index only

  Three of the five DNA repair genes (MRE11A, RAD50, XRCC4) do not conform to a contiguous haplotype block structure; instead SNPs in high LD can be non-contiguous, fitting a more flexible LD group paradigm

  unrelated same haplotype caucasian snp haplotype group

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

  PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

  Full-text index only

  GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

  chromosome genomic comparative phylohmmcons conserved

• Bayesian prediction of microbial oxygen requirement.

  PMID 26913185 · PMC4743139 · F1000Research · 2013 · 7 claims · 8 setups

  Has reproduction · 76

  A naive Bayesian classifier based on presence/absence of class-associated Pfam-A domains can distinguish three oxygen requirement classes (aerobe, anaerobe, facultative anaerobe) from genome sequence, unlike prior studies that only made pairwise distinctions.

  bacterial selected predicted pfam-a genome gene domain

• FeatureScan: revealing property-dependent similarity of nucleotide sequences.

  PMID 16845077 · PMC1538849 · Nucleic acids research · 2006 · 6 claims · 5 setups

  Full-text index only

  FeatureScan transforms nucleotide sequences into numerical signals of physico-chemical/conformational properties and compares them via a convolution/correlation (Fourier transform) method rather than comparing letters

  randomly fully same chimpanzee signal-theoretic featurescan blast

• Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates.

  PMID 16620374 · PMC1464127 · BMC genomics · 2006 · 8 claims · 6 setups

  Full-text index only

  Syndecan-encoding sequences are present in Cnidaria and throughout the Bilateria, showing deep conservation of the family.

  invertebrate syndecan full-length chicken wu-blastp clustalw tcoffee

• Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods.

  PMID 16522644 · PMC1390679 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Align-GVGD predicts loss of transactivation activity with high specificity (~88%) but lower sensitivity (67.9-71.2%) for neutral mutants

  p53 tp53 yeast-based sequence align-gvgd

• 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

• Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

  PMID 17895298 · PMC2533592 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 7 setups

  Full-text index only

  Nucleotide and amino acid substitution trends between human-mouse orthologs are highly asymmetric and polarized in opposite directions for high-GC versus low-GC gene groups.

  human-mouse high aarm orthologous content pairwise

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational