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).

• Mitochondrial localization and function of a subset of 22q11 deletion syndrome candidate genes.

  PMID 18775783 · PMC2729512 · Molecular and cellular neurosciences · 2008 · 8 claims · 8 setups

  Full-text index only

  Six 22q11 genes (Mrpl40, Prodh, Slc25a1, Txnrd2, T10, Zdhhc8) encode proteins that localize to mitochondria, including neuronal/synaptic mitochondria.

  orthologues nih-3t3 3t3 mefs bioinformatic egfp co-transfection

• Reconstruction of human protein interolog network using evolutionary conserved network.

  PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

  Full-text index only

  A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

  ppi sequences interaction predicted interolog orthology quasi-clique

• ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

  PMID 16845048 · PMC1538778 · Nucleic acids research · 2006 · 6 claims · 4 setups

  Full-text index only

  ProMiR II improves on the original ProMiR by integrating free energy, G/C ratio, conservation score and entropy for more controllable miRNA prediction

  genome cytomegalovirus six probabilistic 5-fold directional

• Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae.

  PMID 34489462 · PMC8421402 · Scientific data · 2021 · 8 claims · 8 setups

  Has reproduction · 92

  Chromosome-scale genomes of six Leishmaniinae species (five L. (Mundinia) species and one Porcisia species) were sequenced, assembled and annotated, providing genome, proteome, transcriptome and GFF outputs for taxa previously lacking public reference genomes

  six same polished each nanopore illumina novo

• Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.

  PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 7 claims · 7 setups

  Has reproduction · 71

  A custom ECF pipeline identified 13,401 lncRNAs in the A. crassicauda transcriptome (12,642 novel, 759 known).

  androctonus crassicauda paired-end coding homology

• Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

  PMID 16925842 · PMC1810557 · Genome biology · 2006 · 8 claims · 4 setups

  Full-text index only

  MARS, an extension of the Twinscan algorithm, uses multiple pairwise informant genomes to predict human alternatively spliced transcripts de novo without expressed sequence information.

  genome tissues novo pairwise rt-pcr

• Comprehensive benchmarking of large language models for RNA secondary structure prediction.

  PMID 40205851 · PMC11982019 · Briefings in bioinformatics · 2025 · 7 claims · 4 setups

  Has reproduction · 88

  Existing RNA-LLMs had not previously been evaluated for secondary structure prediction in a unified, fair experimental setup with the same datasets and prediction model.

  archiveii bprna large-scale secondary cross-family self-supervised

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups

  Has reproduction · 50

  A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation

  pre-treatment domingo geo bulk bulk external spatial

• Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

  PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups

  Full-text index only

  SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers

  serum seldi seldi-tof serum univariate

• Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.

  PMID 41826827 · PMC13202766 · BMC microbiology · 2026 · 8 claims · 8 setups

  Has reproduction · 71

  R. artemisiae harbors six prokaryotic taxa: two plant pathogens ('Ca. P. solani', 'Ca. A. phytopathogenicus') and four insect endosymbionts ('Ca. Vidania', 'Ca. Purcelliella', 'Ca. Karelsulcia', and Wolbachia).

  individual long endosymbiont artemisiae pcr-free pcr nucleic

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

  triticum taiqd wheat promoter genome-wide phylogenetic synteny

• Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes.

  PMID 17916580 · PMC2533590 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 7 claims · 7 setups

  Full-text index only

  Adult and weaned-children gut microbiota show high functional (gene-content) uniformity despite taxonomic differences, while unweaned infant microbiota show high inter-individual variation in both taxonomic and gene composition.

  fecal assembled predicted gut whole-genome gene reciprocal

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients.

  PMID 38650649 · PMC11034498 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 83

  188 differentially expressed genes (DEGs) between IS and control blood samples were identified and enriched in immune-related biological pathways

  blood degs peripheral hub microarray kegg cibersort

• Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals.

  PMID 13678422 · PMC222960 · BMC bioinformatics · 2003 · 8 claims · 8 setups

  Full-text index only

  The human genome encodes at least 71 kelch-repeat proteins

  genome yeast kelch-repeat full-length blast blastp cross-referencing

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• Phosphoproteomics: new insights into cellular signaling.

  PMID 16168091 · PMC1242200 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  Protein kinases are one of the largest gene families in humans and mice, accounting for 1.7% of the human genome

  yeast hela beta2-adrenergic erk phosphopeptide targeted silac