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).

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups

  Has reproduction · 59

  Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.

  metastatic tcga-brca homo gse40622 gene bulk rt-pcr

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.

  v6.5 mes icshape rt-qpcr western

• BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

  PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length

  rfam plant lncrna-mirna sequences unsupervised mirna-lncrna length-binned

• Large-scale structural analysis of the core promoter in mammalian and plant genomes.

  PMID 16049029 · PMC1181242 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  DNA encodes at least two independent levels of functional information: protein/TF-binding sequence information and physical/structural properties of the molecule itself.

  core-promoter arabidopsis rice computational adaptive linear

• An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

  PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

  oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel

• Discovery and hypothesis generation through bioinformatics.

  PMID 16522224 · PMC1431734 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Bioinformatics should be used as a tool for discovery and hypothesis generation, not merely to manage biological data

  genome chemokine gene-expression proteins genome-wide phylogenetic microarray

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

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  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

  PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

  Has reproduction · 93

  24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

  jatropha geo bulk semi-quantitative quantitative

• Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.

  PMID 41407883 · PMC12712020 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 32

  PTRs are highly conserved across 44 AML samples and 30 different human tissues, indicating broadly conserved post-transcriptional mechanisms

  blasts aml impaired top integrative proteomics sequencing

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Variation resources at UC Santa Cruz.

  PMID 17151077 · PMC1781230 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  The UCSC Genome Browser variation resources integrate polymorphism data from public collections (dbSNP, HapMap, Affymetrix, Perlegen, SeattleSNPs) into a common format with additional annotations and genomic context.

  chimpanzee affymetrix hapmap perlegen snp fixed linkage

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

  saanen goat testicular saanen_v1 pacbio illumina hi-c