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).

• Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.

  PMID 19964620 · PMC5003034 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 3 setups

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  omniBiomarker, a web-based application, uses prior biological knowledge to identify the most biologically relevant gene ranking metric for a given clinical problem

  renal microarray qrt-pcr computational

• MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.

  PMID 41918857 · PMC13034871 · PeerJ · 2026 · 7 claims · 6 setups

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  MetaPepticon is a modular, end-to-end Snakemake pipeline that predicts ACP candidates directly from raw genomic, metagenomic, transcriptomic, metatranscriptomic reads, assembled contigs, or peptide sequences.

  validated gut representative predicted acp shotgun genome

• Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

  PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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  The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

  sequence genes proteins sequences snp interspecies sequence

• IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

  PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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  IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

  standard thp-1 replicate lc-ms manual cross-instrument

• Dissecting microregulation of a master regulatory network.

  PMID 18294391 · PMC2289817 · BMC genomics · 2008 · 8 claims · 6 setups

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  143 human miRNAs (termed p53-miRs) each contain at least one putative p53 binding site within 10 kb flanking sequence and are predicted to target at least one known gene

  genome mirnas mirna-target predicted p53 mirna cross-referencing

• A DNA microarray survey of gene expression in normal human tissues.

  PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups

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  Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.

  normal common computational each two-color comparative unsupervised

• Integrative microRNA and transcriptome analysis reveals sex-specific molecular divergence in human bladder cancer.

  PMID 41578372 · PMC12911049 · Biology of sex differences · 2026 · 8 claims · 8 setups

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  48 tumor-specific sex-biased (TSSB) microRNAs were identified in bladder cancer, mostly located on autosomes rather than sex chromosomes

  tcga tssb blca mirna-seq bulk kegg

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 50

  Only two of seven published sepsis gene signatures (derived from adult/pediatric/geriatric cohorts) showed good concordance (>80% accuracy) when applied to infant sepsis, showing limited generalizability of non-infant signatures.

  blood merged deg microarray coconut pseudotime

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

  PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups

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  Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.

  barley extracted tool novel nanopore illumina transcriptome

• The integrated world of functional genomics.

  PMID 12537543 · PMC151279 · Genome biology · 2003 · 8 claims · 8 setups

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  Integrating chromatin immunoprecipitation (promoter-binding) data with expression data reveals the yeast cell-cycle transcriptional regulatory network, including network motifs such as autoregulation, multi-component loops, and feedforward loops.

  cerevisiae sequenced elegans drosophila chromatin integration comparative