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).

• 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

• Accurate splice site prediction using support vector machines.

  PMID 18269701 · PMC2230508 · BMC bioinformatics · 2007 · 8 claims · 5 setups

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  Weighted degree (WD) kernel SVMs outperform Markov Chains, GeneSplicer and SpliceMachine for genome-wide splice site recognition

  nn269 dgsplicer caenorhabditis arabidopsis svm genome-wide

• DDBJ dealing with mass data produced by the second generation sequencer.

  PMID 18927114 · PMC2686496 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  DDBJ collected and released 2,368,110 entries (1,415,106,598 bases) of original DNA sequence data from July 2007 to June 2008.

  plasmodium oryzias gut drosophila solexa wgs metagenomic

• Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

  PMID 18816392 · PMC2566984 · BMC evolutionary biology · 2008 · 7 claims · 7 setups

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  Ultraconserved coding regions (UCRs, ≥120 nt with no synonymous or nonsynonymous substitutions) exist outside the homeobox in mammalian Hox genes

  orthologous hox concatenated intronic sliding comparative molecular

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• Connecting synthetic chemistry decisions to cell and genome biology using small-molecule phenotypic profiling.

  PMID 19825513 · PMC2787914 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Multidimensional phenotypic profiling leverages information content from multiple parallel or multiplexed measurements of compound action on cells, unlike hierarchical screening which filters to few 'interesting' compounds.

  one nci60 cerevisiae cancer multidimensional cellular two-color

• SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

  PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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  A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

  bombyx whole-genome snp novo

• Integrative transcriptome-wide association analyses reveal PRKCG-linked GABAergic dysfunction in Fragile X-associated tremor/ataxia syndrome.

  PMID 41507195 · PMC12881518 · Nature communications · 2026 · 8 claims · 8 setups

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  A multi-omics strategy combined with TWAS reveals brain-region-specific molecular signatures and striking gene dysregulation concentrated in inhibitory neurons in an FXTAS mouse model.

  brain prefrontal pfc gabaergic bulk single-nuclei immunofluorescent

• Developing a comprehensive database and search tool for single-cell ATAC-seq data.

  PMID 41545440 · PMC12816011 · Scientific reports · 2026 · 5 claims · 6 setups

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  scATAC.Explorer is a curated database containing 39 publicly available scATAC-seq datasets in a consistent format

  hematopoietic drosophila cancer scatac-seq sci-atac-seq sci-car

• Repeatability of gene expression evolution in experimental environmental adaptation.

  PMID 41587990 · PMC12946262 · Nature communications · 2026 · 6 claims · 8 setups

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  Gene expression evolution during experimental adaptation is far more repeatable across replicate populations than expected by chance, whether measured by shared DEGs, shared direction of change, or shared direction plus magnitude of change

  coli yeast fly copepod microarray rna-seq

• An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation.

  PMID 41922356 · PMC13212934 · Nature communications · 2026 · 8 claims · 7 setups

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  BioSeq2Seq is a transformer-based deep learning framework that predicts genome-wide transcriptional regulatory profiles at 128-bp resolution by jointly using RO-seq data and DNA sequence as tri-modal input

  k562 gm12878 imr-90 ro-seq chip-seq functional

• Systems biology of gene regulation fulfills its promise.

  PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

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  Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

  unspecified embryonic five yeast chip-chip chip-pet computational

• pTARGET: a web server for predicting protein subcellular localization.

  PMID 16844995 · PMC1538910 · Nucleic acids research · 2006 · 7 claims · 3 setups

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  pTARGET web server predicts nine distinct subcellular localizations in eukaryotic non-plant proteins using an algorithm based on location-specific Pfam domain occurrence patterns and amino acid composition (AAC)

  eukaryotic complete pfam amino subcellular

• Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.

  PMID 40233745 · PMC12143324 · Cell genomics · 2025 · 8 claims · 6 setups

  Has reproduction

  SGS is a user-friendly, collaborative, versatile browser for integrative visualization of single-cell and spatial multimodal (scMulti-omics) data

  dorsal hematopoietic brain onek1k sn-m3c-seq scatac-seq spatial

• Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

  PMID 16061936 · PMC1182164 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  Oct-1, Oct-2, PU.1, Sp1 and Sp3 interact in vitro with the pol gene HS7 region

  nuclear spodoptera hiv-infected nih3t3 electrophoretic supershift emsa

• The many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

  PMID 24304889 · PMC3964963 · Nucleic acids research · 2014 · 8 claims · 6 setups

  Has reproduction · 84

  Expression Atlas is a value-added database providing gene, protein and splice variant expression across cell types, organism parts, developmental stages, diseases and other biological/experimental conditions, built from manually curated high-quality microarray and RNA-sequencing experiments from ArrayExpress.

  organisms arrayexpress-derived pride rna-sequencing single-channel two-colour

• 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

• ECgene: an alternative splicing database update.

  PMID 17132829 · PMC1716719 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  ECgene provides functional annotation (domain, GO, expression pattern) for alternatively spliced genes

  nine genome sage cdna genome-based chi-squared sage

• Lipids join the post-genomic era.

  PMID 17076911 · PMC1794566 · Genome biology · 2006 · 8 claims · 8 setups

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  Infrared-laser MALDI-MS can image biological tissue while avoiding the matrix-preparation artifacts of UV-laser MALDI

  biological intact mixtures yeast maldi esi faims