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).

• Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.

  PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups

  Has reproduction · 78

  An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.

  proteins microarray ad-associated pahs target differential wgcna

• Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm.

  PMID 33295865 · PMC8116671 · Microbial genomics · 2020 · 8 claims · 4 setups

  Has reproduction · 98

  wCtub and wDcau (863 988 bp and 863 427 bp) are the smallest Wolbachia genomes sequenced to date and are the first genomes representing supergroup J.

  wolbachia filarial six target-enrichment whole-genome novo

• Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

  PMID 34825285 · PMC8616721 · Journal of computer-aided molecular design · 2022 · 8 claims · 6 setups

  Has reproduction · 63

  Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.

  curated repurposed glycosylated interior inverse molecular exploratory

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs

  afb1 breast training candidate computational bulk weighted

• Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

  PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

  Has reproduction · 98

  Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

  hg38 hela hek293t induced genome-wide high-throughput chip-seq

• The promise of biomarkers in colorectal cancer detection.

  PMID 15322316 · PMC3839323 · Disease markers · 2004 · 8 claims · 8 setups

  Full-text index only

  A panel/combination of biomarkers is likely to provide better predictive value for early CRC detection than any single biomarker.

  stool specimens serum multi-target afb1-n7-guanine mutation

• A computational study of off-target effects of RNA interference.

  PMID 15800213 · PMC1072799 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  The chance of RNAi off-target effects is considerable, ranging from 5% to 80% depending on organism and parameters, when using exact sequence identity between siRNA and transcripts.

  schizosaccharomyces caenorhabditis homo pombe off-target mismatch-tolerant rational

• miRGator: an integrated system for functional annotation of microRNAs.

  PMID 17942429 · PMC2238850 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  miRGator integrates target prediction, functional enrichment analysis (GO/pathway/disease), and expression data (miRNA/mRNA/protein) into one system for functional annotation of miRNAs

  genome predicted tissues organs computational functional mirna

• Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

  PMID 17697348 · PMC2042502 · BMC genetics · 2007 · 8 claims · 5 setups

  Full-text index only

  CTCE eliminates the need for laboratory optimization of separation conditions for each exonic target sequence.

  pcr-amplified target exonic cycling ctce

• A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

  PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

  Has reproduction · 87

  A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

  compositae same species helianthus targeted genome genomic

• INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events.

  PMID 17517762 · PMC1933116 · Nucleic acids research · 2007 · 8 claims · 3 setups

  Full-text index only

  Pair-wise sequence alignment-based indel identification lacks discrimination of species specificity and cannot distinguish insertions from deletions.

  chromosomes hg18 ucsc sequence pair-wise

• Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

  PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

  Full-text index only

  Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

  k-562 targeted sanger

• Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data.

  PMID 35473573 · PMC9044877 · Genome biology · 2022 · 8 claims · 8 setups

  Has reproduction

  Combining multiple enhancer-definition and enhancer-gene link data sources yields 1860 genome-wide EnTDefs covering >500 cell types

  types encode chip-seq chromhmm dnase-seq

• T cell receptor usage and fine specificity of human immunodeficiency virus 1-specific cytotoxic T lymphocyte clones: analysis of quasispecies recognition reveals a dominant response directed against a minor in vivo variant.

  PMID 8666925 · PMC2192525 · The Journal of experimental medicine · 1996 · 8 claims · 6 setups

  Full-text index only

  Despite heterogeneous TCR usage among clones from different HLA-B14 subjects, the fine specificity for the gp41/584-592 epitope and its variants is strikingly similar.

  gp41 hiv-1 pbmc freshly 51cr-release tcr-α limiting

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• A genome annotation-driven approach to cloning the human ORFeome.

  PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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  Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

  chromosome pooled t-tailed naga comparative rt-pcr sanger

• Multiplexed genetic analysis using an expanded genetic alphabet.

  PMID 15319316 · PMC1592527 · Clinical chemistry · 2004 · 7 claims · 6 setups

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  MultiCode PLx is a three-step platform (PCR, target-specific extension, liquid chip decoding) performed in a single reaction vessel and completed in ~3 h

  genomic synthetic subset newborn multicode eracode automated

• RiboSubstrates: a web application addressing the cleavage specificities of ribozymes in designated genomes.

  PMID 17076887 · PMC1634876 · BMC bioinformatics · 2006 · 7 claims · 4 setups

  Full-text index only

  RiboSubstrates is a web-based Perl application that scans a cDNA database for all potential substrates of a given ribozyme, including perfect matches, Wobble base-pair matches, and mismatch-containing matches.

  homo hcv substrate ribozyme

• The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

  PMID 17932789 · PMC2140095 · Journal of structural and functional genomics · 2007 · 8 claims · 6 setups

  Full-text index only

  A family-based target selection approach (rather than genome-wide or fold-novelty based selection) maximizes cross-member methodological transfer and biological insight

  recombinant target coli x-ray differential analytical

• Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

  PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

  inhbb cloned same fresh-frozen rnase masscleave clonal