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).

• ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse.

  PMID 17984078 · PMC2238997 · Nucleic acids research · 2008 · 6 claims · 4 setups

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  ARED Organism and ARED-Integrated are new/updated public databases cataloguing ARE-containing mRNAs/genes in human, mouse and rat

  6x6 ortholog 3'utr comparative chi-squared

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

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  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag

• Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

  PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

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  A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

  blood whole-genome unsupervised class

• Tipping the balance in autoimmune disease.

  PMID 18001485 · PMC2246277 · Genome biology · 2007 · 8 claims · 8 setups

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  Human autoimmune diseases are fundamentally diseases of immune dysfunction, evidenced by predisposing genes being immune-function genes, some shared and some unique across MS, T1D, SLE, CD and RA

  patients congenic nzm2410 mrl-lpr snp induced genetic

• Fatty acid synthesis suppresses dietary polyunsaturated fatty acid use.

  PMID 38167725 · PMC10762034 · Nature communications · 2024 · 7 claims · 8 setups

  Has reproduction · 94

  FASN activity critically determines the use/incorporation of dietary PUFA into complex lipids in mice and humans

  index nash patient-derived hek293t lipidomics 14c-acetate cycloheximide

• Integrating herbarium specimen observations into global phenology data systems.

  PMID 30937223 · PMC6426164 · Applications in plant sciences · 2019 · 7 claims · 5 setups

  Has reproduction · 60

  A new PPO release adds terms and properties to relate observations of parts of plants to whole plants, enabling integration of herbarium phenology data with field observation data.

  plant prunus serotina ontology phenological integration

• ddRAD-seq reveals the genetic structure and detects signals of selection in Italian brown trout.

  PMID 35100964 · PMC8805291 · Genetics, selection, evolution : GSE · 2022 · 7 claims · 9 setups

  Has reproduction · 87

  Italian brown trout populations are genetically differentiated but show strong admixture from stocking practices, especially with the Atlantic lineage.

  brown snp subset salmo ddrad-seq admixture newhybrids

• Evaluation of classification and forecasting methods on time series gene expression data.

  PMID 33156855 · PMC7647064 · PloS one · 2020 · 8 claims · 4 setups

  Has reproduction · 74

  Deep learning based methods generally outperform traditional approaches for time series gene expression classification.

  gene gse6186 time short convolutional

• Tumor-specific but immunosuppressive CD39(+)CD8(+) T cells exhibit double-faceted roles in clear cell renal cell carcinoma.

  PMID 40961944 · PMC12629791 · Cell reports. Medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  CD39+CD8+ TILs constitute a terminally exhausted, tumor-antigen-specific subset of CD8+ T cells

  memory sorted caix-specific cd39+pd-1bright scrna-seq bulk mhc

• Identity rather than 3D position informs splicing of rare introns in the human genome.

  PMID 41561379 · PMC12814444 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 98

  Rare intron classes (minor, minor-like, hybrid, non-canonical) are largely dispersed across the linear human genome, with only two notable clusters (GBP on chr1, TSPY on chrY)

  reference genome k562 computational genome-wide chromomap hi-c

• QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

  PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

  Has reproduction · 78

  QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

  hiv-1 same paired-end reads ngs-based concordance read

• A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

  PMID 16271140 · PMC1309616 · BMC genomics · 2005 · 8 claims · 4 setups

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  149 putative MHC gene loci and their paralogues were identified in the zebrafish genome using sequence similarity searches against the Zv4 draft assembly.

  zebrafish sequence comparative cross-validation

• Functional coverage of the human genome by existing structures, structural genomics targets, and homology models.

  PMID 16118666 · PMC1188274 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Existing PDB structures provide single-domain coverage for 37% of functional classes in the human genome and complete (whole-protein) structure coverage for 25%.

  genome functional registered omim comparative kendall's homology

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

  PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

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  IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

  igvh germline non-igv immunogenetics flow cdna bioinformatic

• 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

• Non-linear mapping for exploratory data analysis in functional genomics.

  PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.

  leukaemia small srbct brain relaxation self-organising sammon's

• Cyrface: An interface from Cytoscape to R that provides a user interface to R packages.

  PMID 24715956 · PMC3962008 · F1000Research · 2013 · 8 claims · 6 setups

  Has reproduction · 67

  Cyrface is a Cytoscape app/Java library providing a general interface from Cytoscape (Java) to any R function or package.

  cytoscape generated prior-knowledge iris software datarail logic

• Association of poly-purine/poly-pyrimidine sequences with meiotic recombination hot spots.

  PMID 16846522 · PMC1543642 · BMC genomics · 2006 · 7 claims · 6 setups

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  PPT frequency is significantly elevated in yeast meiotic recombination hot spots compared with cold spots

  cerevisiae genome chimpanzee hot computational microarray comparative

• Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

  PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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  Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

  orthologous random cattle aligned three-way pairwise bac