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).

• Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

  PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

  postmortem genes gene proteins microarray protein-protein hierarchical

• Computation of haplotypes on SNPs subsets: advantage of the "global method".

  PMID 17067372 · PMC1636337 · BMC genetics · 2006 · 6 claims · 4 setups

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  The global method for subhaplotyping always yields a lower error rate than the direct method across datasets and SNP subset sizes

  gh1 apoe coalescent-model-simulated griv computational genetic

• Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

  PMID 20017903 · PMC2803168 · BMC medical genetics · 2009 · 6 claims · 5 setups

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  Only three nucleotide variations in ITGB1BP2 were found among 928 screened subjects, indicating a high degree of conservation of the gene in the populations analyzed

  genomic hela itgb1bp2 melusin direct minigene in-silico

• Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

  PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

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  A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

  ebv-transformed serum combined rf-filtered snp serum random

• Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

  PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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  Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

  pooled computational identified additional label-free lspad pathway-associated

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics.

  PMID 18957120 · PMC2628390 · BMC bioinformatics · 2008 · 8 claims · 2 setups

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  Sili2DGel represents recursive gel matching results as a weighted undirected graph and identifies SAP by finding cliques and pseudocliques (dense subgraphs) after edge-weight filtering, strength-metric-based graph reduction, and cluster refinement.

  urine matching gel graph-theoretic

• SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

  PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

  chromosome 16p array probe-by-probe sw-array

• Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

  PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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  42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

  genomic metaphase computational array-cgh fish real-time

• High-density SNP genotyping to define beta-globin locus haplotypes.

  PMID 18829352 · PMC4251776 · Blood cells, molecules & diseases · 2009 · 8 claims · 5 setups

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  RFLP analysis lacks sufficient site density/coverage to accurately reflect the genomic complexity of the β-locus

  genomic rflp subset rflp high-density haploview

• Protective effect of paraoxonase 1 gene variant Gln192Arg in age-related macular degeneration.

  PMID 20042177 · PMC3026437 · American journal of ophthalmology · 2010 · 6 claims · 4 setups

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  The Gln192Arg PON1 polymorphism is associated with decreased susceptibility to AMD, particularly wet AMD, indicating a protective effect

  genomic pcr-amplified case-control pon1 single-strand direct genetic

• A single-cell compendium of human cerebrospinal fluid identifies disease-associated immune cell populations.

  PMID 39744938 · PMC11684814 · The Journal of clinical investigation · 2025 · 8 claims · 4 setups

  Has reproduction · 78

  Integration of public and newly generated scRNA-seq datasets yields a compendium of 139 subjects (193 samples, 403,973 immune cells) spanning CSF and blood across healthy controls and multiple neurologic diseases.

  csf scrna-seq trajectory flow

• Identification of serum biomarkers for colon cancer by proteomic analysis.

  PMID 16755300 · PMC2361335 · British journal of cancer · 2006 · 8 claims · 8 setups

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  Complement C3a des-arg, α1-antitrypsin and transferrin were identified as serum proteins with diagnostic potential for CRC.

  serum pooled seldi seldi-tof seldi artificial

• Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

  PMID 19112531 · PMC2610290 · Molecular vision · 2008 · 8 claims · 4 setups

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  A novel STRA6 missense variant (p.G217E, exon 8) and a novel STRA6 nonsense variant (p.Q592X, exon 18) were identified in one A/M subject and absent from 89 controls, implicating STRA6 in this subject's A/M phenotype.

  genomic stra6 direct variant

• SNP selection for genes of iron metabolism in a study of genetic modifiers of hemochromatosis.

  PMID 18366708 · PMC2289803 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  Illumina validation/design scores above 0.6 are not strongly correlated with actual SNP genotyping performance (Gentrain score)

  randomly heirs seattlesnps african resequencing genome-wide tag

• The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.

  PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups

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  PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs

  sophie mammalian xenopus lymphoblastoid resequencing cellular heterologous

• A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

  PMID 19728872 · PMC2745377 · BMC medical genetics · 2009 · 8 claims · 7 setups

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  A novel homozygous missense mutation, c.1922G>A (p.Arg641His), in MANBA was identified in a patient with severe neurological disease featuring pyramidal and cerebellar involvement, a phenotype not previously reported in β-mannosidosis.

  family hek293t lymphoid pcr-amplified fluorometric site-directed western