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).

• Natural clines and human management impact the genetic structure of Algerian honey bee populations.

  PMID 38114899 · PMC10729559 · Genetics, selection, evolution : GSE · 2023 · 7 claims · 8 setups

  Has reproduction · 55

  No significant admixture from European subspecies was detected in Algerian honey bees, suggesting large-scale queen imports have not occurred in Algeria.

  apis algerian ld-pruned reference whole-genome read identity-by-descent

• TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

  PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 2 setups

  Has reproduction · 50

  TOSCA is the first automated, open-source, end-to-end tumor-only somatic calling workflow for WES and targeted panel sequencing data.

  t-cell hcc1395 targeted whole-exome

• Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

  PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

  Full-text index only

  A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

  coriell myeloma duplicate snp targeted genotyping machine

• Preselection of cases through expert clinical and radiological review significantly increases mutation detection rate in multiple epiphyseal dysplasia.

  PMID 17133256 · PMC2670452 · European journal of human genetics : EJHG · 2007 · 7 claims · 3 setups

  Full-text index only

  Expert clinical-radiological preselection significantly increases mutation detection rate in MED

  patients genomic single clinical pcr

• Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

  PMID 35296718 · PMC8927422 · Scientific reports · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Four FBN1-negative patients from three families with a MASS-like phenotype carry likely pathogenic or uncertain-significance missense variants in the propeptide-coding regions of COL2A1

  blood-derived four patients col2a1 targeted clinical transthoracic

• 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

  Full-text index only

  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

• A review on the molecular diagnostics of Lynch syndrome: a central role for the pathology laboratory.

  PMID 19929944 · PMC3837620 · Journal of cellular and molecular medicine · 2010 · 8 claims · 7 setups

  Full-text index only

  Lynch syndrome is caused by germline mutations in the mismatch repair genes MLH1, MSH2, MSH6 or PMS2

  colorectal tumour sporadic germline msi immunohistochemistry mlh1

• A Decentralized Kidney Transplant Biopsy Classifier for Transplant Rejection Developed Using Genes of the Banff-Human Organ Transplant Panel.

  PMID 35619722 · PMC9128066 · Frontiers in immunology · 2022 · 6 claims · 6 setups

  Has reproduction · 90

  A random forest model trained solely on B-HOT panel genes (B-HOT Model) accurately classifies kidney transplant biopsies as NR, ABMR, or TCMR.

  kidney gene combined microarray machine sequential

• Needles in the haystack: identifying individuals present in pooled genomic data.

  PMID 19798441 · PMC2747273 · PLoS genetics · 2009 · 8 claims · 7 setups

  Full-text index only

  The distribution of T for null samples (individuals not in F or G) deviates strongly from the assumed standard normal, in both location and width.

  cgems hapmap genetic-distance within-population snp-count

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class machine learning models built from cross-platform microarray meta-analysis can distinguish bacterial, viral and no-infection states with high accuracy (best model: 93% bacterial, 89% viral correct).

  blood merged affymetrix-optimized gene feature out-of-sample

• Emerging strategies and applications of pharmacogenomics.

  PMID 15606999 · PMC3500198 · Human genomics · 2004 · 7 claims · 7 setups

  Full-text index only

  Effective pharmacogenomics requires infrastructure including informed consent processes, accurate phenotypic data collection, high-throughput genotyping technology, and integrated information technology systems.

  subjects ethnically patients genome-wide gene case-control

• Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

  PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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  Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

  qbl pgf classical ceph bac comparative gene

• Genomic screen for loci associated with tobacco usage in Mission Indians.

  PMID 16472381 · PMC1386651 · BMC medical genetics · 2006 · 8 claims · 5 setups

  Full-text index only

  Regular tobacco use (h2=0.37±0.11) and persistent tobacco use (h2=0.34±0.12) are moderately heritable in this Mission Indian sample

  mission pedigrees same participants genotyping multipoint heritability

• The Genographic Project public participation mitochondrial DNA database.

  PMID 17604454 · PMC1904368 · PLoS genetics · 2007 · 7 claims · 4 setups

  Full-text index only

  The Genographic Project created the largest standardized human mtDNA database to date, comprising 78,590 genotypes from the first 18 months of public participation.

  buccal reference entire direct coding-region leave-one-out

• Development of a fluorescent multiplex assay for detection of MSI-High tumors.

  PMID 15528789 · PMC3839403 · Disease markers · 2004 · 8 claims · 7 setups

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  Mononucleotide markers are the most sensitive and specific microsatellite marker type for detecting MSI-H tumors with MMR defects

  colorectal blood healthy non-msi-h microsatellite fluorescent immunohistochemistry

• Multilocus analysis of SNP and metabolic data within a given pathway.

  PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

  healthy plasma genomic chi-square combinatorial leave-one-out

• Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

  PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

  Full-text index only

  Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

  cervical independent computational long real-time gene

• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

  PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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  A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

  personal genomic pcr-validated unrelated short-read pcr sanger

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 7 claims · 8 setups

  Has reproduction

  Tabular ML classifiers (TabNet, XGBoost, LightGBM) trained on tumor-only-derived features achieve state-of-the-art somatic vs germline classification, with AUC>94% on TCGA holdout and AUC>85% on metastatic melanoma.

  tcga metastatic tumor-only whole-exome wes copy-number

• Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

  PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

  Full-text index only

  Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

  family additional unrelated mutant direct linkage targeted