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).

• SNP@Evolution: a hierarchical database of positive selection on the human genome.

  PMID 19732458 · PMC2755008 · BMC evolutionary biology · 2009 · 7 claims · 6 setups

  Full-text index only

  SNP@Evolution is a hierarchical database integrating HET, FST, and iHS from HapMap Phase II and III to identify genome-wide positive selection signals

  hapmap autosomes simulated sliding snp sliding haplotype-based

• Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

  PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

  Full-text index only

  R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

  bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation

• A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.

  PMID 41513996 · PMC12872441 · Nature microbiology · 2026 · 8 claims · 7 setups

  Full-text index only

  The global cellular tRNA pool is not substantially altered during APMV infection, despite the virus encoding its own tRNA genes.

  acanthamoeba apmv rna-seq ribo-seq mim-trna-seq

• Compressing DNA sequence databases with coil.

  PMID 18489794 · PMC2426707 · BMC bioinformatics · 2008 · 8 claims · 1 setups

  Full-text index only

  coil achieves higher compression ratio than state-of-the-art general-purpose compression tools on a large GenBank EST database file

  large sequence

• MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

  PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

  pooled genomic aneuploid dog mlga

• Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

  PMID 18831757 · PMC2572624 · BMC bioinformatics · 2008 · 6 claims · 4 setups

  Full-text index only

  A dye intensity bias between the two channels (X/Y, Cy5/Cy3) of the Infinium II assay remains after BeadStudio's proprietary normalization.

  urothelial hapmap snp plot baf

• Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

  PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

  representative illumina six snp serial concentration

• Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

  PMID 18302728 · PMC2291454 · BMC medical genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Functional assays of TSC1–TSC2 complex activity can distinguish pathogenic TSC2 mutations from rare polymorphisms when multiple variants segregate in one family

  hek immunoprecipitated tsc2 peripheral coimmunoprecipitation rheb s6k-t389

• Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

  PMID 19788805 · PMC2819883 · Emerging infectious diseases · 2009 · 8 claims · 7 setups

  Full-text index only

  A 7-locus MLST scheme selected from conserved housekeeping genes shared across 4 Chlamydiaceae species (7 genomes) can genotype diverse C. trachomatis reference and clinical isolates.

  genome-sequenced trachomatis same concatenated whole-genome multilocus ompa

• MZPAQ: a FASTQ data compression tool.

  PMID 31171931 · PMC6547476 · Source code for biology and medicine · 2019 · 7 claims · 3 setups

  Has reproduction · 58

  MZPAQ, a hybrid of MFCompress and ZPAQ, outperforms state-of-the-art and general-purpose compression tools on all benchmark datasets in terms of compression ratio

  fastq same compression overall

• Increased risk of breast cancer among female relatives of patients with ataxia-telangiectasia: a causal relationship?

  PMID 16222317 · PMC2361617 · British journal of cancer · 2005 · 6 claims · 3 setups

  Full-text index only

  Breast cancer risk is strongly and significantly elevated specifically among mothers of AT patients (SIR=7.14), consistent with Olsen et al's finding (SIR=6.7)

  blood same retrospective atm weighted

• PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome.

  PMID 16845094 · PMC1538814 · Nucleic acids research · 2006 · 7 claims · 2 setups

  Full-text index only

  Selecting primers using the stringent hybridization ratio (requiring an 'executable temperature' where target hybridization ratio >0.99 and off-target ratio <0.05) yields more specific genomic primers than the conventional melting-temperature-based approach, which only guarantees >0.5 vs <0.5

  chrx entire multiplex computational

• Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

  PMID 33690630 · PMC7978347 · PLoS genetics · 2021 · 8 claims · 4 setups

  Has reproduction · 97

  Paramutation between R and S HPT epialleles occurs only in tetraploid (RRSS) F2 progeny, not in diploid (RS) F2 progeny, reducing the ratio of hygromycin-resistant plants below Mendelian expectation.

  diploid 14-day-old tetraploid type hygromycin small crispr-cas9

• Quantitative analysis of SMN1 gene and estimation of SMN1 deletion carrier frequency in Korean population based on real-time PCR.

  PMID 15608400 · PMC2816285 · Journal of Korean medical science · 2004 · 7 claims · 6 setups

  Full-text index only

  Developed a reliable quantitative real-time PCR assay using SMN1-specific primers, SYBR Green I dye, and the comparative Ct (ΔΔCt) method, normalized to albumin, to determine SMN1 copy number

  genomic peripheral quantitative multiplex pcr-restriction

• Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

  PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

  Full-text index only

  Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

  atm hybridized probe oligonucleotide transcription microarray

• Mosaicism in von Hippel-Lindau disease: an event important to recognize.

  PMID 18205710 · PMC4401302 · Journal of cellular and molecular medicine · 2007 · 7 claims · 5 setups

  Full-text index only

  The proband's father is a somatic mosaic for a VHL missense mutation (R161Q), explaining his mild, late-onset phenotype compared to his daughter's severe early-onset disease.

  peripheral father's pcr proband dhplc sanger semiquantitative

• The CYP2J2 G-50T polymorphism and myocardial infarction in patients with cardiovascular risk profile.

  PMID 19105833 · PMC2626571 · BMC cardiovascular disorders · 2008 · 7 claims · 4 setups

  Full-text index only

  T-allele carriers of the CYP2J2 G-50T polymorphism had significantly more myocardial infarctions than G/G carriers in univariate analysis (21.6% vs 13.7%, p=0.026)

  whole-blood patients pooled genotyping clinical multivariate

• Genotype-phenotype associations: modulation by diet and obesity.

  PMID 19037211 · PMC2771769 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 7 setups

  Full-text index only

  Obesity modulates the association between APOE genotype and fasting insulin/glucose levels in men, with obese APOE4 carriers showing higher insulin and glucose than other obese genotype groups.

  framingham spanish caucasian population apoe edn1 lpl

• Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population.

  PMID 18776593 · PMC3827795 · Disease markers · 2008 · 8 claims · 5 setups

  Full-text index only

  The CNR1 4895G allele is associated with waist-to-hip ratio (WHR)

  peripheral same pcr-rflp anthropometric biochemical

• CGH-Profiler: data mining based on genomic aberration profiles.

  PMID 16042799 · PMC1183191 · BMC bioinformatics · 2005 · 8 claims · 3 setups

  Full-text index only

  CGH-Profiler circumvents ISCN nomenclature by importing CGH data from different vendor systems and converting it into a table format suitable for statistical analysis.

  tumour cgh metaphase comparative metaphase