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).

• CCL genes in multiple sclerosis and systemic lupus erythematosus.

  PMID 18602166 · PMC5301077 · Journal of neuroimmunology · 2008 · 7 claims · 5 setups

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  Previously suggested borderline CCL marker/haplotype associations with MS are rejected after Bonferroni correction for multiple testing

  genomic patients 17q11.2-q12 buccal snp linkage hardy-weinberg

• Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha.

  PMID 18559093 · PMC2440550 · Molecular cancer · 2008 · 7 claims · 6 setups

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  Gain of chromosome 5p is the most frequent genomic alteration in invasive cervical cancer

  cervical tumors pap tumor snp fluorescence fish

• HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

  PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 66

  HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

  embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq

• Transcriptome analysis reveals differential splicing events in IPF lung tissue.

  PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

  Has reproduction · 81

  873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

  lung discovery gene gse24206 sequencing rna-seq real-time

• A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

  PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

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  A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

  cases patients postmortem whole-genome cox linear

• Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells.

  PMID 17267408 · PMC1865061 · Nucleic acids research · 2007 · 6 claims · 6 setups

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  Measuring allelic imbalance (AI) of two SNP alleles within the same sample is an effective approach for identifying cis-acting rSNPs, since each allele serves as an internal control for the other.

  tumor promoter hela cdna bead tag-microarray

• Current and future directions in genomics of amyotrophic lateral sclerosis.

  PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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  Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

  american sals dutch irish genome laser expression

• In B-CLL, the codon 72 polymorphic variants of p53 are not related to drug resistance and disease prognosis.

  PMID 16109171 · PMC1208864 · BMC cancer · 2005 · 7 claims · 5 setups

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  The p53 codon 72 polymorphism is not associated with drug resistance or overall survival in B-CLL

  peripheral fresh b-cll sscp-pcr disc kaplan-meier

• EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

  PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups

  Has reproduction · 54

  EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology

  populus nigra genome variant clustering

• Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.

  PMID 16912992 · PMC1538848 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  PANTHER HMMs built from family/subfamily multiple sequence alignments can classify novel protein sequences into functional groups based on statistically significant HMM match scores

  input gene genome-wide genes sequence gene numerical

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• Gene co-expression network analysis in human spinal cord highlights mechanisms underlying amyotrophic lateral sclerosis susceptibility.

  PMID 33707641 · PMC7970949 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA on control human cervical spinal cord RNA-seq identifies 13 co-expression modules (SC.M1-M13), each representing distinct biological processes or cell types.

  cervical als top yeast bulk stratified protein-protein

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.

  PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups

  Has reproduction · 89

  Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM

  european cis-pqtl myocardial geo mendelian bayesian differential

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

  PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups

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  151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations

  leukocytes leukocyte-derived archived comparison whole-genome quantitative snp

• Methods for genome-wide analysis of DNA methylation in intestinal tumors.

  PMID 19854208 · PMC2891386 · Mutation research · 2010 · 8 claims · 8 setups

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  Aberrant DNA methylation, including CpG island hypermethylation of tumor suppressors and genome-wide hypomethylation, is strongly linked to the origin and progression of colorectal cancer.

  cd19+ lung gpx1 tumor mira medip goldengate

• Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

  PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

  tissues inter-subspecies placenta genomic microarray rt-pcr sequencing

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

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  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

  PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

  Has reproduction · 58

  The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

  developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr