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).

• Correlation of microsynteny conservation and disease gene distribution in mammalian genomes.

  PMID 19909546 · PMC2779822 · BMC genomics · 2009 · 7 claims · 8 setups

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  Density of mouse orthologs of human disease genes correlates with regions of conserved microsynteny in the mouse genome

  genes autosomes dog genome comparative blat sliding-window

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

  PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 58

  PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA

  cancer tcga-stad stomach ges1 rna-seq pearson gsva

• Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

  PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

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  Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

  squamous ophid degs oligonucleotide interaction connectivity

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• Widespread ectopic expression of olfactory receptor genes.

  PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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  OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

  tissues olfactory intact probesets microarray est custom

• Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

  PMID 18086709 · PMC2241899 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Preferred nucleotide sequences around the initiation codon are diverse among eukaryote species, but differences roughly reflect evolutionary relationships between species

  eukaryote genes hexanucleotide saccharomyces comparative cluster hexanucleotide

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 4 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is trivially high regardless of condition and gives misleading estimates of the replicability of conditional (differential) variation in expression.

  encode liver bulk rna-seq meta-analysis

• Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments.

  PMID 15850479 · PMC1127068 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  A step-down quadratic regression method (fitting quadratic, then linear, then null models per gene) identifies differentially expressed genes and classifies them into 9 temporal expression patterns using continuous time information.

  olfactory present same anova-significant microarray step-down peddada

• Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

  PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

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  Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

  perfused lung microarray principal wilcoxon

• PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.

  PMID 18925948 · PMC2605471 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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  Gonna, a supervised k-nearest-neighbor Guilt-By-Association predictor, proposes GO annotations for a gene based on similarity of its transcriptome, proteome, or interactome profile to genes already annotated by GeneDB

  plasmodium genedb-annotated k-nn leave-one-out

• Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.

  PMID 19744994 · PMC2773259 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 5 setups

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  560 genetic skin diseases can be decomposed into 71 elementary phenotypic features (42 dermatologic, 29 systemic) that combine to represent each disease as a point in a multidimensional phenotype space

  genodermatoses phenotype disease gene-phenotype manual correlation principal

• A Bayesian approach to accurate and robust signature detection on LINCS L1000 data.

  PMID 32003771 · PMC7203754 · Bioinformatics (Oxford, England) · 2020 · 6 claims · 4 setups

  Has reproduction · 37

  A novel Bayesian-based peak deconvolution algorithm gives unbiased likelihood estimations for peak locations and characterizes peaks with probability-based z-scores.

  lincs simulated l1000 l1000 simulated student's

• Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

  PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups

  Has reproduction · 75

  RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.

  pbmcs pbmc aligned bulk read transcript

• Gene- and evidence-based candidate gene selection for schizophrenia and gene feature analysis.

  PMID 19944577 · PMC2826526 · Artificial intelligence in medicine · 2010 · 8 claims · 5 setups

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  The SCOR method outperforms the CCOR method for prioritizing schizophrenia candidate genes

  schizophrenia genes ranked gene-based gene expression

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs

  afb1 breast training candidate computational bulk weighted

• COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.

  PMID 36350658 · PMC9825429 · Nucleic acids research · 2023 · 8 claims · 6 setups

  Has reproduction · 84

  COXPRESdb version 8 adds CoexMap (UMAP-based genome-scale coexpression visualization), KEGG pathway enrichment summaries, and CoexPub (literature-linking tool) as new analysis features.

  animal same coexpression gene rnaseq-based microarray-based pathway

• Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data.

  PMID 18560577 · PMC2409962 · PloS one · 2008 · 7 claims · 5 setups

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  Ranked Coexpression Groups (RCG) built from k=6 nearest coexpressed genes, combined with a majority-rule functional characterization, integrate multiple datasets/coexpression measures to generate high-confidence functional annotation predictions

  normal genome-wide same omim microarray sage computational

• The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

  PMID 19912342 · PMC2868947 · FEMS immunology and medical microbiology · 2010 · 7 claims · 5 setups

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  The types of vaginal bacterial communities found in Japanese women closely resemble those previously found in White and Black North American women.

  vaginal japanese t-rflp clone cluster

• Comprehensive Analysis of Cell Population Dynamics and Related Core Genes During Vitiligo Development.

  PMID 33679890 · PMC7933673 · Frontiers in genetics · 2021 · 8 claims · 7 setups

  Has reproduction · 67

  Immune cell infiltration and abnormal gene expression are closely related to vitiligo pathogenesis

  skin peripheral vitiligo deg gene immune coexpression