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).

• Compound heterozygosity for a novel and a recurrent MFRP gene mutation in a family with the nanophthalmos-retinitis pigmentosa complex.

  PMID 19753314 · PMC2742641 · Molecular vision · 2009 · 8 claims · 8 setups

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  Compound heterozygosity for two distinct MFRP mutations (a novel nonsense mutation and a recurrent frameshift mutation) causes the nanophthalmos-retinitis pigmentosa-foveoschisis-optic disc drusen complex in this sibling pair

  patients eyes genomic ophthalmological a-mode electroretinogram

• Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains.

  PMID 19750224 · PMC2735778 · PLoS pathogens · 2009 · 7 claims · 5 setups

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  The IRGM −261TT genotype is negatively associated with (protective against) pulmonary TB caused by M. tuberculosis

  pulmonary tuberculosis reporter genotyped case-control gene spoligotyping

• Genomic views of distant-acting enhancers.

  PMID 19741700 · PMC2923221 · Nature · 2009 · 8 claims · 8 setups

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  Meta-analysis of ~1200 top GWAS SNPs found that in 40% of cases (472/1170) no known exons overlap the linked SNP or its haplotype block, implying noncoding variation causally contributes to many traits.

  genome patients embryos ret gwas targeted transgenic

• A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

  PMID 19725976 · PMC2742551 · BMC cancer · 2009 · 7 claims · 5 setups

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  Three protein spots (beta-actin, HSP60, PDI) show low expression variability across tumourous, non-tumourous cirrhotic, and normal liver tissues by 2-DE (ANOVA p>0.99 ranking)

  liver 2-de western immunohistochemistry

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

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  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

  PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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  85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

  paired list differentially oscc 2-de gene interaction

• A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy.

  PMID 19649163 · PMC2718742 · Molecular vision · 2009 · 7 claims · 7 setups

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  A novel heterozygous UBIAD1 mutation, G98S, was identified in two affected members (proband and her father) of a Chinese SCCD family.

  genomic cornea corneas blood direct pcr laser

• Deconvoluting the 'omics' for organ transplantation.

  PMID 19644370 · PMC2993238 · Current opinion in organ transplantation · 2009 · 8 claims · 5 setups

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  High-throughput 'omic' technologies (genomics, proteomics, metabolomics, antibiomics) can uncover novel biomarkers for acute rejection, chronic rejection, and operational tolerance without a priori pathway bias

  kidney sera peripheral microarray non-parametric antibiomics

• Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.

  PMID 37160956 · PMC10169776 · Scientific reports · 2023 · 7 claims · 8 setups

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  Spontaneous ΦD5-resistant D. solani mutants DsR34 and DsR207 show significantly reduced virulence and colonization ability in planta compared to wild-type

  potato solani planta maceration genome

• Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

  PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

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  10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

  aorta cardiovascular peripheral blood methylation mirna expression

• Revealing potential interfering genes between abdominal aortic aneurysm and periodontitis through machine learning and bioinformatics analysis.

  PMID 40857330 · PMC12380325 · PloS one · 2025 · 6 claims · 8 setups

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  90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

  abdominal gingival overlapping interacting microarray weighted kegg

• Gut microbiome signatures associated with depression and obesity.

  PMID 41615149 · PMC13011431 · mSystems · 2026 · 8 claims · 4 setups

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  Taxonomic gut microbiome profiles classify depressed vs non-depressed subjects with a balanced accuracy of 0.90 using machine learning

  stool subjects shotgun alpha machine

• Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.

  PMID 41800382 · PMC12967217 · Bioinformatics advances · 2026 · 6 claims · 8 setups

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  Annotation tools show substantial variation in isoform detection, structural completeness, splicing classification, and handling of 5' read truncation when applied to plant dRNA-seq data.

  barley extracted tool novel nanopore illumina transcriptome

• Shotgun metagenomic analysis of the oral microbiomes of children with noma.

  PMID 41860897 · PMC13029773 · PLoS neglected tropical diseases · 2026 · 8 claims · 6 setups

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  Noma oral microbiomes show marked dysbiosis with significant enrichment of Treponema, Porphyromonas, and Bacteroides, and depletion of Streptococcus and Rothia, compared to healthy controls

  oral saliva noma previously shotgun comparative metagenome

• MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.

  PMID 41917425 · PMC13201759 · Communications biology · 2026 · 7 claims · 6 setups

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  MIMIC is a reproducible, semi-automated workflow that co-registers and jointly analyzes MALDI-MSI and IMC data using a chain of before/after microscopy images.

  liver regions artificial maldi-msi imaging multi-step

• SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.

  PMID 41993886 · PMC13082578 · Computational and structural biotechnology journal · 2026 · 6 claims · 6 setups

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  SnakeAltPromoter is the first unified, reproducible Snakemake workflow that automates alternative promoter analysis from raw RNA-seq data using 3 complementary methods (ProActiv, Salmon, DEXSeq)

  heart brain gm12878 simulated bulk cage rna-seq

• DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

  PMID 42152108 · PMC13185202 · Genome medicine · 2026 · 8 claims · 5 setups

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  Relatively simple ML models (logistic regression) outperform complex algorithms such as deep neural networks for methylation-based cancer classification

  validation cns healthy genes methylation copy-number gene-set

• Spatial Transcriptomics of Human Decidua Identifies Molecular Signatures in Recurrent Pregnancy Loss.

  PMID 41031483 · PMC13242933 · Genomics, proteomics & bioinformatics · 2026 · 7 claims · 8 setups

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  The human decidua contains two coherent spatial domains, the implantation zone (IZ) and glandular-secretory zone (GZ), corresponding to the decidua compacta and spongiosa

  first-trimester decidual spots dnk 10x h&e type

• TEDD: a comprehensive database for translation efficiency dynamics.

  PMID 41217970 · PMC12807600 · Nucleic acids research · 2026 · 8 claims · 4 setups

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  TEDD integrates 1518 RNA-seq, Ribo-seq, and RNC-seq samples from 143 human projects (279 datasets) spanning 24 tissues/cell types, 74 cell lines, and 52 conditions.

  tissues reference rna-seq ribo-seq rnc-seq

• Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages.

  PMID 41231218 · PMC12865363 · Cancer immunology research · 2026 · 6 claims · 8 setups

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  TAMs arise from two distinct origins: C1QC+ TAMs likely derive from resident tissue macrophages, while SPP1+ TAMs and ISG15+ TAMs likely originate from circulating monocytes.

  myeloid melanoma monocyte-to-macrophage coad-read scrna-seq differential developmental