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).

• 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

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  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

• Mouse-Geneformer: A deep learning model for mouse single-cell transcriptome and its cross-species utility.

  PMID 40106407 · PMC11964219 · PLoS genetics · 2025 · 7 claims · 6 setups

  Has reproduction · 95

  Mouse-Geneformer, a Transformer Encoder model pre-trained via masked-token self-supervised learning on mouse-Genecorpus-20M, was successfully constructed following the original human Geneformer architecture.

  healthy scrna-seq disease scrna-seq type perturbation

• 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

• Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

  PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

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  Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

  p53 1bpi mutations disease-associated graph correlation structural

• An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions.

  PMID 18445289 · PMC2386494 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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  Using RNAsubopt suboptimal solutions computed once for the wild-type sequence, specific multiple-point mutations likely to cause conformational rearrangement can be selected without brute-force enumeration.

  example hepatitis minimum suboptimal multiple-point

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.

  PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.

  schizosaccharomyces pombe rna-seq lasso lariat-specific

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

  Full-text index only

  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

  PMID 18922159 · PMC2614521 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

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  PGRMC1 protein spots are differentially abundant between ER-negative and ER-positive breast tumors, with two of three spots more abundant in ER-negative tumors

  sections pooled mcf7 paraffin-embedded 2d-page shrimp viability

• Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

  PMID 20003452 · PMC2801500 · BMC medical genetics · 2009 · 8 claims · 5 setups

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  TCOF1 transcript levels are significantly reduced (~18%) in leucocytes of TCS patients compared to controls

  leucocytes mesenchymal leucocyte real-time direct flow

• A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

  PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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  Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

  serum plasmids coli pcr oligonucleotide chip

• cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer.

  PMID 19671129 · PMC2731783 · BMC cancer · 2009 · 8 claims · 6 setups

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  cDNA sequencing detects P53 missense mutations in colorectal cancer more frequently and reliably than DNA sequencing

  colorectal paired sequencing cdna real-time

• 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

• An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

  PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.

  liver hcv-infected serum bulk chip-seq serum

• Chemical genomics informs antibiotic and essential gene function in Acinetobacter baumannii.

  PMID 40153700 · PMC11975115 · PLoS genetics · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  The vast majority of A. baumannii essential genes show significant chemical-gene interactions upon knockdown

  baumannii ranked lpta representative pooled string mic

• Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

  PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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  A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

  bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow

• Genomic variability within an organism exposes its cell lineage tree.

  PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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  Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

  robinia arabidopsis randomly genotyping multiplex computer

• Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

  PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

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  Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

  neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic

• Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

  PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

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  B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

  paraffin-embedded cloned same predicted pcr cloning blastx

• Human SNPs resulting in premature stop codons and protein truncation.

  PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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  Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

  genome transcripts validated x-snp-encoded database blast exon-intron