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).

• Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.

  PMID 41767255 · PMC12936829 · iScience · 2026 · 8 claims · 7 setups

  Has reproduction · 100

  A novel computational (Snakemake) pipeline quantifies intratumoral heterogeneity in MSI status at single-cell resolution

  colorectal cancer aggregated msisensor-rna single-cell cnv-based

• Identity rather than 3D position informs splicing of rare introns in the human genome.

  PMID 41561379 · PMC12814444 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 98

  Rare intron classes (minor, minor-like, hybrid, non-canonical) are largely dispersed across the linear human genome, with only two notable clusters (GBP on chr1, TSPY on chrY)

  reference genome k562 computational genome-wide chromomap hi-c

• A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

  PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

  Has reproduction · 76

  58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

  asfv b602l porcine sardinian whole-genome sanger haemoadsorption

• Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.

  PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups

  Has reproduction · 92

  A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)

  panax ginseng whole-genome genome rna-seq

• Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

  PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

  Full-text index only

  The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

  elegans whole-genome rnase pharmacological

• Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance.

  PMID 16168060 · PMC1249558 · BMC biotechnology · 2005 · 8 claims · 6 setups

  Full-text index only

  Increased gDNA input into the MDA WGA reaction increases the proportion of double-stranded and human-specific PCR-amplifiable wgaDNA and improves genotyping performance.

  lymphoblastoid gdna ntc wgadna quantification displacement str

• A chromosomally integrated bacteriophage in invasive meningococci.

  PMID 15967821 · PMC2212043 · The Journal of experimental medicine · 2005 · 8 claims · 7 setups

  Full-text index only

  An 8-kb genetic island (NMA1792-NMA1799) is specifically associated with hyperinvasive meningococcal clonal complexes

  meningitidis culture czech patients comparative pcr nuclease

• Empirical codon substitution matrix.

  PMID 15927081 · PMC1173088 · BMC bioinformatics · 2005 · 8 claims · 5 setups

  Full-text index only

  The authors present the first empirical codon substitution matrix built entirely from alignments of vertebrate coding DNA sequences.

  orthologous million codon same pairwise empirical comparative

• EGASP: the human ENCODE Genome Annotation Assessment Project.

  PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

  encode computational manual rt-pcr

• Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

  PMID 17895298 · PMC2533592 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 7 setups

  Full-text index only

  Nucleotide and amino acid substitution trends between human-mouse orthologs are highly asymmetric and polarized in opposite directions for high-GC versus low-GC gene groups.

  human-mouse high aarm orthologous content pairwise

• Evolution of organelle-associated protein profiling.

  PMID 19110081 · PMC2680700 · Journal of proteomics · 2009 · 8 claims · 8 setups

  Full-text index only

  Traditional biochemical organelle isolation followed by MS cataloguing suffers high false-positive rates because organelles cannot be purified to homogeneity and are structurally heterogeneous

  golgi nuclear lipid clathrin-coated density qualitative silac

• Identification of genomic regions contributing to etoposide-induced cytotoxicity.

  PMID 19089452 · PMC2714550 · Human genetics · 2009 · 7 claims · 6 setups

  Full-text index only

  Etoposide-induced cytotoxicity in CEPH lymphoblastoid cell lines is heritable, with genetics explaining 17-25% of variation

  ceph subset hapmap simulated growth heritability non-parametric

• Salivary proteomics for oral cancer biomarker discovery.

  PMID 18829504 · PMC2877125 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 5 setups

  Full-text index only

  Subtractive salivary proteomics reveals proteins differentially present/expressed between OSCC patients and matched healthy controls.

  pooled saliva shotgun two-dimensional elisa

• Potential biomarkers of human salivary function: a modified proteomic approach.

  PMID 18804197 · PMC2633945 · Archives of oral biology · 2009 · 6 claims · 6 setups

  Full-text index only

  Two SDS-PAGE bands, identified by MS-MS as statherin and a truncated (N-terminal 8-aa-missing) cystatin S, are the strongest and most consistent predictors of HAA/LAA group membership and clinical/microbiological outcomes

  resting pooled saliva quantified preparative sds-page western

• BRAF, KRAS and PIK3CA mutations in colorectal serrated polyps and cancer: primary or secondary genetic events in colorectal carcinogenesis?

  PMID 18782444 · PMC2553419 · BMC cancer · 2008 · 8 claims · 7 setups

  Full-text index only

  KRAS, BRAF and PIK3CA mutations occur in the majority of colorectal polyps and are mutually exclusive

  formalin-fixed colorectal sporadic polyps pcr bisulfite pentaplex

• An integrated genomic analysis of human glioblastoma multiforme.

  PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

  Full-text index only

  IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

  gbm additional missense exome targeted snp

• A biomarker panel for peripheral arterial disease.

  PMID 18687758 · PMC3133945 · Vascular medicine (London, England) · 2008 · 7 claims · 6 setups

  Full-text index only

  β2-microglobulin (β2M) and cystatin C had the highest correlation with ABI among all plasma markers tested, higher than age, smoking, or diabetes status

  plasma fasting subjects biomarker nephelometric clinical ankle-brachial

• A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

  PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

  Full-text index only

  Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

  faecal rsr 16s sargasso shotgun blastn-based 16s

• Associations between polycyclic aromatic hydrocarbon-related exposures and p53 mutations in breast tumors.

  PMID 20064791 · PMC2854728 · Environmental health perspectives · 2010 · 8 claims · 5 setups

  Full-text index only

  PAH-related exposures are associated with breast cancer differently according to tumor p53 mutation status, type, effect, and number

  archived breast peripheral study surveyor immunohistochemistry competitive

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter