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).

• The promise and reality of personal genomics.

  PMID 19723346 · PMC2768970 · Genome biology · 2009 · 7 claims · 6 setups

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  Despite being the most complete and accurate individually sequenced human genome to date, AK1 sequencing still misses a substantial fraction of variants, showing sequencing technology remains far from complete/reliable.

  ak1 six whole-genome copy-number genotyping-based

• Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

  PMID 19698114 · PMC2749045 · BMC infectious diseases · 2009 · 8 claims · 7 setups

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  Three PRNP mutations—D178N, E200K, and M232R—were identified in heterozygosity in Korean probable CJD patients, marking their first report in this population.

  csf 293t genomic pcr western recombinant sequencing

• Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry.

  PMID 19654045 · PMC2818068 · Methods (San Diego, Calif.) · 2010 · 8 claims · 5 setups

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  Voxelation combined with LC-MS enables high-throughput spatial mapping of protein abundance across mouse brain voxels

  brain digested voxel amt-tag lc-ms bca

• Proteomic-based identification of maternal proteins in mature mouse oocytes.

  PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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  625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

  mature mii identified tissues sds-page acid gene

• A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

  PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

  tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided

• Solute exchange through gap junctions lessens the adverse effects of inactivating mutations in metabolite-handling genes.

  PMID 36107487 · PMC9534548 · eLife · 2022 · 8 claims · 8 setups

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  Colorectal cancer (CRC) cells are coupled by gap junctions assembled predominantly from Cx26 (GJB2)

  colorectal normal crc microarray tcga single-cell

• The Chromosome-Scale Genome Assembly of the Redlip Blenny, Ophioblennius macclurei (Blenniidae).

  PMID 41378738 · PMC12758960 · Genome biology and evolution · 2026 · 8 claims · 12 setups

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  A chromosome-scale genome assembly of O. macclurei was generated (529.6 Mb, scaffold N50 23.7 Mb, GC 43.49%) using ONT long reads, Illumina short reads, and Hi-C scaffolding.

  blood muscle tissues assembled oxford illumina hi-c

• Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies.

  PMID 41501078 · PMC12780049 · Nature communications · 2026 · 8 claims · 7 setups

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  MAGPIE is a computational framework (Snakemake workflow) that co-registers Visium spatial transcriptomics with MSI metabolomics and tissue morphology images from same or consecutive sections

  lung brain publicly rodent spatial desi h&e

• Directing stem cell differentiation by chromatin state approximation.

  PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

  cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr

• The Genetic Architecture of Venom Resistance: A Novel Approach to Target Identification and Coevolutionary Discovery.

  PMID 41739857 · PMC12978544 · Molecular biology and evolution · 2026 · 8 claims · 5 setups

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  12 consensus candidate genes were identified across E&R and XQTL techniques as associated with venom resistance

  scolopendra drosophila sequenced genome phenotypic evolve

• AMR-GNN: a multi-representation graph neural network framework to enable genomic antimicrobial resistance prediction.

  PMID 41792137 · PMC13087051 · Nature communications · 2026 · 7 claims · 8 setups

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  AMR-GNN, a graph neural network integrating multiple genomic representations (unitigs, SNPs, FCGR) via low-rank multimodal fusion, improves AMR phenotype prediction in P. aeruginosa compared to single-representation baseline models.

  pseudomonas aeruginosa escherichia coli whole-genome elastic convolutional

• Much ado about nothing: modeling amino acid replacement with predicted protein structures.

  PMID 42036821 · PMC13171170 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 7 setups

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  AFSM was constructed from over 660,000 structural alignments across ~21,000 proteins (297 InterPro families), following the BLOSUM log-odds methodology.

  proteins balibase pfam cath structural sequence remote

• The Nuclear and Mitochondrial Genomes of the Lined Rockskipper, Istiblennius lineatus (Teleostei: Blenniidae).

  PMID 42117780 · PMC13195801 · Genome biology and evolution · 2026 · 7 claims · 8 setups

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  A chromosome-scale nuclear genome assembly of I. lineatus (643.23 Mb, 24 pseudochromosomes) was generated using PacBio HiFi reads and Arima Hi-C scaffolding.

  istiblennius lineatus pacbio hi-c rna-seq

• Sequential RNA polymerase II activation drives human hematopoiesis.

  PMID 41520338 · PMC13067999 · Cell reports · 2026 · 7 claims · 7 setups

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  sciCUT&Tag2in1 enables simultaneous single-cell combinatorial-indexing profiling of Pol II occupancy (Ser5/Ser2-phospho CTD) together with histone modifications (H3K4me1-2-3 or H3K27me3) in up to 50,000 cells per experiment

  g-csf-mobilized cd34+ 10-donor lineage-depleted scicut&tag2in1 individual souporcell

• S3RL: Enhancing Spatial Single-Cell Transcriptomics With Separable Representation Learning.

  PMID 41556263 · PMC13042551 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  S3RL is a separable representation learning framework that denoises sparse spatial transcriptomic data and enhances biologically relevant signals by integrating gene expression, spatial coordinates, and histological image features.

  dorsolateral dlpfc nanostring spatial cell-type multi-platform

• Oxidative stress-associated genes TPPP3 and VEGFA in COPD revealed by bulk and single-cell sequencing analysis.

  PMID 41620539 · PMC12916760 · Scientific reports · 2026 · 8 claims · 9 setups

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  76 overlapping genes were identified between COPD-associated DEGs and oxidative stress-related genes.

  lung genecards differentially bronchial bulk database functional

• The gene expression landscape of disease genes.

  PMID 41664080 · PMC12983648 · Genome biology · 2026 · 8 claims · 8 setups

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  In tissues and cell types with established disease relevance, disease genes show higher and more specific gene expression than control genes

  gtex pubmed tabula archs4 differential magma anderson-darling

• SNP haplotype tagging from DNA pools of two individuals.

  PMID 12709267 · PMC156884 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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  An algorithm can reconstruct haplotypes from pools of two individuals' DNA under very general conditions, without requiring Hardy-Weinberg equilibrium.

  add2 pooling computational exhaustive

• Detection of large deletions in the LDL receptor gene with quantitative PCR methods.

  PMID 15842735 · PMC1087844 · BMC medical genetics · 2005 · 7 claims · 3 setups

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  MLPA was cheaper, more accurate and more precise than Real-Time PCR for detecting LDL receptor gene deletions

  genomic real-time multiplex long-range

• Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.

  PMID 17088437 · PMC2705832 · Molecular cancer therapeutics · 2006 · 8 claims · 3 setups

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  137 oncogenic mutations were identified across 14 of 24 screened cancer genes (APC, BRAF, CDKN2A, CTNNB1, HRAS, KRAS, NRAS, SMAD4, PIK3CA, PTEN, RB1, STK11, TP53, VHL) in the NCI-60 panel

  nci-60 pcr multiplex snp