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).

• RPS4Y gene family evolution in primates.

  PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

  primate chromosomes rps4x concatenated pcr fluorescence repeat

• Geographic distribution and genetic diversity of the Ehrlichia sp. from Panola Mountain in Amblyomma americanum.

  PMID 18433500 · PMC2394526 · BMC infectious diseases · 2008 · 8 claims · 6 setups

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  PME was not recently introduced to the United States, given its extensive geographic distribution, multi-year persistence at sites, and genetic variability

  amblyomma pme-positive map1 nested pcr sanger

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Divergence of exonic splicing elements after gene duplication and the impact on gene structures.

  PMID 19883501 · PMC3091315 · Genome biology · 2009 · 8 claims · 7 setups

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  ESEs and ESSs diverge especially fast shortly after gene duplication, correlating with time since duplication (Ks)

  paralogous human-mouse duplicated comparative ortholog binomial

• Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

  PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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  A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

  pca malignant tcga mda single-cell infercnv pseudotime

• Epidemiology and phylogenomic characterization of the Clade IIb C.1 Mpox outbreak in Phnom Penh, Cambodia (2023-2024).

  PMID 41575511 · PMC12978180 · Emerging microbes & infections · 2026 · 8 claims · 8 setups

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  All Cambodian Mpox genomes belong to lineage C.1, nested within Clade IIb

  skin mpxv-positive raw cambodian real-time viral bioinformatic

• Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV V2 apex broadly neutralizing antibody development.

  PMID 41686912 · PMC13015429 · Science immunology · 2026 · 8 claims · 8 setups

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  Efficiency of B cell priming, not complexity of Env-guided affinity maturation, is the primary obstacle to V2 apex bNAb elicitation in SHIV-infected macaques.

  shiv-infected plasma igg+ rhesus plasma single-genome next-generation

• The genomic diversity of SARS-CoV-2 Omicron lineages collected during routine sentinel surveillance in Tanzania between November 2022 and July 2023.

  PMID 41688918 · PMC13011721 · BMC genomics · 2026 · 8 claims · 5 setups

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  Seven Omicron Nextstrain clades were identified among Tanzanian sequences, with clades 22F (XBB*) and 22E (BQ.1) predominant, comprising 56.3% and 21.35% of samples respectively

  nasal sars-cov-2-positive multiplexed tanzanian rt-qpcr whole-genome bioinformatic

• Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate.

  PMID 41758556 · PMC12948150 · Microbial genomics · 2026 · 8 claims · 8 setups

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  Autocycler (consensus long-read-only assembler) circularised the most chromosomes, 95% (87/92), significantly more than Unicycler, Unicycler bold, Flye and Hybracter (hybrid)

  clinical enterobacterales assembled assembler-polisher nanopore illumina comparative

• Divergent clonal evolution and tumor microenvironment remodeling shape gastric cancer peritoneal metastasis.

  PMID 41882239 · PMC13181027 · Communications biology · 2026 · 8 claims · 7 setups

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  Substantial intra-patient heterogeneity exists between GCPM and primary tumors at both genetic and functional (transcriptomic) levels

  gastric wgs paired genes whole-genome whole-transcriptome mutational

• A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

  PMID 41484771 · PMC12882460 · Molecular cancer · 2026 · 7 claims · 5 setups

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  Integration of pan-cancer scRNA-seq data yields a comprehensive single-cell atlas of 157,025 high-quality DNT cells across 23 cancer types.

  tumor dnt ffpe mc38 scrna-seq tcr multiplex

• Chimeric brain models to study human glial-neuronal and macroglial-microglial interactions.

  PMID 41499239 · PMC12974579 · Cell reports · 2026 · 8 claims · 8 setups

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  Co-transplantation of pNPCs and PMPs into neonatal mouse brain generates chimeric brains (hMAN) containing human microglia, astroglia, oligodendroglia, and neurons

  hipsc chimeric hpsc-derived flow sequencing immunohistochemistry

• A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium.

  PMID 24809511 · PMC4014436 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 30

  The Helicosporidium nuclear genome is small and compact (~2.5-fold smaller than Chlorella and Coccomyxa) yet shows almost no evidence of functional/metabolic reduction.

  helicosporidium ten whole-genome transcriptome gene

• Sex-Based Differences in Cell Types and Gene Expression within the Anterior Cruciate Ligament.

  PMID 41587266 · PMC13011956 · The Journal of bone and joint surgery. American volume · 2026 · 8 claims · 5 setups

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  ACL tissue is heterogeneous, containing 5 major cell types: fibroblasts, pericytes, endothelial cells, macrophages, and T cells.

  acl differentially study flow single-cell immunofluorescence

• Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.

  PMID 41777052 · PMC13010820 · Genome biology and evolution · 2026 · 8 claims · 3 setups

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  tRNA genes and their flanking regions show signatures of high historical transcription-associated mutagenesis (TAM) combined with strong purifying selection on the gene body

  reference strains computational population full-length

• Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

  PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

  Has reproduction · 75

  Endothelial cell-specific deletion of Adgrl2 impairs cerebrovascular integrity in mice

  wild-type cortex brain single-molecule single-cell immunohistochemistry

• epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.

  PMID 35178872 · PMC9311447 · Molecular ecology resources · 2022 · 8 claims · 8 setups

  Has reproduction · 52

  epiGBS2 provides a laboratory protocol and revised bioinformatics pipeline for de novo cytosine methylation and SNP calling in species with or without a reference genome

  arabidopsis great epigbs2 demultiplexed epigbs2 pcr demultiplexing

• PhylomeDB: a database for genome-wide collections of gene phylogenies.

  PMID 17962297 · PMC2238872 · Nucleic acids research · 2008 · 7 claims · 6 setups

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  PhylomeDB is a publicly accessible database storing complete, genome-wide collections of gene phylogenies (phylomes).

  seed homologous trimmed homology sequence neighbor

• SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

  PMID 19036790 · PMC2686452 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  SUPERFAMILY provides structural, functional and evolutionary annotation for proteins from all completely sequenced genomes using SCOP-based hidden Markov models

  user-submitted query genomes proteins domain profile-profile comparative

• Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

  PMID 41663577 · PMC12982125 · Nature methods · 2026 · 6 claims · 3 setups

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  Most SARS-CoV-2 genomes were sequenced using tiled amplicon methods, which introduce systematic errors unless assembly software is aware of the amplicon scheme and the error modes of amplicon sequencing

  sars-cov-2 amplicon-aware simulation global