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).

• Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

  PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

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  Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

  g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic

• MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome.

  PMID 19702866 · PMC3985121 · Journal of applied microbiology · 2010 · 8 claims · 4 setups

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  Danish C. jejuni isolates from gastroenteritis, RA and GBS patients are highly genetically diverse, comprising 51 STs within 18 clonal complexes among 122 isolates.

  campylobacter concatenated clonal multilocus upgma clonalframe

• Migratory Tumor Cells Cooperate with Cancer Associated Fibroblasts in Hormone Receptor-Positive and HER2-Negative Breast Cancer.

  PMID 38892065 · PMC11172245 · International journal of molecular sciences · 2024 · 8 claims · 8 setups

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  HR+/HER2-BC tumor epithelial cells comprise four single-cell-defined functional (SC-f) subtypes: migratory, secretory, proliferating, and dysfunctional.

  hr+ epcam-sorted tumor tcga-brca droplet sidr-seq bulk

• CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation.

  PMID 41400832 · PMC12790814 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 6 setups

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  CholeraSeq is an automated, V. cholerae-specific Nextflow pipeline that processes WGS outbreak data from raw reads/assemblies to high-quality SNPs and phylogenies in near-real-time.

  cholerae recombination-masked pis read reference-based recombination

• metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.

  PMID 41530917 · PMC12818822 · Gut microbes · 2026 · 8 claims · 8 setups

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  metaFun is an open-source, end-to-end Nextflow/Apptainer pipeline integrating quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomics, network analysis, and strain-level microdiversity analysis into a unified framework

  simulated selected gut mags novo binning pangenome-based

• Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.

  PMID 41641705 · PMC12873609 · Nucleic acids research · 2026 · 7 claims · 8 setups

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  Screening 202 cyanobacterial genomes identified 402 CRSs matching known RNA families (Rfam and Rho-independent terminators) and 409 novel CRSs.

  cyanobacterial peptide aligned local comparative genome sequence

• The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.

  PMID 41671394 · PMC12951522 · Genome biology and evolution · 2026 · 8 claims · 8 setups

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  Gouania slender and stout morphotypes evolved convergently at least twice within the genus, confirmed by 3D morphometrics and phylogenomics

  pelvic individuals draft gouania geometric barcoding phylogenomics

• Single-cell immunophenotyping identifies CD8+GZMK+IFNG+ T cells as a key immune population in cutaneous Lyme disease.

  PMID 41729083 · PMC12956012 · JCI insight · 2026 · 8 claims · 7 setups

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  A clonally expanded CD8+GZMK+IFNG+ T cell population (subdivided into IFNGhi and IFNGint groups) is enriched in the EM lesion and shows an inflammatory, tissue-resident phenotype (GZMBlo/PRF1-) resembling tissue-enriched GZMK+ TteK cells

  whole-skin cd8+gzmk+ifnghi identified skin scrna-seq pseudobulk immune

• rMAP 2.0: a modular, reproducible, and scalable WDL-Cromwell-Docker workflow for genomic analysis of ESKAPEE pathogens.

  PMID 41782684 · PMC12955837 · Bioinformatics advances · 2026 · 8 claims · 8 setups

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  rMAP 2.0 standardizes end-to-end bacterial WGS analysis (QC, trimming, assembly, annotation, AMR/virulence/mobile-element profiling, sequence typing, pangenome inference, phylogenetics) via containerized WDL/Cromwell execution

  enterobacterales illumina aeruginosa pneumoniae whole-genome wgs amr

• Evaluating deep learning based structure prediction methods on antibody-antigen complexes.

  PMID 41863324 · PMC13061134 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  Increased sampling improves the chance of generating a correct antibody-antigen model in a roughly log-linear manner with sample size

  alphafold2.3 alphafold3 boltz-1 chai-1 complex structural

• Segmental copy number amplifications are more stable than aneuploidies in the absence of selection.

  PMID 41968576 · PMC13107562 · Molecular biology and evolution · 2026 · 8 claims · 6 setups

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  Segmental amplifications are stable in the absence of selection, whereas aneuploidies are rapidly lost and revert to single-copy genotype

  cerevisiae computational long-term pairwise content

• Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.

  PMID 42007585 · PMC13245728 · The ISME journal · 2026 · 8 claims · 8 setups

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  Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (Nematoda, Mollusca, and Cnidaria)

  pseudoalteromonas mollusca individual live pangenomic core-genome average

• TE-SCALE: a comprehensive database for exploring transposable element expression across human cancers at single-cell resolution.

  PMID 41296555 · PMC12807651 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  TE-SCALE is a comprehensive single-cell database integrating TE expression across 20 human cancer types and 12 tissue origins

  tumor quality-controlled scrna-seq metacells scrna-seq subfamily automated

• Longitudinal Profiling of Tumor and Immune Compartments Uncovers Patterns of Dysregulation and Associations with Response in Multiple Myeloma.

  PMID 41364805 · PMC13012255 · Blood cancer discovery · 2026 · 7 claims · 8 setups

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  IFN-γ signaling after autologous stem cell transplant (ASCT) is associated with markers of impaired CD8+ T-cell memory phenotype

  cd138neg cd138pos bone cd8+ single-cell bulk whole-genome

• Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

  PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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  Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

  luad pan-cancer tumor scrna-seq spatial bulk

• Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations.

  PMID 41520091 · PMC12905261 · Communications biology · 2026 · 8 claims · 8 setups

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  18 B cell subpopulations were identified spanning the full developmental continuum from early progenitors to plasma cells, including 4 previously unappreciated minor subpopulations (FTLhi, S100A8hi immature; FOShi, HSPA1Ahi naïve).

  in-house enriched tonsil peripheral scrna-seq scvdj-seq velocity

• Differential neuronal survival defines a novel axis of sexual dimorphism in the Drosophila brain.

  PMID 41529688 · PMC7618834 · Cell genomics · 2026 · 8 claims · 7 setups

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  Sex differences in the Drosophila central brain do not result from large-scale transcriptional reprogramming, but from selective modifications within shared developmental lineages mediated by dsx and fru.

  drosophila central dsx+ dsx-gal4>mcd8 single-cell differential scenic

• Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models.

  PMID 41543530 · PMC12811152 · Microbial genomics · 2026 · 8 claims · 8 setups

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  HBV splicing efficiency (coSI) correlates more strongly with disease progression than the overall proportion of spliced HBV RNA.

  hbv same host bulk splicing splicebert

• Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.

  PMID 41560697 · PMC13042525 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  Mitochondrial somatic mutations from scRNA-seq can be repurposed as endogenous genetic barcodes for lineage tracing in hPSC-derived organoids.

  hpsc hemo larry-barcoded pdgfrα+ scrna-seq mitochondrial cospar

• Dynamic single-cell transcriptomics reveals lsamp-guided neural network formation in male S. japonicum driving female reproduction.

  PMID 41571647 · PMC12905319 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a high-resolution single-cell transcriptomic atlas of 104,671 cells from male and female S. japonicum across four developmental stages, identifying 76 distinct cell populations

  dissociated japonicum reproductive gscs single-cell fluorescence-activated whole-mount