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).

• Multi-omics feature engineering driven by biomedical foundation models improves drug response prediction for inflammatory bowel disease patients.

  PMID 41844950 · PMC13129071 · Scientific reports · 2026 · 8 claims · 7 setups

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  FM (MAMMAL)-derived drug-target binding affinity (BA) inference can be used to rank/select biologically relevant protein targets and their associated genes/SNPs for a drug of interest without knowledge of protein structure or active sites

  reference top surgical snp-mutated inference gene genomic

• A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen.

  PMID 41505094 · PMC12781895 · Nucleic acids research · 2026 · 7 claims · 6 setups

  Has reproduction · 78

  MERLIN-P-TFA network inference on 18 curated public RNA-seq datasets produced a genome-wide GRN resource for A. fumigatus called GRAsp.

  aspergillus fumigatus bulk computational chip-seq-based

• GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.

  PMID 33193602 · PMC7541957 · Frontiers in genetics · 2020 · 7 claims · 4 setups

  Has reproduction · 80

  GenomeChronicler is the first pipeline able to run offline or in the cloud to generate personal genomics reports (not limited to disease) from whole genome or whole exome sequencing data.

  wgs na12878 pgp-uk1 genomes ancestry germline genome

• Tracing human genetic histories and natural selection with precise local ancestry inference.

  PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

  Has reproduction · 76

  Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

  1kgp-16pops independent simulated 1kgp simulated population-level local

• Charting spatial ligand-target activity using Renoir.

  PMID 42086556 · PMC13144314 · Nature communications · 2026 · 8 claims · 8 setups

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  Renoir computes a neighborhood activity score for curated ligand-target pairs at each spatial spot/cell by integrating cell type abundance, cell type-specific mRNA abundance, receptor expression, gene entropy, and mutual information between ligand and target genes.

  intestine triple-negative dorsolateral dlpfc semi-synthetic spatial single-cell

• Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal.

  PMID 41746282 · PMC12998610 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  dominoSignal extends the Domino algorithm to enable statistical testing of differential cell-cell signaling between experimental conditions.

  single-cell simulated pdac per-sample single-cell simulation cell-cell

• GRNFormer: accurate gene regulatory network inference using graph transformer.

  PMID 41883144 · PMC13069479 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  GRNFormer is a generalizable graph transformer framework for GRN inference from single-cell or bulk transcriptomics data across species, cell types, and platforms without cell-type annotations or prior regulatory information

  hematopoietic embryonic dendritic hepatocytes scrna-seq chip-seq string

• AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures.

  PMID 41871930 · PMC13064981 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 3 setups

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  AutoGERN explicitly models regulatory information in the message-passing space via learned link (edge) embeddings, which are scored by a lightweight MLP to infer TF–target interactions.

  seven same scrna-seq-based chip-seq cold-start

• Tractor workflow: a scalable Nextflow framework for local ancestry-aware genome-wide association studies.

  PMID 41838407 · PMC13197121 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 6 setups

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  Developed a scalable Nextflow workflow that automates phasing, local ancestry inference (LAI), and Tractor GWAS into a reproducible end-to-end pipeline

  biobank phased two-way simulated haplotype local gwas

• IMIREG: a lineage-resolved regulon signature unveiling immune engagement archetypes and predicting immunotherapy response across diverse cancers.

  PMID 42092126 · PMC13234301 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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  IMIREG, a 14-regulon transcriptional signature, robustly predicts clinical benefit from ICB across 50 immunotherapy cohorts (52 treatment arms) spanning 16 cancer types with mean AUROC = 0.71

  imvigor210 matched gtex healthy bulk scrna-seq pathway

• Spider: a flexible and unified framework for simulating spatial transcriptomics data.

  PMID 41237053 · PMC12790819 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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  Spider simulates ST data without requiring real ST data as a reference

  simulated hypothalamus dorsolateral spatial clustering cell-cell

• 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

• A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

  PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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  MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

  crc epithelial rcrc tcga-read scrna-seq copy gene

• Ultra-precision deconvolution of spatial transcriptomics decodes immune heterogeneity and fate-defining programs in tissues.

  PMID 41862467 · PMC13168514 · Nature communications · 2026 · 8 claims · 8 setups

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  UCASpatial is a novel deconvolution algorithm that uses Shannon entropy-based gene weighting combined with weighted non-negative least squares to estimate cell-type composition from spatial transcriptomics data

  simulated colorectal hippocampus ear simulated runtime spatial

• Therapeutic Targeting of Oxidative Phosphorylation in Microsatellite Instability-High Gastric Cancer.

  PMID 42038020 · PMC13104725 · Journal of Cancer · 2026 · 7 claims · 8 setups

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  MSI gastric cancer samples show significantly greater T cell infiltration and a lower proportion of epithelial cells compared to GS samples

  gastric epithelial stomach nod-scid single-cell cnv differential

• Modeling genetic inheritance of copy number variations.

  PMID 18832372 · PMC2588508 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  A joint HMM framework for parents-offspring trios significantly improves CNV call rates and boundary inference accuracy compared to existing methods.

  simulated parent-offspring hapmap hmm-based snp genotype

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory

• Dissecting tumor heterogeneity in colorectal cancer: uncovering the role of BCL2L1(+) cells through single-cell analysis.

  PMID 41958675 · PMC13056825 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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  scRNA-seq identifies five CRC tumor cell subtypes, with the C4 BCL2L1+ subtype predominantly enriched in liver metastases and showing enhanced proliferation, metabolic reprogramming, and anti-apoptotic activity

  crc epcs malignant tcga scrna-seq infercnv cytotrace

• Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

  PMID 42063567 · PMC13127482 · iScience · 2026 · 8 claims · 8 setups

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  LUSC arising within UIP originates from AT2-derived metaplastic basal cells

  fresh-frozen same scrna-seq paired single-cell copy ligand-receptor

• Genomic analysis of bacteria in the Acute Oak Decline pathobiome.

  PMID 30625111 · PMC6412055 · Microbial genomics · 2019 · 7 claims · 7 setups

  Has reproduction · 100

  All studied members of the AOD lesion microbiota possess virulence genes associated with phytopathogens

  gibbsiella lonsdalea brenneria miseq genome novo comparative