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).

• Omics-aided design genome editing strategy for challenging human immortalized cell models.

  PMID 41678468 · PMC12900285 · PloS one · 2026 · 6 claims · 4 setups

  Full-text index only

  Omics profiling identifies bottlenecks associated with poor precise KI efficiency in hard-to-engineer cells

  mcf7 deep-targeted bulk dia-based

• Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota.

  PMID 41741451 · PMC13046836 · NPJ biofilms and microbiomes · 2026 · 6 claims · 6 setups

  Full-text index only

  High inulin supplementation (4%) significantly altered caecal microbial composition and promoted broader microbial metabolic adaptations, indicating a strong fermentative response to soluble fibre

  caecal shotgun metatranscriptomics eukaryotic

• Water mass specific genes dominate the Southern Ocean microbiome.

  PMID 41803086 · PMC12972064 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  The Southern Ocean microbial gene catalog is highly original and largely distinct from existing marine gene catalogs

  seawater ace tara polar-specific shotgun comparative agnostos

• VHL synthetic lethality screens uncover CBF-β as a negative regulator of STING.

  PMID 41820368 · PMC13121600 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  CBFB (CBF-β) is a synthetic lethal interactor of VHL in ccRCC cell lines

  786o ccrcc tcga genome-wide competitive immunoblot

• Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.

  PMID 41890980 · PMC13015239 · One health (Amsterdam, Netherlands) · 2026 · 8 claims · 7 setups

  Full-text index only

  Agricultural drainage ditches consistently harbor higher fecal-associated bacterial diversity than mixed-use or forested sites, with pronounced seasonal shifts (higher during spring/fall high-flow periods).

  surface shotgun trimmed co-assembled 16s shotgun short-read

• Phosphorylation of SF3B1 by CDK11 orchestrates spliceosome activation via SNIP1-dependent RES complex recruitment.

  PMID 41904131 · PMC13194972 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  CDK11 inhibitor OTS964 traps the spliceosome in a previously uncharacterized intermediate (B_OTS964) that has the NTR complex integrated but the NTC complex not yet associated.

  hct116 gst-sf3b1 ip-mass subcellular iclip-seq

• Umi-pipeline-nf: a modular and scalable workflow for UMI-tagged nanopore amplicon analysis with real-time sequencing integration and GPU-acceleration.

  PMID 41923360 · PMC13070649 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

  Full-text index only

  umi-pipeline-nf is a portable, fully containerized, modular Nextflow DSL2 workflow that generates single-molecule consensus sequences from UMI-tagged nanopore amplicon data and scales linearly from single samples to large cohorts.

  lpa zymo sars-cov-2 nanopore real-time umi

• Full-length 16S rRNA nanopore sequencing enables species resolution of Fusobacterium associated with colorectal cancer.

  PMID 41963777 · PMC13078227 · Gut microbes · 2026 · 8 claims · 7 setups

  Full-text index only

  Full-length 16S rRNA ONT sequencing combined with custom demultiplexing (nanoMux) enables robust species-level discrimination within the Fusobacterium genus

  gtdb rrndb zymobiomics host-bacteria ani phylogenetic 16s

• 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

  Full-text index only

  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

• Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.

  PMID 41987828 · PMC13077298 · ISME communications · 2026 · 8 claims · 5 setups

  Full-text index only

  Transplantation of a microbiome from heat-primed donor clams into non-acclimated recipients is sufficient to enhance host resilience during a subsequent simulated heatwave.

  ruditapes philippinarum 16s host enzymatic

• DNA methylation profiles at hospital admission are associated with subsequent severe COVID-19 outcomes.

  PMID 42021404 · PMC13251264 · Clinical epigenetics · 2026 · 7 claims · 5 setups

  Full-text index only

  DNA methylation profiles at hospital admission differ among disease trajectory groups (TGs) and are associated with subsequent disease progression.

  pbmcs blood immune end-stage targeted rna-seq mass

• Expansion of the geranylgeranyl pyrophosphate synthase gene family underlies the evolution of terpenoid biosynthesis in termites.

  PMID 42044146 · PMC13143122 · PLoS biology · 2026 · 8 claims · 8 setups

  Full-text index only

  A gene family arose through a series of duplications of geranylgeranyl pyrophosphate synthase (GGPPS) in the common ancestor of Neoisoptera, the terpene-producing termite lineage.

  body diterpenoids neotenicus fpps gc-ms nmr genome

• TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.

  PMID 42277027 · PMC13260335 · Nature communications · 2026 · 8 claims · 5 setups

  Full-text index only

  TOFU-MAaPO yields significantly more high-quality MAGs than metaFun, nf-core/mag, and ATLAS due to integration of multiple complementary binning tools with unified MAGScoT refinement

  gut same uniquely metagenome quality assembly-free

• TEDD: a comprehensive database for translation efficiency dynamics.

  PMID 41217970 · PMC12807600 · Nucleic acids research · 2026 · 8 claims · 4 setups

  Full-text index only

  TEDD integrates 1518 RNA-seq, Ribo-seq, and RNC-seq samples from 143 human projects (279 datasets) spanning 24 tissues/cell types, 74 cell lines, and 52 conditions.

  tissues reference rna-seq ribo-seq rnc-seq

• Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development.

  PMID 41355514 · PMC12848575 · Development (Cambridge, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  NR5A2 chromatin binding is dynamic, changing genome-wide from the 2-cell to the morula stage, with peak numbers and target regions (e.g. SINE B1/Alu) shifting over developmental time

  2-cell embryonic 8-cell zygotes cut&tag chip-seq h3k27ac

• Berberine suppresses colon inflammation via integrated modulation of host metabolism, microbial ecology, and innate immune signaling.

  PMID 41356191 · PMC12680593 · Theranostics · 2026 · 6 claims · 8 setups

  Full-text index only

  Berberine enhances energy metabolism (oxidative phosphorylation, ATP biosynthesis, fatty acid metabolism) in intestinal epithelial cells of DSS-induced mice, preserving normal physiological function

  colon feces serum dss-induced single-cell targeted 16s

• Tight junction-high and CDH17-positive cell population is the source of colorectal cancer liver metastases.

  PMID 41484106 · PMC12881549 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Loss/inhibition of IKKα unexpectedly promotes, rather than suppresses, CRC liver metastasis in patient-derived organoid (PDO) xenograft models.

  pdo5 pdo5-derived crc dld1 intrasplenic immunohistochemistry kaplan-meier

• Single-Nucleus Multi-Omics Reveals Hypoxia-Driven Angiogenic Programs and Their Epigenetic Control in Sinonasal Squamous Cell Carcinoma.

  PMID 41498635 · PMC12948189 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  Five distinct malignant cell populations exist in SNSCC, with hypoxic (TC1) and proliferative (TC2) subtypes associated with adverse clinical outcomes.

  snscc bulk single-nucleus bulk single-nucleus methylation

• A cellular epigenetic classification system for glioblastoma.

  PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

  gbm healthy pseudo-bulk tcga illumina single-cell deconvolution

• Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.

  PMID 41501628 · PMC12870380 · BMC genomics · 2026 · 8 claims · 6 setups

  Full-text index only

  ChromHMM integration of 7 histone marks/variants, ATAC-seq accessibility, and HP1 ChIP-seq across ring, trophozoite, and schizont stages defines 11 chromatin states as optimal for the P. falciparum genome at 200 bp resolution

  plasmodium chip-seq atac-seq chromhmm