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).

• Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

  PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 71

  CAI is positively correlated with translational efficiency, validating its use as a proxy for translational efficiency at the elongation level.

  unstimulated cd4+ kidney liver bulk single-cell

• Nucleosome deposition and DNA methylation at coding region boundaries.

  PMID 19723310 · PMC2768978 · Genome biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Nucleosomes and DNA methylation form distinct peaks just downstream of the start codon and just upstream of the stop codon, marking both ends of protein coding units genome-wide.

  yeast drosophila resting naive nucleosome methylation pol

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue

  tcga degs cd4-gzma prognostic scrna-seq cibersortx differential

• Single-Cell Analysis Reveals Characterization of Infiltrating T Cells in Moderately Differentiated Colorectal Cancer.

  PMID 33584715 · PMC7873865 · Frontiers in immunology · 2020 · 8 claims · 7 setups

  Has reproduction · 45

  Eight distinct T cell populations are identifiable in CRC tumor tissue and seven in peripheral blood by unsupervised clustering of scRNA-seq data.

  tumor peripheral cd4+ eight single-cell unsupervised ligand-receptor

• Intergenic risk variant rs56258221 skews the fate of naive CD4(+) T cells via miR4464-BACH2 interplay in primary sclerosing cholangitis.

  PMID 38901430 · PMC11293351 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 58

  rs56258221 (BACH2/MIR4464) associates with a distinct peripheral blood T cell immunophenotype in people with PSC

  peripheral liver facs-sorted cd4+ flow bulk cite-seq

• Novel approaches for identifying target antigens of autoreactive human B and T cells.

  PMID 19763575 · PMC2845891 · Seminars in immunopathology · 2009 · 8 claims · 8 setups

  Full-text index only

  CD8+ T cells infiltrating MS brain and IM muscle tissue show clonal expansions consistent with antigen-driven selection

  muscle brain morphologically autopsy cdr3-spectratyping single-cell immunohistochemistry

• Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

  PMID 17587445 · PMC1913537 · BMC genetics · 2007 · 6 claims · 4 setups

  Full-text index only

  CCR7 gene variants occur at extremely low frequency (allelic frequencies ≤5%) in the German population

  genomic hut78 t-cells direct pcr dual

• HIV-1 sequence evolution in vivo after superinfection with three viral strains.

  PMID 17716368 · PMC2020475 · Retrovirology · 2007 · 8 claims · 8 setups

  Full-text index only

  gag and env-V3 nucleotide evolution follows a similar pattern in all three strains: low substitution rate in the first 2-3 years of infection, then an increase driven mainly by synonymous substitutions

  blood seminal pbmcs biological strain-specific bulk in-house

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

  Full-text index only

  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• Mutation analysis in primary immunodeficiency diseases: case studies.

  PMID 19841577 · PMC2774237 · Current opinion in allergy and clinical immunology · 2009 · 8 claims · 8 setups

  Full-text index only

  Genomic DNA Sanger sequencing is the standard first-line approach for identifying PIDD-causing mutations but has limitations that can yield false-negative or false-positive results

  mother parents ebv-transformed nemo genomic flow northern

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

  Has reproduction · 83

  A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

  peripheral pbmcs blood normal gene-expression lymphocyte gene

• Circulating mucosal-associated invariant T cells identify patients responding to anti-PD-1 therapy.

  PMID 33723257 · PMC7961017 · Nature communications · 2021 · 7 claims · 7 setups

  Has reproduction · 70

  Proportions of activated and proliferating CD8+ T cells (cluster C16/activated EM) are significantly higher in responders before and during therapy

  pbmc cd3+cd8+ pbmc-derived metastatic high-dimensional single-cell polychromatic

• Spatial transcriptomics demonstrates the role of CD4 T cells in effector CD8 T cell differentiation during chronic viral infection.

  PMID 36450262 · PMC9792173 · Cell reports · 2022 · 8 claims · 6 setups

  Has reproduction · 50

  IL-21-producing Tfh CD4 T cells repopulate after CD4 depletion but remain at reduced frequency compared with control mice

  cd44+ splenocytes spleen tcr scrna-seq flow spatial

• An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.

  PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 6 setups

  Has reproduction · 67

  An individualized Bayesian causal discovery framework can learn tumor-specific intercellular communication networks (ICNs) by combining single-cell gene expression module (GEM) discovery, bulk tumor deconvolution, and individualized causal network learning.

  hnscc cd45+ cd8+ tcga single-cell bulk pseudo-time

• Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators.

  PMID 34680414 · PMC8533457 · Biomedicines · 2021 · 7 claims · 8 setups

  Has reproduction · 67

  A set of 15 TFs was identified as sepsis-specific master regulators of pediatric sepsis, dividing into two non-overlapping clusters.

  blood cd4+ pbmc regulons microarray differential master

• To Explore the Key Subgroup and Their Immune Microenvironment During the Formation of Coronary Plaque With scRNA-seq.

  PMID 40454289 · PMC12126265 · Cardiology research and practice · 2025 · 6 claims · 8 setups

  Has reproduction · 33

  C1 RACK1+ NK cells are a crucial subgroup for understanding coronary plaque formation, exhibiting the highest cell stemness/differentiation potential and positioned at the start of the pseudotime trajectory

  coronary scrna-seq five type single-cell doublet copy

• Metabolic profiling during malaria reveals the role of the aryl hydrocarbon receptor in regulating kidney injury.

  PMID 33021470 · PMC7538157 · eLife · 2020 · 8 claims · 8 setups

  Has reproduction · 62

  Plasma AHR ligands derived from heme metabolism (biliverdin, bilirubin) and tryptophan/kynurenine pathway metabolites increase during acute Pc malaria in mice and acute cerebral malaria in humans

  c57bl pediatric littermate untargeted targeted bilirubin

• Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics.

  PMID 17331236 · PMC1868942 · Genome biology · 2007 · 8 claims · 8 setups

  Full-text index only

  moDCs and KG-1 cells show significant proteomic differences from primary mDCs, particularly in proteins involved in cell growth/maintenance and cell-cell interaction/integrity.

  mdcs mdc freshly peripheral two-dimensional maldi-tof capture

• Polymorphism in the tumour necrosis factor receptor II gene is associated with circulating levels of soluble tumour necrosis factor receptors in rheumatoid arthritis.

  PMID 16277675 · PMC1297570 · Arthritis research & therapy · 2005 · 8 claims · 6 setups

  Full-text index only

  The TNF-RII T676G polymorphism is associated with circulating levels of sTNF-RI and sTNF-RII in RA, with a trend TT > TG > GG

  serum genomic peripheral synovial elisa pcr-rflp clinical

• Irisin ameliorates obesity and insulin resistance via adipose tissue IL-33 and regulatory T cells.

  PMID 41933175 · PMC13052164 · Nature metabolism · 2026 · 8 claims · 8 setups

  Has reproduction · 48

  Irisin modulates adipose tissue inflammation by increasing IL-33 production and preserving ST2+ regulatory T cells in white adipose tissues, thereby improving obesity and glucose intolerance.

  4-week-old hfd-fed bat iwat aav8-mediated body intraperitoneal