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).

• mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.

  PMID 31799603 · PMC6954439 · Nucleic acids research · 2020 · 5 claims · 5 setups

  Has reproduction · 89

  mitoXplorer integrates transcriptome, proteome, and mutation data with a manually curated mitochondrial interactome of ~1200 genes grouped into 38 mitochondrial processes across four model species.

  rpe-1 trisomic rpe yeast bulk proteomics mitotracker

• The ubiquitin ligase KLHL6 drives resistance to CD8(+) T cell dysfunction.

  PMID 41535474 · PMC12979199 · Nature · 2026 · 8 claims · 8 setups

  Full-text index only

  KLHL6 is a dual-negative regulator of both T cell exhaustion and mitochondrial dysfunction

  cd8+ cas9+ sgklhl6-transduced klhl6 bulk pooled flow

• Oxidative stress and GPX2 control pancreatic vs. non-pancreatic cell fate in human endoderm.

  PMID 41484137 · PMC12881361 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  GPX2 is a critical regulator of human posterior foregut differentiation, with oxidative stress acting as a key determinant of pancreatic vs. non-pancreatic cell fate

  hpsc-derived hpsc fetal bulk immunofluorescence flow

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells.

  PMID 41485059 · PMC12930946 · Journal of ovarian research · 2026 · 8 claims · 6 setups

  Full-text index only

  Acute 10 Gy X-ray irradiation does not significantly affect viability (ATP levels, mitochondrial dehydrogenase activity) of cPOCs and mPOCs over 7 days.

  kgn cpocs celltiter-glo mtt immunofluorescence

• Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.

  PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups

  Has reproduction · 23

  The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies

  adriatic mitochondrial autosomal brain whole-genome phylogenetic d-statistics

• The Molecular and Functional Landscape of Resistance to FOLFIRI Chemotherapy in Metastatic Colorectal Cancer.

  PMID 40981426 · PMC12877753 · Cancer discovery · 2026 · 8 claims · 7 setups

  Full-text index only

  FOLFIRI-resistant PDX tumors show transcriptional upregulation of innate immunity and mitochondrial metabolism genes and reduced expression of DNA polymerase POLD1

  mcrc pdx patients patient-derived drug whole-exome bulk

• Single-cell resolution of an open chromatin signature in persister tumor cells.

  PMID 41485222 · PMC12978573 · Cell reports · 2026 · 8 claims · 8 setups

  Full-text index only

  Single-nucleus multi-omic (snRNA-seq + snATAC-seq) profiling of fallopian tube, treatment-naive, and NACT-treated HGSOC tissue identifies a persister cell signature (PCS) defining the chemotherapy-tolerant state.

  non-malignant same epithelial tumor single-nucleus mitochondrial copy-number

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.

  mammary aggregated single-cell quality doublet

• Immuno-metabolic dysregulation in type 2 diabetes is associated with altered neutrophil functional plasticity, mitochondrial dysfunction, and compromised responses in sepsis.

  PMID 41520116 · PMC12882159 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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  Proportions of functionally restricted neutrophil subpopulations (phagocytosis-only vs NETosis-only) are significantly altered in T2D and fail to elicit an immune response upon sepsis induction

  peripheral bone plasma neutrophils flow bulk global

• Improved chromosome-level genome assembly of the American cockroach, Periplaneta americana.

  PMID 41123565 · PMC12774602 · G3 (Bethesda, Md.) · 2026 · 8 claims · 7 setups

  Full-text index only

  Produced the first chromosome-level genome assembly of P. americana, scaffolded into 17 chromosome-scale scaffolds consistent with karyotype

  leg midgut assembled blattodea pacbio hi-c bulk

• Monocarboxylate Transporter-2 Expression Restricts Tumor Growth in a Murine Model of Lung Cancer: A Multi-Omic Analysis.

  PMID 34638954 · PMC8508890 · International journal of molecular sciences · 2021 · 8 claims · 8 setups

  Has reproduction · 53

  MCT2 knockout (KO) increases tumor weight, volume, and local invasiveness in the TC1 lung carcinoma model

  testis tc1 tumor tumor-associated western tumor electron

• CD74 deficiency protects against doxorubicin cardiotoxicity through RRM2-mediated regulation of ferroptosis.

  PMID 42180553 · PMC13198236 · Acta pharmaceutica Sinica. B · 2026 · 8 claims · 8 setups

  Has reproduction · 29

  CD74 levels are elevated in plasma of DOX-exposed breast cancer patients and in DOX-challenged mouse hearts and cardiomyocytes

  plasma cd74− cardiomyocytes hearts elisa echocardiography cardiomyocyte

• The Chromosome-Scale Genome Assembly of the Redlip Blenny, Ophioblennius macclurei (Blenniidae).

  PMID 41378738 · PMC12758960 · Genome biology and evolution · 2026 · 8 claims · 12 setups

  Full-text index only

  A chromosome-scale genome assembly of O. macclurei was generated (529.6 Mb, scaffold N50 23.7 Mb, GC 43.49%) using ONT long reads, Illumina short reads, and Hi-C scaffolding.

  blood muscle tissues assembled oxford illumina hi-c