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).

• Proteomic identification of non-Gal antibody targets after pig-to-primate cardiac xenotransplantation.

  PMID 18957049 · PMC2586876 · Xenotransplantation · 2008 · 8 claims · 6 setups

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  Non-Gal antibody response after cardiac xenotransplantation is directed to a diverse set of stress response, inflammation-related, cytoskeletal and metabolic pig EC antigens, with several immunodominant targets remaining undefined

  gt-ko spots explanted flow western nanolc

• Mitochondrial dysregulation of osteoarthritic human articular chondrocytes analyzed by proteomics: a decrease in mitochondrial superoxide dismutase points to a redox imbalance.

  PMID 18784066 · PMC2713027 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 5 setups

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  A mitochondria-enriched 2-D DIGE plus MALDI-TOF/TOF proteomics workflow can define a characteristic mitochondrial protein profile of OA chondrocytes.

  articular chondrocytes 2-d real western

• NUSAP1 Could be a Potential Target for Preventing NAFLD Progression to Liver Cancer.

  PMID 35431924 · PMC9010788 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups

  Has reproduction · 45

  NUSAP1 is a hub gene linking NAFLD fibrosis progression and NAFLD-associated HCC

  liver common hl-7702 c57bl deg kegg rt-pcr

• Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.

  PMID 16980117 · PMC7159276 · Lancet (London, England) · 2006 · 8 claims · 5 setups

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  An SVM classifier trained on serum proteomic profiles discriminated patients with active tuberculosis from controls with clinically overlapping conditions

  serum computational kda spin-column seldi-tof supervised peptide

• Identification of Poor Prognosis-Associated Fibroblast Subpopulation Signature Genes Utilizing the Scissor Algorithm to Classify Colorectal Cancer Subtypes and Evaluate the Immune Landscape.

  PMID 41787974 · PMC13180509 · Gut and liver · 2026 · 8 claims · 8 setups

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  Scissor+ fibroblast subpopulations significantly correlated with prognosis were identified in CRC using the Scissor algorithm integrating scRNA-seq, bulk RNA-seq, and clinical data

  tcga gse39582 gse166555 scrna-seq bulk single-cell cell-cell

• Identification and validation of lymphangiogenesis-related genes for predicting acute myeloid leukemia prognosis: insights from bulk RNA sequencing and single-cell RNA sequencing analyses.

  PMID 41772327 · PMC12979290 · Clinical and experimental medicine · 2026 · 7 claims · 8 setups

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  A 6-LYMRG risk model (ANGPT1, HGF, MAPK8, PCNA, TBL1XR1, TLR4) is the optimal prognostic signature for AML

  gse142698 tcga-laml tcga-laml1 gse116256 differential univariate kaplan-meier

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups

  Has reproduction · 86

  TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR

  tnbc unique 719-gene gene term machine

• Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

  PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

  preimplantation single uniparental embryos rna-seq paired gene

• Comparative proteomics of clathrin-coated vesicles.

  PMID 17116749 · PMC2064594 · The Journal of cell biology · 2006 · 8 claims · 4 setups

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  A comparative proteomics strategy contrasting CCV fractions from control and clathrin-depleted (CHC siRNA knockdown) HeLa cells can distinguish genuine CCV proteins from copurifying contaminants

  hela western sds-page difference

• Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

  PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

  est unannotated trans-sa tus computational coding hybridization

• TARPON-A Telomere Analysis and Research Pipeline Optimized for Nanopore.

  PMID 41637390 · PMC12871981 · PLoS computational biology · 2026 · 7 claims · 6 setups

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  TARPON is the first complete, experimentally validated end-to-end pipeline for Nanopore-based telomere analysis requiring no data pre-processing or prior bioinformatics expertise.

  hg002 blood hek pod5 ont read capture

• 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

• Antigen specificity of clonally enriched CD8(+) T cells in multiple sclerosis.

  PMID 41644766 · PMC12956596 · Nature immunology · 2026 · 8 claims · 7 setups

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  A subset of 23 highly expanded, CSF-enriched CD8+ T cell clonotypes exists predominantly in the CSF of the MS/CIS cohort.

  paired cd8+ cd4+ csf single-cell differential pseudotime

• CircleBase V2: an eccDNA annotation platform across cancers and species.

  PMID 41273082 · PMC12807720 · Nucleic acids research · 2026 · 8 claims · 7 setups

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  CircleBase V2 provides a 12-fold increase in human eccDNA data, comprising over 3.8 million entries from >300 cell types/tissues

  raw eccdna tissues cancer circle-seq motif gene

• Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in Arabidopsis thaliana L.

  PMID 35457273 · PMC9026532 · International journal of molecular sciences · 2022 · 7 claims · 6 setups

  Has reproduction · 88

  Meta-analysis of five transcriptomic experiments identified 1151 differentially expressed genes that compose a coordinated gene network responding to high light stress

  arabidopsis deg promoter selected meta-analysis transcription hexamer

• Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

  PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups

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  Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome

  pooled albumin-bound analysis mudpit immunoaffinity bca

• Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

  PMID 41563441 · PMC13007207 · Diabetes · 2026 · 8 claims · 7 setups

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  5′ single-cell library preparation protocols outperform 3′ protocols for transcript identification and read length

  lines pancreatic spleen dtc single-cell bulk ngs

• CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data.

  PMID 17962311 · PMC2238989 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  CEBS is a public repository that integrates study design, timeline, clinical chemistry and histopathology data with microarray and proteomics data

  subcellular laboratory cebs microarray gel clinical

• Expression and Secretion of Circular RNAs in the Parasitic Nematode, Ascaris suum.

  PMID 35711944 · PMC9194832 · Frontiers in genetics · 2022 · 8 claims · 7 setups

  Has reproduction · 20

  A. suum expresses 1,997 distinct circRNAs identified via next-generation sequencing in adult female body wall and ovary-enriched tissue

  suum circrna qrt-pcr drug

• Improved methods for the enrichment and analysis of glycated peptides.

  PMID 18989935 · PMC2752342 · Analytical chemistry · 2008 · 7 claims · 4 setups

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  Replacing off-line desalting with an online 50 mM NH4OAc wash (10 min) of boronate-bound glycated proteins improves the enrichment workflow while minimizing sample loss

  glucose-glycated tryptic glycated lc-ms boronate lc-etd-ms database