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).

• Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets.

  PMID 18925947 · PMC2600787 · BMC structural biology · 2008 · 8 claims · 3 setups

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  The extended matrix PP10 (built from a proline-containing peptide library) shows significant improvement in binding prediction over the original nine-residue matrix P9

  recombinant peptides awcsdealplgsprcd peptide-mhc quantitative x-ray

• Prognostic biomarker discovery in pancreatic cancer through hybrid ensemble feature selection and multi-omics data.

  PMID 41957754 · PMC13188360 · BioData mining · 2026 · 8 claims · 2 setups

  Has reproduction · 92

  hEFS integrates data subsampling with multiple (nine) survival prediction models, combining embedded and wrapper-based feature selection strategies

  pancreatic pdac multi-omics gene

• More biology from the sequence.

  PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

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  The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

  schizosaccharomyces chromosome genome cervical whole-genome sequence genome

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• The mitochondrial genome, a growing interest inside an organelle.

  PMID 18488415 · PMC2526360 · International journal of nanomedicine · 2008 · 8 claims · 8 setups

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  mtDNA mutations are causally linked to a wide range of mitochondrial diseases, aging, and chronic degenerative diseases

  post-mitotic mtdna homozygous high-fat southern rflp-pcr dhplc

• The Universal Protein Resource (UniProt) in 2010.

  PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.

  uniprotkb oceanic proteome manual automated sequence

• Web-based resources for comparative genomics.

  PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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  Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

  yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood

• Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis.

  PMID 34079055 · PMC8172904 · Communications biology · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  Integration of five mouse scRNAseq datasets reveals a trifurcating lineage trajectory originating from embryonic mammary stem cells (MaSCs) that differentiates into three epithelial lineages (Basal, L-Alv, L-Hor) via unipotent progenitor clusters

  mammary surgically normal single-cell whole-mount integration

• GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.

  PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups

  Has reproduction · 73

  GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.

  mcf10a nde&dt hypoxia bulk correlation pca

• Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

  PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups

  Has reproduction · 95

  Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells

  kidney live blood snrna-seq snatac-seq bulk

• Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.

  PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups

  Has reproduction · 55

  352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples

  endometrial degs hub decidua microarray wgcna machine

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• Monocytes serve as Shiga toxin carriers during the development of hemolytic uremic syndrome.

  PMID 39871175 · PMC11773931 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  Monocytes are the primary carriers that transport Stx2 from the periphery to the kidney during STEC-induced HUS

  peripheral thp-1 cfse-labeled evs single-cell flow toxin-cell

• Age Deceleration and Reversal Gene Patterns in Dauer Diapause.

  PMID 41104926 · PMC12686545 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 88

  Dauer arrest, regardless of duration, does not cause lasting functional decline in lifespan, brood size, or developmental resumption

  daf-2 wild-type same dauer developmental lifespan brood

• 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

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• Enhanced Bioremediation Potential of Shewanella decolorationis RNA Polymerase Mutants and Evidence for Novel Azo Dye Biodegradation Pathways.

  PMID 35391736 · PMC8981235 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  Unbiased RNAP (rpoB) mutation screening via rifampicin resistance is an effective method to obtain bacterial mutants with enhanced bioremediation activity

  shewanella decolorationis rifampicin pcr minimum

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Similarities and differences in genome-wide expression data of six organisms.

  PMID 14737187 · PMC300882 · PLoS biology · 2004 · 8 claims · 8 setups

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  Coexpression of functionally related genes is frequently conserved across evolutionarily distant organisms

  saccharomyces caenorhabditis escherichia arabidopsis genome-wide large-scale developmental