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).

• Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE) study.

  PMID 19997623 · PMC2780352 · PLoS genetics · 2009 · 8 claims · 6 setups

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  Functionally associated gene modules, not individual genes, underlie CAD development and can be identified via multi-organ expression clustering

  liver atherosclerotic 128-gene independent two-way gene bioinformatic

• SGCRNA: spectral clustering-guided co-expression network analysis without scale-free constraints for multi-omic data.

  PMID 41615289 · PMC12856952 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  WGCNA's reliance on a scale-free topology assumption is problematic because real co-expression networks do not consistently exhibit scale-free properties

  gse114007 gse261545 dryad.37pvmcvsg prjna762466 bulk spatial merfish

• DNA demethylation is associated with malignant progression of lower-grade gliomas.

  PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.

  gliomas neural analysis tcga methylation whole-exome sequencing

• The molecular characterization and clinical management of multiple myeloma in the post-genome era.

  PMID 19657360 · PMC3686133 · Leukemia · 2009 · 8 claims · 8 setups

  Full-text index only

  GEP identifies distinct molecular subgroups of MM associated with differing clinical features and survival outcomes

  myeloma cd138-immunomagnetically plasma bone-marrow filter-based gene-expression targeted

• Bioinformatics Analysis of the Characteristics and Correlation of m6A Methylation in Breast Cancer Progression.

  PMID 35655723 · PMC9148239 · Contrast media & molecular imaging · 2022 · 8 claims · 8 setups

  Has reproduction · 48

  Breast cancer samples can be classified into 4 m6A subtypes (quiescent, m6A methylation, protein-binding, mixed) based on Z-score median of Set1 (writer+reader) and Set2 (eraser) gene expression

  breast tcga-brca gse25066 bioinformatics survival alternative

• Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

  PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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  Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

  genome poly est cdna est blast cdna

• Emerging genomic and proteomic evidence on relationships among the animal, plant and fungal kingdoms.

  PMID 15629046 · PMC5172449 · Genomics, proteomics & bioinformatics · 2004 · 8 claims · 7 setups

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  Sequence-based molecular phylogenies widely support a sister relationship between animals and fungi, grouped as the Opisthokonta

  nine animals completed fungal combined sequence biochemical

• Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?

  PMID 41627342 · PMC12862982 · Briefings in bioinformatics · 2026 · 7 claims · 3 setups

  Has reproduction · 89

  No single existing SOTA imputation method consistently performs well across newer SRT platforms/datasets

  datasets srt same computational proposed

• Widespread ectopic expression of olfactory receptor genes.

  PMID 16716209 · PMC1508154 · BMC genomics · 2006 · 8 claims · 6 setups

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  OR genes show widespread, locus-dependent, heterogeneous ectopic expression across dozens of non-olfactory human and mouse tissues

  tissues olfactory intact probesets microarray est custom

• Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.

  PMID 24830797 · PMC4022483 · PLoS computational biology · 2014 · 8 claims · 8 setups

  Has reproduction · 75

  A convolved Gaussian process model of pol-II occupancy across gene segments captures the transcription wave and yields estimates of transcription speed and promoter-proximal pol-II activity.

  mcf7 promoter gene signals pol-ii clustering transcription

• MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

  PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups

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  High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status

  high ovarian mir-29a mirna unsupervised significance

• Species-Wide Phylogenomics of the Staphylococcus aureus Agr Operon Revealed Convergent Evolution of Frameshift Mutations.

  PMID 35044202 · PMC8768832 · Microbiology spectrum · 2022 · 8 claims · 7 setups

  Has reproduction · 79

  AgrVATE, a novel kmer-based BLASTn and in silico PCR/Snippy pipeline, enables fast, standardized agr group typing and frameshift/null mutation detection from genome assemblies

  aureus complete extracted agr kmer-based sheep mash

• The protein-phosphatome of the human malaria parasite Plasmodium falciparum.

  PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups

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  P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.

  sapiens ppp-domain metallophosphatase pf14_0142 hmm sequence neighbour-net

• Retentive Network promotes efficient RNA language modeling of long sequences.

  PMID 41814064 · PMC13111708 · Communications biology · 2026 · 8 claims · 6 setups

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  RNAret, a RetNet-based RNA language model with O(n) complexity, achieves training parallelism and low computational overhead while processing long RNA sequences

  million rnacentral mirtarraw rnastralign self-supervised t-sne mirna-mrna

• pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.

  PMID 16381926 · PMC1347407 · Nucleic acids research · 2006 · 8 claims · 3 setups

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  pSTIING is a publicly accessible web-based knowledgebase integrating protein-protein, protein-lipid, protein-small molecule interactions, transcriptional regulatory associations, ligand-receptor-cell type information, and signal transduction modules, with a focus on inflammation, cell migration and cancer.

  model gene molecular sequence clustering literature

• Cell fixation and preservation for droplet-based single-cell transcriptomics.

  PMID 28526029 · PMC5438562 · BMC biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  Methanol fixation stabilizes and preserves dissociated cells for weeks without compromising single-cell RNA-seq data quality

  hek293 dissociated facs-sorted hek drop-seq bulk trizol

• Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

  PMID 36681937 · PMC10025442 · Briefings in bioinformatics · 2023 · 8 claims · 8 setups

  Has reproduction · 94

  HiCAT is a hierarchical, marker-based cell-type identifier that uses gene set analysis (GSA) scoring with markers structured in a three-level taxonomy tree (major-type, minor-type, subset)

  pbmc cord melanoma lung scrna-seq computational

• Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

  PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions

  compendium ffpe simulated frna-seq statistical bulk integrity

• Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

  PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

  Has reproduction · 86

  CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

  tissues predicted tss-enhancer cattle cage extraction coexpression

• MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.

  PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 70

  MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling

  bat stromal paraffin-embedded aortic bulk proteomics scrnaseq