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).

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

  meta-geo tcga-blca bca genomics unsupervised lasso weighted

• A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

  PMID 38157249 · PMC10781479 · Aging · 2023 · 7 claims · 8 setups

  Has reproduction · 85

  Consensus clustering of 74 oxidative stress-related genes identifies three distinct HNSCC molecular subgroups (Cluster1-3) with significantly different overall survival and tumor stage distribution

  tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunohistochemistry

• Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

  PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 73

  Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

  fresh tcga gbm bulk rna-seq consensus

• Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

  PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments

  tcga-blca famc1-3 differentially gse32894 bulk consensus gene

• Whole genome association mapping by incompatibilities and local perfect phylogenies.

  PMID 17042942 · PMC1624851 · BMC bioinformatics · 2006 · 8 claims · 8 setups

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  Blossoc scores the perfect phylogenetic tree spanning the largest compatible region around each marker as a decision tree for case/control status to detect association

  coalescent-simulated artificial empirical same perfect-phylogeny hapminer haplotype

• The flexible pocketome engine for structural chemogenomics.

  PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups

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  A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.

  pdb bacteriorhodopsin enr asn automated virtual energy-based

• Multiomic machine learning on lactylation for molecular typing and prognosis of lung adenocarcinoma.

  PMID 39856156 · PMC11760357 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 83

  Ten multiomics clustering algorithms identify two distinct lactylation cancer subtypes (CS1 and CS2) in LUAD

  tcga gse13213 gse31210 multiomics closest ssgsea

• targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

  PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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  A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

  tuberculosis mtb protein-protein flux transposon

• Structure of protein interaction networks and their implications on drug design.

  PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups

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  Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.

  budding pin yeast protein-protein graph-theoretic gene

• Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

  PMID 19649302 · PMC2709445 · PLoS computational biology · 2009 · 7 claims · 4 setups

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  A computational framework can build disease-specific drug-protein connectivity maps by integrating protein interaction networks and PubMed literature mining, without gene expression profiles from drug perturbation experiments

  seed ad-related retrieved combined protein-protein network-based pubmed

• Illuminating cell states by a comprehensive and interpretable single cell foundation model.

  PMID 41839876 · PMC13139411 · Nature communications · 2026 · 6 claims · 6 setups

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  CellVQ, incorporating a Single-Cell Discretization (SCD) module that converts cell embeddings into a discrete 'cell code' via a unified codebook, mitigates data heterogeneity and batch effects while improving interpretability

  pancreas sampled bulk lines scrna-seq type property

• Embeddings from language models are good learners for single-cell data analysis.

  PMID 41726097 · PMC12921509 · Patterns (New York, N.Y.) · 2026 · 8 claims · 8 setups

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  scELMo combines LLM-derived embeddings of gene and cell metadata with raw single-cell expression data via matrix operations to generate cell embeddings without pretraining a new model

  scrna-seq multi-batch diseased perturbation clustering batch cell-type

• 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

• The COMBAT-TB Workbench: Making Powerful Mycobacterium tuberculosis Bioinformatics Accessible.

  PMID 35138128 · PMC8827006 · mSphere · 2022 · 8 claims · 5 setups

  Has reproduction · 90

  The COMBAT-TB Workbench combines the IRIDA web platform and the Galaxy workflow platform into a single easy-to-install, Docker-based application

  tuberculosis outlier whole-genome maximum-likelihood read

• Construction of a SEMA3 family-based model to predict prognosis and molecular subtypes in pancreatic ductal adenocarcinoma.

  PMID 41792569 · PMC13079247 · Discover oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  SEMA3 family expression defines two molecular subtypes (A and B) of PDAC with significantly different overall survival

  pdac bulk ssgsea differential

• Expression genomics in breast cancer research: microarrays at the crossroads of biology and medicine.

  PMID 17397520 · PMC1868923 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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  Genome-wide expression microarray studies reveal transcriptional networks/signatures that explain breast cancer biological and clinical heterogeneity

  breast early-stage diffuse dlbcl gene

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation

• Shared patterns of dysregulated gene expression across squamous cell carcinomas unveil predictors for prognosis and drug sensitivity.

  PMID 41803163 · PMC13096486 · Scientific reports · 2026 · 8 claims · 6 setups

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  SCCs from head and neck (HNSC), esophagus (ESCC), and cervix (CESC) share highly similar dysregulated gene expression patterns (DGEPs), whereas lung (LUSC) and skin (CSCC) SCCs are more molecularly distinct

  tumor combined tcga differential sequencing weighted

• Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

  PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

  aml hovon cancer tcga bulk consensus machine

• 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