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).

• Systematic design of combination therapy by targeting master regulators of coexisting diffuse midline glioma cell states.

  PMID 42020604 · PMC13175895 · Nature genetics · 2026 · 8 claims · 6 setups

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  A generalizable, network-based framework was established to systematically identify combination therapies targeting complementary coexisting tumor cell states

  malignant eight patient-derived dmg single-cell pooled plate-seq

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk

• Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.

  PMID 34875090 · PMC8887463 · Nucleic acids research · 2022 · 6 claims · 8 setups

  Has reproduction · 56

  Halo-seq pairs a light-activatable Halo-DBF ligand with Click chemistry to label and purify spatially defined RNA populations in living cells with high spatial specificity (~100 nm radius)

  hela apex-seq proximity dot comparative

• An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection.

  PMID 39209804 · PMC11362569 · Nature communications · 2024 · 7 claims · 7 setups

  Has reproduction · 50

  Human hepatocytes engrafted in liver chimeric mice display a large rhythmic transcriptome of ~1700 protein-coding orthologous genes, including transcription factors, chromatin modifiers, and metabolic enzymes.

  liver hcv-infected serum bulk chip-seq serum

• Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

  PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups

  Has reproduction · 68

  GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance

  gtex genetic lncap heart rna-seq meta-analysis electronic

• AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.

  PMID 27082953 · PMC4833304 · PLoS computational biology · 2016 · 7 claims · 6 setups

  Has reproduction · 88

  Sample-sample correlation of transcript abundances is a misleading measure of replicability for assessing differential expression, because it is dominated by gene-specific dynamic ranges rather than condition-dependent variation.

  liver encode publicly co-expressed rna-seq meta-analysis computational

• CellPolaris: Transfer Learning for Gene Regulatory Network Construction to Guide Cell State Transitions.

  PMID 41498638 · PMC12948241 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  CellPolaris is a unified computational framework performing TF-centered GRN construction, master TF identification, and TF perturbation simulation

  bulk previously round paired transfer-learning cross-species

• EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.

  PMID 41832145 · PMC13133354 · Nature communications · 2026 · 8 claims · 7 setups

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  EPInformer outperforms existing gene expression prediction models (Xpresso, CREaTor, Seq-GraphReg, Enformer, Borzoi) in rigorous 12-fold cross-chromosome validation for both RNA-seq and CAGE expression prediction

  k562 lines likely cell-type-specific rna-seq cage abc

• iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.

  PMID 42108258 · PMC13158306 · Signal transduction and targeted therapy · 2026 · 8 claims · 5 setups

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  iS2C2 integrates the S2C2 cell-cell communication algorithm with LLMs to generate biologically interpretable hypotheses from scRNA-seq and spatial transcriptomics data

  single-cell algorithm domain scrna-seq single-cell perturbation llm-based

• A mechanistic model captures the emergence and implications of non-genetic heterogeneity and reversible drug resistance in ER+ breast cancer cells.

  PMID 34316714 · PMC8271219 · NAR cancer · 2021 · 7 claims · 8 setups

  Has reproduction · 85

  EMT and tamoxifen-resistance (TamR) regulatory axes can drive one another, enabling non-genetic heterogeneity via six co-existing phenotypes (ES, ER, HS, HR, MS, MR)

  gene same randomized publicly racipe stochastic randomized

• Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.

  PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups

  Has reproduction · 63

  >700 tissue-specific transcriptomes generated from w1118 and 141 DGRP Drosophila lines, forming a circadian gene expression atlas

  w1118 dgrp drosophila dgrp-796 bulk high uas-rnai

• CCL3+ Neutrophil Signature Predicts Response to Neoadjuvant Toripalimab plus Chemotherapy in Patients with Hypopharyngeal Squamous Cell Carcinoma: A Phase II Trial.

  PMID 41817286 · PMC13223550 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2026 · 7 claims · 8 setups

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  A proinflammatory, CCL3-high neutrophil subset (Neu_CCL3) is significantly enriched in the pretreatment tumor microenvironment of patients who respond to nCIT.

  pretreatment microarray cohorts moc1 single-cell bulk immunohistochemistry

• AI-guided multi-omics analysis identifies NPC1-modulated susceptibility to SARS-CoV-2 infection under PM(2.5) exposure.

  PMID 41912520 · PMC13194984 · Nature communications · 2026 · 8 claims · 6 setups

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  A fine-tuned Geneformer (single-cell transcriptomics transformer) model classifies PM2.5 exposure status and generalizes better than BERT models trained from scratch, especially with limited data.

  lung fine-tuned biobank single-cell bulk gene

• Single-cell analysis highlights the significance of malignant cell IFN/MHC-II for immunotherapy response in head and neck squamous cell carcinoma.

  PMID 41923630 · PMC13130666 · Cell reports. Medicine · 2026 · 8 claims · 4 setups

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  A malignant cell subset expressing IFN-response and MHC-II genes (IFN/MHC-II) increases in proportion after pembrolizumab treatment and is associated with response

  hnscc ffpe syngeneic independent single-cell multiplexed tumor

• sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

  PMID 31114926 · PMC6602500 · Nucleic acids research · 2019 · 8 claims · 1 setups

  Has reproduction

  sRNAtoolbox 2019 update adds automatic processing of the most used small RNA library preparation protocols, including UMI-based protocols, to sRNAbench

  srp046046 small

• Comprehensive comparison of gene expression diversity among a variety of human stem cells.

  PMID 36458020 · PMC9706419 · NAR genomics and bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 71

  Tissue origin has a stronger influence on gene expression in iPSCs than in other stem cell types

  escs stem batch-corrected degs bulk batch dimensionality

• Modeling nascent transcription from chromatin landscape and structure with CLASTER.

  PMID 41691282 · PMC13011747 · Genome biology · 2026 · 7 claims · 8 setups

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  CLASTER, a deep neural network combining chromatin landscape tracks and 3D contact maps, accurately predicts kilobasepair-resolution nascent RNA (EU-seq) profiles in a DNA-sequence-agnostic manner

  embryonic mescs chromatin k562 eu-seq chip-seq micro-c

• Characterizing gene perturbations in single cells via network divergence analysis.

  PMID 41965857 · PMC13249949 · Nature communications · 2026 · 8 claims · 8 setups

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  scDNS quantifies gene-specific functional perturbations by measuring Jensen-Shannon divergence between condition-specific gene interaction network configurations

  ipsc-derived embryonic panc-1 triple scrna-seq single-nucleus

• AICellType: a large language model-based platform for accurate cell type annotation.

  PMID 42001469 · PMC13092268 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  Claude 3.5 Sonnet achieved the best overall performance among 79 benchmarked LLMs for cell type annotation, balancing accuracy, robustness, speed, and cost-efficiency

  single-cell immune pbmc in-house llm-based scrna-seq spatial

• PRDM1 Is Associated with Chemoradiotherapy-Associated Enrichment of Adaptive NK Cells in Cervical Cancer.

  PMID 42110212 · PMC13150072 · Computational and structural biotechnology journal · 2026 · 8 claims · 8 setups

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  CRT enriches adaptive NK (aNK) cells within the cervical cancer immune microenvironment, with enrichment apparent after the first fraction and persisting after the second

  cervical subclusters ank overlapping single-cell cluster differential