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).

• Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

  PMID 34825285 · PMC8616721 · Journal of computer-aided molecular design · 2022 · 8 claims · 6 setups

  Has reproduction · 63

  Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.

  curated repurposed glycosylated interior inverse molecular exploratory

• A ligand-centered framework for γδ T cell activation in colorectal cancer revealed by single-cell and transformer-based perturbation.

  PMID 41607803 · PMC12835328 · Frontiers in immunology · 2025 · 8 claims · 8 setups

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  CRC-infiltrating γδ T cells show varied activation levels, with the TRM-like population being the major tumor-infiltrating subtype and exhibiting the lowest effector and exhaustion signature scores.

  crc-infiltrating crc scrna-seq gene nichenet

• PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

  PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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  PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

  pah scrna-seq pah-former candidate scrna-seq transfer perturbation

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• 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

• PSGRN: Gene regulatory network inference from single-cell perturbational data through self-training with synthetic gold standards.

  PMID 42054465 · PMC13127566 · Science advances · 2026 · 8 claims · 4 setups

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  PSGRN infers GRNs by generating pseudoannotations from gene-gene correlations and iteratively refining them via a self-training classifier using pre/post-intervention expression features.

  k562 rpe1 processed single-cell computational biological

• Toward stem cell systems biology: from molecules to networks and landscapes.

  PMID 19329576 · PMC2738746 · Cold Spring Harbor symposia on quantitative biology · 2008 · 7 claims · 6 setups

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  Stem-cell-fate specification is an extremely complex process regulated by multiple mutually interacting molecular mechanisms with numerous regulatory feedback loops.

  stem embryonic promyelocytic genome-wide serial chip-chip

• Temporal control of progenitor competence shapes maturation in GABAergic neuron development in mice.

  PMID 40629142 · PMC12321585 · Nature neuroscience · 2025 · 8 claims · 8 setups

  Has reproduction · 82

  Ganglionic eminence (ventral) progenitors maintain stable differentiation competence throughout neurogenesis, generating a consistent set of postmitotic precursor states at all stages, unlike dorsal cortical progenitors whose differentiation competence changes gradually.

  dlx5 progenitors sections cortical scrna-seq trackerseq flashtag

• 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

• BMP and NODAL paracrine signalling regulate the totipotent-like cell state in embryonic stem cells.

  PMID 41660012 · PMC12876259 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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  BMP and NODAL (TGF-β) paracrine signalling are key routes of intercellular communication that respectively enhance or diminish the totipotent-like cell (TLC) state in mouse ESCs

  escs esc scrna-seq cellchat differential

• A multi-omic single-cell landscape of perinatal mouse skin maps lineage specification and reveals shared dynamics in human fetal skin.

  PMID 41998142 · PMC13144478 · Experimental & molecular medicine · 2026 · 7 claims · 8 setups

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  Integrated scATAC/scRNA multi-omics analysis of developing mouse skin identifies gene network axes underlying skin lineage specification

  dorsal scrna-seq skin fibroblast scatac-seq scrna-seq spatial

• Lipids join the post-genomic era.

  PMID 17076911 · PMC1794566 · Genome biology · 2006 · 8 claims · 8 setups

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  Infrared-laser MALDI-MS can image biological tissue while avoiding the matrix-preparation artifacts of UV-laser MALDI

  biological intact mixtures yeast maldi esi faims

• Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

  PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups

  Has reproduction · 100

  A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001

  post-mortem combined sub-studies down-regulated microarray differential statistical

• 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

• The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos.

  PMID 41917015 · PMC13201599 · Nature communications · 2026 · 8 claims · 8 setups

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  eccDNA is widespread in mouse preimplantation embryos across all six developmental stages examined

  ivf-derived 2-cell preimplantation fibroblasts mda-based reverse chip-seq