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).

• Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.

  PMID 41547351 · PMC13069856 · Cell genomics · 2026 · 8 claims · 8 setups

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  Otari, an attention-based graph neural network trained on long-read transcriptomes across 30 tissues/brain regions, predicts tissue-specific differential isoform abundance

  tissues genomic gtex hgmd long-read variant splice

• CaHoT-GRN: context-aware high-order topology learning for robust single-cell gene regulatory network inference.

  PMID 42059479 · PMC13130071 · Briefings in bioinformatics · 2026 · 7 claims · 5 setups

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  CaHoT-GRN integrates pretrained biological language model embeddings (DNABERT for DNA, ESM for protein) with scRNA-seq expression data to improve GRN inference

  embryonic gene dataset-specific same scrna-seq-based sequence protein-protein

• EpiXFormer: a cross-attention neural network for predicting cell type-specific transcription factor binding sites.

  PMID 41527854 · PMC12796812 · Briefings in bioinformatics · 2026 · 8 claims · 8 setups

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  EpiXFormer achieves high accuracy (mean AUROC ~0.99) predicting binding sites of both TFs and non-sequence-specific DBPs across 199 DBP-cell type pairs

  dbps tfs common ctcf deep comparative feature-ablation

• 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

• Multiomics and deep learning dissect regulatory syntax in human development.

  PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

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  The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

  fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact

• A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0.

  PMID 41923359 · PMC13090826 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  LncADeep 2.0 outperforms LncADeep and other existing tools for lncRNA identification on both GENCODE annotated transcripts and independent RNA-seq data

  lncrna hypertrophic gencode lncrna-protein-mirna mlp-based independent ablation

• Cross-species prediction reveals chromatin regions with increased accessibility in humans.

  PMID 41984952 · PMC13082337 · Science advances · 2026 · 8 claims · 8 setups

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  CNNs trained exclusively on human ATAC-seq data achieve cross-species prediction performance in chimpanzees and macaques comparable to species-specific models

  lymphoblastoid prefrontal six chimpanzee bulk single-cell cnn

• Characterization of Human Genes Modulated by Porphyromonas gingivalis Highlights the Ribosome, Hypothalamus, and Cholinergic Neurons.

  PMID 34194426 · PMC8236716 · Frontiers in immunology · 2021 · 8 claims · 8 setups

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  Genes in the SRP-dependent cotranslational protein targeting to membrane (ER translocation) pathway and ribosomal subunit genes are strongly and specifically enriched for arginine and lysine residues, suggesting high susceptibility to gingipain cleavage.

  protein-coding coli recombinant postmortem proteome-wide gene gingipain

• Cosmopolitan Gene Families With Known Functions Are Hotspots for the Evolution of Novel Genes in Stony Corals.

  PMID 41873503 · PMC13044578 · Genome biology and evolution · 2026 · 8 claims · 8 setups

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  Dark gene families in corals form cosmopolitan (broadly shared) families that originated via bursts of lineage-specific duplication, often from genes with known function

  genome same montipora stylophora orthogroup busco bulk