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).

• Accurate chromatin marks peak calling with Omnipeak.

  PMID 41521664 · PMC12784980 · Nucleic acids research · 2026 · 8 claims · 6 setups

  Has reproduction · 77

  Omnipeak is a universal unsupervised peak-calling algorithm based on a constrained three-state hidden Markov model (zero, noise, signal states)

  gm12878 roadmap abf immgen chip-seq ultra-low-input atac-seq

• Aligned cross-modal integration and regulatory heterogeneity characterization of single-cell multiomic data with deep contrastive learning.

  PMID 41588477 · PMC12833949 · Genome medicine · 2026 · 8 claims · 4 setups

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  scMDCF outperforms existing state-of-the-art scMulti-omics integration and clustering models across various types of scMulti-omics datasets, including robustness against batch effects

  single immune dorsolateral cite-seq scrna-atac-seq snmulti-omics

• Developing a comprehensive database and search tool for single-cell ATAC-seq data.

  PMID 41545440 · PMC12816011 · Scientific reports · 2026 · 5 claims · 6 setups

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  scATAC.Explorer is a curated database containing 39 publicly available scATAC-seq datasets in a consistent format

  hematopoietic drosophila cancer scatac-seq sci-atac-seq sci-car

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and BAP1 loss.

  PMID 41719400 · PMC12922754 · Science advances · 2026 · 8 claims · 8 setups

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  Subclustering of ccRCC tumor cells reveals four shared epigenetic programs (C0-C3) recurrent across patients, cohorts, and disease stages

  rcc internal tumor state-specific single-cell multiome copy

• A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

  PMID 19911041 · PMC2766639 · PLoS genetics · 2009 · 8 claims · 7 setups

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  Padlock probes combined with high-throughput sequencing enable accurate, quantitative, low-bias digital RNA allelotyping of allele-specific expression

  genomic pgp1 skin fibroblasts padlock quantitative gene