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).

• SiCmiR Atlas: Single-Cell miRNA Landscape Reveals Hub-miRNA and Network Signatures in Human Cancers.

  PMID 41691474 · PMC13042402 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  SiCmiR, a two-layer neural network, predicts mature miRNA expression profiles from only 977 LINCS L1000 landmark genes

  tcga k562 pancreatic acth-secreting paired bulk scrna-seq-based

• maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

  PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups

  Has reproduction · 98

  maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors

  lines hepg2 types single chip-seq omni-atac-seq atac-seq

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

  hymenophyllum caudiculatum annotated rna-seq chlorophyll relative

• Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

  PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

  Has reproduction · 95

  Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

  embryonic escs dem-cgis demg methylation chip-seq gene

• MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

  PMID 24599324 · PMC3944147 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 29

  MOSAIK is the only aligner that consistently aligns reads from all major sequencing platforms (Illumina, AB SOLiD, Roche 454, Ion Torrent, Pacific Biosciences SMRT) using the same algorithmic approach.

  simulated million coli illumina short-read mapping neural-network

• Classification of ALS molecular subtypes: a literature review on machine learning applications and their clinical value.

  PMID 41731547 · PMC13037183 · BMC medicine · 2026 · 8 claims · 5 setups

  Full-text index only

  Unsupervised ML analysis of ALS transcriptomes consistently identifies molecular subtypes reflecting distinct biological processes, primarily oxidative stress (ALS-Ox) and glial activation/neuroinflammation (ALS-Glia), found in every study reviewed.

  post-mortem peripheral bulk rna-seq blood

• Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites.

  PMID 41778583 · PMC12959880 · eLife · 2026 · 8 claims · 8 setups

  Full-text index only

  H3K115ac is enriched at the TSS of active CpG island (CGI) promoters, far more than non-CGI promoters

  embryonic mescs synthetic mesc chip-seq atac-seq dot