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).

• 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

• Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.

  PMID 42203797 · PMC13216315 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Generated 20 near-complete haplotypes from 10 Japanese male individuals using PacBio HiFi, ONT ultra-long, and Omni-C reads, all with contig N50 exceeding 100 Mbp

  japanese pacbio oxford omni-c

• FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

  PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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  FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

  prostate targeted single-nucleus scatac-seq

• Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

  PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

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  Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

  plasma ppp reference identification quantitative specimen

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• pmid-41691474

  PMID 41691474 · PMC13042402 · 8 claims · 8 setups

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  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