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).

• Wide-Open: Accelerating public data release by automating detection of overdue datasets.

  PMID 28594819 · PMC5464523 · PLoS biology · 2017 · 7 claims · 5 setups

  Has reproduction · 74

  Wide-Open is a general text-mining approach that automatically detects overdue datasets by scanning PubMed articles for dataset accession identifiers and querying repositories to determine if the datasets remain private.

  open-access geo sra text database web

• Approaching the genomics of risk-taking behavior.

  PMID 20109660 · PMC3961474 · Advances in genetics · 2009 · 8 claims · 8 setups

  Full-text index only

  Candidate genes (e.g., DRD4, SERT, MAOA) explain only a small fraction of total genetic variation in risk-taking-related behaviors, motivating a whole-genome approach.

  wild-caught three-spined sticklebacks open-field-like predator repeated-measures

• The RYR2-encoded ryanodine receptor/calcium release channel in patients diagnosed previously with either catecholaminergic polymorphic ventricular tachycardia or genotype negative, exercise-induced long QT syndrome: a comprehensive open reading frame mutational analysis.

  PMID 19926015 · PMC2880864 · Journal of the American College of Cardiology · 2009 · 8 claims · 6 setups

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  Comprehensive open-reading-frame RYR2 mutational analysis reveals possible CPVT1 mutations located outside the three canonical hot-spot domains

  genomic hair-root reference patients pcr screening multi-tissue

• Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.

  PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 6 setups

  Has reproduction

  CD4 T cells and B cells independently mediate MS GWAS genetic signals through their open chromatin regions, beyond shared regulatory landscapes.

  flow-sorted cd4 gwas bulk ldsc

• Temporal trends in methane emissions from a small eutrophic reservoir: the key role of a spring burst.

  PMID 35126532 · PMC8815417 · Biogeosciences (Online) · 2021 · 8 claims · 7 setups

  Has reproduction · 72

  Acton Lake had cumulative areal CH4 emission rates of 45.6 ± 8.3 g CH4 m-2 in 2017 and 51.4 ± 4.3 g CH4 m-2 in 2018 (109 ± 14 and 123 ± 10 Mg CH4 whole-reservoir, respectively)

  whole-reservoir sediment-water water reservoir eddy active floating

• Molecular dynamics and mutational analysis of a channelopathy mutation in the IIS6 helix of Ca V 1.2.

  PMID 18836301 · PMC3196984 · Channels (Austin, Tex.) · 2008 · 8 claims · 4 setups

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  I781T in CaV1.2 shifts the voltage-dependence of activation and inactivation to hyperpolarized voltages, reproducing the channelopathy-like gating phenotype of CaV1.4 I745T

  homology tsa-201 cav1.2 molecular whole-cell confocal

• Kinetoplastid genomics: the thin end of the wedge.

  PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups

  Full-text index only

  Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.

  brucei major cruzi kinetoplastid whole-genome gene shotgun

• X-linked isolated growth hormone deficiency: expanding the phenotypic spectrum of SOX3 polyalanine tract expansions.

  PMID 19654509 · PMC2763399 · Clinical dysmorphology · 2009 · 7 claims · 5 setups

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  A 21bp in-frame insertion causing a 7-alanine expansion in the SOX3 polyalanine tract causes X-linked isolated growth hormone deficiency (IGHD) without learning disability.

  affected family patients pedigree sanger pcr-based endocrine

• Electroacupuncture reshapes the microbial co-occurrence networks related to the behavioral and psychological symptoms of dementia in Alzheimer's disease.

  PMID 41676443 · PMC12806058 · iMetaOmics · 2025 · 6 claims · 7 setups

  Has reproduction · 77

  Electroacupuncture reshapes microbial co-occurrence network topology and drives keystone species in AD-related BPSD, with R. gnavus emerging as a likely keystone species post-intervention.

  appswe app gut 16s open picrust2

• Missense polymorphisms in the adenomatous polyposis coli gene and colorectal cancer risk.

  PMID 18612690 · PMC2768068 · Diseases of the colon and rectum · 2008 · 7 claims · 4 setups

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  Germline missense APC alterations (S130G, E1317Q, D1822V, G2502S) identified in a CRC-multiple-polyp cohort do not confer significantly increased CRC risk when tested in a large population-based case-control series

  germline same population-based ofccr manual dhplc nuclease

• PRNP variation in UK sporadic and variant Creutzfeldt Jakob disease highlights genetic risk factors and a novel non-synonymous polymorphism.

  PMID 20035629 · PMC2806268 · BMC medical genetics · 2009 · 8 claims · 7 setups

  Full-text index only

  All UK vCJD cases tested (147/147) are methionine homozygous (MM) at PRNP codon 129

  vcjd scjd scottish controls pcr-rflp full chi-squared

• Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

  PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 6 claims · 3 setups

  Has reproduction · 90

  Representing the genome as a binary string (1/0) of peak presence and computing Hamming distances enables hierarchical clustering of ATAC-seq samples with reduced computational cost while preserving cell-type classification.

  leukemia hematopoietic atac-seq rna-seq

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• Prediction of condition-specific regulatory genes using machine learning.

  PMID 32329779 · PMC7293043 · Nucleic acids research · 2020 · 8 claims · 6 setups

  Has reproduction · 85

  ConSReg integrates expression, DAP-seq TF-DNA binding, and ATAC-seq open chromatin data into machine learning models to predict condition-specific regulatory genes

  arabidopsis zea bulk dap-seq atac-seq

• A virtual computer lab for distance biomedical technology education.

  PMID 18366629 · PMC2292716 · BMC medical education · 2008 · 6 claims · 4 setups

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  A 'virtual computer lab' combining videoconferencing with VNC-based desktop sharing can replicate the functionality of a physical computer lab for distance biomedical technology education

  graduate students nlm five-point open-ended informal

• Using prototyping to choose a bioinformatics workflow management system.

  PMID 33630841 · PMC7906312 · PLoS computational biology · 2021 · 8 claims · 6 setups

  Has reproduction

  Prototyping a subset of a project's actual workflow in candidate software offers a low-cost (time and effort) way to make a more informed software selection than relying solely on reviews and recommendations.

  riboviz bioinformatics open-source prototyping web-search-based repository

• A common genetic factor for Parkinson disease in ethnic Chinese population in Taiwan.

  PMID 17187665 · PMC1764029 · BMC neurology · 2006 · 6 claims · 4 setups

  Full-text index only

  The G2385R variant in LRRK2 contributes significantly to the etiology of PD in ethnic Han Chinese individuals

  peripheral g2385r patients genotype pcr full clinical

• The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.

  PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se

  sez-derived computational nsc npc atac-seq bulk lisa

• Cis-Regulation of the CFTR Gene in Pancreatic Cells.

  PMID 40332394 · PMC12027686 · International journal of molecular sciences · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  Multiple active CREs exist upstream and downstream of the CFTR gene in pancreatic (Capan-1) cells, identified via ATAC-seq, CUT&RUN-seq (H3K27ac), 4C-seq, and the ABC model

  capan-1 caco-2 hepg2 atac-seq cut&run-seq 4c-seq

• Characteristics of small breast and/or ovarian cancer families with germline mutations in BRCA1 and BRCA2.

  PMID 10188893 · PMC2362698 · British journal of cancer · 1999 · 7 claims · 7 setups

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  Presence of at least one ovarian cancer case in a small family strongly predicts finding a BRCA1 or BRCA2 mutation.

  genomic pcr family truncation pcr multiplex