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).
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Spontaneous symmetry breaking in genome evolution.
PMID 18367477 · PMC2377439 · Nucleic acids research · 2008 · 6 claims · 3 setups
Exon size distributions in sequenced genomes follow a lognormal pattern typical of a random Kolmogoroff fractioning process
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The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.
PMID 19911046 · PMC2768904 · PLoS computational biology · 2009 · 8 claims · 3 setups
The replication rate of the strain that initiates an infection has a strong effect on the fitness of the infection at the between-host level, even though the virus evolves rapidly within the host.
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Antigenic diversity, transmission mechanisms, and the evolution of pathogens.
PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups
Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode
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Adaptation, aging, and genomic information.
PMID 20157529 · PMC2806027 · Aging · 2009 · 8 claims · 6 setups
Aging is caused primarily by the absence of adaptive genomic information for later-age survival and function, due to declining forces of natural selection with adult age; this absence secondarily produces misallocation and damage at every level of biological organization.
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STAN, a computational framework for inferring spatially informed transcription factor activity.
PMID 41521668 · PMC12784991 · Nucleic acids research · 2026 · 7 claims · 7 setups
STAN, a linear mixed-effects (spatially weighted regression) model, integrates TF-target gene priors, gene expression, spatial coordinates, and histological image features to predict spot-specific TF activity in spatial transcriptomics data
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Mutation analysis of the c-mos proto-oncogene in human ovarian teratomas.
PMID 9635841 · PMC2150066 · British journal of cancer · 1998 · 6 claims · 3 setups
Mutations in the coding region of the c-MOS gene do not play a significant role in the genesis of human ovarian teratomas
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Protein co-evolution, co-adaptation and interactions.
PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups
The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).
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Has reproduction · 97
Easy and efficient ensemble gene set testing with EGSEA.
PMID 29333246 · PMC5747338 · F1000Research · 2017 · 8 claims · 2 setups
EGSEA combines results from up to 12 prominent gene set testing algorithms to obtain a consensus ranking of biologically relevant gene sets
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Has reproduction · 69
A blood-based DNA damage signature in patients with Parkinson's disease is associated with disease progression.
PMID 40913219 · PMC12443628 · Nature aging · 2025 · 8 claims · 2 setups
A blood-based DNA damage signature is present in PD patients and is associated with disease progression.
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Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.
PMID 15099405 · PMC411067 · BMC bioinformatics · 2004 · 7 claims · 2 setups
Two-way ANOVA and Mack-Skillings tests on probe-level data with FDR control are substantially more powerful than t-test/Wilcoxon on probe-set level data for detecting differential expression
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A case of intolerance to warfarin dosing in an intermediate metabolizer of CYP2C9.
PMID 16385662 · PMC2810600 · Yonsei medical journal · 2005 · 7 claims · 2 setups
A patient heterozygous for CYP2C9*3 (genotype CYP2C9*1/*3) developed an extremely elevated INR on standard warfarin dosing, indicating impaired warfarin metabolism.
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Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.
PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups
A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size
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How can developing countries harness biotechnology to improve health?
PMID 18053180 · PMC2238767 · BMC public health · 2007 · 8 claims · 2 setups
Five Executive Courses on Genomics and Public Health Policy were held in five developing-world regions (Africa, India, Eastern Mediterranean, Latin America/Caribbean, Western Pacific/Southeast Asia) to generate recommendations on harnessing biotechnology for health.
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BLASTO: a tool for searching orthologous groups.
PMID 17483516 · PMC1933156 · Nucleic acids research · 2007 · 7 claims · 2 setups
BLASTO treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences
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A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics.
PMID 18957120 · PMC2628390 · BMC bioinformatics · 2008 · 8 claims · 2 setups
Sili2DGel represents recursive gel matching results as a weighted undirected graph and identifies SAP by finding cliques and pseudocliques (dense subgraphs) after edge-weight filtering, strength-metric-based graph reduction, and cluster refinement.
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Genome-wide analysis of subependymomas shows underlying chromosomal copy number changes involving chromosomes 6, 7, 8 and 14 in a proportion of cases.
PMID 18397339 · PMC2659379 · Brain pathology (Zurich, Switzerland) · 2008 · 8 claims · 2 setups
Whole-genome aCGH reveals chromosomal copy number abnormalities in 5 of 12 (42%) subependymoma cases
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Environmental genomics: an opportunity for the NIEHS.
PMID 16393638 · PMC1332673 · Environmental health perspectives · 2006 · 8 claims · 5 setups
Intrauterine exposure to endocrine-disrupting pesticides can produce transgenerational adverse effects on male fertility
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Single-cell dissection of regulated cell death dynamics in ovarian aging.
PMID 41689119 · PMC13005338 · Journal of ovarian research · 2026 · 8 claims · 8 setups
The RCD landscape of ovarian aging had not previously been characterized at single-cell resolution
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Has reproduction · 84
An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations.
PMID 32425511 · PMC7218276 · Bioinformatics and biology insights · 2020 · 8 claims · 6 setups
An integrated methodology combining nonnegative matrix factorization (NMF), the WebGestalt functional enrichment tool, and an ad hoc gene extraction procedure automatically identifies informative gene subsets from microarray data matrices that differ in number of genes (rows) and patients (columns)
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Has reproduction · 30
First step toward gene expression data integration: transcriptomic data acquisition with COMMAND>_.
PMID 30691411 · PMC6348648 · BMC bioinformatics · 2019 · 8 claims · 2 setups
COMMAND>_ is a flexible multi-user web-application that allows users to search and download gene expression experiments, extract relevant information from experiment files, re-annotate microarray platforms, and present data in a coherent data model.