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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An integrative genomic and epigenomic approach for the study of transcriptional regulation.
PMID 18365023 · PMC2266992 · PloS one · 2008 · 8 claims · 7 setups
Integrative analysis combining gene expression, DNA methylation, and H3K9 acetylation data reveals hundreds of additional differentially expressed genes missed by gene expression arrays alone
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Has reproduction · 71
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.
PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics
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Has reproduction · 93
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.
PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups
Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.
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Iterative class discovery and feature selection using Minimal Spanning Trees.
PMID 15355552 · PMC520744 · BMC bioinformatics · 2004 · 7 claims · 5 setups
Iterating between MST-based clustering and t-statistic feature selection removes noise genes step-wise while sharpening the sample clustering
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Independent component analysis reveals new and biologically significant structures in micro array data.
PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups
ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone
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DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups
Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.
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Has reproduction · 90
Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.
PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 6 claims · 3 setups
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.
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Has reproduction · 73
Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma.
PMID 32629858 · PMC7408437 · Cancers · 2020 · 8 claims · 8 setups
Unsupervised biclustering of 283 NB-specific immune genes stratifies HR-NB into two reproducible subtypes: ultra-high-risk (UHR-NB) and (revised) HR-NB.
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Non-linear mapping for exploratory data analysis in functional genomics.
PMID 15661072 · PMC548129 · BMC bioinformatics · 2005 · 8 claims · 8 setups
A relaxation method for non-linear mapping adapts one pair of points per step rather than all points at once, and was originally shown by Chang and Lee to outperform Sammon's mapping in cluster detection effectiveness and computational efficiency.