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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Boosting accuracy of automated classification of fluorescence microscope images for location proteomics.
PMID 15207009 · PMC449699 · BMC bioinformatics · 2004 · 8 claims · 8 setups
New classifiers (SVMs, ensembles) and new wavelet-derived (Gabor, Daubechies) features improve recognition of protein subcellular location patterns over the previous neural network approach
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LOCATE: a mammalian protein subcellular localization database.
PMID 17986452 · PMC2238969 · Nucleic acids research · 2008 · 8 claims · 6 setups
LOCATE is a curated, web-accessible database housing membrane organization and subcellular localization data for mouse and human proteins.
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A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.
PMID 19647519 · PMC2772893 · Molecular cell · 2009 · 8 claims · 6 setups
A genome-wide siRNA screen in HeLa cells using γH2AX as a readout identifies genes whose knockdown elevates DNA damage/genome instability
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Has reproduction · 100
The mouse gastric surface epithelial cell and its response to early Helicobacter pylori infection.
PMID 41824631 · PMC13020875 · Virulence · 2026 · 8 claims · 5 setups
LCM followed by RNA-Seq is a feasible methodology for characterizing gastric SMCs and their host response to H. pylori infection in vivo
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.
PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups
The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.
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An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.
PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups
shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.
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Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.
PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups
Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain
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Has reproduction · 55
Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.
PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups
Microglia, endothelial cells, and pericytes exhibit the highest type I interferon (IFN-I) activity among PD midbrain cell types, with microglia showing markedly higher activity in PD.
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Has reproduction · 96
Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.
PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups
ID-seq combines antibody-based protein detection with DNA-sequencing of DNA-tagged antibodies to measure large numbers of (phospho-)proteins in many samples in parallel
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Has reproduction · 85
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.
PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups
COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).
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Has reproduction · 70
MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.
PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups
MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling
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Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.
PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups
Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells
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Transcriptional and proteomic profiling in a cellular model of DYT1 dystonia.
PMID 19665049 · PMC2774817 · Neuroscience · 2009 · 8 claims · 7 setups
Accumulation of mutant torsinA(ΔE) in the nuclear envelope is not sufficient to cause transcriptional dysregulation
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Has reproduction · 85
Distinct sympathetic projections to brown fat regulate thermogenesis and glucose tolerance.
PMID 41559445 · PMC12945688 · Nature metabolism · 2026 · 8 claims · 8 setups
Distinct sympathetic neuron subpopulations in the stellate ganglion (SG) innervating iBAT parenchyma versus its vasculature mediate separable functions of the depot.