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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Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.
PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups
42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH
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A DNA microarray survey of gene expression in normal human tissues.
PMID 15774023 · PMC1088941 · Genome biology · 2005 · 6 claims · 6 setups
Unsupervised hierarchical clustering of gene expression groups normal tissue samples largely according to anatomic location, cellular composition, or physiologic function.
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Disruption of the EGFR E884-R958 ion pair conserved in the human kinome differentially alters signaling and inhibitor sensitivity.
PMID 19015641 · PMC2633425 · Oncogene · 2009 · 8 claims · 8 setups
E884K works in concert with L858R in-cis, in a dominant fashion, to differentially alter EGFR downstream signaling and inhibitor sensitivity in an inhibitor-specific manner
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Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.
PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups
Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks
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Has reproduction · 91
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles.
PMID 32111252 · PMC7049190 · Genome medicine · 2020 · 8 claims · 8 setups
DeClust is a reference profile-free deconvolution method that simultaneously deconvolves bulk tumor expression into cancer, immune, and stromal compartments and clusters samples into cancer cell-intrinsic molecular subtypes, outputting subtype-specific reference profiles for the cohort rather than for individuals.
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Gene-centric characteristics of genome-wide association studies.
PMID 18060058 · PMC2092383 · PloS one · 2007 · 8 claims · 5 setups
High-density SNP chips using either direct or indirect selection approaches provide very high coverage in genic regions and capture most known common disease variants under the HapMap framework.
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Relation of response to treatment with dorzolamide in X-linked retinoschisis to the mechanism of functional loss in retinoschisin.
PMID 18834580 · PMC2668603 · American journal of ophthalmology · 2009 · 6 claims · 4 setups
A positive response of macular cysts to dorzolamide can occur across all three known mechanisms of retinoschisin dysfunction (absent secretion, decreased expression, non-functional secretion).
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Has reproduction · 35
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer.
PMID 32365491 · PMC7281456 · Cancers · 2020 · 8 claims · 7 setups
ZBTB38 expression is decreased in localised prostate cancer and further decreased in metastatic prostate cancer compared to non-cancerous prostate tissue
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Human PAML browser: a database of positive selection on human genes using phylogenetic methods.
PMID 17962310 · PMC2238824 · Nucleic acids research · 2008 · 8 claims · 5 setups
The Human PAML Browser is a web-accessible database of codeml-based positive selection test results for 13,721 human genes with orthologs in UCSC multispecies alignments.
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Chips to hits.
PMID 11983055 · PMC139346 · Genome biology · 2002 · 8 claims · 8 setups
Illumina's fiber-optic bead array technology allows ~2,000 oligonucleotide-based assays per bead array for high-throughput genotyping
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Has reproduction · 67
Therapeutic Stress-Induced Remodeling of Transposable Elements and TE-Gene Chimeras in KYSE150 Esophageal Squamous Cell Carcinoma Cells.
PMID 42074115 · PMC13116134 · International journal of molecular sciences · 2026 · 8 claims · 8 setups
Combined 125I radiation and carfilzomib treatment causes structured, non-random remodeling of the TE transcriptome in KYSE150 ESCC cells.
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Viral and host determinants of RNA virus vector replication and expression.
PMID 15734041 · PMC7115378 · Vaccine · 2005 · 7 claims · 4 setups
BMV RNA replication occurs in a virus-induced, membrane-bounded compartment rather than in the open cytoplasm.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Validation of analytic methods for biomarkers used in drug development.
PMID 18829475 · PMC2744124 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups
Analytical method validation (assessing assay performance/reproducibility) is a distinct process from clinical qualification (linking a biomarker to biological processes and clinical endpoints), though the two are intertwined.