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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Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy.
PMID 19842929 · PMC2923222 · Pharmacogenomics · 2009 · 8 claims · 8 setups
Approximately 15-20% of nonsynonymous variants in membrane transporters exhibit reduced function
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Genomics: applications in mechanism elucidation.
PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups
Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.
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Utilization of genomic signatures to identify phenotype-specific drugs.
PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups
A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin
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Has reproduction
Pre-implantation embryo metabolism identified by PEMA reveals endogenous lactate insufficiency contributes to pre-implantation development arrest.
PMID 42272466 · PMC13247451 · Fundamental research · 2026 · 7 claims · 7 setups
PEMA, a Ribo-seq-weighted computational framework, characterizes metabolic states of human and mouse pre-implantation embryos more accurately than Compass
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Has reproduction · 81
Enabling Single-Cell Drug Response Annotations from Bulk RNA-Seq Using SCAD.
PMID 36762572 · PMC10104628 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023 · 7 claims · 7 setups
SCAD, a transfer learning framework integrating adversarial discriminative domain adaptation (ADDA), can infer single-cell drug sensitivities by transferring knowledge from bulk RNA-seq pharmacogenomic data (GDSC) to scRNA-seq target domains
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Has reproduction · 59
Refining breast cancer biomarker discovery and drug targeting through an advanced data-driven approach.
PMID 38253993 · PMC10810249 · BMC bioinformatics · 2024 · 8 claims · 8 setups
The BGWO_SA_Ens algorithm (hybrid BGWO + simulated annealing with an ensemble classifier objective function) selects predictive breast cancer biomarker genes with high classification performance
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Genomics research and malaria control: great expectations.
PMID 14624242 · PMC261879 · PLoS biology · 2003 · 8 claims · 8 setups
Genomics research on humans, P. falciparum, and An. gambiae holds great promise for developing new drugs, vaccines, diagnostics, and vector control tools for malaria.
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From Pasteur to genomics: progress and challenges in infectious diseases.
PMID 15516917 · PMC7096024 · Nature medicine · 2004 · 8 claims · 8 setups
Genomic sequencing has revealed the blueprint of most pathogens, enabling new diagnostics, therapeutics and vaccines including for previously uncultivable agents.
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Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.
PMID 17318599 · PMC1915625 · Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007 · 7 claims · 7 setups
The T309V mutation shifts the CYP2D6 heme spin equilibrium toward the six-coordinate low-spin (6cLS) state, decreasing the five-coordinate high-spin (5cHS) fraction relative to wild type.
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In silico promoters: modelling of cis-regulatory context facilitates target predictio.
PMID 18505473 · PMC3823354 · Journal of cellular and molecular medicine · 2009 · 8 claims · 8 setups
An integrated 'profiling of transcriptional targets' (PTT) strategy by Freebern et al. identified IGF-1 as a co-modulator of immune cell function genes in mitogen/drug-activated T cells.
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GoMiner: a resource for biological interpretation of genomic and proteomic data.
PMID 12702209 · PMC154579 · Genome biology · 2003 · 8 claims · 4 setups
GoMiner organizes 'interesting' gene lists (e.g., differentially expressed genes) into the Gene Ontology hierarchy for biological interpretation, displaying results as both a tree and a directed acyclic graph (DAG).
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Probing the cancer genome.
PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups
Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level
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The pharmacogenomics of membrane transporters project: research at the interface of genomics and transporter pharmacology.
PMID 19940846 · PMC2923224 · Clinical pharmacology and therapeutics · 2010 · 8 claims · 8 setups
PMT identified sequence variants in 129 membrane transporter genes in the SLC and ABC superfamilies, discovering over 3100 SNPs
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The flexible pocketome engine for structural chemogenomics.
PMID 19727619 · PMC2975493 · Methods in molecular biology (Clifton, N.J.) · 2009 · 8 claims · 8 setups
A comprehensive structural Pocketome combined with ensemble docking enables de novo, structure-based prediction of ligand binding poses and activities for new proteins and new chemical scaffolds.
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Has reproduction · 61
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.
PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups
T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.
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Structural genomics: a new era for pharmaceutical research.
PMID 11864367 · PMC139010 · Genome biology · 2002 · 8 claims · 6 setups
Automation of crystal mounting, diffraction data collection, and structure determination/refinement is a critical factor enabling large-scale structural genomics projects.
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From microarrays to genome duplications.
PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups
Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life
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Translating genome sequences into biological understanding.
PMID 12801409 · PMC193614 · Genome biology · 2003 · 8 claims · 7 setups
Gene-trap insertional mutagenesis in mouse ES cells (BayGenomics) generates a large resource of cell lines and knockout mice for studying gene expression patterns and function.
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Has reproduction · 92
Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.
PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 8 setups
MCF-7 cell lines and human breast cancer tissues share only minimal similarity in biological processes, though fundamental functions such as cell cycle are conserved
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Has reproduction · 100
Identification of a PRDM1-regulated T cell network to regulate atherosclerotic plaque inflammation.
PMID 41039608 · PMC12490039 · Genome medicine · 2025 · 6 claims · 7 setups
A distinct gene co-expression module with a prominent T cell signature is enriched in unstable plaques and distinguishes high-risk from low-risk lesions.