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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targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.
PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups
A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb
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Has reproduction · 20
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.
PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups
AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats
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Human synthetic lethal inference as potential anti-cancer target gene detection.
PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups
Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design
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Has reproduction · 84
Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.
PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups
TEPs in NSCLC show 111 upregulated and 108 downregulated genes versus non-cancer control platelets, enriched in ECM interaction, cytoskeleton, immune signaling, and platelet activation pathways.
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Structure of protein interaction networks and their implications on drug design.
PMID 19876376 · PMC2760708 · PLoS computational biology · 2009 · 8 claims · 6 setups
Budding yeast and human PINs are scale-rich and configured as highly optimized tolerance (HOT) networks similar to Internet router-level topology, rather than scale-free networks formed by preferential attachment.
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Has reproduction · 83
Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.
PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups
Twenty-two genes lie at the intersection of AFB1-predicted targets and breast cancer-associated co-expression modules/DEGs
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Has reproduction · 78
Machine learning and free energy clustering reveal PAH protein binding linked to AD risk.
PMID 41953002 · PMC13053772 · iScience · 2026 · 7 claims · 8 setups
An integrated framework of bioinformatics, machine learning, and ΔG clustering can prioritize PAHs for AD-associated neurotoxicity.
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Has reproduction · 85
Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.
PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups
Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) were identified for HCM by intersecting DEGs with MR-derived HCM-associated eQTLs.
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The post-genomic era for a select few.
PMID 14759254 · PMC395745 · Genome biology · 2004 · 8 claims · 8 setups
The Exofish comparative-genomics tool identifies protein-coding DNA segments by comparing two genome sequences and was used to compare pufferfish (Takifugu, Tetraodon) genomes with mammalian genomes, improving annotation of the human and mouse genomes.
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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 · 74
Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.
PMID 40721291 · PMC12305944 · Life science alliance · 2025 · 8 claims · 7 setups
Acute MYC (T58I) and BCL2 overexpression drives an aberrant B-cell differentiation phenotype with altered surface marker expression while functional antibody secretion is retained
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Phenotypic variation meets systems biology.
PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups
Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'
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Has reproduction · 63
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.
PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups
More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes
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A survey of integral alpha-helical membrane proteins.
PMID 19760129 · PMC2780624 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups
An automated annotation pipeline defines the integral membrane genome and family associations for 21,379 proteins from 34 genomes, most belonging to 598 Pfam-derived membrane protein families.