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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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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Tumor mapping in 2 large multigenerational families with CYLD mutations: implications for disease management and tumor induction.
PMID 19917957 · PMC2935681 · Archives of dermatology · 2009 · 8 claims · 4 setups
The clinical distinction between FC, BSS, and MFT has little prognostic or clinical utility, even within the same family, warranting a unifying diagnosis of 'CYLD cutaneous syndrome'.
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Proteomics-derived cerebrospinal fluid markers of autopsy-confirmed Alzheimer's disease.
PMID 19863188 · PMC2824250 · Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals · 2009 · 8 claims · 8 setups
2D gel electrophoresis screening of pooled postmortem CSF identified ApoA1, hemopexin (HPX), transthyretin (TTR) and PEDF as differentially abundant among AD, ND and NADD groups
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Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.
PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups
BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay
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Proteomic analyses of the effects of drugs of abuse on monocyte-derived mature dendritic cells.
PMID 19811410 · PMC2812871 · Immunological investigations · 2009 · 6 claims · 7 setups
Cocaine differentially regulates expression of several functional classes of proteins (apoptosis, protein folding, kinase activity, metabolism, signal transduction) in monocyte-derived mature dendritic cells
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Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates.
PMID 19768705 · PMC3030255 · Electrophoresis · 2009 · 8 claims · 8 setups
Commercial plasma-derived FVIII/VWF concentrates contain significant amounts of non-FVIII/VWF plasma proteins as impurities
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Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.
PMID 34282405 · PMC8285288 · Frontiers in cellular and infection microbiology · 2021 · 8 claims · 7 setups
iPSC-derived pancreatic endocrine and exocrine (acinar/ductal) cultures express ACE2 and TMPRSS2, enabling SARS-CoV-2 entry
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Has reproduction · 69
Fluent genomics with plyranges and tximeta.
PMID 32528659 · PMC7243206 · F1000Research · 2020 · 6 claims · 3 setups
A three-step fluent genomics workflow (import, model, integrate) using plyranges and tximeta provides a coherent, reproducible framework for integrating RNA-seq and ATAC-seq data within the Bioconductor ecosystem.
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Molecular genetic diagnosis of von Hippel-Lindau disease: analysis of five Japanese families.
PMID 8641976 · PMC5921130 · Japanese journal of cancer research : Gann · 1996 · 5 claims · 3 setups
Four of five Japanese VHL disease families showed germ line VHL gene mutations, comprising 2 missense mutations, 1 deletion, and 1 splice-site mutation
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Has reproduction · 92
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia.
PMID 32581241 · PMC7314847 · Nature communications · 2020 · 8 claims · 8 setups
IL7R interacts with CXCR4 to recruit BCR-ABL1 and JAK kinases into close proximity, forming a molecular platform for transformation
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Has reproduction · 84
Genetically engineered stem cell-derived retinal grafts for improved retinal reconstruction after transplantation.
PMID 34409267 · PMC8361135 · iScience · 2021 · 8 claims · 6 setups
Bhlhb4−/− and Islet1−/− pluripotent cell lines differentiate into retinal organoids with similar timing, morphology, and gene expression to wt lines up to around DD15
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Has reproduction · 30
Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.
PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 8 setups
Single-cell transcriptomic analysis of GBA-N370S iPSC-derived dopamine neurons identifies a progressive axis of gene expression variation leading to endoplasmic reticulum stress.
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Has reproduction · 10
RADAR: differential analysis of MeRIP-seq data with a random effect model.
PMID 31870409 · PMC6927177 · Genome biology · 2019 · 8 claims · 6 setups
RADAR is a novel analytical tool for differential methylation analysis of MeRIP-seq data combining gene-level INPUT normalization with a Poisson random effect model.
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Has reproduction · 91
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.
PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups
A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)
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Has reproduction · 74
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.
PMID 27583132 · PMC4972086 · F1000Research · 2016 · 6 claims · 6 setups
An open-source, reproducible RNA-seq pipeline delivered as an IPython notebook and Docker image can process raw RNA-seq data into interactive PCA/HC plots, enrichment results, and small-molecule predictions with minimal setup overhead
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Has reproduction · 85
PDGFRA defines the mesenchymal stem cell Kaposi's sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment.
PMID 31881074 · PMC6980685 · PLoS pathogens · 2019 · 8 claims · 8 setups
Pα(+)S (PDGFRA-positive/SCA-1-positive) bone marrow-derived MSCs are KS spindle-cell progenitors
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Has reproduction · 85
Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.
PMID 33634984 · PMC7882098 · Clinical and translational medicine · 2021 · 8 claims · 8 setups
JMJD6 is identified as a potent epigenetic vulnerability/fitness gene in RCC by integrating GeCK CRISPR screening data with TCGA-KIRC epigenetic regulator survival analysis
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Has reproduction · 59
Integrative network modeling reveals mechanisms underlying T cell exhaustion.
PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 7 setups
TCE arises from changes in diverse gene regulatory interactions across a shared network rather than dysregulation of a single gene
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Has reproduction · 50
Dissecting lncRNA-mRNA competitive regulatory network in human islet tissue exosomes of a type 1 diabetes model reveals exosome miRNA markers.
PMID 36440209 · PMC9682028 · Frontiers in endocrinology · 2022 · 7 claims · 7 setups
LncRNA-mRNA competitive regulatory network topology and function differ substantially between control and cytokine-treated (IL-1β+IFN-γ) islet exosomes
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Has reproduction · 62
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.
PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups
Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.