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).

• Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.

  PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups

  Has reproduction · 53

  Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)

  crc colorectal crcos crco organoid drug bulk

• New strategies in drug discovery.

  PMID 16671397 · PMC7120019 · Methods in molecular biology (Clifton, N.J.) · 2006 · 8 claims · 8 setups

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  A new integrated drug discovery paradigm has emerged combining clinical, genetic, genomic, and molecular phenotype data with cheminformatics, managed via informatics

  animal normal low-abundance mice situ microarray taqman

• Personalized medicine: the future is not what it used to be.

  PMID 19958922 · PMC2844719 · Surgery · 2009 · 8 claims · 8 setups

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  Many rare tumors harbor a genomic Achilles heel that can be exploited for targeted therapy

  sw13 h295r drosophila acc drug synthetic gene

• Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

  PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups

  Has reproduction · 59

  NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering

  tcga-nsclc geo bulk microarray unsupervised

• Biomarkers of lupus nephritis determined by serial urine proteomics.

  PMID 18596723 · PMC2614389 · Kidney international · 2008 · 7 claims · 6 setups

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  SELDI-TOF-MS screening of the LMW urine proteome identifies protein ions that are differentially expressed across phases of the lupus nephritis flare cycle (baseline, pre-flare, flare, post-flare)

  low-molecular-weight lmw urine kidney seldi-tof-ms on-chip capillary

• Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

  PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

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  HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

  plasma proviral cloned pbmc hiv-1 nested clonal

• Clinico-pathogenetic findings and management of chondrodystrophic myotonia (Schwartz-Jampel syndrome): a case report.

  PMID 12839625 · PMC166146 · BMC neurology · 2003 · 8 claims · 7 setups

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  The patient is a compound heterozygote with a different splicing mutation in each Perlecan allele, causing a significant reduction in production of the normal (wild-type) protein.

  8-year-old muscle lower skeletal molecular immunostaining electromyogram

• Malaria genomics meets drug-resistance phenotyping in the field.

  PMID 19664295 · PMC2745762 · Genome biology · 2009 · 8 claims · 8 setups

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  Significantly longer parasite clearance times in Pailin (western Cambodia) versus Wang Pha (Thailand-Myanmar border) establish the presence of artemisinin resistance in western Cambodia.

  falciparum plasmodium drug clinical high-throughput

• Molecular genomic approaches to infectious diseases in resource-limited settings.

  PMID 19855820 · PMC2745561 · PLoS medicine · 2009 · 8 claims · 5 setups

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  Researchers in most developing countries lack the technology, resources, and capacity to participate fully in genomics research.

  clinical mycobacterium trypanosoma theileria pcr-based molecular whole-genome

• Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

  PMID 34825285 · PMC8616721 · Journal of computer-aided molecular design · 2022 · 8 claims · 6 setups

  Has reproduction · 63

  Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.

  curated repurposed glycosylated interior inverse molecular exploratory

• Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

  PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups

  Has reproduction · 80

  The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences

  mpm mesomics whole-genome bulk methylation

• Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

  PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments

  tcga-blca famc1-3 differentially gse32894 bulk consensus gene

• GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.

  PMID 34461978 · PMC8407037 · Genome medicine · 2021 · 8 claims · 6 setups

  Has reproduction · 78

  GenTB is a free, open, web-based application offering two ML predictors (Random Forest and WDNN) that predict resistance to 13 and 10 anti-TB drugs, respectively.

  clinical tuberculosis registered whole-genome targeted retraining

• Genomic and proteomic approaches for studying human cancer: prospects for true patient-tailored therapy.

  PMID 15601541 · PMC3525069 · Human genomics · 2004 · 8 claims · 6 setups

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  DNA microarray gene expression profiling generates robust molecular classifications for many tumour types (brain, breast, colon, gastric, kidney, leukaemia, lymphoma, lung, melanoma, ovary, prostate, etc.)

  breast sars serum tumour microarray custom mass

• Diet and DNA.

  PMID 15174456 · PMC1315985 · Environmental health perspectives · 2004 · 8 claims · 8 setups

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  The tombusvirus CIRV p19 protein selectively binds short (21-22 nt) silencing siRNAs, using tryptophan residues Trp39 and Trp42 as molecular 'calipers' that stack with the ends of the siRNA duplex

  cirv blood rice smokers x-ray site-directed mass

• Zebrafish functional xenograft vasculature platform identifies PF-502 as a durable vasculature normalization drug.

  PMID 37680473 · PMC10480778 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  The zebrafish functional xenograft vasculature platform (zFXVP) enables visualization and quantification of structurally and functionally realistic tumor vasculature formation.

  zebrafish endothelial tumor fluorescence edu dextran-tomato

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

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  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray

• L2L: a simple tool for discovering the hidden significance in microarray expression data.

  PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

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  L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

  mammalian user-supplied diabetic uniprot compiled l2l re-analysis

• Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

  PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

  aml hovon cancer tcga bulk consensus machine

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  Key genes AR, AKT1, UBC, CDH1, SMAD3, ROR1, and ROR2 are associated with chemotherapy resistance and poor prognosis in metastatic breast cancer

  breast tcga-brca geo gse40622 gene pan-cancer differential