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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Has reproduction · 85
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.
PMID 38157249 · PMC10781479 · Aging · 2023 · 6 claims · 7 setups
A nine-gene oxidative stress-related scoring (OSRS) model (AREG, CES1, CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2, SPINK6) predicts overall survival in HNSCC.
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A distinct epigenetic signature at targets of a leukemia protein.
PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups
Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve
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TFBScluster web server for the identification of mammalian composite regulatory elements.
PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups
TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.
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Has reproduction · 63
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
Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.
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Has reproduction · 73
Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.
PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups
Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.
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Has reproduction · 71
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
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
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Has reproduction · 73
A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.
PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups
COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity
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Has reproduction · 69
Machine learning-based identification of an immunotherapy-related signature to enhance outcomes and immunotherapy responses in melanoma.
PMID 39355255 · PMC11442245 · Frontiers in immunology · 2024 · 8 claims · 8 setups
66 consensus immunotherapy prognostic genes (CITPGs) were identified from the intersection of WGCNA modules, immunotherapy responder-vs-non-responder DEGs, and tumor-vs-normal DEGs
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A third approach to gene prediction suggests thousands of additional human transcribed regions.
PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups
A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.
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Human stool contains a previously unrecognized diversity of novel astroviruses.
PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups
Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1
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Nursing advocacy in a postgenomic age.
PMID 19850180 · PMC2766592 · The Nursing clinics of North America · 2009 · 8 claims · 3 setups
Nurses need genetics/genomics competency (knowledge, reasoning, and action) to be effective patient advocates in the post-genomic era
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Has reproduction · 67
An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.
PMID 36548438 · PMC9822106 · PLoS computational biology · 2022 · 8 claims · 7 setups
An individualized causal analysis framework can discover tumor-specific intercellular communication networks (ICNs) from transcriptomic data
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PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
PMID 17135190 · PMC1747181 · Nucleic acids research · 2007 · 8 claims · 6 setups
PeroxisomeDB integrates the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae into interrelated 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases' sections with links to NCBI, ENSEMBL and UCSC
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PigGIS: Pig Genomic Informatics System.
PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups
PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons
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Ensembl 2006.
PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups
Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.
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Has reproduction · 59
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
NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering
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Has reproduction · 84
Towards reliable whole genome sequencing for outbreak preparedness and response.
PMID 35945497 · PMC9361258 · BMC genomics · 2022 · 7 claims · 4 setups
Amplicon-based Nanopore sequencing can rapidly generate whole genome sequences in samples with viral load up to Ct 33.
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Use of modified U1 snRNAs to inhibit HIV-1 replication.
PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups
U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA
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Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.
PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups
A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.
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Has reproduction · 93
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.
PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups
Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.