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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Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.
PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups
PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301
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Has reproduction · 42
Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.
PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups
PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.
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Has reproduction · 87
CoINcIDE: A framework for discovery of patient subtypes across multiple datasets.
PMID 26961683 · PMC4784276 · Genome medicine · 2016 · 8 claims · 6 setups
CoINcIDE is a methodological framework that discovers replicable patient subtypes (meta-clusters) across multiple datasets by finding consensus across dataset-specific clusterings, requiring no between-dataset transformations.
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Has reproduction · 99
Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.
PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups
Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.
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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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Automatic discovery of cross-family sequence features associated with protein function.
PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups
A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.
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Has reproduction · 73
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.
PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups
GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.
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Has reproduction · 71
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 · 7 claims · 7 setups
AML patients can be categorized into two distinct PANRG-based clusters with differing prognosis and immune characteristics
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Has reproduction · 67
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda.
PMID 35455012 · PMC9026859 · Life (Basel, Switzerland) · 2022 · 8 claims · 5 setups
Most transposable elements are commonly shared across all eight geographically distant S. frugiperda samples, except Maverick and PIF/Harbinger elements which show divergent repeat copies
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Has reproduction · 93
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.
PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups
Most of the 17 m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis.
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Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.
PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups
A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.
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Has reproduction · 55
Gene module regulation in dilated cardiomyopathy and the role of Na/K-ATPase.
PMID 35901050 · PMC9333241 · PloS one · 2022 · 5 claims · 8 setups
Several co-expressed gene modules are significantly associated with left ventricle ejection fraction (LVEF) and the DCM phenotype, enriched in fibrosis-related, small molecule transporting-related, and immune response-related pathways.
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Skittle: a 2-dimensional genome visualization tool.
PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups
Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales
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A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.
PMID 16271148 · PMC1310624 · BMC genomics · 2005 · 8 claims · 5 setups
Integrating EST-based expression data with phylogenetic analysis is a valid new method for functionally annotating multigenic protein families
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Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.
PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups
A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome