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 · 90
Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.
PMID 37444556 · PMC10340377 · Cancers · 2023 · 7 claims · 4 setups
Different EV isolation methods vary in reproducibility for isolating small RNAs and have characteristic effects on small RNA composition, with differential ultracentrifugation showing the highest variability/lowest replicability.
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Has reproduction · 89
miRge 2.0 for comprehensive analysis of microRNA sequencing data.
PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups
miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification
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Has reproduction · 78
Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data.
PMID 28045932 · PMC5207757 · PloS one · 2017 · 7 claims · 5 setups
Metavisitor is an open-source suite of modular Galaxy tools and preset workflows enabling non-experts to detect and assemble viral genomes from deep sequence data.
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Has reproduction · 100
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.
PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 7 claims · 7 setups
Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [miR-141-3p], Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic sites in colorectal cancer.
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Has reproduction · 78
IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.
PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 8 claims · 2 setups
IsomiR Window is an integrated, user-friendly platform that systematically identifies, quantifies, and functionally explores isomiR expression in small-RNA-seq datasets without requiring computational skills
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Has reproduction
miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.
PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 6 claims · 5 setups
miRge3.0 with 12 CPUs consistently has the best execution speed compared to miRge2.0, Chimira and sRNAbench
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Has reproduction · 64
Starvation-induced transgenerational inheritance of small RNAs in C. elegans.
PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups
L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.
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The androgen receptor CAG repeat polymorphism and modification of breast cancer risk in BRCA1 and BRCA2 mutation carriers.
PMID 15743497 · PMC1064126 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups
The AR CAG repeat polymorphism does not modify breast cancer risk in BRCA1 mutation carriers
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Patterns of somatic mutation in human cancer genomes.
PMID 17344846 · PMC2712719 · Nature · 2007 · 8 claims · 5 setups
Systematic resequencing of a large gene family (protein kinases) across diverse cancers reveals a larger repertoire of cancer genes than previously anticipated
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Has reproduction · 89
MirDIP 5.2: tissue context annotation and novel microRNA curation.
PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups
mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 7 claims · 8 setups
Six genes (CST7, HSP90AB1, PADI4, PLBD1, RAB32, SLAMF6) are signature diagnostic biomarkers for aSAH identified by LASSO and SVM-RFE.
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The application of genomic technology to combat parasitic disease.
PMID 16454893 · PMC1914215 · Parasitology · 2004 · 8 claims · 8 setups
Genomic resources from mammalian hosts can be exploited to understand parasitic processes from the host's standpoint, illustrated by host cell penetration by Trypanosoma cruzi.
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Has reproduction · 55
Identification and verification of diagnostic biomarkers in recurrent pregnancy loss via machine learning algorithm and WGCNA.
PMID 37691920 · PMC10485775 · Frontiers in immunology · 2023 · 8 claims · 8 setups
352 DEGs (198 up-regulated, 154 down-regulated) were identified between RPL and control endometrial samples
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Has reproduction · 71
Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.
PMID 33633149 · PMC7907363 · Scientific reports · 2021 · 7 claims · 7 setups
A custom ECF pipeline identified 13,401 lncRNAs in the A. crassicauda transcriptome (12,642 novel, 759 known).
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Has reproduction · 89
Identification of potential therapeutic targets for nonischemic cardiomyopathy in European ancestry: an integrated multiomics analysis.
PMID 39267096 · PMC11396958 · Cardiovascular diabetology · 2024 · 8 claims · 7 setups
Two-sample MR analysis identified 255 circulating plasma proteins associated with NISCM
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Has reproduction · 61
TEMP: a computational method for analyzing transposable element polymorphism in populations.
PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups
TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.