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 · 76
Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.
PMID 34287005 · PMC8386447 · mSphere · 2021 · 8 claims · 7 setups
Periodontitis significantly alters dental plaque microbial community diversity and structure compared to healthy and treated states
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Has reproduction · 100
poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.
PMID 34394197 · PMC8355734 · Frontiers in genetics · 2021 · 8 claims · 8 setups
poreCov is an easy-to-use, fast, and robust Nextflow-based workflow for reference-based SARS-CoV-2 genome reconstruction and lineage determination from nanopore sequencing data
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Has reproduction · 92
Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK.
PMID 34427554 · PMC8549364 · Microbial genomics · 2021 · 8 claims · 8 setups
bla_CTX-M-27 is located on IncFII pKSR100-like plasmids, flanked by IS26 and IS903B
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Has reproduction · 96
Calibration-free NGS quantitation of mutations below 0.01% VAF.
PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups
QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation
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Has reproduction · 69
Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.
PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups
Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis
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Has reproduction · 64
Candidates for Balancing Selection in Leishmania donovani Complex Parasites.
PMID 34865011 · PMC8717319 · Genome biology and evolution · 2021 · 7 claims · 8 setups
Five genetically distinct, well-sampled populations exist within the L. donovani complex: EA1, EA2 (East Africa), ISC1, ISC2 (Indian subcontinent), and BM (Brazil-Mediterranean)
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Has reproduction · 67
snpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data.
PMID 34900230 · PMC8637247 · F1000Research · 2021 · 8 claims · 4 setups
snpQT is a scalable, stand-alone software pipeline using nextflow and BioContainers for comprehensive, reproducible, interactive QC of human genomic data.
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Has reproduction · 58
Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.
PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups
Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)
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Has reproduction · 69
TC-hunter: identification of the insertion site of a transgenic gene within the host genome.
PMID 35184734 · PMC8859905 · BMC genomics · 2022 · 7 claims · 4 setups
TC-hunter is an open-source Nextflow pipeline that identifies transgene insertion sites using chimeric reads and discordant read pairs from NGS data.
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Has reproduction · 95
Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.
PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups
Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input
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Has reproduction · 75
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups
XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations
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Has reproduction · 100
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.
PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.
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Has reproduction · 75
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.
PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups
RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.
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Has reproduction · 65
Estimating biodiversity across the tree of life on Mount Everest's southern flank with environmental DNA.
PMID 36148432 · PMC9486557 · iScience · 2022 · 8 claims · 6 setups
eDNA from ten high-alpine ponds and streams (4,500-5,500 m) on Mt. Everest's southern flank revealed 187 potential orders from 36 phyla across the Tree of Life.
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Has reproduction · 81
Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.
PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups
A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020
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Has reproduction · 67
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.
PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups
binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)
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Has reproduction · 88
Wochenende - modular and flexible alignment-based shotgun metagenome analysis.
PMID 36368923 · PMC9650795 · BMC genomics · 2022 · 8 claims · 6 setups
Wochenende is a modular, transparent alignment-based pipeline for shotgun metagenome analysis supporting short and long reads across all kingdoms of life
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Has reproduction · 83
MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.
PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups
MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences
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Has reproduction · 50
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.
PMID 36451166 · PMC9710047 · Genome biology · 2022 · 7 claims · 6 setups
MoDLE is a high-performance stochastic model that simulates DNA-DNA contacts from loop extrusion genome-wide in minutes using less than 1 GB of RAM
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Has reproduction · 43
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.
PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups
TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.