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 · 67
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads.
PMID 36321867 · PMC9805576 · Bioinformatics (Oxford, England) · 2023 · 7 claims · 4 setups
GAVISUNK is an open-source pipeline that validates phased diploid HiFi assemblies by assessing concordance of inter-SUNK distances against orthogonal Oxford Nanopore (ONT) reads.
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Has reproduction · 91
Comparative Genomics of Listeria monocytogenes Isolates from Ruminant Listeriosis Cases in the Midwest United States.
PMID 36314928 · PMC9769944 · Microbiology spectrum · 2022 · 8 claims · 6 setups
73 ruminant listeriosis isolates classified by WGS/cgMLST fall into three lineages: 31.5% lineage 1, 53.4% lineage 2, 15.1% lineage 3
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Has reproduction · 79
RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.
PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups
RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report
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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.
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Has reproduction · 98
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.
PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups
maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors
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Has reproduction · 80
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
The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences
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Has reproduction
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.
PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups
Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.
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Has reproduction · 63
A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.
PMID 33892623 · PMC8063339 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date
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Has reproduction · 92
Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.
PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups
A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)
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Has reproduction · 69
Discovery and characterization of Alu repeat sequences via precise local read assembly.
PMID 26503250 · PMC4666360 · Nucleic acids research · 2015 · 7 claims · 8 setups
Combining Alu-supporting read detection (RetroSeq) with local de novo assembly (CAP3) reconstructs the full sequence of non-reference Alu insertions from Illumina paired-end WGS reads
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Has reproduction · 89
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.
PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa
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Has reproduction · 23
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.
PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups
Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations
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Has reproduction · 95
A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.
PMID 35115531 · PMC8813906 · Nature communications · 2022 · 8 claims · 8 setups
ST58 contains a major sub-lineage (BAP2, n=363) characterized by near-ubiquitous carriage of ColV plasmids
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Has reproduction · 85
PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.
PMID 35338232 · PMC8956664 · Communications biology · 2022 · 8 claims · 8 setups
Two computational approaches (sub-sampling and phenotype-simulation) can be implemented to perform power calculations for bacterial GWAS using existing genome collections, packaged as the PowerBacGWAS pipeline
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Has reproduction · 54
A 14-bp motif in the KIT active promoter region is critical for melanin accumulation in yaks, mice, and humans.
PMID 40629379 · PMC12239316 · BMC biology · 2025 · 8 claims · 7 setups
A 14-bp deletion in the KIT gene promoter region is associated with the all-white phenotype in yaks, identified via GWAS
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Has reproduction · 89
Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.
PMID 36752777 · PMC9997745 · Microbial genomics · 2023 · 8 claims · 8 setups
Dogs are the dominant host of E. coli ST372, and clusters within the ST372 population structure exhibit distinctive O:H types.
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Has reproduction · 74
Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.
PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups
The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.
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Full-text index only
Comparative genomics and understanding of microbial biology.
PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups
GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.
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Has reproduction · 83
Hobbes: optimized gram-based methods for efficient read alignment.
PMID 22199254 · PMC3315303 · Nucleic acids research · 2012 · 8 claims · 4 setups
Hobbes, a gram-based short-read mapper supporting Hamming and edit distance, is faster than all other read-mapping programs tested while maintaining high mapping quality.
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Has reproduction · 78
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).
PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups
METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.