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 · 89
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups
TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency
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Has reproduction · 95
Base editing in human cells with monomeric DddA-TALE fusion deaminases.
PMID 35821233 · PMC9276701 · Nature communications · 2022 · 8 claims · 8 setups
mDdCBEs built from non-toxic full-length DddA_tox variants enable mitochondrial DNA base editing with efficiencies of up to 50% upon transient expression in human cells
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SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.
PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups
SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.
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Has reproduction · 91
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.
PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups
SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes
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Has reproduction · 66
RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups
S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.
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A comprehensive resequence analysis of the KLK15-KLK3-KLK2 locus on chromosome 19q13.33.
PMID 19823874 · PMC2793378 · Human genetics · 2010 · 7 claims · 7 setups
Deep resequencing of a 56 kb region on chr19q13.33 identified 555 polymorphic loci, including 116 novel SNPs and 182 novel indels.
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Has reproduction · 87
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings.
PMID 39039281 · PMC11319204 · Nature genetics · 2024 · 6 claims · 5 setups
A structured multidisciplinary exome sequencing framework established molecular genetic diagnoses in 32% of patients with suspected ultrarare disorders, comprising 370 distinct molecular causes.
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Has reproduction · 80
Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.
PMID 35714765 · PMC9283944 · The Journal of biological chemistry · 2022 · 8 claims · 4 setups
Genome-wide Ψ mapping using HydraPsiSeq and small RNA Ψ-seq identifies Ψ sites on snoRNA, 7SL RNA, vtRNA, SL RNA, and tRNA in T. brucei
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Has reproduction · 50
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.
PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups
A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.
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Has reproduction · 76
Estimation of peptide elongation times from ribosome profiling spectra.
PMID 33885812 · PMC8136808 · Nucleic acids research · 2021 · 8 claims · 3 setups
A maximum-likelihood model that separates context-dependent bias factors from elongation-time factors enables bias-corrected estimation of peptide elongation times at single-codon resolution from Ribo-Seq spectra.
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Has reproduction · 97
Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation.
PMID 34471117 · PMC8410849 · Nature communications · 2021 · 7 claims · 5 setups
Chromosome 3D structure in S. ambofaciens correlates with genetic compartmentalization during exponential phase, with the central region segmented into domains and quiescent terminal compartments
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Has reproduction · 81
Comparing the utility of in vivo transposon mutagenesis approaches in yeast species to infer gene essentiality.
PMID 32681306 · PMC7599172 · Current genetics · 2020 · 7 claims · 7 setups
A Random Forest machine-learning approach can predict gene essentiality from in vivo transposon insertion data across multiple yeast species and transposon systems
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Has reproduction · 50
Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.
PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups
BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).
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Has reproduction · 68
Identification of new ETV6 modulators through a high-throughput functional screening.
PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups
A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity
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Has reproduction · 57
Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection.
PMID 35072628 · PMC8887901 · eLife · 2022 · 8 claims · 3 setups
mRNA vaccination induces antibody binding to additional Spike epitopes (NTD and CTD in S1) beyond those seen after mild infection (FP and SH-H in S2)
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Has reproduction · 50
DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning.
PMID 33662629 · PMC9801043 · Genomics, proteomics & bioinformatics · 2022 · 7 claims · 3 setups
DeeReCT-APA, a CNN-LSTM deep learning architecture, quantitatively predicts the usage level of all alternative PASs within a gene regardless of PAS number, treating it as a variable-length regression task.
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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 · 73
Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.
PMID 29221171 · PMC5707065 · Oncotarget · 2017 · 8 claims · 6 setups
A customised SAAV peptide database built from RNA-seq/WGS variant calls can be used to search proteomics data and detect single amino acid variant (SAAV)-containing peptides at the protein level
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DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups
Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.
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Has reproduction · 87
High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies.
PMID 34010620 · PMC8096189 · Cell · 2021 · 7 claims · 3 setups
Phage-DMS comprehensively maps the effect of all possible single mutations across the SARS-CoV-2 spike protein on polyclonal plasma antibody binding, defining antibody escape pathways.