ArticleNAR genomics and bioinformatics2020
Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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Who cites it
24 citing papers in PubMed.
- Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns.medRxiv : the preprint server for health sciences · 2026Article
- Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.Nature biotechnology · 2026Article
- Multi-Tissue Genetic Regulation of RNA Editing in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- MBNL loss of function in smooth muscle as a model for myotonic dystrophy associated gastrointestinal dysmotility.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The promises and pitfalls of automated variant interpretation: a comprehensive review.Briefings in bioinformatics · 2025Review
- Whole-genome sequencing reveals three follicular lymphoma subtypes with distinct cell of origin and patient outcomes.Cell reports. Medicine · 2025Article
- Chromosome-Level Genome Assembly of the Meishan Pig and Insights into Its Domestication Mechanisms.Animals : an open access journal from MDPI · 2025Article
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- Genome-wide association study reveals mechanisms underlying dilated cardiomyopathy and myocardial resilience.Nature genetics · 2024Article
- Integrated multi-omics analysis of PBX1 in mouse adult neural stem- and progenitor cells identifies a transcriptional module that functionally links PBX1 to TCF3/4.Nucleic acids research · 2024Article
- StableLift: Optimized Germline and Somatic Variant Detection Across Genome Builds.bioRxiv : the preprint server for biology · 2024Article
- MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts.Nature communications · 2024Article
- Tumour microenvironment programming by an RNA-RNA-binding protein complex creates a druggable vulnerability in IDH-wild-type glioblastoma.Nature cell biology · 2024Article
- Article
- Genome annotation: From human genetics to biodiversity genomics.Cell genomics · 2023Review
- Bioinformatics for wet-lab scientists: practical application in sequencing analysis.BMC genomics · 2023Article
- Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies.Science advances · 2023Article
- SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets.Bioinformatics (Oxford, England) · 2023Article
- GAGAM v1.2: An Improvement on Peak Labeling and Genomic Annotated Gene Activity Matrix Construction.Genes · 2022Article
- VPMBench: a test bench for variant prioritization methods.BMC bioinformatics · 2021Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As reference genome assemblies are updated there is a need to convert epigenome sequence data from older genome assemblies to newer versions, to facilitate data integration and visualization on the same coordinate system. Conversion can be done by re-alignment of the original sequence data to the new assembly or by converting the coordinates of the data between assemblies using a mapping file, an approach referred to as 'liftover'. Compared to re-alignment approaches, liftover is a more rapid and cost-effective solution. Here, we benchmark six liftover tools commonly used for conversion between genome assemblies by coordinates, including
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.