ArticleBioinformatics (Oxford, England)2020
HALPER facilitates the identification of regulatory element orthologs across species.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
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21 citing papers in PubMed, 36 citations in OpenAlex.
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- A consensus spinal cord cell type atlas across mouse, macaque, and human.bioRxiv : the preprint server for biology · 2026Article
- The evolution of gene regulation in mammalian cerebellum development.Science (New York, N.Y.) · 2026Article
- Cross-species consensus atlas of the primate basal ganglia.bioRxiv : the preprint server for biology · 2025Article
- A Multimodal Atlas Reveals the Anatomical Distribution of Medium Spiny Neuron Subtypes and a Novel RGS6+ Population in the Primate Striatum.bioRxiv : the preprint server for biology · 2025Article
- A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording.Nature biotechnology · 2025Article
- Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability.bioRxiv : the preprint server for biology · 2025Article
- Combining Machine Learning and Multiplexed,bioRxiv : the preprint server for biology · 2025Article
- Genome synteny reveals hidden enhancer conservation.Nature genetics · 2025Article
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition.Cell reports · 2024Article
- A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.Nature communications · 2024Article
- Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation.Bioinformatics (Oxford, England) · 2024Article
- Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.Science (New York, N.Y.) · 2024Article
- Genome evolution and divergence in cis-regulatory architecture is associated with condition-responsive development in horned dung beetles.PLoS genetics · 2024Article
- Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.Science (New York, N.Y.) · 2023Article
- Evolutionary constraint and innovation across hundreds of placental mammals.Science (New York, N.Y.) · 2023Article
- A chromosome-level reference genome and pangenome for barn swallow population genomics.Cell reports · 2023Article
- Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin.BMC genomics · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
summaryDiverse traits have evolved through cis-regulatory changes in genome sequence that influence the magnitude, timing and cell type-specificity of gene expression. Advances in high-throughput sequencing and regulatory genomics have led to the identification of regulatory elements in individual species, but these genomic regions remain difficult to align across taxonomic orders due to their lack of sequence conservation relative to protein coding genes. The groundwork for tracing the evolution of regulatory elements is provided by the recent assembly of hundreds of genomes, the generation of reference-free Cactus multiple sequence alignments of these genomes, and the development of the halLiftover tool for mapping regions across these alignments. We present halLiftover Post-processing for the Evolution of Regulatory Elements (HALPER), a tool for constructing contiguous regulatory element orthologs from the outputs of halLiftover. We anticipate that this tool will enable users to efficiently identify orthologs of regulatory elements across hundreds of species, providing novel insights into the evolution of traits that have evolved through gene expression. AVAILABILITY AND IMPLEMENTATION: HALPER is implemented in python and available on github: https://github.com/pfenninglab/halLiftover-postprocessing. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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 OpenQuestion graph.