ArticleCommunications biology2019
Systematic discovery of conservation states for single-nucleotide annotation of the human genome.
Article in Communications biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Pervasive cryptic selection in the human noncoding genome.bioRxiv : the preprint server for biology · 2026Article
- Pan-cell type continuous chromatin state annotation of 1,698 epigenomes from the International Human Epigenome Consortium.Genome biology · 2026Article
- MissenseHMM: state-based annotations for missense variants through joint modeling of pathogenicity scores.bioRxiv : the preprint server for biology · 2026Article
- A conserved 3'UTR short motif regulates gene expression in vertebrates.Nucleic acids research · 2026Article
- Computational Evidence for Digenic Contribution ofInternational journal of molecular sciences · 2025Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Where do obesity and male infertility collide?BMC medical genomics · 2024Article
- Article
- Machine-learning of complex evolutionary signals improves classification of SNVs.NAR genomics and bioinformatics · 2022Article
- A mammalian methylation array for profiling methylation levels at conserved sequences.Nature communications · 2022Article
- Universal annotation of the human genome through integration of over a thousand epigenomic datasets.Genome biology · 2022Article
- Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.PLoS computational biology · 2021Review
- NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality.Genome biology · 2021Article
- Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.Communications biology · 2021Article
- Learning a genome-wide score of human-mouse conservation at the functional genomics level.Nature communications · 2021Article
- Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.Nature communications · 2020Article
- ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation.NAR genomics and bioinformatics · 2020Article
- Single-nucleotide conservation state annotation of the SARS-CoV-2 genome.bioRxiv : the preprint server for biology · 2020Article
- Identifying functions and prognostic biomarkers of network motifs marked by diverse chromatin states in human cell lines.Oncogene · 2020Article
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2 authors.
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Abstract
Comparative genomics sequence data is an important source of information for interpreting genomes. Genome-wide annotations based on this data have largely focused on univariate scores or binary elements of evolutionary constraint. Here we present a complementary whole genome annotation approach, ConsHMM, which applies a multivariate hidden Markov model to learn de novo 'conservation states' based on the combinatorial and spatial patterns of which species align to and match a reference genome in a multiple species DNA sequence alignment. We applied ConsHMM to a 100-way vertebrate sequence alignment to annotate the human genome at single nucleotide resolution into 100 conservation states. These states have distinct enrichments for other genomic information including gene annotations, chromatin states, repeat families, and bases prioritized by various variant prioritization scores. Constrained elements have distinct heritability partitioning enrichments depending on their conservation state assignment. ConsHMM conservation states are a resource for analyzing genomes and genetic variants.
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