Roles of transposable elements in the regulation of mammalian transcription
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often
contain sequences capable of recruiting the host transcription machinery, which they use to …
contain sequences capable of recruiting the host transcription machinery, which they use to …
Characterizing cis-regulatory elements using single-cell epigenomics
Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …
A genomic mutational constraint map using variation in 76,156 human genomes
The depletion of disruptive variation caused by purifying natural selection (constraint) has
been widely used to investigate protein-coding genes underlying human disorders,,–, but …
been widely used to investigate protein-coding genes underlying human disorders,,–, but …
Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution
Genomic (DNA) sequences encode an enormous amount of information for gene regulation
and protein synthesis. Similar to natural language models, researchers have proposed …
and protein synthesis. Similar to natural language models, researchers have proposed …
Nucleotide Transformer: building and evaluating robust foundation models for human genomics
The prediction of molecular phenotypes from DNA sequences remains a longstanding
challenge in genomics, often driven by limited annotated data and the inability to transfer …
challenge in genomics, often driven by limited annotated data and the inability to transfer …
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
C Bravo González-Blas, S De Winter, G Hulselmans… - Nature …, 2023 - nature.com
Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …
A joint NCBI and EMBL-EBI transcript set for clinical genomics and research
J Morales, S Pujar, JE Loveland, A Astashyn, R Bennett… - Nature, 2022 - nature.com
Comprehensive genome annotation is essential to understand the impact of clinically
relevant variants. However, the absence of a standard for clinical reporting and browser …
relevant variants. However, the absence of a standard for clinical reporting and browser …
Evolutionary constraint and innovation across hundreds of placental mammals
Zoonomia is the largest comparative genomics resource for mammals produced to date. By
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect …
Effective gene expression prediction from sequence by integrating long-range interactions
How noncoding DNA determines gene expression in different cell types is a major unsolved
problem, and critical downstream applications in human genetics depend on improved …
problem, and critical downstream applications in human genetics depend on improved …
Human genetic diversity alters off-target outcomes of therapeutic gene editing
CRISPR gene editing holds great promise to modify DNA sequences in somatic cells to treat
disease. However, standard computational and biochemical methods to predict off-target …
disease. However, standard computational and biochemical methods to predict off-target …