The technological landscape and applications of single-cell multi-omics

A Baysoy, Z Bai, R Satija, R Fan - Nature Reviews Molecular Cell …, 2023 - nature.com
Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

PANTHER: Making genome‐scale phylogenetics accessible to all

PD Thomas, D Ebert, A Muruganujan… - Protein …, 2022 - Wiley Online Library
Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their
evolutionary relationships to other proteins. However, phylogenetics analyses can be …

A genomic mutational constraint map using variation in 76,156 human genomes

S Chen, LC Francioli, JK Goodrich, RL Collins, M Kanai… - Nature, 2024 - nature.com
The depletion of disruptive variation caused by purifying natural selection (constraint) has
been widely used to investigate protein-coding genes underlying human disorders,,–, but …

CADD v1. 7: using protein language models, regulatory CNNs and other nucleotide-level scores to improve genome-wide variant predictions

M Schubach, T Maass, L Nazaretyan… - Nucleic acids …, 2024 - academic.oup.com
Abstract Machine Learning-based scoring and classification of genetic variants aids the
assessment of clinical findings and is employed to prioritize variants in diverse genetic …

hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

S Morabito, F Reese, N Rahimzadeh, E Miyoshi… - Cell reports …, 2023 - cell.com
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …

Efficient site-specific integration of large genes in mammalian cells via continuously evolved recombinases and prime editing

S Pandey, XD Gao, NA Krasnow, A McElroy… - Nature Biomedical …, 2024 - nature.com
Methods for the targeted integration of genes in mammalian genomes suffer from low
programmability, low efficiencies or low specificities. Here we show that phage-assisted …

Evolutionary constraint and innovation across hundreds of placental mammals

MJ Christmas, IM Kaplow, DP Genereux, MX Dong… - Science, 2023 - science.org
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 …

Fusobacterium infection facilitates the development of endometriosis through the phenotypic transition of endometrial fibroblasts

A Muraoka, M Suzuki, T Hamaguchi… - Science translational …, 2023 - science.org
Retrograde menstruation is a widely accepted cause of endometriosis. However, not all
women who experience retrograde menstruation develop endometriosis, and the …

Characterizing cis-regulatory elements using single-cell epigenomics

S Preissl, KJ Gaulton, B Ren - Nature Reviews Genetics, 2023 - nature.com
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 …

The sequences of 150,119 genomes in the UK Biobank

BV Halldorsson, HP Eggertsson, KHS Moore… - Nature, 2022 - nature.com
Detailed knowledge of how diversity in the sequence of the human genome affects
phenotypic diversity depends on a comprehensive and reliable characterization of both …