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 …

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 …

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 …

[HTML][HTML] A single-cell atlas of chromatin accessibility in the human genome

K Zhang, JD Hocker, M Miller, X Hou, J Chiou… - Cell, 2021 - cell.com
Current catalogs of regulatory sequences in the human genome are still incomplete and lack
cell type resolution. To profile the activity of gene regulatory elements in diverse cell types …

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

S Chen, LC Francioli, JK Goodrich, RL Collins, M Kanai… - BioRxiv, 2022 - biorxiv.org
The depletion of disruptive variation caused by purifying natural selection (constraint) has
been widely used to investigate protein-coding genes underlying human disorders, but …

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 …

The genomic landscape of 2,023 colorectal cancers

AJ Cornish, AJ Gruber, B Kinnersley, D Chubb… - Nature, 2024 - nature.com
Colorectal carcinoma (CRC) is a common cause of mortality, but a comprehensive
description of its genomic landscape is lacking,,,,,,–. Here we perform whole-genome …

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 …

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

P Ebert, PA Audano, Q Zhu, B Rodriguez-Martin… - Science, 2021 - science.org
INTRODUCTION The characterization of the full spectrum of genetic variation is critical to
understanding human health and disease. Recent technological advances have made it …