García-Pérez et al. perform a multi-tissue analysis of the association between demographic and clinical traits and human transcriptome variation. Ancestry, sex, age, and BMI and certain diseases make...

Integrated analysis of single-cell transcriptomes and epigenomes with a simple, permutation-based procedure detects cell-type-specific enhancer-gene associations. This procedure establishes stringent...

Brown, Wang et al. introduce MCFA, an approach to multi-modal dataset integration that generalizes canonical correlation analysis. MCFA is broadly applicable to data integration challenges but has...

Li et al. develop a new approach to estimate protein-level regulatory activity of 55 different transcription factors (TFs) from RNA-seq profiles in an individual-specific manner across 49 tissues....

Through RNA sequencing of individuals with sex chromosome aneuploidy, San Roman et al. identify modular “active” (Xa) and “inactive” (Xi) X chromosome transcriptomes. Looking beyond classical X...

Gunsalus et al. use a deep learning model to screen the human genome for regions where sequence changes have particularly large predicted effects on 3D genome folding. They find that sequence...

Single-cell methods for measuring chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) are rapidly evolving, but tools to integrate data and infer gene-regulatory relationships remain...

Establishing a comprehensive map of trans-gene regulatory effects is a critical step toward understanding complex trait and disease genetics. However, detecting these effects is extremely difficult...

Wang et al. conducted extensive simulations and empirical analyses, revealing that incorporating greater diversity from discovery GWASs improved PRS accuracy in comparison to using large-scale,...

Sadler et al. compared and benchmarked genetically informed approaches combined with network diffusion to prioritize drug target genes. Gene prioritization methods were based on large-scale genetic...

Spatial transcriptomics is a rapidly growing field, but there is a lack of standardized tools for analyzing high-resolution experiments, leading many groups to write their own in-house tools. To...

Fully understanding the impact of the human retrotransposon L1 requires that each of ∼500,000 L1 copies be evaluated as a potentially unique genomic entity. In this issue of Cell Genomics, Lanciano...

Mechanisms underlying phenotypic divergence across species remain unresolved. In this issue of Cell Genomics, Hansen, Fong, et al. systematically dissect human and rhesus macaque gene expression...

Li et al. investigate the functional impact of rare genetic variation across the regulatory cascade from RNA to protein. Using multi-omics data from diverse individuals, they demonstrate that rare...

Wu and colleagues developed OPERA, a method that integrates genetic analysis of multi-omics data with GWASs to explore the biology of genetic associations. They found that 50% of GWAS signals are...

Ma et al. developed scPagwas, a method that integrates coordinated transcriptional features in biological pathways from scRNA-seq data and GWAS summary statistics to prioritize trait-relevant genes...

Li et al. review recent advances and existing challenges in the development and application of CRISPR-based functional genomics screening in human-pluripotent-stem-cell-derived cell models. This...

The CRISPR toolbox continues to expand at a rapid pace, leaving researchers scrambling to assess the latest tools in their systems of interest. McGee et al. have developed a modular assembly platform...

Barnett et al. profile the chromatin-accessibility landscape across B cell lineage acute lymphoblastic leukemia (B-ALL) patient samples, identifying differences among individual patients, B-ALL...

Zhang et al. identified thousands of potentially functional non-coding SNPs showing allele-specific open chromatin. They prioritized schizophrenia GWAS risk variants for functional studies in NGN2...

Li et al. review recent advances and existing challenges in the development and application of CRISPR-based functional genomics screening in human-pluripotent-stem-cell-derived cell models. This...

Protein quantitative trait loci (pQTLs) are a valuable resource for drug target development. Here, Suhre shows that a systematic analysis of ratios between protein pairs strengthens associations at...

L1 retrotransposons are abundant sequences in the human genome, implicated in disease and evolution. Lanciano, Philippe et al. profile their DNA methylation patterns at single-locus resolution in...

Corvò et al. present a GA4GH htsget implementation enabling RD-Connect GPAP users to remotely visualize genomic alignments at the EGA in real time, avoiding the need for large downloads. This has...

In a recent Cell Genomics article, Tsouris et al. analyze the transcriptomes of a large diallel panel of hybrids from Saccharomyces cerevisiae natural isolates to study cis- and trans-regulatory...

A remaining challenge in the use of iPSCs to study neurodevelopment is the variability of differentiation outcomes. Puigdevall et al. analyzed 238 iPSC lines and showed that those with deleterious...

EpiNN is a method that uses epigenetic data to detect genomic regions that are relevant for immune-system function. Regions detected using EpiNN have a high concentration of variants associated with...

Zawistowski et al. present the Michigan Genomics Initiative, a biobank of linked genotype and clinical data among patients at Michigan Medicine. This health-system-based biobank opportunistically...

Genetic fine-mapping across the IKZF1 gene revealed a variant associated with childhood ALL that contributes to the increased risk of this disease in Hispanic/Latino individuals. The ALL risk allele...

Establishing a comprehensive map of trans-gene regulatory effects is a critical step toward understanding complex trait and disease genetics. However, detecting these effects is extremely difficult...

DeForest et al. analyzed protein-coding variants in the gene HNF1A, which is associated with diabetes and hepatic physiology. They found that 1 in 5 rare protein-coding HNF1A variants in the general...

Ma et al. systematically mapped the somatic expression of recently duplicated genes in nematodes across developmental stages using both whole-organism and single-cell transcriptomic data. Young...

Hansen, Fong, et al. present an experimental framework for large-scale determination of mechanisms of gene regulatory divergence between species. Their approach demonstrates that both DNA sequence...

Through temporally resolved single-cell analysis of transcriptional responses to estrogen, Ginley-Hidinger et al. discovered that the presence of multiple estrogen-receptor alpha-bound enhancers is...

L1 retrotransposons are abundant sequences in the human genome, implicated in disease and evolution. Lanciano, Philippe et al. profile their DNA methylation patterns at single-locus resolution in...

Detection of somatic mutations in single cells is challenging, in part because whole-genome amplification causes many artificial mutations. Middelkamp et al. developed the computational PTA Analysis...

By intersecting and deconvoluting extracellular RNAs (exRNAs) and eCLIP datasets, LaPlante and Stürchler et al. predict and validate novel extracellular RNA-binding proteins (exRBPs) associated with...

de Jong et al. evaluated the seventh assembly of the rat reference genome, mRatBN7.2, and found that it reduces base-level errors and increases contiguity, although some misassemblies remain. Gene...

In this webinar—the first in a “Women in Science” series co-hosted by GEN and the Rosalind Franklin Society—British biologist and author Dr. Matthew Cobb explores Franklin’s contribution to DNA...

Tuncay et al. investigate the genetics of autism in an East African cohort. They discover 2.13 million private variants and detect rare variants that segregate with autism in known genes and in new...

An analysis of the mutational landscape in five cell types reveals diverse relationships between mutation rate, the prevalence of mutational pathways, and replicative strand asymmetry, all in...

Hodonsky et al. perform gene expression profiling and a multifaceted genetic analysis of gene regulation in coronary artery tissues from an ancestrally diverse patient cohort. This new resource...

Using multi-omics data from monocyte-derived macrophages before and after influenza infection, Chen et al. characterize transcriptional and epigenetic changes in transposable elements (TEs). They...

Genome-wide associations studies (GWASs), often performed as meta-analyses, have identified tens of thousands of disease-associated loci. Kanai et al. demonstrate via large-scale simulations and real...

Isobe et al. profiled 269,048 single-cell transcriptomes of hematopoietic stem and progenitor cells from eight preleukemic mouse models, revealing mutation-specific perturbations in cell abundance,...

Zhang, Zhang, Forrest et al combine allele-specific open chromatin (ASoC) mapping and CRISPR-editing to evaluate the functional impact of schizophrenia risk variants on human neuronal gene expressi...

Caudal et al. review emerging molecular technologies used to unpack the influence of genetic variants in the heart. The authors focus on applications of genetic toolkits in human induced pluripotent...

Joshi et al. present a whole-genome sequencing dataset from 449 samples spanning 47 unique self-reported ethnolinguistic groups in Nigeria, briefly characterizing the genetic structure of the...

Combining six biobanks in Europe, the United States, and Asia, Mars et al. evaluated cross-ancestry transferability of polygenic risk scores for four common diseases: coronary artery disease, type 2...