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We introduce MIMIC a generative multimodal foundation model trained across biomolecular sequences 3D structures and functional assays. MIMIC performs unified representation learning and conditional generation across nucleic acids …

Non-functioning pituitary adenomas (NFPAs) exhibit considerable cellular heterogeneity. Using single-cell multi-omics we map chromatin accessibility tumor microenvironment interactions and core transcription factor networks driving NFPA …

Alternative splicing generates functional transcript diversity across human tissues. We present a graph-based neural attention architecture that predicts variant-resolved context-specific RNA isoform proportions directly from …

Non-coding somatic mutations play critical roles in cancer development. We implement a deep-learning framework to predict the functional regulatory impact of non-coding somatic variants across …

Single-cell RNA sequencing of human kidney allograft biopsies reveals key transcriptional programs altered during BK polyomavirus infection. We delineate distinct epithelial sub-populations undergoing viral-induced stress …

Understanding how perturbations influence gene function in a tissue-specific manner is key to uncovering novel drug targets. However, current computational approaches emphasize global network or sequence-derived …

New approaches that generate long-lasting therapeutic responses in patients with therapy-resistant metastatic cancer are urgently needed. To address this challenge, we developed Spot Neoantigens in Metastases …

… the traditional tandem mass tag (TMT) data-dependent acquisition (DDA) TPCA workflow. This work provides insights into denaturation-based assays, highlights the value of insoluble fractions, and …

Passively collected wearable data offers scalable sleep phenotyping in autism spectrum disorder. We address domain shift and compliance challenges to establish reliable machine-learning biomarkers of sleep disruption …

Acute kidney injury (AKI) and chronic kidney disease (CKD) are two interconnected clinical conditions, both defined by degree of functional impairment, but with heterogeneous clinical trajectories. Using new …

The growing availability of biological data resources has transformed research, yet their effective use remains challenging: selecting appropriate sources requires domain knowledge, data are fragmented across databases, and …

Parkinson’s Disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc), which is associated with changes in microglia function. While …

Building upon a foundational Human Kidney resource, we present a comprehensive multi-modal atlas that defines spatially resolved versus unresolved repair states and mechanisms in human kidney disease …

3D chromatin structure is critical for the regulation of gene expression during development. Here we used Micro-C assays at 100-bp resolution to map genome organization in …

Viral infections can induce prolonged changes in innate immunity. Here, we use blood samples from a human influenza H3N2 challenge study (NCT03883113) to perform comprehensive multi-omics analyses …

IgA nephropathy (IgAN), focal segmental glomerulosclerosis (FSGS), membranous nephropathy (MN), and minimal change disease (MCD) account for the majority of idiopathic glomerulopathies (GN). However, there are no powered …

Endurance exercise induces multisystem adaptations that improve performance and benefit health. Gene regulatory circuit responses within individual skeletal muscle cell types, which are key mediators of exercise effects …

Viruses exploit host cell reliance on compartmentalization to facilitate their replication. Herpes simplex virus type 1 (HSV-1) modulates the subcellular localization of host proteins to suppress immune …

Cells modified outside of the body and then reintroduced provide an advantage over most small-molecule therapeutics in that cells can be designed to recognize target molecules in …

To facilitate single-cell multi-omics analysis and improve reproducibility, we present single-cell pipeline for end-to-end data integration (SPEEDI), a fully automated end-to-end …

… differed by their level of expression of mitochondrial genes, suggesting decreased aerobic capacity associated with the GT- tumor subgroup. Interestingly, differential analyses between the healthy and the …

Viral infections can induce changes in innate immunity that persist after virus clearance. Here, we used blood samples from a human influenza H3N2 challenge study to perform comprehensive …

Unraveling the phenotypic and genetic complexity of autism is extremely challenging yet critical for understanding the biology, inheritance, trajectory, and clinical manifestations of the many forms of the …

Diffuse midline glioma (DMG), including Diffuse intrinsic pontine glioma (DIPG), is an aggressive brain tumor in children with limited treatment options. Recent developments of phase 1 clinical trials …

In recent years deep learning has become one of the central approaches in a number of applications, including many tasks in genomics. However, as models grow in depth …

Deciphering the regulatory code of gene expression and interpreting the transcriptional effects of genome variation are critical challenges in human genetics. Modern experimental technologies have resulted in an …

Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer’s disease. Gaining insight into the …

Protein–protein interactions (PPIs) drive cellular processes and responses to environmental cues, reflecting the cellular state. Here we develop Tapioca, an ensemble machine learning framework for studying global …

Single same cell RNAseq/ATACseq multiome data provide unparalleled potential to develop high resolution maps of the cell-type specific transcriptional regulatory circuitry underlying gene expression. We present …

Finely-tuned enzymatic pathways control cellular processes, and their dysregulation can lead to disease. Creating predictive and interpretable models for these pathways is challenging because of the complexity …

Human biology is rooted in highly specialized cell types programmed by a common genome, 98% of which is outside of genes. Genetic variation in the enormous noncoding space …

Resolving chromatin-remodeling-linked gene expression changes at cell-type resolution is important for understanding disease states. Here we describe MAGICAL (Multiome Accessibility Gene Integration Calling and Looping …

Assays detecting blood transcriptome changes are studied for infectious disease diagnosis. Blood-based RNA alternative splicing (AS) events, which have not been well characterized in pathogen infection, have …

Periodontal disease is more common in individuals with rheumatoid arthritis (RA) who have detectable anti-citrullinated protein antibodies (ACPAs), implicating oral mucosal inflammation in RA pathogenesis. Here, we …

Marine recruits training at Parris Island experienced an unexpectedly high rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, despite preventive measures including a supervised …

Astrocytes have been shown to play a central role in Alzheimer’s Disease (AD). However, the genes and biological pathways underlying disease manifestation are unknown, and it is …

Male sex is a major risk factor for SARS-CoV-2 infection severity. To understand the basis for this sex difference, we studied SARS-CoV-2 infection in …

Epigenomic profiling has enabled large-scale identification of regulatory elements, yet we still lack a systematic mapping from any sequence or variant to regulatory activities. We address this …

Kidney Precision Medicine Project (KPMP) is building a spatially specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of …

Although membranous nephropathy (MN) is one of the most common causes of nephrotic syndrome, the molecular characteristics of the kidney damage in MN remain poorly defined. In this …

Neurons from layer II of the entorhinal cortex (ECII) are the first to accumulate tau protein aggregates and degenerate during prodromal Alzheimer’s disease. Here, we use a …

There is a need for better classification and understanding of tumor-infiltrating lymphocytes (TILs). Here, we applied advanced functional genomics to interrogate 9,000 human tumors and multiple …

… infections in young adults, including potential targets for developing new therapies and prognostic tests.

Despite their importance in tissue homeostasis and renewal, human pituitary stem cells (PSCs) are incompletely characterized. We describe a human single nucleus RNA-seq and ATAC-seq resource …

The mRNA-1273 vaccine is effective against SARS-CoV-2 and was granted emergency use authorization by the FDA. Clinical studies, however, cannot provide the controlled response to …

Interpreting the effects of genetic variants is key to understanding individual susceptibility to disease and designing personalized therapeutic approaches. Modern experimental technologies are enabling the generation of massive …

Experimental approaches to study tissue specificity enable insight into the nature and organization of the cell types and tissues that constitute complex multicellular organisms. Machine learning provides a …