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 …

Although more studies are demonstrating that a father's environment can influence child
health and disease, the molecular mechanisms underlying non-genetic inheritance remain …

Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …

The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

Single-cell atlases often include samples that span locations, laboratories and conditions,
leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets …

Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …

Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

Bulk sequencing methodologies have allowed us to make great progress in cancer
research. Unfortunately, these techniques lack the resolution to fully unravel the epigenetic …

Advances in multi-omics have led to an explosion of multimodal datasets to address
questions from basic biology to translation. While these data provide novel opportunities for …

Alzheimer's disease (AD) is the most common form of dementia, characterized by
progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic …