We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …

Deep neural networks (DNNs) have greatly advanced the ability to predict genome function
from sequence. However, elucidating underlying biological mechanisms from genomic …

Conventional biological experiments often focus on in vitro assays because of the inherent
limitations when handling multiple variables in vivo, including labor-intensive and time …

Microbes are increasingly employed as cell factories to produce biomolecules. This often
involves the expression of complex heterologous biosynthesis pathways in host strains …

The effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory
element (CRE) depend on the local sequence context. In rod photoreceptors, binding sites …

Understanding the influence of cis‐regulatory elements on gene regulation poses numerous
challenges given complexities stemming from variations in transcription factor (TF) binding …

Massively parallel reporter assays (MPRAs) represent a set of high-throughput technologies
that measure the functional effects of thousands of sequences/variants on gene regulatory …

Constructing a directed cyclic graph (DCG) is challenged by both algorithmic difficulty and
computational burden. Comparing multiple DCGs is even more difficult, compounded by the …

Insect host defense comprises two complementary dimensions, microbial killing-mediated
resistance and microbial toxin neutralization-mediated resilience, both jointly providing …

Cellular transcription enables cells to adapt to various stimuli and maintain homeostasis.
Transcription factors bind to transcription response elements (TREs) in gene promoters …