Modern genome-scale methods that identify new genes, such as proteogenomics and
ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open …

The ability to accurately model the fitness landscape of protein sequences is critical to a
wide range of applications, from quantifying the effects of human variants on disease …

Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins to address our most pressing …

Human immunodeficiency virus (HIV) infections and HIV-induced acquired
immunodeficiency syndrome (AIDS) continue to represent a global health burden. There is …

Protein design holds immense potential for optimizing naturally occurring proteins, with
broad applications in drug discovery, material design, and sustainability. However …

Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …

Understanding the emergence of novel viruses requires an accurate and comprehensive
annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have …

Predicting the effects of mutations in proteins is critical to many applications, from
understanding genetic disease to designing novel proteins that can address our most …

Over the past years, much knowledge has been gained about the HIV-1 virus structure and
infection cycle. This knowledge has been used to conceive different types of potential …

The Tat proteins of HIV-1 and simian immunodeficiency virus (SIV) are essential for
activating viral transcription. In addition, Tat stimulates nuclear factor κB (NF-κB) signaling …