Although the significance of chemical modifications on RNA is acknowledged, the
evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication …

The development of synthetic biological circuits that maintain functionality over application-
relevant time scales remains a significant challenge. Here, we employed synthetic …

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 …

Background Sexual transmission of human immunodeficiency virus (HIV) is inefficient and
results in selection of viral variants based on incompletely understood factors. Functional …

Mutations in amino acid sequences can disrupt protein structures and functions. Accurate
and unsupervised prediction of mutation effects is critical in biotechnology and biomedicine …

Synonymous mutations in a protein coding gene lead to a remarkably similar average
“collateral” mutation effect size across alternative reading frames (1). Here we quantify the …

Overlapping genes, wherein two different proteins are translated from alternative frames of
the same DNA sequence, provide a means to stabilize an engineered gene by directly …

HIV is not efficiently transmitted between hosts, and selection of viral variants occurs during
the process of sexual transmission. The factors that confer selective advantage at the …