Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a
genome. TFs recognize DNA in a specific manner; the mechanisms underlying this …

Each language has standard books describing that language's grammatical rules. Biologists
have searched for similar, albeit more complex, principles relating enhancer sequence to …

Identifying master regulators of biological processes and mapping their downstream gene
networks are key challenges in systems biology. We developed a computational method …

A large body of evidence indicates that genome annotation pipelines have biased our view
of coding sequences because they generally undersample small proteins and peptides. The …

Identifying the molecular origins by which new morphological structures evolve is one of the
long-standing problems in evolutionary biology. To date, vanishingly few examples provide …

A wide variety of RNAs encode small open-reading-frame (smORF/sORF) peptides, but their
functions are largely unknown. Here, we show that Drosophila polished-rice (pri) sORF …

Animal development fundamentally relies on the precise control, in space and time, of
genome expression. Whereas we have a wealth of information about spatial patterning, the …

The excretory system of the nematode Caenorhabditis elegans is a superb model of tubular
organogenesis involving a minimum of cells. The system consists of just three unicellular …

The cuticular exoskeleton of insects and other arthropods is a remarkably versatile material
with a complex multilayer structure. We made use of the ability to isolate cuticle synthesizing …

To achieve a highly differentiated state, cells undergo multiple transcriptional processes
whose coordination and timing are not well understood. In Drosophila embryonic epidermal …