The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants. But these ampli ...
Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitnes ...
Ecosystems are the stage on which the play of evolution is acted. Inferring evolutionary processes from the spatial and temporal genetic patterns they produce in populations is challenging because ecosystems are highly complex, spatially structured, and te ...
This thesis consists of five papers published in peer-reviewed journals, two of which focus on method development of time-serial inference, represented by publications in methodology journals, and three others that describe collaborative data applications ...
The highly polymorphic human leukocyte antigen (HLA) locus encodes cell surface proteins that are critical for immunity. HLA-A expression levels vary in an allele-dependent manner, diversifying allele-specific effects beyond peptide-binding preference. Ana ...
American Association for the Advancement of Science2018
The standard framework to study vision is typically hierarchical and feedforward, which facilitates deconstructing complex mechanisms into smaller, more tractable problems. However, this framework can fail when elements are presented in context, as they ar ...
Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with novel mechanisms of action. Favipiravir is an antiviral drug that acts by increasing the genome-wide mu ...
A fundamental goal of population genetics is to determine and quantify the interplay of mutation, natural selection, genetic drift and migration in shaping allelic frequency changes that underpin evolution-ary change. In this dissertation, I present comput ...
Transcription factors (TFs) are a family of DNA-binding proteins whose gene regulatory capabilities are of vital importance in defining the molecular state of a cell. Despite their biological significance, our understanding of TF behavior and function is s ...
