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Genome evolution in structured systems
(2016-05-14)
The evolution of a genome is shaped by spatial interactions at multiple scales. At the angstrom level, structural constraints on both RNA molecules and proteins contribute to the evolution of a gene sequence. Such optimized ...
Towards Perfect Molecular Measurement
(2016-09-16)
The rapid pace of technological innovation has profoundly transformed life sciences research. Whereas less than 100 years ago researchers were often confined to descriptive and theoretical practices, modern scientists can ...
Global Signatures of Selection in Humans
(2018-05-13)
This thesis studies the properties and prevalence of natural selection operating on our species on a global or genome-wide scale. It is still not known how negative selection against deleterious mutations operates genome-wide, ...
Probabilistic Models of Structure in Biological Sequences
(2018-09-25)
The machinery of life is encoded in biological polymers for which sequence, structure, and function are intimately connected. This dissertation presents new probabilistic models for uncovering these connections from ...
Genetic and Molecular Dissection of the Integration of Galactose and Glucose Signaling in Saccharomyces Cerevisiae Strains
(2015-05-21)
Cells need to sense the environment in order to survive, in particular they need to detect nutrients which will provide different building blocks and energy for the cell. This task is complicated by the fact that there can ...
Genetic Engineering Toward a 57-Codon Genome
(2017-01-09)
Scientific progress in fundamental biology has drastically transformed our ability to engineer biological systems, with diverse applications in medicine and industry, from insulin and artemisin production in prokaryotes ...
Fitness Tradeoffs, Bimodality, and the Genetics of Natural Variation in Glucose-Galactose Sensing Across Saccharomyces Cerevisiae
(2017-01-26)
In nature, cells must constantly sense their environment and respond appropriately. These cellular “decisions” are implemented by molecular components that can mutate and evolve. How do mutations lead to changes in cellular ...
Genomic Analysis of Viral Outbreaks
(2018-05-11)
Due to recent advances in sequencing technologies, genomics has emerged as a powerful tool for combating viral outbreaks. In this dissertation, I show how genomic data can be used to understand the transmission, as well ...
Evolutionary dynamics of CRISPR gene drives
(2018-09-16)
The alteration of wild populations has been discussed as a solution to a number of humanity’s most pressing ecological and public health problems. Enabled by the recent revolution in genome editing, CRISPR gene drive ...
Uncovering Genes Underlying Quantitative Trait Variation Using S. cerevisiae as a Model System
(2017-05-09)
Individuals from the same species often differ quantitatively in many phenotypes. Understanding the genetic causes of such individuality may improve our understanding of the corresponding phenotypes, and our ability to ...