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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 ...
Finding Cis-Regulatory Regions in Long Noncoding RNA Loci
(2018-04-18)
We currently understand very little about how the genome functions. Up to 80% of the genome is transcribed, but much of biology focuses on the ~1-5% that codes for proteins. This narrow focus leaves many newly cataloged ...
Mitochondrial Calcium Signaling in Brown Fat Bioenergetics
(2018-09-26)
Calcium is a ubiquitous signaling molecule that coordinates biological processes over a wide range of length and timescales. For decades, it has been known that respiring mitochondria can take up large amounts of calcium ...
When the Circadian Clock Cannot Be Set: An Unstable Singularity Underlies Stochastic Phasing of the Circadian Clock in Individual Cyanobacterial Cells
(2018-05-15)
The endogenous circadian clock synchronizes with environmental time by appropriately resetting its phase in response to external cues. Of note, some resetting stimuli induce attenuated oscillations of clock output, which ...
A Computational Approach to Analysis and Control\\of the Mammalian Circadian Oscillator
(2018-05-11)
Circadian rhythms, endogenous, entrainable, near-24 h oscillations in metabolism, are a nearly ubiquitous feature of life on Earth. Circadian rhythms function as a feedforward biological control system that reorganizes ...
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 ...
Engineering Bacteria for Bio-Based Chemicals Production and Gut Microbiota Applications
(2018-09-16)
Microbes have been used for production of food and beverages for thousands of years. In the last century we have begun to modify them by means of genetic engineering to produce more complex compounds and we have gained ...
Programming molecular behavior: development and applications of autonomous DNA synthesis cascades
(2018-09-25)
DNA serves many functional roles in living organisms, and dynamic DNA nanotechnology seeks to expand this set of DNA-based behaviors through the rational design of new functions. In the past 20 years, the predictable and ...