Browsing by FAS Department "Systems Biology"
Now showing items 1-20 of 31
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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 ... -
Charting Evolutionary Paths of Least Resistance
(2017-04-12)The efficacy of therapeutics such as antibiotics and cancer immunotherapy is double-edged: as they eradicate agents of disease, they simultaneously select for resistant populations, eventually causing their own obsolescence. ... -
Cyanobacteria and Friends: Engineered Photosynthetic Microbial Communities
(2017-02-10)Microbial communities are the rule rather than the exception. Laboratories using model organisms often focus on monoclonal, axenic cultures overlooking the importance of the interactions, division of labor, and robustness ... -
Defining the Essential Function of Yeast Hsf1 Reveals a Compact Transcriptional Program for Maintaining Eukaryotic Proteostasis
(2016-05-14)Despite its eponymous association with proteotoxic stress, heat shock factor 1 (Hsf1 in yeast and HSF1 in mammals) is required for viability of yeast and many human cancer cells, yet its essential role remains undefined. ... -
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 ... -
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 ... -
Experimental and Computational Tools to Study P53 Dynamics at the Single-Cell Level
(2015-09-21)One of the most commonly mutated genes found in cancer is the tumor suppressor p53. p53 is a transcription factor capable of inducing cell-cycle arrest, apoptosis, senescence, and other cellular processes thought to halt ... -
Experiments and Analysis of Mitochondrial DNA Segregation, Yeast Polarization and RNA Polymerase Dynamics
(2015-03-27)This thesis presents work done in three different topics in biology with a combination of experiments, mathematical modeling and quantitative data analysis. All cellular materials are partitioned between daughters at cell ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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, ... -
Identifying Mechanisms of Apoptotic Pore Formation With Programmatic Ensemble Modeling
(2016-02-05)Mitochondrial outer membrane permeabilization is a key step in the apoptotic cell death program, regulating life-death decisions in response to cytotoxic drugs and other forms of cell stress. In this thesis I use mathematical ... -
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 ... -
On the growth of microtubule asters spanning millimeter-sized cells
(2016-01-12)The large cells in early vertebrate embryos are organized by radial arrays of microtubules called asters. Asters grow, interact, and move to precisely position the cleavage planes of for each cell division. Cell-spanning ... -
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 ... -
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 ...