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Leveraging latent patterns in the study of living systems
(Massachusetts Institute of Technology, 2019)
The development of high-throughput techniques to observe and perturb biological systems has led to remarkable progress in the last several decades. From the tremendous amounts of data being accumulated, new opportunities ...
Synthetic analog feedback control circuits in living cells
(Massachusetts Institute of Technology, 2019)
Models of biochemical reaction networks in cells are important for advancing our understanding of complex biological systems and for designing functional synthetic biological circuits. However, most models are based on a ...
Integrating Omics data : a new software tool and its use in implicating therapeutic targets in Huntington's disease
(Massachusetts Institute of Technology, 2018)
High-throughput "omics" data are becoming commonplace in biological research and can provide important translational insights, but there is a need for well-crafted user-friendly tools for integrating and analyzing these ...
The mechanism and function of pervasive noncoding transcription in the mammalian genome
(Massachusetts Institute of Technology, 2014)
The vast majority of the mammalian genome does not encode proteins. Only 2% of the genome is exonic, yet recent deep survey of human transcripitome suggested that 75% of the genome is transcribed, including half of the ...
Measuring the effects of drugs on single cancer cell growth
(Massachusetts Institute of Technology, 2012)
Understanding the effectiveness of a drug therapy on halting disease progression is an essential aspect of cancer biology. Conventional assays that study cell behavior after a drug intervention report the average response ...
Computational insights into the ecology of the human microbiota
(Massachusetts Institute of Technology, 2016)
The vast community of microbes that inhabit the human body, the human microbiota, is important to human health and disease. These microbes contribute to human metabolism, the development of the immune system and pathogen ...
c-Myc regulates transcriptional pause release and is a global amplifier of transcription
(Massachusetts Institute of Technology, 2012)
Elevated expression of the c-Myc transcription factor occurs frequently in human cancers and is associated with tumor aggression and poor clinical outcome. However, the predominant mechanism by which c-Myc regulates global ...
Investigating the longitudinal dynamics of the human gut microbiome and immune system
(Massachusetts Institute of Technology, 2024-02)
This thesis reports three explorations of two human-associated biological systems: the gut microbiome and the adaptive immune system. These two systems are closely intertwined, and engage in significant crosstalk with each ...
Unfolding genome organization in interphase
(Massachusetts Institute of Technology, 2019)
Genomic contact frequency maps obtained from high throughput chromosome conformation capture technologies have revealed several organizing patterns of mammalian interphase chromosomes, including self-interacting topologically ...
Deciphering the mitotic and meiotic phases of spermatogenesis in the mouse
(Massachusetts Institute of Technology, 2016)
Mammalian spermatogenesis includes two types of cell divisions. First, germ cells undergo transit-amplifying mitotic divisions, which enable prodigious output of mature spermatozoa. Second, they undergo reductive meiotic ...