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Browsing Computational and Systems Biology - Ph.D. / Sc.D. by Title

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Browsing Computational and Systems Biology - Ph.D. / Sc.D. by Title

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  • Novel phylogenetic approaches to problems in microbial genomics 
    David, Lawrence A. (Lawrence Anthony) (Massachusetts Institute of Technology, 2010)
    Present day microbial genomes are the handiwork of over 3 billion years of evolution. Comparisons between these genomes enable stepping backwards through past evolutionary events, and can be formalized using binary tree ...
  • Order, disorder, and protein aggregation 
    Gurry, Thomas (Massachusetts Institute of Technology, 2015)
    Protein aggregation underlies a number of human diseases. Most notably, it occurs widely in neurodegenerative diseases, including Alzheimer's and Parkinson's. At the molecular level, neurotoxicity is thought to originate ...
  • Origins of cell-to-cell variability in apoptosis 
    Spencer, Sabrina Leigh (Massachusetts Institute of Technology, 2009)
    Diversity within a population of organisms is typically ascribed to genetic differences. However, even members of a genetically identical group of cells or organisms in identical environments can exhibit variability in ...
  • Pervasive degeneracy and epistasis in a protein-protein interface 
    Podgornaia, Anna Igorevna (Massachusetts Institute of Technology, 2014)
    Signal transduction pathways rely on transient yet specific protein-protein interactions. How a limited set of amino acids can enforce cognate protein interactions while excluding undesired pairings remains poorly understood, ...
  • Predicting and testing determinants of histidine-kinase functions by leveraging protein sequence information 
    Ashenberg, Orr (Massachusetts Institute of Technology, 2013)
    All cells sense and respond to their environments using signal transduction pathways. These pathways control a sweeping variety of cellular processes across the domains of life, but the pathways are often built from a ...
  • Rational drug combinations design against intratumoral heterogeneity and clonal evolution 
    Zhao, Boyang (Massachusetts Institute of Technology, 2016)
    Cancer is a clonal evolutionary process. This results in complex clonal architecture and intratumoral heterogeneity in each patient. This also presents challenges for effective therapeutic intervention - with constant ...
  • The role of unfolded states in collagen degradation 
    Salsas Escat, Ramon (Massachusetts Institute of Technology, 2010)
    Excessive collagen degradation (collagenolysis) has been implicated in a series of diseases such as tumor metastasis, atherosclerosis and arthritis. There are still several unresolved questions about the mechanism of ...
  • Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution 
    Guo, Yuchun (Massachusetts Institute of Technology, 2012)
    I present three novel computational methods to address the challenge of identifying protein-DNA interactions at high spatial resolution from noisy ChIP-Seq data. I first present the genome positioning system (GPS) algorithm ...
  • The specificity and evolution of gene regulatory elements 
    Friedman, Robin Carl (Massachusetts Institute of Technology, 2010)
    The regulation of gene expression underlies the morphological, physiological, and functional differences between human cell types, developmental stages, and healthy and disease states. Gene regulation in eukaryotes is ...
  • Transcriptional and structural control of cell identity genes 
    Fan, Zi Peng (Massachusetts Institute of Technology, 2015)
    Mammals contain a wide array of cell types with distinct functions, yet nearly all cell types have the same genomic DNA. How the genetic instructions in DNA are selectively interpreted by cells to specify various cellular ...
  • Understanding regulation of mRNA by RNA binding proteins 
    Robertson, Alexander De Jong (Massachusetts Institute of Technology, 2014)
    Posttranscriptional regulation of mRNA by RNA-binding proteins plays key roles in regulating the transcriptome over the course of development, between tissues and in disease states. The specific interactions between mRNA ...
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