Premature birth interrupts the typical development of the human fetus, leaving the infant born with underdeveloped gastrointestinal and immune systems. Preterm infants have reduced stomach acidity, reduced digestive protease activity, more permeable intestinal membranes, impaired innate and adaptive immune response, and poor microbiome development. Due to these factors, preterm infants...
Software testing is of critical importance for the success of software projects. Current inefficient testing methods often still take up half or more of a software project's budget. Automatic test data generation is the most promising way to lower the software testing cost. Manually creating testing data is expensive and...
We consider the problem of supervised classification of bird species from audio recordings in a real-world acoustic monitoring scenario (i.e. audio data is collected in the field with an omnidirectional microphone, without human supervision). Obtaining better data about bird activity can assist conservation efforts, and improve our understanding of their...
Metabolomics has recently gained momentum in biomolecule research and complements the genomics and proteomics research space. Metabolomics strives to detect, identify, and quantify all metabolites present in biological samples. In particular, biomolecular analysis using ultra-performance liquid chromatography combined with mass spectrometry (UPLC-MS) has become increasingly important for metabolomic analyses. Similarly,...
Hop (Humulus lupulus L. var. lupulus) is a diploid, dioecious plant with an extensive history of cultivation and use in brewing, as a textile, and for its therapeutic properties. Hop is prized for its ability to produce a variety of aromatic and flavor compounds, as well as compounds with anti-microbial...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....