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High Throughput Sequencing

This page is dedicated to my work in the Knight Lab at UCSD. The Knight Lab "... uses and develops state-of-the-art computational and experimental techniques to ask fundamental questions about the evolution of the composition of biomolecules, genomes, and communities in different ecosystems, including the complex microbial ecosystems of the human body. We subscribe to an open-access scientific model, providing free, open-source software tools and making all protocols and data publicly available in order to increase general interest in and understanding of microbial ecology, and to further public involvement in scientific endeavors more generally." 


The Knight Lab takes advantage of highly parallelized, automated experimental procedures to process hundreds of samples with high reproducibility and ease of execution. We cooperate with robotic devices in order to handle miniaturized volumes for molecular biology techniques at sample sizes that would otherwise burden a research team. The lab has proposed and published highly standardized experimental protocols and software tools to engage the active participation of a wider scientific workforce. The software tools allow the users to channel their raw data through common microbiome analysis workflows, such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs. The wide use of standardized bioinformatic workflows and shared data repositories allow for meta-analysis of thousands of samples across multiple studies.


As the software tools become more robust and widely adopted, the molecular biology techniques have to be continuously developed in order to generate increasing amounts of data at a decreasing cost. To achieve this goal, our team borrows high throughput methodologies used in drug discovery, such as working in quantized sample sizes for microplate compatibility, miniaturizing reaction volumes, and incorporating specialized automation devices, and applies them to the next generation sequencing realm. We have successfully adopted liquid handling technologies optimized for high throughput screening, like acoustic droplet ejection, sub-microliter pipetting, and plate washing,  to carry out next generation sequencing workflows at a fraction of the cost relative to traditional methods. 


Our highly automated robotic infrastructure extends our scientists' agency by enabling them to work on developing new knowledge instead of  performing repetitive tasks. We often find ourselves investing the time away from instrument optimizing protocols to increase sample throughput, reproducibility, experimental robustness, and cost efficiency, or developing new experimental procedures at the bench top that will ultimately be ported into our automated infrastructure. This pursuit pushes us to think of robotics as our extensions when developing experimental procedures, because they will be the tools executing our ideas, and to acknowledge the limitations of the systems involved, both organic and synthetic. 

My participation in academic research with the Knight Lab has been the catalyst for a pursuit of a doctorate degree. Working with a team of passionate scientists dedicated to the acquisition of new knowledge is the best everyday routine I can think of. 

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