Wei Wei

Wei Wei

The Wei lab focuses on highly cross-disciplinary research within the realms of molecular and cellular analysis and cancer systems biology. Our areas of focus include the development and implementation of innovative single-cell multi-omics tools and systems-level computational approaches, aimed at unraveling the complexities of tumor heterogeneity and the tumor-immune microenvironment (TME). We are engaged in exploring treatment-induced cell lineage state transition, epigenetic plasticity, and signaling network dynamics, which are key factors in the development of adaptive therapy resistance in cancer. Additionally, our lab is at the forefront of functional precision medicine, utilizing tumor-derived materials from liquid biopsy and needle biopsy samples for predictive cancer diagnostics and immunotherapy. Read More

Naeha Subramanian

Naeha Subramanian at her desk

Our lab studies the molecular basis of innate immunity, a primordial antimicrobial defense mechanism that is conserved from invertebrates to higher animals. In particular, we focus on a class of intracellular immune sensors called the NOD-like receptors (NLRs) that play essential roles in host defense against pathogens, but also carry genetic variants that are associated with several human autoinflammatory and autoimmune syndromes. We use an ensemble systems immunology approach involving high-throughput experimental, computational, and engineering tools to investigate NLR signaling and regulation at the transcriptional, post-transcriptional, cellular, and organismal scales in various infectious and complex disease contexts. Read More

Anika Gupta

Anika Gupta

As a graduate student in Anna Kuchina’s lab at the Institute for Systems Biology, Anika is utilizing microbial split-pool ligation transcriptomics to study host-pathogen interactions. Transcriptomic analyses of single bacterial cells allow for high-resolution profiling of gene expression within systems where bacteria may act and exist as both a host for bacteriophages and pathogens against eukaryotic cells. Anika received her B.S. in Biochemistry from the University of Wisconsin-Madison and enjoys hiking, road biking, and dancing in her free time. Read More

Alyssa Easton

Alyssa is a graduate student co-advised in Dr. Sean Gibbon’s microbial ecology lab at the Institute for Systems Biology and Dr. Abbie Schindler’s trauma and stress lab at VA Puget Sound. She is using data science to study the molecular gut-brain axis and how this system is impacted by trauma, stress, and aging. She is an NIH T32 Fellow in the University of Washington Alzheimer’s Disease Training Program. Alyssa holds a B.S. in Biological Engineering with a concentration in Cellular and Biomolecular Engineering from Purdue University. Read More

Anna Kuchina

Kuchina lab research interests lie in the development and application of high-resolution technologies toward understanding the single-cell biology of bacteria within complex samples such as biofilms, and in challenging environments such as the human host. We develop and apply single-cell genomic tools for unbiased, high-throughput expression profiling of bacterial consortia. Our custom technology based on combinatorial barcoding is scalable, versatile, and customizable for use in various settings including the host-pathogen interface, environmental microbial communities, or the bioengineered bacterial consortia used for biomanufacturing. Read More

Evan Pepper

As a graduate student in the Baliga Lab at the Institute for Systems Biology, Evan is researching the emergence of antibiotic resistant pathogens and looking to reveal the mechanisms that facilitate this phenomenon. Through a systems biology perspective, Evan hopes to understand how to exploit new transcriptional or metabolic vulnerabilities in clinical pathogens that have evolved to resist a specific type of antibiotic. Evan holds a B.S. in Biomolecular Engineering from the University of California, Santa Cruz. Read More

Nick Quinn-Bohmann

Nick in a blue suit outside.

Nick is a graduate student in Dr. Sean Gibbons lab at the Institute for System Biology. He is interested in using computational tools to enhance the predictive capability of models of the microbiome, eventually using insights from these models to develop interventions for disease. Ultimately, he hopes to apply new understanding gained through a systems biology approach to translational medicine, improving human health and wellness in the process. He was selected as a College of Engineering Dean’s fellow in 2019. Nick holds a B.S. Read More

Jingyi Xie

As a graduate student in Dr. James Heath’s lab at the Institute for Systems Biology, Jingyi is developing new methods to analyze antigen-specific T-cell populations by incorporating multiple biomolecular technologies. These technologies were applied to improve personalized cancer immunotherapy and understand the host immune response against SARS-CoV-19. She holds a B.S. in Biomedical Engineering from Southeast University (Nanjing, China) and an M.S. in Bioengineering from the University of Washington. Read More

Yeon Mi Hwang

Yeon is a graduate student in the lab of Drs. Jennifer Hadlock and Lee Hood at the Institute for Systems Biology. She is investigating adverse maternal outcomes by integrating multi-omics and electronic health record (EHR) data. More specifically she is characterizing the association between the continuation of antidepressant use during pregnancy and the risk of preterm birth using Providence EHR data. She was awarded the 2018 College of Engineering Dean’s Fellowship. She has a B.S. in Genetics and Plant Biology from the University of California, Berkeley. Read More

Alex Carr

Alex is co-advised by Drs. Sean Gibbons and Nitin Baliga at the Institute for Systems Biology. He is interested in how interspecies interactions and environmental factors facilitate the formation and functions of microbial communities as well as the ways by which these communities adapt to changes in their environment, and the roles they play in both the environment and human health. He hopes to develop a deeper understanding of the complex interspecies and evolutionary dynamics of soil and human gut microbial communities through the characterization of individual species and synthetic consortia. Read More