PhD Program

As a graduate student in Professor Alshakim Nelson’s lab in the department of chemistry, Gökçe is working on in situ production and continuous delivery of therapeutics by 3D printed engineered living materials. She received the Scientific and Technological Research Council of Turkey (TÜBİTAK) Scholarship in support of her graduate work and holds a B.Eng. and M.S. in Food Engineering from Istanbul Technical University.

Larissa is interested in designing de novo proteins that can modulate and stimulate powerful immune responses. By engineering immune responses, she wants to circumvent immunodeficiencies present in chronic diseases, improve vaccine efficacy, and tailor individual immune systems to be a ’natural therapeutic’. As an undergraduate, Larissa performed research in a variety of fields such as retroviral genetics, cancer cell biology, immunotherapy cure strategies for HIV chronic infection, and computational approaches for studying antibody development following vaccination. After obtaining her B.S. in Molecular Cell Biology from the University of Hawai’i at Manoa, she completed a 2-year postbac at the NIH Vaccine Research Center, where she learned how to use yeast display to engineer improved antibodies against HIV for use in passive immunization. As a MolE PhD student, she plans to master protein engineering techniques in order to improve immune responses as well as expand her experience in biotechnology entrepreneurship in hopes of co-founding a start-up company dedicated to these pursuits. Larissa is a recipient of the Molecular Engineering & Sciences Institute Director’s Fellowship.

Gabrielle is a graduate student in Dr. Elizabeth Nance’s disease-directed engineering lab. She is interested in the sustainable applications of nanotechnology involving therapeutics and diagnostics for critical diseases. Her research focuses on the characterization and investigation of cellulose drug delivery systems to the brain. Her previous undergraduate work focused on porous silicon materials as an alternative imaging technique for human diagnosis and treatment of gastrointestinal stromal tumors. She received her B.S. in Chemistry at the University of California San Diego.

Reagan is interested in leveraging her past research experience to study nanomaterials for sustainable technology at the UW. As an undergraduate at UCSD, she used porous silicon nanoparticles to immobilize catalysts for the purpose of chemical warfare agent and photosensitizer dye degradation. She also spent a summer interning at the National Renewable Energy Laboratory (NREL) where she researched corrosion of metal alloys in liquid desiccants to help construct an energy efficient air conditioning system. She received a B.S. in Chemistry from UC San Diego.

As a graduate student in the Baker lab at the Institute for Protein Design, Nate is developing computational methods to improve the design of polar protein-protein interfaces. These methods will allow researchers to design mini-protein binders towards a more diverse set of natural targets. He was selected as a College of Engineering Dean’s fellow in 2019. Nate holds a B.S. in Chemical Engineering and a minor in Computer Science from the University of Wisconsin-Madison.

As a graduate student in Dr. E. Virginia Armbrust’s lab in the School of Oceanography, Stephen is developing computational tools for the discovery and characterization of novel molecular mechanisms in ocean microbial communities. Previously, he worked as a research associate on high throughput cell-based assays assessing the efficacy of HIV vaccine candidates in the lab of Dr. Victoria Polonis, and on the development of novel bacterial genome engineering tools at the SF bay area based biotech company Zymergen. Stephen holds a B.S. in Molecular Cellular Developmental Biology and Neuroscience from the University of Colorado Boulder.

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. in Biological Systems Engineering from Virginia Tech.

Samantha is working with Georg Seelig and Jeff Nivala as part of the Molecular Information Systems Lab. With Georg, she is working on scaling up DNA strand displacement circuit architectures for more complex computations. With Jeff, she is developing a CRISPR-based system for in vivo neural network computation. Both projects have potential applications in diagnostics and environmental monitoring as well as synthetic biology. She holds a B.A. in Molecular Biology from Pomona College, where she previously worked on chemical synthesis and synthetic biology.

As a graduate student in the labs of James Carothers and Jesse Zalatan, Ryan is developing CRISPR-based gene regulation tools to improve our ability to engineer microorganisms for the production of high-value compounds. Ryan holds a B.S. in Bioengineering from Stanford University.

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. Alex holds a B.S. in Chemistry from the University of California, San Diego.

As a graduate student in the lab of bioengineering professor James Bryers, and in collaboration with the Mulligan/Hwang lab in the Department of Surgery, Nathan is investigating the role of monocytes and macrophages in porous scaffolds to understand wound healing and the factors that regulate the outcome of implanted biomaterials. Nathan previously worked in industry at Stemcell Technologies on nanoparticle development and researched at the Michael Smith Laboratories on cellular therapies and aptamer selection. He holds a BASc in Chemical and Biological Engineering from the University of British Columbia in Vancouver, Canada.

Adam Chazin-Gray is a graduate student in David Baker’s lab. He is using computational protein design to expand the tools to communicate between cells. His project combines aspects of protein design, and synthetic biology to design synthetic cell signaling systems. This research has potential applications in treating a wide variety of human diseases, including many types of cancer and drug-resistant bacterial infections. He holds a B.A. in Biology & Neuroscience from Oberlin College.

Under the guidance of Chemistry Professor David Ginger and Materials Science & Engineering Professor Christine Luscombe, Emerson is studying interactions between solvated conjugated polymers, ions, and electrons in order to effectively engineer a polymer with better ion and electron transport. These polymers, known as Organic Mixed Ionic Electronic Conductors (OMIECs), have potential applications in energy storage, biosensors, and neuromorphic computing. He holds a B.S. in Chemical Engineering from National Taiwan University.

Louis is interested in polymer science, smart biomaterials and tissue engineering. As an undergraduate researcher in the Ratner Lab, Louis’ research focused on developing engineered polymeric biomaterials for multiple applications. One of his projects involves synthesizing materials to prevent biofilm formation through surface modifications. He is also developing a biomaterial scaffold for better kidney organoid integration. He holds a B.S in Biology from the University of Washington.

As a graduate student in Richard James’s lab at the Center for Immunity and Immunotherapies at Seattle Children’s Research Institute, Rene studies how to experimentally reprogram human B cells to long-lived antibody secretion cells by developing a mathematical model of cell differentiation. This research will help design new protein deficiency therapies as a life-long treatment and antibody vaccine. Rene holds a B.S. in Clinical Laboratory Science and Medical Biotechnology from National Taiwan University.

Maggie is interested in leveraging synthetic biology to address environmental issues. As an undergraduate at Arizona State University, she focused on developing a computational gene regulatory network for mesothelioma in the Plaisier lab. She also rehabilitated the ASU iGEM team to focus on the bioremediation of arsenic out of local water sources. Maggie is a recipient of the NSF Graduate Research Fellowship. She received a B.S.E. in Biomedical Engineering from ASU.

Brian is interested in leveraging synthetic biology and metabolic engineering to address ecological issues ranging from food production to water pollution. As an undergrad, he studied gene regulatory networks involved in plant stem cell differentiation, with an eye toward creating more water-efficient crops. Afterward, he worked at a food biotech startup where he engineered strains of filamentous fungi to optimize heterologous production of dairy proteins for food applications. Brian received a B.S. in Biochemistry and Ecology, Evolution and Conservation Biology from North Carolina State.

As a graduate student in David Baker’s lab at the Institute for Protein Design, Fatima is working on designing scaffolds and protein interfaces to interact with iron oxide surfaces. She hopes to engineer new ways of directing inorganic synthesis of materials by understanding these molecular recognition problems. She is also interested in engineering biomaterials with properties spanning to the meso scale. She holds a B.S. in Biotechnology Engineering from the Monterrey Institute of Technology and Higher Education in Mexico.

As a graduate student in the labs of Dr. Kelly Stevens and Dr. Cole DeForest, Olivia is developing a new 3D printed biomaterials that can serve as mechanically tunable and functional liver tissue to trigger regeneration in an injured or diseased liver. This research will offer a novel therapy to treat liver disease and advance the field of tissue engineering and regenerative medicine. She holds a B.S in Chemical Engineering from the University of Michigan.

Alyssa is interested in applying engineering principles to uncover the molecular mechanisms of human diseases. At Purdue, she spent three years investigating changes in gene expression that may lead to age-related neurodegenerative disease with Dr. Hana Hall. Alyssa also spent a year as a bioinformatics TA for Dr. Kari Clase, conducting exploratory research on the relationship between protein structure and function through bacteriophage phylogeny. She went on to join Dr. Susan Tsutakawa and Dr. Greg Hura at Berkeley National Laboratory, where she performed X-ray scattering data analysis to assess the ability of AI to predict proteins’ functional flexibility. Alyssa holds a B.S. in Biological Engineering with a concentration in Cellular and Biomolecular Engineering from Purdue University.

Andrew is a researcher in the lab of David Baker, at the Institute for Protein Design. His research focuses on the design of symmetric protein complexes to serve as scaffolds for the development of new types of medicine and nanomaterials. In his previous research experience, in academia and industry, he focused on utilizing modified bacteriophage proteins to create drug-delivery vehicles and antimicrobial agents. He holds a B.S in Chemical Biology and M.S. in Materials Science and Engineering from the University of California, Berkeley.

Julian is a graduate student in the lab of physiology and biophysics professor Fred Rieke investigating how natural scenes are encoded by the retina. His work has applications in prosthetics, computer vision, and cortical neuroscience. He holds a B.S in Nanoscale Science and Mathematics from SUNY Albany.

Patrick is interested in the development of novel drug delivery platforms. As an undergrad, he characterized drug loading and size of polymer nanoparticles to investigate the impact of intermolecular interactions between a screen of cancer drugs and the polymer. He has also worked on projects involving drug release from biodegradable foams and scaffolds. He received a B.E. in Chemical Engineering from Vanderbilt University.

Jacob is interested in using the principles of synthetic biology and protein engineering to address prominent issues facing our world including environmental rehabilitation, clean water, and the sustainable manufacturing of textiles, goods, and chemicals. As a graduate student in the Baker lab, Jacob is working on developing deep generative models for protein design, hoping to someday use these tools to design new materials that support sustainable fashion. Traditional textile manufacturing generates toxic byproducts, but this may be alleviated with the use of de novo enzymes. In his free time he loves to eat tomatoes, make riddles, and watch F1. He has a B.S. and M.S. in Biomedical Engineering from SUNY, Binghamton.

Gizem is a doctoral student in the laboratory of Gaurav Bhardwaj in Medicinal Chemistry and interested in de novo peptide design to inhibit the activity of macromolecules. She is currently designing cyclic peptides against protein targets including extracellular ones such as SARS-CoV-2 main protease because cyclic peptides have some advantages over linear peptides which are high stability, high specificity and their ability to bind protein surfaces that cannot generally be drugged. She is primarily interested in computationally achieving the best binders that reach global energy minima by analytical calculations and also to test & approve their binding by experimental analyses. She previously did one of her internships in the Baneyx Lab in Chemical Engineering at the University of Washington and holds an M.S. in Biomedical Engineering from the TOBB University of Economics and Technology from Ankara, Turkey.

Marc is interested in using genetic engineering and computational biology approaches to increase our understanding of biological systems and precisely engineer new biological functions. His previous research experience includes both molecular biology work to accelerate the development of rapid antigen tests for emerging viruses (Gehrke lab, MIT) and dry lab experience in using machine learning to predict the outcomes of CRISPR/Cas9 genome editing (Güell lab, UPF). He also started a team to develop a gluten sensor for people with celiac disease, which was presented in the 2018 iGEM competition. He holds a B.S. in Biotechnology from University of Girona, a M.Sc. in Bioengineering from IQS School of Engineering, and a M.Sc. in Bioinformatics and Biostatistics from Open University of Catalonia.

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Anika is interested in studying the mechanisms of CRISPR/Cas9-mediated genome editing in vivo in addition to protein engineering with medical applications. As an undergraduate, Anika worked in research labs specializing in computational chemistry and plant biochemistry. Her honors thesis focused on the regulatory properties of enzymes in the plant shikimate pathway and methods of preventing aromatic amino acid-mediated inhibition of the pathway. Additionally, she investigated cation-pi interactions in biological systems using theoretical models to search for vibrational shifts associated with aromatic structures near positive charges. She received a B.S. in Biochemistry from the University of Wisconsin-Madison.

As a graduate student in the Lutz lab, Josef is developing next-generation diagnostic tests for upper respiratory infections and HIV. Josef’s research focuses on using advanced molecular diagnostics on paper microfluidics to produce rapid, inexpensive, and highly multiplexed point-of-care diagnostics. His research will help to make diagnostic testing more accessible and comprehensive. He holds a B.S. in Bioengineering and Nano-Molecular Engineering with a minor in Applied Mathematics from the University of Washington, and certificates in nanotechnology and data science.

Steven is interested in understanding why people with diabetes have a higher risk of having heart attacks than those without. Under the mentorship of Dr. Karin Bornfeldt in the Department of Medicine, he is studying the role of inflammatory macrophage cell death on the development of advanced plaques (atherosclerosis lesion) concomitant with diabetes. This research will provide novel mechanistic insights into the culprit for accelerating the buildup of plaques under diabetic conditions and provide new ways to prevent heart attacks in people with diabetes in the future. Steven holds a B.S. in Bioengineering: Nanoscience & Molecular Engineering from the University of Washington.

As a graduate student in chemistry professor Xiaosong Li’s research group, Hang is developing new computational tools to analyze complex electron interactions in molecules or materials. He is also applying these tools to better understand how molecules emit light (fluorescence) and to design new fluorophores. This research could provide a lot of theoretical perspectives for experimentalists and help us understand the general light-matter interactions in molecules or materials. Hang was named a 2020 Clean Energy Institute Graduate Fellow. He received his B.S. in Materials Science and Engineering from Shanghai Jiao Tong University and an M.S. in Materials Science and Engineering from the University of Washington.

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.

Neurodegenerative diseases like Alzheimer’s and ALS are characterized by the aggregation of disordered proteins. Recent discoveries suggest that these same disordered proteins also demonstrate phase separation behavior, in which disordered proteins prefer each other to mixing evenly in aqueous solution. Working with Professors Abhi Nath and Mike Guttman in the department of Medicinal Chemistry, Ellie seeks to understand the dynamics and structural intricacies that govern aggregation and phase separation. This knowledge may enable the use of small molecule drugs to influence disordered proteins on the pathways to aggregation or phase separation. Ellie holds a B.S. in Biochemistry and a minor in Materials Science from Western Washington University.

Naveen is interested in using synthetic biology to develop biologic solutions in global health and is mentored by Neil King. He hopes to design protein nanoparticles that further vaccine development and provide insight into the role of specific interactions during immune responses. He received a B.S. in Cell and Molecular Biology from the University of Michigan.  

David Juergens is a doctoral student in the David Baker lab in Biochemistry. His work focuses on using deep learning and data science to solve problems in computational protein design. These problems include the prediction of protein structure, prediction of amino acid sequences that fold into a desired state, and the design of functional proteins. David holds a B.S. in Chemical Engineering from the University of Washington.

As a graduate student in the labs of chemical engineering professor James Carothers and chemistry professor Jesse Zalatan, Ice is developing CRISPR-based transcriptional activation methods in multiple bacteria to apply in industrial biotechnological applications. He previously worked as a researcher at Vidyasirimedhi Institute of Science and Technology (VISTEC) in Thailand developing biocatalytic systems for chemical synthesis from food/agricultural wastes. Ice holds a B.S. and M.S. in Chemistry from Mahidol University, Thailand.

Paul is interested in developing machine learning models with applications in structural biology. Previously he worked at Bayer (Berlin) and the Simons Machine Learning Center (New York) in machine learning research and development roles. Paul received a B.A. in Statistics from UC Berkeley.

Daniel is a graduate student in the lab of Neelendu Dey, a professor in the division of gastroenterology in the School of Medicine. He is interested in relationships between the gut microbiome and colorectal cancer. His research focuses on how interspecific interactions influence the production of carcinogenic bacterial metabolites. He holds a B.S. in Biochemistry/Biophysics from Rensselaer Polytechnic Institute (NY).

Kacper’s work in Professor Lilo Pozzo’s group revolves around spontaneously formed lipid coated droplets for use as biomedical ultrasound imaging and therapeutic agents. In addition to developing better agents, he hopes to improve the fundamental understanding of this spontaneous emulsification phenomenon. Kacper holds a B.S. in Materials Science and Engineering from the University of Illinois in Urbana-Champaign.

As a graduate student in Professor Alshakim Nelson’s lab, LeAnn is working on the development and characterization of bio-hybrid materials, commonly known as Engineered Living Materials (ELMs). Using 3D printing techniques, LeAnn aims to design more responsive and sustainable materials for both the health and industry sectors. LeAnn is a recipient of the Molecular Engineering & Sciences Institute Director’s Fellowship. She holds a B.S. in Microbiology, Immunology, and Molecular Genetics from the University of California, Los Angeles.

Under the mentorship of Professor Andre Berndt in the department of bioengineering, Justin is developing molecular tools and methods for optical phenotyping of hiPSC-based disease models. Before joining the Berndt lab, his work encompassed mechanobiology and stem cell-derived tissue engineering for disease modeling. Outside of academia, Justin has extensive experience in biomedical entrepreneurship, and he cofounded UW spin-off startup Curi Bio. In 2022, Justin was awarded a prestigious F31 Fellowship from the NIH. Justin received a B.S. in Physiology and M.S. in Applied Bioengineering from the University of Washington.

Bonni is a PhD student in the Asbury laboratory in the Physiology and Biophysics department. She studies microtubules (MTs), which are long, hollow cylinders of repeating protein subunits that switch stochastically between phases of lengthening and shortening. In most eukaryotic cells, bundles of several MTs drive cell division by synchronously lengthening and shortening to align and segregate chromosomes. Uncovering how MTs remain synchronized to correctly separate the cell’s genome is critical to understanding how cell division goes awry, as in many cancers. Bonni’s thesis work will use optical trapping and Monte Carlo simulations to examine the role of mechanical coupling in MT coordination.  In addition to providing pathological insights, understanding MT mechanics will instruct the design of sophisticated synthetic nanomachines, which thus far cannot recapitulate naturally occurring protein nanomachinery. Bonni earned her B.S. in Bioengineering at the University of Washington in 2019.

As a graduate student in David Baker’s lab at the Institute for Protein Design, Phil is trying to make proteins that have two defined structural states. His current approach uses helical bundles. He hopes to use these proteins as bistable switches for the applications of information storage, biological programming, and nanomachinery. He was awarded an NSF Graduate Research Fellowship in 2018. Phil holds a B.S. in Biochemistry and Genetics from the University of Minnesota.

Ariel is interested in developing analytical tools to investigate cellular mechanisms. The focus of her research as both an undergraduate and research scientist at the UW has involved the use of biochemical techniques to study membrane trafficking proteins in budding yeast. She received a B.S. in Chemistry from California State University, San Bernardino.

As a graduate student in the lab of Dr. Suzie Pun, Melissa is working on drug delivery platforms, including biologically testing polymeric drugs bypassing the blood-brain barrier. This could improve drug targeting to the brain for diseases such as Alzheimer’s and Parkinson’s. In addition, she is identifying biomaterials that will promote CAR-T cell therapy, which will improve this cancer treatment in the future. She holds a B.S. in Biomedical Engineering at The Pennsylvania State University.

Yulai is co-advised by Professors David Baker in the Department of Biochemistry and William Catterall in the Department of Pharmacology. Yulai is interested in studying the physicochemical properties of transmembrane proteins. Based on this knowledge he aims to use computational approaches to design transmembrane nanopores for selective filtration, molecular sensing and sequencing. He holds a B.S. in Chemistry from Fudan University.

Peik is interested in designing de novo proteins for environmental applications, such as the degradation of pollutants and the sustainable industrial synthesis of chemicals. During his undergraduate he used molecular modeling and molecular dynamics simulations to investigate protein-protein interactions and to predict protein structure and function. He holds a B.S in Molecular Biology and Biotechnology from the University of Idaho.

As a graduate student in the lab of chemical engineering professor François Baneyx, Jinrong is investigating solid binding protein-peptoid hybrid materials and their application in nanoparticle regulation and biomineralization. A better understanding of how interactions between solid binding proteins (proteins fused with solid binding peptide) and inorganic nanoparticles vary under different conditions (pH, redox, etc) will allow researchers to manipulate nanoparticle behavior (such as aggregation/deaggregation or crystallization). He holds a B.Eng. in Chemical Engineering from Xi’an Jiaotong University and an M.S. in Chemical Engineering from the University of Washington.

As a graduate student in David Baker’s lab at the Institute for Protein Design, Sanaa is using deep learning (specifically generative models) for protein structure refinement and design. She holds a B.S. in Chemistry and Computer Science from Mount Holyoke College.

Cassandra is a graduate student in the Nemhauser lab in the Biology department. She is interested in using CRISPR dCas9 and serine integrase technology to build externally responsive genetic circuits in plants, genetically engineering them for eventual applications in agriculture, medicine, and climate resilience. She aims to advance the field of plant synthetic biology and use the multicellular nature of plants for novel and exciting applications. Cassandra holds a B.S. in Chemical Engineering from UW.

Rory is advised by Jeff Nivala, an assistant research professor in the Molecular Information Systems Laboratory in the Allen School of Computer Science and Engineering. He is investigating digital microfluidics as a tool for automating bacterial and cell-free synthetic biology. The result of this research will be a versatile, high-throughput, and entirely open-source platform for automating and tuning synthetic biology experiments. He holds a B.S. in Biological Science from Cornell University, where he focused on microbiology research.

As a graduate student in Hugh Hillhouse’s research group, Yuhuan is investigating bismuth rudorffites, a promising new material for the top cell in solution processed tandem perovskites. These lead-free wide bandgap semiconductors could potentially serve as a high-performance alternative to the lead-based materials in hybrid perovskite solar cells currently used to increase the power conversion efficiency of solar cells while lowering their overall cost. A deeper understanding of bismuth rudorffites could enable the development of low-cost tandem solar cells from non-toxic elements. Yuhuan holds a B.S. in Materials Science and Engineering from Tianjin University and a M.S. in Materials Science and Engineering from the University of Washington.

Abdul is interested in integrating machine learning or artificial intelligence to develop materials for energy conversion and storage applications. Previously, he was a Fulbright fellow and masters student in the Department of Materials Science & Engineering at the UW. His thesis focused on improving the electrochemical cycling stability of cathodes for sodium ion batteries. Prior to joining the MolE program, he worked as a lecturer in MSE department at the Institute of Space Technology in Pakistan. He has a B.S. in Materials Science & Engineering from the Institute of Space Technology, Islamabad in Pakistan and an M.S. in Materials Science & Engineering from the UW.

Davi is interested in using computational approaches to understand biology and solve problems in molecular engineering. During his undergrad, he developed deep learning systems for predicting how complexes of proteins fold with Dr. Mu Gao in Dr. Jeffrey Skolnick’s lab. He believes machine learning models are very useful in answering scientific questions and hopes these methods can help solve problems in healthcare and sustainability. He earned his B.S. in Computer Science at Georgia Tech with a Minor in Chemistry and Biochemistry.

Phuong is a PhD student performing her graduate research in the lab of Elizabeth Nance in the Department of Chemical Engineering. Her research focuses on characterizing and investigating the role of brain-derived extracellular vesicles in injury response in neonatal ischemia models. Extracellular vesicles are membrane bound vesicles that have emerged as a new pathway of cellular communication and a valuable source for injury stage-specific information and as ‘fingerprints’ of injury progression. They have become an exciting new research thrust in therapeutics due to their intrinsic capability to carry active biomolecules, endogenous bioavailability, and biocompatibility. The long-term goal of her research is to develop targeted therapies for neonatal ischemic injury, which is an underserved population in translational research. Phuong obtained her B.S. and M.S. degrees in Materials Science & Engineering at Stanford University and the University of Washington, respectively.

Ben is co-advised by Professors Suzie Pun and Patrick Stayton in the Bioengineering department. He is developing polymeric biomaterials for targeted drug delivery, with a particular interest towards advancing the state-of-the-art of cancer vaccines and kidney therapeutics. The efficacy of promising drug candidates is often hampered by delivery constraints, such as rapid clearance from the body and/or off-target toxicity – more simply, they do not stay at the right place for the right amount of time to work. Ben’s work can change that – incorporating drugs into polymers can help them stay in certain bodily compartments for longer, and adding targeting molecules to polymer chains can help them “hone in” to certain cells that they need to act upon. He likes to think of his work as bringing “miracle molecule kills cancer cells in a petri dish” drugs from news articles to full clinical approval and into patients’ hands. He holds a B.E. in Chemical Engineering from Vanderbilt University.

With a background in computational biology, Kira has spent the last 3 years working at the Broad Institute of MIT and Harvard where she studied new pan-cancer immunotherapy targets and their mechanisms of action. Kira is interested in exploring synthetic biology systems as it applies to environmental biotech or medicine. She holds a B.S. in Bioinformatics from Wheaton College (MA).

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.

Ayumi is a grad student in Patrick Stayton’s lab within the department of Bioengineering. The Stayton lab explores novel polymer architectures to create prodrug platforms that target specific tissues while reducing peripheral effects. Ayumi is interested in infectious disease treatments, and currently studies polymeric treatments for the radical cure of Plasmodium vivax malaria. Her previous work focused on sub-anesthetic ketamine treatments for levodopa-induced dyskinesia in Parkinson’s disease. She received her B.S. in Molecular and Cellular Biology from the University of Arizona.

As a graduate student in bioengineering professor Valerie Daggett’s lab, Tatum is studying self-aggregating proteins known as amyloids. Amyloid proteins are a hallmark of disease in mammalian systems, but are also used by bacteria as part of an extracellular scaffold known as a biofilm. She is targeting functional bacterial amyloid in biofilms by engineering peptides that interfere with amyloid aggregation. By preventing continued aggregation of alpha sheet oligomers through specific binding to alpha sheet peptides, bacterial biofilms cannot form efficiently, effectively increasing their susceptibility to common antibiotics. Tatum received the 2018 College of Engineering Dean’s Fellowship. She holds a B.S. in Bioengineering and a minor in Chemistry from Santa Clara University.

As a graduate student in the laboratory of David Ginger in Chemistry, Yangwei  is interested photovoltaics, energy storage, synthesis and characterization of functional nanomaterials. He is currently working on a project that focuses on developing new methods to alleviate the impact of defects in perovskite solar cells. This research will help improve the efficiency of perovskite solar cells. He holds B.E. and M.E. in chemical engineering from Dalian University of Technology.

Janis is a member of Dr. Herbert Sauro’s lab. She collaborates with Dr. James Carothers to develop a method for systematically reengineering metabolic pathways in microorganisms. Specifically, she utilizes machine learning to build kinetic models from perturbation data. Her research will decrease humanity’s reliance on fossil fuels by lowering the cost of sustainable industrial chemical production. She holds a B.S. in Bioengineering from the University of Washington. 

Amy is co-advised by Jim De Yoreo, Chief Scientist for Materials Synthesis and Simulation Across Scales at PNNL and an affiliate professor of materials science and engineering and of chemistry at the UW, and David Baker, Director for the Institute for Protein Design and a UW professor of biochemistry. Amy is investigating the self-assembly and nucleation of hybrid organic/inorganic nanostructures. She is specifically studying protein directed mineralization in order to facilitate the rational design of self-assembling hierarchical structures for clean energy applications. Amy was named a 2020 Clean Energy Institute Graduate Fellow and previously received an NSF Graduate Research Fellowship in 2018. She holds a B.S. in Materials Science & Engineering from the University of Washington.

As a graduate student in the lab of Dr. John K. Lee at the Fred Hutch Research Institute, Huiyun is developing pipelines to deconvolute diverse population of cells marked by combinations of lentiviral barcodes using next-generation sequencing technologies. She is interested in using computational methods to solve biological problems. Her Master’s research focused on analyzing gene expression downstream of TP53 under different genetic contexts in malignant melanoma cells. Huiyun graduated with a B.S. in Biological Sciences from Nanjing University and a M.S. in Biology with a concentration in Microbial and Cellular Biology from Emporia State University.

Hao is a Ph.D. student in the lab of materials science & engineering professor Bruce Hinds, where he is developing photocatalytic materials that facilitate more efficient chemical reactions for use in solar cells and other photovoltaic devices as well as biomedical devices. He is part of a collaboration with UW Medicine’s Center for Dialysis Innovation (CDI), which seeks to improve the health and well-being of people with advanced kidney disease initiating and receiving dialysis treatment. Hao holds a M.S in Materials Science and Engineering (MSE) from the University of Washington and a B.S in MSE from Georgia Tech.

Mattias is interested in all things synthetic biology, including de novo protein design, engineered metabolic pathways and synthetic cellular circuits. Mattias has a background in mathematics, biotechnology and pharmacology. He has also worked as a data scientist, designing machine learning systems for public health in New Zealand. He received a B.S. in Mathematics and Biotechnology and a Bachelor of Biomedical Science in Pharmacology & Medicinal Chemistry from Te Herenga Waka – Victoria University of Wellington.

Marti is jointly advised by Drs. Neil King and David Baker within the Institute for Protein Design. She aims to use computational methods to design new nanoparticle cages that will direct specific immune responses. Her goal is to understand more about the complex role of immunity and help generate a vaccine platform with long-lasting protection. She previously worked at Fred Hutchinson Cancer Research Center engineering B cells in their Vaccine and Infectious Disease Division. Marti holds a B.S. in Chemical and Biomolecular Engineering from the University of Tennessee.

Quoc is developing high-throughput technologies in Georg Seelig’s lab to construct and characterize biological networks. This work could one day enable scientists to implement complex, programmable control of gene expression in live cells for applications in disease therapeutics or metabolic engineering. Outside of the lab, Quoc invents foods and develops riddles. He holds a B.S. in Biochemistry and Cell Biology from UC San Diego.

As a graduate student in the lab of Andre Berndt, Sarah is interested in optimizing protein function by coupling machine learning algorithms to directed evolution. This research will help advance the field of protein engineering and develop optogenetic tools that can be used in studies of addiction, pain, and emotion. She recently received the Herbold Data Science Fellowship to continue her work in machine learning. Sarah holds a B.S in Biomedical Engineering from the University of Utah.

Photovoltaic devices are important for the renewable clean energy system. Today, silicon-based solar modules keep dominating the market, but various emerging techniques based on thin-film inorganic semiconductors are rapidly developing. Among thin-film technologies, chalcopyrite Cu(In, Ga)Se2 (CIGS) shows excellent light conversion efficiency. As a graduate student in Dr. Scott Dunham’s lab in the department of electrical & computer engineering, Xiaofeng is developing predictive models for the design and optimization of CIGS solar cell fabrication and device operation processes. These predictive models will help engineers and scientists design the material structure of solar cells to optimize performance. Xiaofeng was selected to be a 2021 Clean Energy Institute Graduate Fellow. He holds a B.S. in Chemistry from Nankai University, China.

In Dr. Aimee Dudley’s research group at the Pacific Northwest Research Institute, Michael uses yeast as a model organism to develop new technologies and high throughput methods to study complex genotype-phenotype relationships. Previously, Michael worked on drug discovery for Cryptococcus neoformans infections in the Farnoud research group at Ohio University, thermoplastic processing as a material science co-op at ContiTech’s research and development department (Akron, Ohio), and protein engineering for enzyme immobilization in the Blenner research group at Clemson University as part of an NSF-REU. Michael holds a B.S. in Chemical and Biomolecular Engineering from Ohio University in Athens, Ohio.

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.

As a graduate student in the lab of materials science & engineering professor Christine Luscombe, Liwen developed a new and greener method to synthesize materials for organic photovoltaics (OPVs). OPVs have drawn lots of attention due to their flexibility, light weight, high charge mobility, and solvent processability. She developed a synthetic method called cross dehydrogenative coupling (CDC) polymerization, which can eliminate the pre-functionalization steps of monomers, thus lowering the cost of the resultant OPV materials and minimizing the generation of hazardous chemical wastes. She was named a 2020 Clean Energy Institute Graduate Fellow. She holds a B.S. in Polymer Materials and Engineering from the Beijing University of Chemical Technology (China) and a M.S. in Polymer Science from the University of Akron.

As a graduate student in the lab of Biomedical Informatics and Medical Education professor Sean Mooney, Yao studied clinical data sharing, synthetic data generation, and machine learning model evaluation. After completing her Ph.D. in 2022, Yao joined Amazon as an Applied Scientist.

As a graduate student in Professor Jennifer Nemhauser’s lab in the department of biology, Eric is interested in engineering native plant promoters to be orthogonally repressible, which has applications in plant synthetic biology and building logic circuits. Eric previously worked on E. coli contamination tracking through strain clustering and helped develop diagnostic test strips for a biotechnology company in Taiwan. He received his B.S. in Biochemistry and minors in Biology and Philosophy from Cal Poly, San Luis Obispo.

Jessie is interested in developing computational methods to design new protein binders and protein materials for therapeutic applications. As an undergraduate, she used yeast surface display to develop protein engineering design technology in the Wittrup Laboratory at MIT. Subsequently, she worked in the biotechnology industry including at early-venture-startup Ab Initio Biotherapeutics where she designed therapeutic antibodies against G-protein coupled receptors and at Genentech where she worked on large molecule pharmaceutical development. She is a recipient of a 2021 UW College of Engineering Dean’s Fellowship. Jessie received a B.S. in Chemical-Biological Engineering from MIT.

As a graduate student in the Pfaendtner Research Group, Marlo uses molecular dynamics simulations to investigate protein dynamics at interfaces. He works closely with experimentalists to characterize the structure-function relationships that dictate protein roles, and hopes to contribute to protein design methodology. Marlo holds a B.S. in Chemistry from the University of Vermont.