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2020 REU Summer Research Projects

Descriptions (Click on link to jump to project)


Eric Appel
Sustained delivery technologies for engineering robust immunity

Project Description: Efficacious vaccines elicit a persistent antibody response and high-affinity broadly neutralizing antibodies (bnAbs) against pathogens of interest ranging from HIV to influenza to malaria. We are developing novel controlled delivery technologies for prolonging exposure of the immune system to vaccines to increase the potency, durability, and quality of the resulting antibody responses. These technologies enable a critical avenue for elucidating what molecular levers must be pulled, how hard, and for how long, to produce robust long-term immunity.

Anticipated Student Responsibilities/Suggested Qualifications: The REU student will gain skills from hydrogel synthesis and characterization to drug delivery to immunoengineering. The student will conduct in vitro release assays of molecular cargo and participate in analysis of vaccine responses.


Lacra Bintu 
Massively Parallelized Discovery of Gene Expression Regulators

Project Description: The human genome contains 20,000 protein-coding genes that are expressed in myriad combinations. Understanding the regulation of gene expression is fundamental to explain cellular behaviors in health and disease, and to engineer the next generation of synthetic cell therapies. We know over 1000 proteins can be found in the human nucleus and may play a role in regulating gene expression. Here, we will employ a new massively parallelized measurement technology to systematically discover which of these proteins can turn a gene on or off. This effort will improve models of mammalian gene regulation and accelerate the development of synthetic epigenome editing technologies.

Anticipated Student Responsibilities/Suggested Qualifications: Students will develop valuable skills in high-throughput mammalian functional genomics and computational analysis of large-scale biological datasets.


Lacra Bintu
Novel Methods for Single-Molecule Detection of Chromatin Modifications using Nanopore Sequencing

Project Description: Transcription factors (TFs) and chromatin modifications collaborate to determine gene expression patterns, and characterizing their function in single cells will be critical to understanding cellular behavior in health and disease. Tremendous progress has been made in mapping the locations of TFs and chromatin modifications genome-wide in as few as 1,000 cells, yet methods to do so in single cells are lacking. To meet this need, we propose a novel method to detect the presence of chromatin modifications on single DNA molecules at near basepair resolution using Nanopore sequencing. The REU student would help to develop this method, with opportunities to learn techniques in molecular biology and sequencing data analysis.

Anticipated Student Responsibilities/Suggested Qualifications: This project would be ideal for a highly enthusiastic student who enjoys troubleshooting and fast iteration. Prior experience in Nanopore sequencing or sequencing data analysis not required.


David Camarillo
Smart Mouthguard for Monitoring Head Impacts

Project Description: Traumatic brain injury (TBI) is a leading cause of death and disability in the U.S., affecting a broad swath of the population, from infants to the elderly and all ages in between due to vehicular accidents, violence, and sports. We study the biomechanics of concussion through the development of diagnostic sensors, preventative equipment, and computational models of the brain and cervical spine. To “sense” concussion, we instrument high school and collegiate athletes in football, lacrosse, MMA, and other contact sports with inertial sensors which measure the severity of impacts. Using this information, we can simulate the response of the brain to impact to better understand the underlying mechanisms of concussion.

Anticipated Student Responsibilities/Suggested Qualifications: Assisting with instrumented mouthguard lab testing and validation, as well as football helmet redesign and impact testing for improved safety. Additionally, video analysis to video verify real vs fake impacts from the previous football season's data.


Wah Chiu
CryoEM of molecules and cells

Project Description: Our lab is interested to advance the methodology of cryoEM to determine biological structures either in purified form or inside a cell at the highest possible resolution. We have state of the art instrumentations for cryo-specimen preparation and data collection. Ample computing resources and graphics workstations are available for 3-D structure determination and visualization. We have a variety of collaborative projects with scientists from engineering to medicine. 

Anticipated Student Responsibilities/Suggested Qualifications: The project involves image processing of cryo-electron microscopic images. Computational skill is preferred. The type of data ranges from molecular machines to cells related to different human diseases.


Jennifer Cochran
Engineering a receptor decoy for lung cancer

Project Description: Particular cytokines have been shown to be upregulated in lung adenocarcinoma making them attractive targets for therapeutic development. This project focuses on engineering a native ligand and receptor to create high affinity decoy antagonists that can prevent downstream signaling and inhibit cancer growth. Our lab uses directed evolution as a non-biased approach to find mutations that improve the binding affinity between receptors and ligands.

Anticipated Student Responsibilities/Suggested Qualifications: The anticipated role will involve characterizing the mutations found through directed evolution screens using yeast binding assays. The student will also assist to make and purify proteins from bacterial and mammalian systems.


Jennifer Cochran
Engineering antibodies as novel cancer therapeutics

Project Description: The Cochran lab uses a technique called yeast display to express millions of protein variants on the surface of yeast cells. We can then sort these cells to discover molecules, like antibodies, with beneficial properties. Our goal for this project is to engineer an antibody which binds specifically to a mutated protein found on the surface of cancer cells but not healthy cells.

Anticipated Student Responsibilities/Suggested Qualifications: The REU student will purify DNA for protein expression and characterize the antibodies in vitro using yeast and mammalian cells. Introductory lab experience (BioE 44) is helpful but not required.


Jennifer Cochran
Targeted Drug Delivery for Pediatric Solid Tumors

Project Description: The Cochran lab has developed a platform for targeted delivery of chemotherapeutic agents based on an engineered peptide that binds selectively to multiple tumor-associated integrin receptors. These particular integrin receptors are overexpressed on tumor cells and their vasculature in a variety of cancers, and facilitate angiogenesis, invasion, and metastasis. When conjugated to fluorescent dyes or radiolabels, the engineered peptide, termed 2.5F, serves as an effective in vivo molecular imaging agent against various solid tumors, ranging from spontaneous intracranial tumors to transgenic lung cancer. The high specificity of 2.5F to tumors versus healthy tissue prompted us to expand the use of 2.5F as a targeting agent for delivery of small molecule chemotherapeutics to numerous tumor types, including glioma, breast, ovarian, pancreatic, melanoma, fibrosarcoma, colon, and lung. More recently, we have started to apply these targeted therapies to the most difficult-to-cure childhood cancers, including osteosarcoma, rhabdomyosarcoma, Ewing sarcoma, diffuse intrinsic pontine glioma (DIPG), and glioblastoma. We have begun characterizing pediatric cancer cell lines to determine the best candidates for our targeted therapy.

Anticipated Student Responsibilities/Suggested Qualifications: The REU student will be developing and optimizing high-throughput assays to assess therapeutic response in pediatric cancer cell lines treated with our tumor-targeted drug conjugates.


Markus Covert 
Whole-cell computational modeling of Escherichia coli

Project Description: The Covert Lab created the first computational model of a cell that took all the genes into account and could successfully predict cellular physiology - an advance that was reported around the world and highlighted by the journal Cell as one of its most important publications during it's 40th anniversary celebration. Now we are working to expand this modeling approach to E. coli - with 10 times as many genes, roughly 50 times as many molecules and far more complexity on the whole, but also with incredible value to both academia and industry.

Anticipated Student Responsibilities/Suggested Qualifications: REU students will work as part of a team to develop modeling strategies, curate and incorporate data, implement the models in python, and test/validate the resulting simulations. There are also opportunities to generate some of the data or test predictions experimentally.


Drew Endy 
Engineering mealworms for waste biodegradation

Project Description: Remember your middle school science fair project on mealworms? Well, those little wrigglers are making a big comeback. As it turns out, mealworms (Tenebrio molitor) have the capacity to eat, metabolize, and biodegrade styrofoam, a notoriously recalcitrant pollutant. All of a sudden, a waste-free future seems within reach; a future with mealworms as a platform organism for substrate-agnostic biodegradation and conversion into useful biomaterials. With the wealth of possible applications for easily modifiable, wiggling bioreactors, this project aims to develop and characterize fast, easy, and universally accessible mealworm genetic engineering techniques.

Anticipated Student Responsibilities/Suggested Qualifications: REU student responsibilities include performing cellular and molecular biological experiments along with handling live mealworms and mealworm beetles. Previous wet lab experience is suggested but not required.


Drew Endy
Synthetic cells: Workflows for testing functional integration of essential systems

Project Description: Want to help build world-first synthetic cells? Cells for which we have a functional understanding of each component used in their creation, and whose genome is fully-specified? Success will result in a deeper understanding of biology and unlock new horizons for the engineering of, and innovation with, biology. A key challenge in cell building is integration testing—how can we build multiple cell systems, compose them in a single context, and determine that all of the components are working as expected. We are investigating whether an advanced microscopy technique, cryo-electron tomography (cryo-ET), can be used to characterize the performance of multiple systems simultaneously, by building a three-dimensional reconstruction of the inside of our prototype synthetic cells.

Anticipated Student Responsibilities/Suggested Qualifications: The REU student will work across one or more of the stages of our integration testing pipeline: building and operating engineered cell-essential constructs in the PURE cell-free system, encapsulating these systems in cell-like liposomes, imaging the liposomes using cryo-ET, or analysing the resultant data. Overall, the student will gain experience in the design, build, test, and measurement of synthetic DNA, using new tools to go beyond simple synthetic circuits and approach the genome scale.


Polly Fordyce
Leveraging lanthanide-encoded beads for high-dimensional mass cytometry

Project Description: The Fordyce Lab has recently developed a technology for high-throughput production of hydrogel beads containing many distinct ratios of lanthanide nanophosphors (MRBLEs). We are interested in exploring 2 novel questions about this technology: (1) Are these beads compatible with CyTOF mass spectrometry techniques (which would open up a wide range of new high-throughput immunoassays)? and (2) Can we increase the coding capacity of these beads by including additional lanthanides?

Anticipated Student Responsibilities/Suggested Qualifications: Generating lanthanide-encoded hydrogel beads, analyzing high-dimensional mass cytometry data, helping build new optical setups, high-throughput computational image analysis.


Pollly Fordyce
MRBLE-path: fast, sensitive, and multiplexed detection of pathogens in blood samples for sepsis

Project Description: We have recently developed a new technology that allows fast, sensitive, and multiplexed detection of pathogens in blood samples for sepsis and demonstrated the ability to identify up to 20 samples with high confidence. For a summer project, we would like to explore the possibility of adding additional probes capable of detecting antibiotic resistance markers to the assay.

Anticipated Student Responsibilities/Suggested Qualifications: Student will be responsible for microfluidic synthesis of lanthanide-encoded hydrogel beads, thermodynamic design of hybridization probes, performing multiplexed hybridization assays, analyzing images, and interpreting data.


Garry Gold
Development of new MRI Technology for Musculoskeletal Imaging

Project Description: The JOINT (Joint and Orthopedic Imaging with Novel Techniques) group develops and tests novel Magnetic Resonance Imaging methods for imaging bone and joint disorders. The project will involve using MRI for muscle, bone, and joint disorders in athletes and patients. We will study the application of advanced quantitative MRI in these subjects.

Anticipated Student Responsibilities/Suggested Qualifications: The student will work with a team of postdocs, graduate students, and faculty to implement and evaluate novel methods of data acquisition or analysis of MRI data in bones and joints. Scanning of subjects, analyzing data, and programming new AI/ML algorithms are all part of the research.


Geoffrey Gurtner
Wearable alternatives for chronic wound care management

Project Description: This project aims to develop a "smart bandage" that will utilize sensors to provide real time tracking of an injury site. Additionally, the data collected by the smart bandage will ideally provide insight into the progress of the healing of the wound and subsequently deliver appropriate real-time electrostimulations to induce galvanotaxis of cells to the injured site. As such, this smart bandage would not only be able to cut down wound-healing times for patients, but also treat them more effectively as well.

Anticipated Student Responsibilities/Suggested Qualifications: The student will collect clinical data on wounds of consenting patients and use this data to train a machine learning algorithm that will optimize wound healing outcomes of the smart bandage. Student should have some familiarity with biology, basic engineering principles. Previous lab experience is desired, but not necessary, in cell biology and data analysis.


Sarah Heilshorn
Injectable Materials to Delivery miRNA Drugs

Project Description: The microRNA (miRNA) profile in many cancers and other diseases is significantly dysregulated. While many promising candidate miRNA drugs have been identified by pharmaceutical chemists, these drugs cannot be efficiently delivered to the patient. Commonly these drugs are delivered systemically through the circulatory system, resulting in severe off-target consequences that are poorly tolerated by the patient. To overcome this challenge, we are developing injectable hydrogels that encapsulate and protect the miRNA drugs. These materials can be delivered to the exact site of action in a minimally invasiveness manner using a catheter or syringe needle. Over time, the materials biodegrade and release the miRNA drugs to the surrounding tissue.

Anticipated Student Responsibilities/Suggested Qualifications: The REU student will participate in the synthesis and characterization of these injectable materials. They will measure and quantify the release rates of different encapsulated miRNA drugs. They will assist in confirming that the miRNA drugs are still active and biologically functional after release.


KC Huang
Developing predictive mathematical models of microbial communities

Project Description: Microbial communities are important to host and environmental health, making microbiome engineering a potentially impactful solution in medicine and environmental remediation. However, engineering applications of microbiome research are hindered by a lack of predictive models. Therefore, this project aims to develop mathematical models to predict growth data for an in vitro system of gut commensals. The project offers an opportunity to model biological complexity and to interact closely with fast-paced experiments.

Anticipated Student Responsibilities/Suggested Qualifications: The student will analyze a large data set of a complex biological system using rigorous statistical methods, and develop a predictive model by applying mathematical techniques used to study disordered systems and nonlinear dynamics. The student should be proficient with ordinary differential equations, linear algebra, and general statistics, and should have a basic knowledge of microbiology.


KC Huang
Quantifying interspecies interactions in microbial communities

Project Description: Microbial communities are important to host and environmental health, making microbiome engineering a potentially impactful solution in medicine and environmental remediation. However, engineering applications of microbiome research are hindered by a lack of understanding of to what extent member species interact to affect the growth of one another. Therefore, this project aims to quantify interspecies interactions in an in vitro system of gut commensals through pairwise co-culture and spent media experiments. The project offers an opportunity to quantitatively characterize microbial systems in high throughput and to interact closely with mathematical models.

Anticipated Student Responsibilities/Suggested Qualifications: The student will quantify the growth of bacterial cultures using plate readers under anaerobic settings and high throughput microscopy. The student should be proficient with basic microbiology experimental techniques, and should be comfortable with understanding mathematical models.


Alison Marsden
Patient-specific computational flow modeling for precision endovascular treatment of complex abdominal aortic aneurysms

Project Description: Branched and fenestrated endografts represent the forefront of minimally-invasive endovascular treatment of complex abdominal aortic aneurysms (EVAR). This project aims to develop computational fluid dynamic arterial models for assessing the hemodynamic performance of branched, fenestrated and mixed endograft designs. We further plan to develop a virtual testing framework to enable patient-specific simulation of complex EVAR strategies, thus allowing surgeons to precisely determine the most optimal device configuration for treating a specific patient.

Anticipated Student Responsibilities/Suggested Qualifications: The student will have the opportunity to learn multiple skills including interpretation of CT imaging, 3D modelling of vascular anatomy using the SimVascular program, and model visualization and interpretation. Project responsibilities include building 3D models, tuning computational models and helping with data analysis. Basic MATLAB and Python coding is helpful but not required. The overall skills and knowledge learned from this project would be useful for those pursuing biomedical engineering or pre-medical careers.


Paul Nuyujukian
Neuroelectrophysiology laboratory development using a Linux-based realtime computational platform

Project Description: This project will utilize LiCoRICE (Linux comodular realtime interactive computation engine - http://licorice.stanford.edu ) to develop several invertebrate neuroelectrophysiology and closed-loop systems neuroscience laboratory experiments which will be deployed as part of the first offering of a lab course the following year (BIOE 248). The projects span single and dual electrode neuroelectrophysiology recording with crickets, roaches, earthworms; and also human-controlled closed-loop neural decoding experiments. Student will develop and test labs in LiCoRICE, spanning experimental setup, data acquisition, and analysis.

Anticipated Student Responsibilities/Suggested Qualifications: Student must be independent, creative, and willing to persevere in the face of failure. Experiments fail often before succeeding, and student must be both attentive to detail and comfortable with uncertainty. No required courses, but familiarity with programming is helpful (CS106A), circuits (EE101A/101B), signal processing (EE102A/102B), and numerical computing (Python, CME 193/108) is helpful.


Paul Nuyujukian
A realtime computational platform for systems neuroscience and brain-machine interfaces

Project Description: This project will continue development on LiCoRICE (Linux comodular realtime interactive computation engine) which was developed as REU projects over the past five summers. LiCoRICE is a flexible platform that implements model-based design in realtime with Python, and is used as the central data processing and collection tool for the neuroelectrophysiology and brain-machine interface work in the group. Student will continue to develop platform, addressing outstanding bugs, and adding features based on need and interest. More information about platform is available at http://licorice.stanford.edu

Anticipated Student Responsibilities/Suggested Qualifications: Student must be fearless and willing to climb a steep learning curve. This platform is challenging and will stretch the knowledge learned from coursework into new territory. Student must also be willing to work independently to solve problems. No required courses. These are useful: programming (CS106A/B), systems (CS107 , CS110), algorithms (CS161), embedded systems (EE 107/109), signal processing (EE102A/102B/264), networking (CS144), numerical methods (CME103/200/108), and compilers (CS143).


Stanley Qi
Synthetic Manipulation of the Genome to Model Disease

Project Description: Spatial genome reorganization and epigenetics have been implied in the etiology of many diseases including those related to aging and cancers, but the direct sufficiency of these events have not been proven. The Stanley Qi lab has developed many targetable synthetic bioengineering tools to reorder and modulate genome organization and/or the epigenetics surrounding specific loci. In an effort to understand the disease etiology based on these events, chemically induced proximity can be forced between certain DNA loci and subnuclear structures, upon which many different data must be bioinformatically analyzed such as chromosome conformation capture, RNA transcriptome, and occupancy of epigenetic factors and/or DNA accessibility. This completion of this project will have fundamental impact in understanding how genome reorganization can promote disease or affect cell biology.

Anticipated Student Responsibilities/Suggested Qualifications: The student will be responsible for learning bioinformatic analysis and/or synthetic genome reorganization techniques under the tutelage of a postdoctoral scientist. Basic familiarity with computer science and/or minimal basic molecular biology experience (PCR) are preferred but not required. Enthusiasm for fundamental genome biology, familiarity with R, cell culture, and plasmid cloning skills are especially preferred.


Stanley Qi
CRISPR technologies for long-lasting gene regulation

Project Description: CRISPR technologies have been rapidly deployed for manipulating the function of the cell via genome engineering and altering gene regulation. This project will investigate the potential of these technologies for inducing durable gene regulation by investigating combinations of CRISPR-based gene regulation domains. These optimized molecules will be assessed for their activity locally and within the genome, and will be characterized thoroughly to understand the bases for effective gene regulation on endogenous genes.

Anticipated Student Responsibilities/Suggested Qualifications: This project will involve molecular cloning, cell biology techniques, sequencing, and data analysis. Experience in any of these will be helpful, but the only requirement is an interest in developing CRISPR gene regulation technologies.


Stanley Qi
A Gene Editing Toolkit for High School students

Project Description: Gene editing and engineering is changing the future of bioengineering, biomedical sciences, and healthcare. Despite enormous advancement in research, there is little connection with the education. It seems a far-reaching goal for K12 students to practice safe and robust gene editing laboratory, prohibiting them from gaining a deeper understanding of this wonderful science. We aim to develop a robust and safe toolkit that can be easily distributed to high schools so they can use it for teaching and perform gene editing, even without routine molecular biology lab setup.

Anticipated Student Responsibilities/Suggested Qualifications: The students should be very motivated to accomplish, goal-driven, and creative in solving this problem. Prior experiences in molecular lab or BIOE44 is a must.


Mark Skylar-Scott
Rapid 3D Printing of Vascularized Cardiac Tissue

Project Description: 3D bioprinting is a promising approach to fabricate custom shaped human tissues with embedded vasculature to maintain tissue viability and function. However, as standard approaches are limited to depositing a single filament at a time, the construction of large and high-resolution tissues is prohibitively slow. Recently, multimaterial multinozzle 3D printing (MM3D) has shown promise to create truly scalable and complex components in 3D. To date, this process has not been used for bioprinting purposes, and offers the ability to produce heterogeneous and vascularized tissue constructs in a rapid and efficient manner. 

Anticipated Student Responsibilities/Suggested Qualifications: Students will be involved in setting up an MM3D printer in Dr Skylar-Scott's new laboratory at Stanford, and will use the system to demonstrate the rapid patterning of vascularized cardiac tissue. The ideal student will have some cell culture experience and a demonstrated interest in tinkering and building things.


Nicholas Telischak & Alsion Marsden
Patient specific treatment of intracranial aneurysms incorporating computation flow dynamic analysis

Project Description: Our summer project entails developing a predictive patient specific model from a database of intracranial aneurysms treated with a flow-diverting stent, correlating procedural outcome to computational flow analysis using Simvascular, an open source software. This is personalized medicine for minimally invasive neurosurgery, and students would be welcome to participate in both the research aspects (building the aneurysm specific models) as well as the clinical aspects (patient care, observation of procedures in neuro cath lab, etc.) if interested. We look forward to having you!

Anticipated Student Responsibilities/Suggested Qualifications: Completing computational flow analysis starting with cross sectional imaging data (CT or MRI) and ending with computational flow dynamic analysis using Simvascular. The student would be taught and mentored in the use of this software. Additional observation of patient care in the hospital and clinic would be available if interested in a career in medicine.


Fan Yang
Modeling primary and metastatic bone cancers using bioengineered 3D in vitro models

Project Description: Malignant bone tumors are aggressive cancer which arise from bone tissue or as a result of metastasis. The most prevalent types of cancer, such as breast cancer, preferentially metastasize to bone, yet the role of the bone niche in promoting cancer progression remains poorly understood. In this project, the REU student will work under the mentorship of a senior Ph.D. student to harness tissue engineering to bridge this knowledge gap by providing 3D in vitro systems that can be specifically designed to mimic key properties of the bone niche in a more physiologically relevant context than standard 2D culture, and apply it for elucidating cancer biology and drug screening.

Anticipated Student Responsibilities/Suggested Qualifications: Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior lab experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.


Fan Yang
Controlled drug delivery to Control Stem Cell fate and Enhance Tissue Regeneration

Project Description: To control stem cell differentiation in situ and enhance desirable tissue regeneration, there remains a critical need to develop controlled drug delivery platforms that can release soluble factors in the body in a spatiotemporally-controlled manner. Biomaterials provide a powerful tool to serve as drug delivery depot for this purpose, but complex parameter needs to be designed and optimized to achieve the target release kinetics. Prospective undergraduate researcher will work with a senior lab member to learn biomaterials fabrication and characterization, conduct in situ drug release studies, evaluate cell responses using in vitro assays and validating the efficacy using relevant animal models. Such tools may be useful for enhancing bone and cartilage regeneration or promoting vasculature formation etc.

Anticipated Student Responsibilities/Suggested Qualifications: Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.


Fan Yang
Engineering pediatric brain cancer using biomimetic hydrogels

Project Description: Brain tumors are the most common solid tumor in childhood and account for 20% of all neoplasms in children. Pediatric brain tumors are distinct from their adult counterparts, and must be studied independently to achieve effective treatment regimes for the children they afflict. The brain tumor microenvironment is a complex niche consisting of biochemical and mechanical cues, and the interplay between multi-factorial niche signals play an important role in regulating brain tumor growth and invasion. To address the urgent need for improving the outcomes for treating pediatric brain tumor, the goal of this project is to develop in vitro models specifically optimized for pediatric brain tumor to advance understanding of the effects of cell-matrix and cell-cell interactions on pediatric brain cancer growth and invasion.

Anticipated Student Responsibilities/Suggested Qualifications: Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior lab experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.


Fan Yang
Novel biomaterials as 3D cell niche to enhance stem cell differentiation and tissue regeneration

Project Description: Stem cells hold great promise as building blocks for regenerating lost tissues, but methods must be developed to control stem cell fate towards desirable lineages before they can be useful for clinical translation. Biomaterials provide a powerful tool for recapitulating the extracellular matrices, and can be engineered as 3D artificial cell niche to promote desirable cellular fates and tissue formation. Prospective undergraduate researcher will work in a highly interdisciplinary group that integrates biology, materials science, engineering and medicine. Such biomaterials platforms can be used for elucidating the mechanisms of stem cell-niche interactions, as well as for translational studies for repairing tissues such as muscle, bone, cartilage etc.

Anticipated Student Responsibilities/Suggested Qualifications: Under the guidance of PI (Prof. Fan Yang) and a senior lab member(e.g. a postdoctoral fellow or graduate student), the student is expected to conduct literature review, experimental design, carrying out experiments, data analyses and provide progress report update in written and oral format. Highly motivated individuals with great hands-on skills are desired. Prior lab experience in cell culture, molecular biology or biomaterials is not required, but would be a plus.


Peter Yang
3D printed medical devices for musculoskeletal tissue engineering

Project Description: Three dimensional (3D) bioprinting technology has been a promising way to make tissue engineering constructs. Previously, we have built an innovative bioprinter to make the combinational tissue engineering constructs with both soft and hard structures by different biocompatible materials. In this new project, we will design and build our next generation bioprinting platform to enable us to control biological presentations spatially and temporally in our combinational constructs and thus provide more functionalities to them. The candidate is expected to complete any mechatronic-related course.

Anticipated Student Responsibilities/Suggested Qualifications: C/C++ or C#, SolidWorks or other CAD software, LabVIEW (not required)


Peter Yang
Development of Prevascularized Endothelial Cell Aggregates for Therapeutic Angiogenesis

Project Description: Cell-based therapeutic angiogenesis has shown a great potential for treatment of the damaged tissues, but there still remain challenges in protecting cells from poor vascularization and maintaining stable vascular network for anastomosis and microcirculation. Here, we will develop prevascularized human umbilical vein endothelial cell (HUVEC) based vasculature capable of enhancing functional vessel formation, preventing vessel regression over time, and recovering blood perfusion quickly. In this project, first, we will develop hydrogel systems with tunable physiochemical and mechanical properties. Second, we will evaluate the interaction between HUVEC, the specific tissue cells, and tunable hydrogels. Finally, we will evaluate the effect of pre-fabricated HUVEC aggregates on neovascularization in a murine ischemia model.

Anticipated Student Responsibilities/Suggested Qualifications: Completion of basic molecular biology /chemistry courses. Prior lab experience is preferred but not required