STARS 2023 - Research Project Descriptions

Dr. Julian Schroeder
Julian Schroeder is a Professor in Plant Sciences at UC San Diego. His research focus is on discovering the signal transduction mechanisms and the underlying signaling networks that mediate resistance to climate change-linked environmental stresses in plants, in particular drought, CO2 responses and heat in plants. These environmental ("abiotic") stresses have substantial negative impacts on plant growth and crop yields. These environmental stresses are also relevant in reference to climate change and to securing crop growth and food production to meet the human needs of the growing world population. Research in Julian Schroeder's laboratory is using multidisciplinary approaches including genetics, genomics, cell signaling, physiological, proteomics, molecular biology, and bioinformatics towards uncovering the signal transduction network and receptors in plants that translate drought stress hormone reception and CO2 sensing to specific resistance responses in plants. Some of the recent research advances are being used in the biotechnology industry with the goal of enhancing the stress resistance of plants and crop yields.
Prerequisites: None. Students, however, must show motivation, interest, honesty, inquisitive thinking. Students should also be careful with respect to adhering to lab safety protocols.
Website: https://www-biology.ucsd.edu/labs/schroeder

Diana Rennison
Diana Rennison is an Assistant Professor in the Ecology, Behavior, and Evolution section of the Biological Sciences department at UC San Diego. For Summer 2023, Dr. Renninson's lab will be examining morphological variation associated with ecological variables along the west coast of North America. Her group generally takes an integrative approach to determine the mechanisms central to the origin and maintenance of the spectacular species diversity observed in the world today. The core questions her group seeks to address are: how do sources of selection interact to shape the course of evolution and the generation of biodiversity and why do organisms follow certain evolutionary trajectories when many are possible? To tackle these questions, they integrate population genomics, field collections, and experimental estimates of natural selection. The research project will look at characterizing patterns of morphological and genetic variation in divergent wild threespine stickleback populations. 
Prerequisites: None. Students must be willing to work on animal specimens.
Website: http://rennisonlab.com 

Dr. Sergey Kryazhimskiy
The overarching goal of the Kryazhimskiy lab is to develop our understanding of how microbes evolve to the point where we can predict their evolution. We take several complementary approaches to solve this problem. We observe and measure how microbes evolve and adapt to various lab conditions, for example, to the presence of antibiotics. We also introduce new mutations on purpose into their genomes and see how these mutations change various important traits. Finally, we construct mathematical models to simulate evolution on the computer. Students working in the lab will have the opportunity to evolve microbial populations and/or analyze their genetic information, traits and fitness. Students who are more math-inclined can also learn how about evolution by modeling it. Basic understanding of evolution by natural selection is required. We also expect students to be interested in advancing their understanding of evolution, to be motivated, curious and careful.
Prerequisites: None. 
Website: http://sklab.science/

Dr. Sara Creel
When a child calls a long-eared animal a "wabbit," do they know they're saying it differently than an adult would? What about learners of a new language? In our current research we are using eye tracking methodologies and (potentially) machine learning approaches to examine how a speaker's PRODUCTIONS of words relate to their UNDERSTANDING, by asking listeners to comprehend their own speech. This will likely focus on college-aged second-language speakers of English.
Prerequisites: At least one course in Psychology, Development, or Education. 
Website: quote.ucsd.edu/creel

Dr. Steven Dow 
 The ProtoLab combines research in design thinking, crowdsourcing, and decision making to create novel social technologies that motivate participation and organize people around complex problems. Our research investigates the underlying social and cognitive mechanisms that impact how different groups— from local communities, to classrooms of students, to online crowds — tackle complex problems creatively and collaboratively. More information on our research projects can be found here: https://protolab.ucsd.edu/projects/
Prerequisites: Computer science and design skills.
Website: spdow.ucsd.edu/ 

Dr. Caren Walker
Dr. Walker's research is in the area of cognitive development: we examine the various learning mechanisms that underlie knowledge acquisition and change in early life. Current projects focus on the emergence of scientific thinking—we study preschool-aged children’s reasoning about the cause and effect relationships in the world. We are particularly interested in how features of the learning context can facilitate (or suppress) children’s understanding of abstract concepts that go beyond their direct perceptual experience.
Prerequisites: At least one course in Psychology, Development, or Education. 
Website: http://elc-lab-ucsd.com/caren 

Dr. Lindsey Powell 
Research in Dr. Powell's Social Cognition and Learning Lab investigates how infants and children think about others' minds, social interactions, and relationships. Studies use both behavioral methods (tracking infant attention, asking children what they think) and neuroimaging methods (measuring brain activation with near infrared light). Students will work on the collection, coding, and statistical analysis of data that test hypotheses regarding the development of social cognition and motivation. The lab also offers professional development sessions, presentation practice, and training in R. Preference for students comfortable working with children and their families. 
Prerequisites: None.
Website: socallab.ucsd.edu

Dr. Timothy Brady 
Timothy Brady is an Assistant Professor of Psychology at UC San Diego. At the UCSD Vision and Memory lab, directed by Dr. Timothy Brady, we aim to understand how the world is represented by the visual system, and how information is encoded and integrated into memory. The lab is interested in the precision with which people can remember information long-term memory and how much we can actively hold the information in our mind (e.g., you may have heard about a working memory capacity of 7+/- 2).  This project will focus on examining visual memory precision -- how well we can remember what we saw and what we can do to improve our memories. You'll get to learn to do some work in MATLAB; run people in experiments, and learn about the data. The experiments will vary from simple examinations of memory precision to questions about what memory looks like when people have false memories.
Prerequisites: Students with a background in psychology or cognitive science and programming experience preferred.
Website: https://bradylab.ucsd.edu 

Dr. John Wixted 
 Dr. Wixted search is concerned with forensic psychology and eyewitness memory. Much of his work investigates the cognitive mechanisms that underlie recognition memory, often using signal detection theory as a guide. A related line of research investigates how episodic memory is represented in the human hippocampus, work that is based mainly on single-unit recording studies performed with epilepsy patients. In recent years, his research has also investigated the applied implications of signal detection-based models of recognition memory. The main focus of this line of research is on the reliability of eyewitness memory.
Prerequisites: None.
Website: https://wixted.weebly.com/

Dr. Christina Gremel 
 Dr. Gremel's research lab will work with animal models of decision-making and addiction investigating brain mechanisms. This requires an understanding of both the behavioral and neural mechanisms involved. We take an integrative approach using mice, in which we can combine both simple and sophisticated quantitative behavioral measurements, with powerful molecular and genetic tools and monitoring techniques to delineate molecular mechanisms within specific cell-types in identified circuits that control decision-making processes.
Prerequisites: None.
Website: N/A  

Dr. Adam Engler
The Engler lab's research is focused on how cell behavior is directed by the extracellular matrix (ECM), a 3-dimensional (3D) fibrillar scaffold to which cells adhere. Investigations in the lab revolve around how the mechanical and biochemical properties of this 3D ECM direct the cell behavior, i.e. mechanobiology. Under this broad conceptual framework, the lab is interested in how mechanobiology influences or misregulates cell function and modifies genetic mechanisms of disease. Specifically, the lab has shown that ECM mechanics can regulate the differentiation of stem cells into specific adult cell types, cause heart cells to contract better/worse with age, and cause cells to transform into cancer and metastasize. To accomplish this, his lab makes natural and synthetic matrices with unique spatiotemporal properties to mimic niche conditions, improve stem cell behavior and commitment in vitro, or direct them for therapeutic use in vivo.
Prerequisites: Must be okay with working with embryonic stem cells. Cell culture is a plus. 
Website: ecm.ucsd.edu

Boris Kramer
Boris Kramer is an Assistant Professor in the Department of Mechanical and Aerospace Engineering at UC San Diego. Looking for a student with good skills in computation (python, matlab) and dynamical systems to work on model predictions for space weather. This may range from data-based model learning, uncertainty quantification or inverse problem solving. Dr. Kramer's lab has some interesting projects in reduced-order modeling for various applications, for instance space weather, Lagrangian and Hamiltonian mechanics. Moreover, other projects in risk-based engineering design (design under uncertainty) would require implementing a computational model for a mechanical system and then collaborating with a Postdoc on methods development.
Prerequisites: Preference for students with computational experience and good knowledge of dynamical systems.
Website: http://kramer.ucsd.edu/

Dr. Sonia Martinez
Implement a particular stochastic control algorithm on the turtlebot/ROS platform for future integration into a trajectory tracking project. The control algorithm is trying to move a turtlebot from a current to a goal location while tracking and avoiding a (possibly hypothetical) moving obstacle. The algorithm accomplishes this by creating a Gaussian distribution in the direction of the goal state, defining a non-sample region around the obstacle (with a safety parameter as an input), then controlling to the sampled point. This process repeats until the robot is at the goal state. Movement behavior combines safety with an optimal bias (through distribution placement toward the goal).
Prerequisites: None. Python knowledge and some knowledge of C++ would be great.
Website: http://muro.ucsd.edu

 Dr. Jorge Cortes
Work on distributed robotics at the MURO Lab (http://muro.ucsd.edu) includes design, analysis, and implementation of motion planning strategies and distributed coordination algorithms on multi-robot networks performing spatially-distributed tasks. Our lab focuses on deployment of heterogeneous robots including ground vehicles and aerial vehicles. We rely on methods from graph theory, dynamics, and control combined with open source software programming. Several project opportunities exist to enhance the range of current capabilities in the lab. These include the implementation of distributed methods for self-localization with on-board cameras, 3D formation control strategies with heterogeneous teams, and human-swarm interaction structures that enable rapid deployment of robot teams. Other projects include research in methods of enabling human interaction with a swarm of robots and design/development of ground and aerial robots.
Prerequisites: Familiarity with open source software; programming experience (either phython or C++, ideally ROS); knowledge of ordinary differential equations and linear algebra.
Website: terrano.ucsd.edu/jorge 

Dr. Oliver Schmidt
STARS students will be integrated into one of our ongoing research projects related to computational fluid mechanics, modeling, and flow physics. These are:

• High-fidelity numerical simulation for active flow control for jet noise reduction
• Gas cooling with minimal aero-optical distortion of high-energy lasers
• Mesh-free methods for flow simulation and hydrodynamic stability
• Nonlinear physics of transitional boundary layers and turbulent open cavity flows
• Reconstruction of gaps in experimental particle image velocimetry flow data
• Predictive modeling of shoaling internal gravity waves in the bay of La Jolla         

Prerequisites: None. Depending on the project, knowledge of programming in Matlab, theoretical and numerical fluid mechanics, linear algebra, and partial differential equations.
Website: https://flowphysics.ucsd.edu/

Dr. Mai ElSherief
Students can expect to do research and training in the following:

• * Inferring mental health states from social media language.
• * Online incitement to violence language detection.
• * Misinformation detection.
• *Online abuse detection in social audio and VR settings. 

Shaochen Chen
Dr. Chen is a Professor and Chair in the NanoEngineering Department at UC San Diego. He is also a faculty member of the Institute of Engineering in Medicine and the Clinical Translational Research Institute at UCSD. His research interests include 3D Printing and Bioprinting, Stem Cells and Tissue Engineering, Biomaterials and Nanomaterials, Organ/Tissue-on-a-Chip. The development of 3D printing and bioprinting processes is used to create functional tissues for tissue repair and regeneration. 
Prerequisites: None.
Website: http://schen.ucsd.edu/lab/

Jinhye Bae
Jinhye Bae is an Assistant Professor in the NanoEngineering Department at UC San Diego. The Bae lab focuses on understanding and exploiting physics, mechanics, and dynamics of soft matter to develop new pathways of programmable assembly and deformation of soft matter at the nano to macro-scales. The group is interested in Integrating material characteristics into new structural design and fabrication approaches for applications in biomedical devices, soft robotics, actuators, and sensors.
Prerequisites: Students should have taken general physics and chemistry classes.
Website: https://jbae.eng.ucsd.edu/

Dr. Monica Allen 
Dr. Monica Allen is an Assistant Professor of Physics at UC San Diego. Her research aims to combine scanning probe microscopy with transport techniques to spatially visualize electronic phases in quantum materials and utilize them for emerging technologies, such as quantum information processing. Students will have the opportunity to build hybrid materials by stacking atomically thin crystals and contribute to the development of novel microscopy instrumentation.
Prerequisites: None. 
Website: https://allen.physics.ucsd.edu/

Dr. Adam Burgasser
Adam Burgasser is a Professor of Physics at UC San Diego. In his lab, students will work with Prof. Adam Burgasser and members of the Cool Star Lab to analyze near-infrared spectral data of stars, galaxies, asteroids, and planets as part of a NASA-funded archival research program. Prior experience in programming (especially Python) is recommended but not required; open to Astronomy, Physics, and Computer Science majors.
Prerequisites: None.
Website: http://www.coolstarlab.org   

The Department of Biomedical Informatics designs, implements, and evaluates informatics algorithms and systems that serve biomedical researchers, other healthcare providers, and public health professionals. Students who are interested in being mentored by DBMI Mentors will participate in both STARS and DBMI activities. DBMI Activities have previously included workshops on topics such as Data Science and Informatics, Computational Environments (R/RStudio), R Basics, Informatics Research Ethics, The Electronic Health Record, Data in Databases and SQL, Using the MIMIC Dataset, Hackers and Healthcare, Visualizing Data and Analysis, and Basic Biostatistics.

Applicants requesting to be matched to DBMI Mentors should pay close attention to project prerequisites and special considerations listed after each project description. DBMI Website: https://dbmi.ucsd.edu.

Faculty Mentors: 

• Ming Tai-Seale
• Jejo Koola
• Rodney Gabriel
• Matteo D'Antonio
• Tsung-Ting Kuo

Dr. Ming Tai-Seale
Dr. Tai-Seale is Professor of Family Medicine and Medicine in UCSD's School of Medicine. She leads the Learning Health Systems Lab which seeks to discover new ways to improve health, to disseminate and implement discoveries into evidence-based practices, and to enhance joy in the practice of medicine.
Prerequisites: Preferences for students with skills in quantitative research and are genuinely curious. Able to program in statistical software such as STATA or R.
Website: https://familymedicine.ucsd.edu/research/faculty-labs/learning-health-systems/index.html

Dr. Rodney Gabriel
Dr. Rodney A. Gabriel holds position as Chief of the Division of Regional Anesthesia and Acute Pain Medicine and is the Medical Director at the Koman Family Outpatient Pavilion surgery center. He is an Associate Professor of Anesthesiology and Associate Adjunct Professor in Biomedical Informatics. His research interests include the development of predictive models for perioperative outcomes using machine learning and in novel regional anesthesia techniques for pain management. Dr. Gabriel is actively involved in the acute pain management of surgical patients, especially focused on the reduction of opioid use.
Prerequisites: Willing to learn (if not already known) statistics and programming in R and/or python.
Website: https://profiles.ucsd.edu/rodney.gabriel 

Dr. Matteo D'Antonio
Matteo D'Antonio is an Assistant Professor in the Division for Biomedical Informatics, Department of Medicine at UC San Diego. As member of the The Center for Admixture Science and Technology (CAST), he is interested in investigating the associations between genetic variation and complex traits, in order to improve patient stratification for disease risk. His main focus is understanding how these associations differ between individuals from different ancestries and how admixed individuals can be characterized. clinicians: https://covid19questions.org along with helping to produce high-end graphics for the results.
Prerequisites: None. Basic programming and statistics (R language preferred).
Website: https://admixgenomics.ucsd.edu/

Dr. Tsung-Ting Kuo
Tsung-Ting Kuo is an Assistant Professor of Medicine in UC San Diego Health Department of Biomedical Informatics (DBMI). The Kuo Lab is focused on blockchain technology (a distributed ledger/database technology adopted by the Bitcoin cryptocurrency) that can advance research by data sharing, especially when data is from multiple healthcare systems. However, current, state-of-the-art data sharing frameworks are mostly still centralized. This centralization carries several risks, e.g., single-point-of-failure at the central server. To improve the security and robustness of data sharing frameworks, they want to develop and implement novel and advanced methods on decentralized blockchain networks and/or review related works. The outcome will be development of approaches or summarization of studies that can enhance the security and robustness of data sharing from multiple healthcare systems through a distributed system.
Prerequisites: None. Computer programming such as Java or Python preferred.
Website: https://profiles.ucsd.edu/tsung-ting.kuo

Alon Goren
The Goren Lab studies the characterization of the roles of mitotic associated histone deacetylation patterns. Our interdisciplinary research focuses on epigenomic mechanisms and their dynamics. We merge basic biology, technological innovations and computational analyses to study the role of chromatin regulation in development and disease states, such as cancer and autism. Candidates should be highly committed, hardworking and enthusiastic.We are looking for a highly motivated student, with interest in molecular and computational biology and epigenomics. Previous experience in experimental or computational biology is an advantage.
Prerequisites: None. 
Website: goren-lab.github.io

Chengbiao Wu
Chengbiao Wu is an Associate Professor in the School of Medicine under the Neurosciences Department. His lab is actively developing cutting-edge technologies to pursue novel hypotheses regarding axonopathy. For the summer 2023 project, the focus is using human iPSC, cell models and animal models as they are interested in understanding the molecular and cellular mechanisms in neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease. Research students also study peripheral sensory neuropathy such as Charcot Marie Tooth disease. 
Prerequisites: Students are required to have taken general biology courses.
Website: https://wulaboratory.weebly.com/