STARS 2024 - Research Project Descriptions

Dr. Julian Schroeder
Julian Schroeder’s laboratory is focused on identifying the molecular mechanisms by which plants respond to and mount resistance to climate change-linked stresses. Stress resistance mechanisms that we are characterizing are directly linked to water, including drought stress-induced signal transduction mechanisms, salinity resistance mechanisms and how plants respond to the continuing rise in the atmospheric CO2 concentration. We have discovered drought stress resistance signal transduction pathways and have recently identified a long-sought CO2 sensor that controls the water use efficiency of plants. An important goal of this research is also developing future strategies for engineering climate stress resistance in plants. Summer research students will receive training in molecular biological, advanced imaging, cell signaling, genomics, genetics and other methods while pursuing their hands on research project. Furthermore, students will be mentored in presenting their research results and in diverse career questions.
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

Claire Meaders 
Claire Meaders is an Assistant Teaching Professor in the Cell and Developmental Biology Section at UC San Diego. Her research is focused on the intersection of instructional practices and student experiences in STEM courses. A current project focuses on identifying aspects of discussion sections that are helpful or unhelpful for student learning. This project will involve analyzing quantitative and qualitative student survey data.
Prerequisites: none
Website: https://biology.ucsd.edu/research/faculty/cmeaders

Diana J Rennison
Characterizing morphological divergence of threespine stickleback across the west coast of North America. The goal of the work is to identify traits and underlying genes that are associated with abiotic and biotic factors that vary across the native range of threespine stickleback fish.
Program: Ecology, Behavior, and Evolution
Lab: Rennison Lab
https://rennisonlab.com/

Noah Rose
We are an ecological and evolutionary genomics lab that uses a combination of population genomics and field ecology, supplemented with behavioral, physiological, and developmental work in a controlled laboratory environment to study how mosquitoes have come to thrive in the human niche, and how this shapes the spread of human disease. This project will involve primarily microscope and computer work to identify morphological differences between different populations of mosquitoes with some opportunity to also assist with behavioral experiments.
Program: Ecology, Behavior, and Evolution
Lab: Rose Lab
https://roselab.biosci.ucsd.edu/

Alina Schimp
Solution-phase synthesis of inorganic nanomaterials.
Prerequisites: students must have taken general chemistry
Website: https://schimpflab.ucsd.edu

Seth Cohen
STARS students will work on the synthesis and characterization of metal-organic frameworks (MOFs). MOFs are a type of metal-organic hybrid material that are of interest for environmental and energy applications. Applicants should be in interested in synthetic chemistry for this experience.
Prerequisites: General and organic chemistry classes completed.
Website: http://cohenlab.ucsd.edu

Kent Griffith
The Griffith Laboratory develops new materials for rechargeable batteries including fast-charging lithium-ion batteries and sustainable next-generation energy storage technologies like sodium-based materials. We are a materials chemistry laboratory with a focus on materials synthesis, characterization methods such as diffraction and spectroscopy, and device (battery) fabrication and testing.
Prerequisites: none
Website: https://griffithlab.ucsd.edu

Andrew Pun
This project will focus on developing new materials for photon upconversion. Students will gain hand-on skills in synthetic organic chemistry, as well as molecular and optical characterization of materials synthesized.
Prerequisites: Taken some chemistry lab courses.
Website: http://aplab.ucsd.edu

Erik Romero
Program: Organic Chemistry
Lab/Website: http://r2g.ucsd.edu/group.html

Wei Wang
Program: Chemistry and Biochemistry
Lab/Website: https://chemistry.ucsd.edu/faculty/profiles/wang_wei.html

Francesco Paesani
Program: Computational Chemistry 
Lab/Website: Paesani Lab https://paesanigroup.ucsd.edu 

Lisa Jones
Students will get hands on experience in using mass spectrometry to study proteins. Specifically, students will use a mass spectrometer to quantify protein expression abundance in a human cell line. Students will learn how to calibrate the instrument, how to prepare samples, and how to run the instrument. Mass spectrometry is an important technology that is widely used in many fields and is a desirable skill set for jobs in the biopharma industry.
Prerequisites: Has some knowledge of proteins and amino acids.
Website: https://chemistry.ucsd.edu/faculty/profiles/jones_lisa.html

Dr. Steven Dow 
UC San Diego’s ProtoLab conducts research at the intersection of social computing and design with the goal of developing tools, processes, and instructional techniques that change the way people solve complex problems creatively and collaboratively. We develop technology related to social media, crowdsourcing, mixed-initiative systems, and physical-digital interactions to enable large-scale online creativity and to study the cognitive, social, and cultural aspects of design.
Prerequisites: UX design skills, programming especially web development, Node.js, python.
Website: https://protolab.ucsd.edu

Lara Rangel 
The Neural Crossroads laboratory studies how the coordination of neural activity in rhythms critically facilitates information processing across brain regions. Our current projects study the rhythmic circuit interactions that support prosocial behaviors, auditory perception, and learning and memory in rodents. Summer students will receive an introduction to animal behavior and electrophysiology skills, and will have an opportunity to analyze behavioral and neural data. Students will have additional opportunities to engage in collaborative efforts during weekly lab meetings and journal clubs.
Prerequisites: Some programming experience in Matlab.
Website: http://neuralcrossroads.ucsd.edu

Sarah Creel 
Sometimes children say words in ways that are difficult for adults to recognize, such as "wock" for rock or calling a small office a "closet." Is this because they think that rock sounds like wock, or that their parent works in a closet, or does it indicate gaps between their comprehension and their production? In our current research we are using eye tracking methodologies to examine how a speaker's PRODUCTIONS of words relate to their UNDERSTANDING, by asking listeners to comprehend their own speech.
Program: Cognitive Science, language acquisition and speech perception.
Lab/Website: http://quote.ucsd.edu/creel

Drew Walker 
Program: Social cognition; teaching and learning.
Lab/Website: https://cogsci.ucsd.edu/people/faculty/drew-walker.html

Deanna Greene
I am an Associate Professor in the Cognitive Science Department at UCSD. I received my BA from UCSD and my PhD from UCLA in the Psychology Department with a focus on Cognitive Neuroscience. I then received postdoctoral training at Washington University in St. Louis. The neuroimaging community at Wash U is fantastic, so I stuck around as faculty in the Psychiatry department. After 10 exciting years at WashU, I made my way back to my alma mater and home state in 2020. My lab studies brain development, network organization, and what goes awry in neurodevelopmental disorders, using a cognitive neuroscience approach. When I am not doing research, I enjoy spending time with my family, eating good food, and watching basketball.
Program:  Developmental Cognitive Neuroscience
Lab/Website: https://greenelab.ucsd.edu/lab_members

Doris Trauner M.D.
Program:  Developmental Cognitive Neuroscience
Lab/Website: https://profiles.ucsd.edu/doris.trauner

Jason Fleischer
Program: Machine Learning & Data Science
Lab/Website: https://cogsci.ucsd.edu/people/faculty/jason-fleischer.html

Dr. Christina Gremel 
Neural bases of decision-making and alcohol use in mice.
Prerequisites: Psychology, biology, or neuroscience major.
Website: https://gremellab.ucsd.edu/

Victor Ferreira 
Help with experiments investigating adult language production: How do speakers think of the words they want to say and assemble them into grammatical sentences, all in real time and with so much else going on?
Prerequisites: none.
Website: http://lpl.ucsd.edu

Miranda Francoeur Koloski
Program: Psychiatry Department/ VA Mental Health, Neural Circuits, Traumatic Brain Injury
Lab: ---

Nadia Brashier
Program: Physiology 
Lab/Website: https://psychology.ucsd.edu/people/profiles/nbrashier.html

Miranda Koloski
We are a neural engineering lab using innovative methods to measure brain activity supporting cognitive functions. Help us better understand how traumatic brain injuries (TBI) lead to neural circuit impairments that affect memory, decision-making, and impulsivity. We use animal models to study the molecular, neural, and behavioral impacts of frontal TBI. We will test brain stimulation as a method to re-engage neural circuits and improve behavior after TBI.
Prerequisites: Knowledge of MATLAB, Python or programming language; Microsoft Excel
Website: https://neatlabs.ucsd.edu/

Christine Smith 
Program: Cognitive Neuroscience
Lab/Website: CNS Laboratory of Memory and Brain

Michael Taffe
Program: Psychiatry
Lab/Website: The Taffe Lab
https://profiles.ucsd.edu/michael.taffe

Gregory Light 
Program: Psychiatry Education and Training
Lab/Website: https://psychiatry.ucsd.edu/research/programs-centers/mirecc/directors-welcome.html

Sarah Gille
The California Current is the region of ocean just upstream of the continental US. Conditions in the California Current drive weather and climate as well as shaping maritime activities (e.g. fisheries). The region is well monitored, and because of that, it is a convenient test bed for exploring research approaches that will later be applied across the planet. The research opportunity will focus on analyzing data and models in the region in the context of multiple projects: understanding how DDT and other contaminants that were dumped on the sea floor could be redistributed in the San Pedro Basin off of Los Angeles, evaluating atmosphere–ocean coupling in high-frequency radar data along the coast, assessing model results that are constrained by the new Surface Water and Ocean Topography satellite, investigating coastal and open ocean exchanges with the help of machine learning tools, or examining biogeochemical processes using profiling floats. There are also possibilities to extend work to examine the Southern Ocean or the tropical Pacific, taking advantage of the global array of profiling floats.
Prerequisites: Experience in Matlab or Python, math including linear algebra (e.g. Math 18) and calculus (e.g. Math 20 A-C).
Website: https://sgille.scrippsprofiles.ucsd.edu/

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: http://ecm.ucsd.edu/

Francisco Contijoch
The Contijoch Research Laboratory develops new CT and MRI imaging methods to better understand cardiopulmonary function and disease. We develop new imaging methods, new ways to analyze clinical images, and frameworks which combine imaging metrics with other measures (for example, pressure recordings). Students will have the opportunity to analyze real-world clinical data to try to answer a pressing clinical question.
Prerequisites: Programming experience is required. However, it can be in any language (python, C++, matlab, etc).
Website: http://contijoch.ucsd.edu

Robert L Sah
Program: ---
Lab: https://iem.ucsd.edu/researchers/people/profiles/robert-sah.html

Shengqiang Cai
Our research is focused on the mechanics and chemistry of soft materials including both synthesized polymers and biological tissues. We aim to understand and model large deformation, instabilities, fracture, fatigue, chemo-mechanical coupling, electro-mechanical coupling in diverse soft materials. We also explore engineering applications of soft materials, such as artificial muscle, soft robots, soft machines and biomedical devices.
Prerequisites: None.
Website: https://sites.google.com/ucsd.edu/caigroup/home?authuser=0

Nicholas Boechler
Mechanical metamaterials. The student will be involved in the design and testing of materials with extraordinary mechanical properties (mechanical metamaterials). This will likely involve dynamic vibration or impact experiments with high speed video or laser-based characterization, as well as manufacturing via 3D printing, casting, laser cutting, or CNC machining.
Prerequisites: Have taken at least statics (like MAE30A) course. Preferably have taken a mechanics of materials or structural mechanics course (like MAE131A), but the latter is not necessary.
Website: http://boechler.ucsd.edu

Antonio Sanchez
Our research encompasses a wide variety of fluid dynamics problems emerging in engineering and biomedical applications. In investigating these flows, we often take advantage of the disparity of the length and time scales encountered in these complex problems to simplify the solutions, often by application of asymptotic methods that help to identify simpler sub-problems and serve to extract the fundamental underlying physics. These perturbation methods are supplemented by numerical simulations and small-scale laboratory experiments.
Prerequisites: Mechanical Engineering, Aerospace Engineering, or Bioengineering are preferable.
Website: http://asanchez.ucsd.edu/

James Friend 
Our group uses micro-nano engineering to produce clinically beneficial technologies, especially using ultrasound, a safe method for imaging and treatment of disease. We have projects on pacing the heart, overcoming type II diabetes, treating peripheral neuropathy, speeding viral diagnosis at the point of care, and delivering genes into cells. We also work on fundamental physical phenomena, including exploration of rogue waves and holes at the microscale, attempting to drive ultra high-speed rotation through levitation, and the behavior of fluids under large stresses at the nanoscale. We've hosted STARS students in the past, and one of our current PhD students is a STARS program alumni.
Prerequisites: For some projects, experimental and bench experience is a plus. For a couple of our projects, extensive math experience and/or a thorough grounding in physics is required.
Website: http://friend.ucsd.edu

Renkun Chen
Program: Mechanical and Aerospace Engineering 
Lab/Website: https://jacobsschool.ucsd.edu/people/profile/renkun-chen

David Saintillan
Program: Fluid Mechanics
Lab/Website: Saintillan Lab
https://jacobsschool.ucsd.edu/people/profile/david-saintillan

Abhishek Saha
Program: Mechanical and Aerospace Engineering 
Lab/Website: https://jacobsschool.ucsd.edu/people/profile/abhishek-saha

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: http://terrano.ucsd.edu/jorge

Olivia Sanchez 
Program:  Sociology of Education
Lab/Website: https://sociology.ucsd.edu/people/graduate-students/olivia_sanchez.html

Irene Hyangseon Ahn
Program: Comparative and Historical Methods
Lab/Website: https://www.hseonahn.com/

Dr. Nikolay Atanasov
Title: Motion Planning and Reinforcement Learning for Robot Manipulation Description: This project focuses on motion planning and reinforcement learning techniques for robot manipulation. The objective is to develop algorithms that compress visual or tactile observations into an environment representation and plan or learn robot arm and end-effector motions to achieve a desired task. The project involves learning manipulation policies in a physics simulator, such as MuJoCo, and transfer of the learned policies to a real robot arm.
Prerequisites: Experience with motion planning (e.g., A*, RRT) or reinforcement learning (e.g., Q learning or policy gradient) as well as proficiency in Python or C++ are required.
Website: http://erl.ucsd.edu/

Tse Nga Ng
Program: Flexible Printed Electronics
Lab/Website: https://jacobsschool.ucsd.edu/faculty/profile?id=394

Imani Munyaka
Students can expect to do research and training in one of the following areas:

• Human-interaction with LLMs.
  Misinformation detection.
• Network or Mobile device security
• STEM Scholar educational tools - Unlike the other topics, this requires a student interested or knowledgeable in developing websites, videos, and designing educational materials. There is no coding involved in this project.

Students should be excited about the applications of computer science for social good.
Prerequisites: Majors similar or related to Marketing and Computer Science
Website: https://www.ujimasp.com/

Gary Cottrell
Program: Deep Learning 
Lab/Website: https://jacobsschool.ucsd.edu/giving/founding-faculty-and-emeriti/gary-cottrell

Nisarg Shah
Dr. Shah is a faculty member in the NanoEngineering Department at UC San Diego. His research focuses on the development of new bio and nanomaterials with unique properties that regulate the fate and function of immune cells with applications in autoimmune diseases. Dr. Shah emphasizes the mentorship of students with the goal of developing their intellectual curiosity and experimental skills through his interdisciplinary research program at the interface of materials science, nanomedicine and immunology.
Prerequisites: Students should have taken general physics, biochemistry and cell biology courses
Website: https://shah.ucsd.edu/

Kesong Yang
Program: Computational Materials Science
Lab/Website: Yang Group
http://materials.ucsd.edu/

Zheng Chen
Program: Nanoengineering 
Lab/Website: Sustainable Materials and Energy Lab (Dr. Z. Chen)
https://zhengchen.eng.ucsd.edu/members

Monica Allen 
Program: Physics, Quantum Materials (experimental).
Lab/Website: https://allen.physics.ucsd.edu/

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: 

• Rodney Gabriel
• Jejo Koola
• Kathleen Curtius
• Tiffany Amariuta
• Matteo D'Antonio

Dr. Rodney Gabriel
Using artificial intelligence technologies to predict surgical and anesthesia outcomes, such as long term opioid use and other complications.
Prerequisites: Willing to learn (if not already known) statistics and programming in R and/or python.
Website: https://profiles.ucsd.edu/rodney.gabriel

Dr. Kathleen Curtius
This project seeks to investigate the bacterial composition associated with human tumor and pre-cancer samples, with a focus on the commensal bacteria Bacteroides fragilis. The study aims to identify specific bacterial strains present within pre-cancer environments in inflammatory bowel disease and analyze their genetic and virulence factors through whole genome sequence mapping. This project aims to explore potential correlations between pathogenic strains of bacteria and cancer progression, or the effectiveness of therapeutic interventions. This project will employ advanced computational analysis to dissect the complex interplay between the human microbiome and cancer, potentially uncovering novel biomarkers or therapeutic targets.
Prerequisites: Knowledge of Python or R required. Knowledge of Bash scripting highly preferred.
Website: https://qcclab.com

Dr. Tiffany Amariuta
Students will work with high dimensional genetic and genomic data to understand mechanisms of disease risk that pertain to specific genes and cell types. In the Amariuta Lab, we develop new statistical methods to interpret disease information from genome-wide association studies (GWAS) using functional genomics data such as gene expression measured by RNA-sequencing at bulk tissue and single cell levels. Integrating these data types, we can infer which genes are disease risk factors in which specific cell types. We are also interested in analyzing other functional genomics data such as protein expression data and chromatin accessibility data, in order to gain new insights into genomic regulation and dysregulation in disease.
Prerequisites: Knowledge of R or python, knowledge of command line (Unix).
Website: https://www.amariutalab.org

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: http://goren-lab.github.io

Kay Tye
The Tye Lab employs a multi-disciplinary approach including optogenetic, in vivo and ex vivo electrophysiological, pharmacological and imaging techniques to find mechanistic explanations for how emotional and motivational states influence behavior, in health and disease.
Prerequisites: Optics or Computational skills a plus.
Website: https://tyelab.org/

Chengbiao Wu
Program: Neurodegenerative Diseases
Lab/Website: The Wu Lab 
https://iem.ucsd.edu/researchers/people/profiles/chengbiao-wu.html

Joseph Herdy
Program: Laboratory of Genetics
Lab: Gage Lab
https://www.cbs8.com/article/news/local/scientists-new-findings-could-lead-to-cure-for-alzheimers-disease/509-b08d9fac-a077-4a20-85fc-6b61ea176a9a

Paula Desplats
Program: Neurosciences
Lab/Website: https://profiles.ucsd.edu/paula.desplatsdegiaconi

Huilin Zhou
http://huilinzhoulab.org
Prerequisites: Prior knowledge of general chemistry and biology.
Website: http://huilinzhoulab.org

Jacques Verstraete
Program: Combinatorics
Lab/Website: https://math.ucsd.edu/people/profiles/jacques-verstraete