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STARS 2019 - Research Project Descriptions

The following UC San Diego faculty members have offered to host STARS students in Summer 2019. Identify the department and three faculty mentors with whom you would like to do research with.  Describe your research interests for your selection in the online application.
***This page is subject to change. Please check for updates prior to submitting your application***

Biological Sciences – Cell and Developmental Biology

Eric Schmelz
The Schmelz laboratory has a research focus on biochemical mechanisms that mediate crop plant defenses against insect and pathogen attack. The first step in activation of defenses is immune recognition of pests, often enabled by specific, germline-encoded receptor proteins. While many receptors for pathogens have been identified, receptors for insects (e.g. Lepidopteran caterpillar larvae) have remained unknown. Schmelz’s research has recently identified candidate receptor genes specific to legumes which are predicted to detect defense elicitors, termed inceptins, found in the oral secretions of insect herbivores. Using newly available crop genomes, orthologous receptor genes have been cloned from legume species in the family Phaseoleae including dry beans (Phaseolus vulgaris), black eye peas (Vigna unguiculata) and mung beans (Vigna radiata), all species which naturally ward off herbivorous pests. In the wild, induced defenses can be directly toxic or indirectly defend against herbivores, e.g. induced volatiles serve as the plant’s ‘cry for help’ by acting as reliable host location signals for predators, parasitoids, and other natural enemies. A STARS summer student will be involved with understanding the maize disease processes instead of bean perception of caterpillars.
Prerequisites: None
Website: https://biology.ucsd.edu/research/faculty/eschmelz

 Julian Schroeder
Julian Schroeder is a distinguished Professor in Plant Sciences. His research is directed at discovering the responses of plants to drought and climate change. His focus is in discovering the signal transduction mechanisms and the underlying signaling networks that mediate resistance to environmental stresses in plants, in particular drought and CO2 responses 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 maintaining crop growth and food production to meet 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 biological 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 recent research advances are being used in the biotechnology industry with the goal of enhancing stress resistance of plants and crop yields.
Prerequisites: Students are trained with laboratory techniques and the lab works with students to learn new techniques independent of previous experience.
Website: http://www-biology.ucsd.edu/labs/schroeder

Biological Sciences – Ecology, Behavior, and Evolution

Sergey Kryazhimskiy
Sergey Kryazhimskiy is an Assistant Professor for the department of Ecology, Behavior, and Evolution. Plants have transitioned into the era when a single species (Homo-sapiens) massively alters ecosystems, genetically engineers other species and even starts to create new species. All these environmental changes exert enormous and extremely poorly understood pressures on many organisms to evolve and adapt. This is especially true for microbes, many of which adapt extremely rapidly and sometimes cause unanticipated and catastrophic situations (think of "superbugs" that are resistant to all known antibiotics). His lab is interested in understanding, predicting and, in long run, manipulating evolutionary responses of microbial populations and microbial communities. To do that, they study how bacterium Escherichia coli, yeast Saccharomyces cerevisiae, and alga Chlamydomonas reinhardtii evolve in the lab. In one project, a STARS student will try to understand the co-evolution in a microbial community.
Prerequisites: General understanding of evolutionary theory; ability and desire to do laboratory experiments.
Website: http://sklab.science/

Biological Sciences – Neurobiology

Cory Root
Cory Root is an Assistant Professor for the department of Neurobiology. He studies sensory systems that detect features of the external world, which are represented in the activity of ensembles of neurons in the brain. His lab seeks to understand how sensory information is represented in the brain and how internal representations acquire meaning that can be used to inform behavior. For his project students will focus on the neural control of mouse olfactory behaviors. Students who decide to participate in this project must not have a problem handling and sacrificing mice.
Prerequisites: Basic knowledge of Neurobiology and/or animal behavior.
Website: http://labs.biology.ucsd.edu/root

Chemistry and Biochemistry

Alina Schimpf
Alina Schimpf is an Assistant Professor with research interest in Spectroscopy, Inorganic Chemistry, Nanoscale Materials. A STARS student will study the assembly of metal oxide frameworks from molecular clusters and metal cations.
Prerequisites: None
Website:schimpflab.ucsd.edu

Guy Bertrand
Guy Bertrand is a chemistry professor currently researching the synthesis of novel stable carbines. Phosphorus is vital not only for food production but also for other agricultural commodities such as ethanol, biofuels, and any bio-renewable chemicals. The annual worldwide production of elemental phosphorus reaches 850,000 tons, from which 18% is transformed by addition of chlorine gas into 700,000 tons/year of PCl3, the industrial precursor to most phosphorus derivatives. Significant environmental risks are involved in the preparation and transport of PCl3; it is highly reactive to atmospheric moisture, and has to be transported in lead-lined, glass-lined or nickel vessels. Lastly, its transformation into the desired chemicals produces an enormous amount of waste and is energy-inefficient. From this short analysis, it can be concluded that it is of utmost importance to discover environmentally sustainable PCl3 alternatives, which allow for the preparation of a variety of phosphorus derivatives. There has been an intense research effort towards the design of molecular catalysts, based on early and late transition metals, as well as on main group elements that could allow for the reaction of elemental phosphorus with organic substrates to form organophosphorus derivatives.  Unfortunately, decades of unsuccessful attempts indicate that the design of catalysts for the one-step transformation of elemental P into valuable organophosphorus compounds is likely unrealistic. As multi-step synthesis appears unavoidable, Bertrand proposes to develop molecular bricks, whose preparation, storage, shipping, and handling are significantly more tolerable than PCl3.The student will learn to synthesize and handle air sensitive chemicals, and will become familiar with different analytical techniques such as NMR and X-ray crystallography.
Prerequisites: Have taken organic chemistry classes.
Website: http://bertrandgroup.ucsd.edu

Cellular and Molecular Medicine

Gene Yeo

Gene Yeo is an Associate Professor of Cellular and Molecular Medicine. A major focus of the Yeo laboratory is an interest in understanding how gene expression is controlled at the RNA level to maintain proper functioning of cells during development and aging. The STARS student will study stem cell models of neurodevelopmental and neurodegenerative diseases.
Prerequisites: Must be okay with lentiviral work; basic molecular biology and cell culture laboratory skills essential, Python desired but not required.
Website: yeolab.github.io

Cognitive Science

Drew Walker
Drew Walker is an Assistant Professor in the Cognitive Science department. She is interested in Social cognition; teaching and learning. For her project students will be exploring questions in visual and/or social cognition.
Prerequisites: None
Website: None

Jacobs School of Engineering (JSOE) - Bioengineering

Francisco Contijoch
Francisco Contijoch is an Assistant Adjunct Professor of Radiology. His research develops novel medical imaging techniques to improve our understanding of cardiovascular physiology, improve diagnosis of patients, and help monitor disease progression and responses to treatments. He recently developed a technique to measure regional myocardial function in a novel way and is interested in comparing the results of this technique with other standard measures of function. The student would measure both new and standard measures of function and explore the potential of the method to improve clinical care. The datasets will include patients with normal function as well as patients with a variety of cardiovascular diseases including congenital heart disease, pulmonary hypertension, and heart failure. This project could advance our understanding of these diseases as well as a result in a new way for clinicians to evaluate their patients. The student will be exposed to cardiovascular medical imaging techniques, computer programming, and image analysis tools.
Prerequisites: Preference for students with some programming experience (python, java, or Matlab).
Website: Contijoch.ucsd.edu

 Robert Sah
Professor Sah's goal is to pave the way for successful tissue-engineered total joint replacement for people who suffer cartilage damage due to injury or aging. The student will research Cartilage Tissue Engineering: Formation, Maintenance, Deterioration, Repair, Regeneration, and Restoration of the Skeleton. Has a group of PhD students who are starting to move along well in their projects, and will all be ready to mentor undergraduate students in the summertime. For most, students majoring in Science or Engineering would be best. There is space for technically oriented art majors (or something like that).
Prerequisites: Majoring in Science, Engineering, and Art
Website: cte.ucsd.edu

Jacobs School of Engineering (JSOE) - Computer Science and Engineering

Vineet Bafna
Professor Bafna is a Professor with expertise in Bioinformatics. He has many projects in 'personalized genomics', relating to the mining of genetic information to better inform about diseases (human cancer), and genetic health.
Prerequisites: The students must be comfortable in Python. If interested in web development, they should be comfortable with JavaScript. Knowledge of algorithms, machine learning is a bonus.
Website: http://www-biology.ucsd.edu/labs/schroeder

 



Jacobs School of Engineering (JSOE) - Electrical and Computer Engineering

Tina Tse Nga Ng
Tina Tse Nga Ng is an Associate Professor in Electrical and Computer Engineering. Her project aims to develop short-wavelength infrared photo sensors by using a new generation of narrow bandgap conjugated polymers. The polymer semiconductors are processed by solution processing techniques and allow printing deposition to bypass the limitations in conventional devices. The proposed research will involve fabrication of photosensors and device characterization to identify the fundamental constraints in the charge generation processes as polymer band gaps are reduced. The resulting knowledge will be applicable not only to infrared sensing applications but also to other areas including photovoltaics and optical communications, and will be essential to theoretical efforts to rapidly predict better photo-active polymers.
Prerequisites: Must have taken classes in physics or learned about semiconductors.
Website: http://flexible-electronics.ucsd.edu/

Jacobs School of Engineering (JSOE) - Mechanical and Aerospace Engineering

David Saintillan
David Saintillan joined the University of California San Diego in 2013 as a Professor in Mechanical and Aerospace Engineering. His research centers in the study of fundamental fluid mechanic problems involving complex fluids and complex flows, typically on small scales. His research group uses a combination of modeling theory, and numerical simulations to study the dynamics and properties of flows involving a microstructure suspended in and interacting with a viscous fluid, as arise in many biophysical, environmental, and technological processes. The exact duties of the student will be determined by Prof Saintillan.
Prerequisites: Undergraduate calculus, and basic knowledge of Matlab
Website: http://stokeslet.ucsd.edu

Joanna McKittrick
Professor Joanna McKittrick's research is concerned with understanding the structure and mechanical properties of biological materials (e.g. bone, teeth, mollusk shells). Student will study structural biological materials and development of bioinspired materials.
Prerequisites: Have taken general physics, math and chemistry classes
Website: CB3M.ucsd.edu

Jorge Cortes
Jorge Cortés is a Professor with the department of Mechanical and Aerospace Engineering. He works 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. His lab focuses on deployment of heterogeneous robots including ground vehicles and aerial vehicles. They 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, human-swarm interaction mechanisms that enable rapid deployment of robot swarms, and design and instrumentation of small ground and aerial robots.
Prerequisites: Experience with open source software and programming (python/C++) in general.
Website: http://carmenere.ucsd.edu/jorge/

Nicholas Boechler
Nicholas Boechler is an Assistant Professor in the Mechanical and Aerospace Engineering department studies materials and its properties. Throughout history, discoveries of materials with new properties have enabled significant technological leaps. Within this context, using a combined experimental, computational, and analytical approach, Boechler strives to uncover new understanding that enables the design of materials with extraordinary properties. Currently, he is focused on materials wherein new mechanical properties are achieved by manipulating the propagation of stress waves via designed microstructure and strong nonlinearities, and has particular interest in the dynamics of self-assembled systems. Students will study and design materials with new properties, particularly under dynamic mechanical loading.
Prerequisites: None
Website: http://boechler.ucsd.edu

Literature

Ameeth Vijay
Ameeth Vijay is an Assistant Professor of Literature, Modern and Contemporary Global Literatures in English. His research examines the intersections between literature, urban planning and geography in order to track the persistence of colonial relationships in the development of contemporary spaces, including in global cities. Methodologically, He studies not only literature but historical materials, planning documents, environmental assessments, and urban aesthetics to theorize the development of colonial and neocolonial relations. He would like to extend the scope of his region to study the Los Angeles and San Diego/border regions as key sites of urban development and thus metonymic for all global cities.
Prerequisites: Need a student both familiar with the cultural history of Southern California and familiar with the techniques and disposition of literary studies and critical theory to aide in this research. Research in the humanities addresses critical and timely issues pertaining to culture, politics, and aesthetics.
Website: https://literature.ucsd.edu/people/faculty/avijay.html

 

Medicine

Alon Goren
Alan Goren is an Assistant Professor in the department of Medicine. His lab focuses on epigenomic mechanisms, and merges basic biology, technological innovations and computational analyses. His major interest is in developmental-epigenomic questions. Both DNA sequence and the organization of DNA associated proteins are transmitted during cell divisions. This organization is disrupted during the cell cycle, and the original structure of chromatin must be restored after each cell division, a process termed ‘epigenetic memory’. This project, in collaboration with the Simon lab, focuses on the mechanisms that provide cellular epigenetic memory. They merge cell cycle synchronization methods, automated ChIP-seq and computational framework to model temporal dynamics of CRs and histone modifications during the cell cycle and predict critical regulators of cell cycle epigenomic maintenance. Students will functionally evaluate these predictions using an inducible degradation system to perturb specific CRs and then follow the dynamics of the histone modifications in the perturbed cells.
Prerequisites: Knowledge of chromatin biology (e.g., ChIP-seq) and/or computational approaches for analysis of genomic datasets (command line tools and e.g. peak calling algorithms).  
Website: https://goren-lab.github.io/index.html

Dan Kaufman
Dan Kaufman is a Professor in the Division of Regenerative Medicine. He is currently the Director of Cell Therapy at University California San Diego. His project will focus on blood and immune cell development from human pluripotent stem cells.
Prerequisites: Students must have specific interest and knowledge about the research in his lab.
Website: kaufmanlab.ucsd.edu

John T. Chang
Dr. John Chang studies the cellular and molecular mechanisms underlying Tlymphocyte fate specification. In particular his laboratory is interested in molecular regulation of CD8+ T cell differentiation & cell polarity as a central theme in regulating the fate and function of a wide range of cell types across many different organisms. They are interested in how rare progenitor cells continually produce terminally differentiated cells while also preserving a self-renewing lineage. The goal of their research is to understand how T cells use asymmetric cell division to balance the demands of terminal differentiation and self-renewal, using cutting-edge methods including immunofluorescence microscopy, animal models of infection and autoimmunity, multi-color flow cytometry, and single-cell RNA sequencing techniques. The importance of the work is that defining the mechanisms regulating asymmetric cell division will contribute to their understanding of a multitude of diverse processes, including embryonic patterning, organ formation and function, stem cell and tissue regeneration, immunity, and cancer.   
Prerequisites: Must be willing to work with mice; interested in immunology
Website: https://changlab.ucsd.edu

Kim Barrett
Kim Barrett is a distinguished professor in the department of Medicine. Her project is based on the study of intestinal epithelial physiology to understand the mechanistic basis of various diarrheal diseases.
Prerequisites: Life sciences or chemistry major
Website: profiles.ucsd.edu/kim.barrett

 

Neurosciences - Institute for Neural Computation (INC)

Leanne Chukoskie
Leanne Chukoskie is a Neuroscientist who has worked at the interface of multiple other disciplines -- from engineering to education -- to engage technology for assessment and intervention of eye and body movement differences in children with learning and developmental disorders. The Research for Autism and Development Laboratory and the Power of NeuroGaming Center (at the Qualcomm Institute) seek to develop and test game-based therapeutics and assessments that address specific challenges that are commonly observed in different neurodevelopmental disorders.  Our gaze-driven games train attention orienting skills are the subject of an NIH-funded clinical trial. The student will help develop and test video games for assessment and intervention in different populations, such as individuals with autism.
Prerequisites: Must be able to work with children and good with technology-- coding preferred.
Website: radlab.ucsd.edu; pong-center.ucsd.edu

Political Science

Erik Gartzke
Professor Gartzke studies the impact of information on war, peace and international institutions and he is in charge of the Center for Peace and Security Studies (CPASS).  CPASS supports and monitors funded research, graduate training, and campus outreach at UCSD in the subject of peace and international security. It currently has projects on new modes of deterrence (gray zone, cross-domain) and emerging modes of conflict (cyber, space, UAVs). They are eager to integrate students into their research agenda and can offer opportunities to work on one of several projects in these substantive areas. For example, an ongoing project involving students seeks to assess the ways in which officials choose the types of actions to threaten or employ in crises and conflict situations.
Prerequisites: Preferred political science, computer science/applied mathematics background, but open to all interested students
Website: cpass.ucsd.edu

Psychology

Adena Schachner
Adena Schachner is an Assistant Professor whose research explores how children and adults reason about the social world, with a particular focus on links between music and social cognition. The Mind and Development Lab investigates children's social and cognitive development. They are interested in how infants and children learn about their social world, by making inferences about the hidden contents of others' minds (like goals, preferences, or beliefs). In particular, they are currently studying how infants, children and adults understand other's intentional actions, and reason about the objects they own and create. Their work has also focused on music cognition, particularly the origins of our capacity to move in time with a beat. Student researchers may be involved with data collection (including recruiting and conducting studies with families of infants, children, and adults), data coding and analysis, weekly lab meetings and reading group.
Prerequisites: Preference for students who can program and code websites, and/or students who can work with young children.
Website: madlab.ucsd.edu

David Barner
Professor David Barner is interested in language, thought, and conceptual development, and studies case studies like number, time, space, and logical reasoning. The Language and Development Lab is interested in how children learn language and develop an understanding of objects and events in the world. Current research projects in the lab investigate a broad range of topics, from how children acquire words and concepts about logic, number, color, and time, to how children make pragmatic inferences in conversation. Summer research students will have the opportunity to work on an existing project under the supervision of a graduate student, postdoc, or lab coordinator. Students will run experiments in preschools, museums, or in the lab with children (e.g. 18-months-old to 5-years-old) or adult controls; enter and code data using various computer software; recruit families via phone, email and at external sites; design stimuli; and participate in weekly lab meetings.
Prerequisites: Students who are able to work with children, and have experience doing so is preferable; undergraduate linguistics or developmental psychology
Website:ladlab.ucsd.edu

Timothy Brady
Assistant Professor Timothy Brady aims to understand how the world is represented by the visual system, and how information is encoded and integrated into memory. His 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 we have a working memory capacity of 7+/- 2). When you are asked to remember a property of a visual object (e.g., what color was that car you saw?), how much does holding it in mind for a longer time hurt your memory? Does your memory get worse primarily because all of your memories get noisier and less precise or because some memories are lost completely but others are preserved almost perfectly? The STARS 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 programming in MATLAB; run people in experiments; and learn to analyze the data in Excel and MATLAB. The experiments will vary from simple examinations of memory precision to questions about what memory looks like when people have false memories.
Prerequisites: MATLAB experience is a plus but not required. Experience running psychology experiments is a plus.
Website: http://bradylab.ucsd.edu

Viola Stormer
Viola Stormer is an Assistant Professor in the Psychology department. Her lab is interested in understanding the cognitive and neural mechanisms of visual attention and multisensory processing. Her research is focused on the question of how attention helps us select and process information efficiently. Furthermore, she is interested in the role of attention in integrating events from different sensory modalities (sight, sound, touch). She uses both behavioral and electrophysiological methods to study these questions in healthy human participants. This summer STARS project will focus on examining how visual and auditory attentions intersect. As a student researcher, you’ll get to do some programming in Matlab, run participants in both behavioral and electrophysiological (EEG) experiments, and analyze data in Excel and Matlab. You will work closely together with the PI and a PhD student.
Prerequisites: Have taken general psychology classes; great if matlab experience (not required though).
Website: http://stoermerlab.ucsd.edu/

Caren Walker
The Early Learning & Cognition Lab, under the direction of Dr. Caren Walker, seeks to understand how children build early theories and learn and reason about the causal structure of the world. They use a model of the child as a "scientist," forming implicit hypotheses and then testing and rationally revising those hypotheses based on incoming evidence. Although children are excellent at scientific reasoning in informal learning contexts, they often find explicit scientific inquiry skills in formal pedagogical contexts quite difficult. Our current line of work explores a variety of techniques in order to facilitate these early skills. All studies will take place in the context of short games, designed to be engaging for young children (between the ages of 1 and 8).
Prerequisites: Some experience with psychology, cognitive science, or a related field. Student must have experience working with children (formally or informally).
Website:elclab.ucsd.edu

 

Pathology

Jonathan Lin
Jonathan Lin, a Professor in the Pathology department studies Tauopathies. They are devastating neurodegenerative diseases that include Alzheimer’s disease, Progressive Supranuclear Palsy, and Chronic Traumatic Encephalopathy. Recent studies have identified a novel gene, EIF2AK3/PERK, as being a risk factor in patients with tauopathies.  The EIF2AK3/PERK gene encodes a kinase with numerous coding and non-coding variants in the human population.  Several of these EIF2AK3/PERK variants are associated with increased risk for tauopathy, but the function of these variants and how they cause neurodegeneration are unknown.  The goal of the STARS project is to test the function of human EIF2AK3/PERK alleles in cells obtained from patients with tauopathies. The student will use stem cell, molecular, and biochemical approaches to identify differences between EIF2AK3/PERK alleles. These studies will reveal how EIF2AK3/PERK contributes to neurodegeneration and may lead to development of novel therapies to prevent disease based on targeting this kinase. Essentially the student will research diseases of the eye and brain.
Prerequisites: None
Website: https://profiles.ucsd.edu/jonathan.lin