2025 MSI STEM Faculty Mentors
Dr. Heather Bradshaw
Email: hbbradsh@iu.edu
Neuroscience
Campus location: Bloomington
Research Area: Endocannabinoids and endogenous lipids in the CNS
Research Link: https://c3a.indiana.edu/
Research Area keywords: endocannabinoids, cannabis, mass spectrometry, lipid signaling
Research Description: We use mass spectrometric techniques to study lipid signaling molecule regulation in a variety of disease and drug abuse models.
Dr. Drew Capone
Email: dscapone@iu.edu
Environmental & Occupational Health
Campus location: Bloomington
Research Area: Flies as Biological Sensors of Terrestrial Fecal Contamination
Research Link: https://caponelab.publichealth.indiana.edu/projects/index.html
Research Area keywords: sanitation, health, enteric pathogens, fecal source tracking
Research Description: Flies act as nature's composite samplers, eating feces and drinking water from the environment. The summer research student will assist with nucleic acid extractions and run PCR for fecal source tracking markers from flies previously captured in Bloomington.
Dr. Kay Choi
Email: kaychoi@iu.edu
Biochemistry
Campus location: Bloomington
Research Area: RNA vs RNA Structure and Function
Research Link: https://mcb.indiana.edu/about/faculty/choi-kay.html
Research Area keywords: biochemistry, structure, RNA, protein, biochemistry, small molecule inhibitors
Research Description: Many RNA viruses, such as dengue, Zika and West Nile viruses, pose significant threats as emerging diseases and potential bio-terror agents. The goal of Choi laboratory is to obtain structural and biochemical information on every step in the virus life cycle, including interaction of virus with receptors, genome release, genome synthesis by the viral replication complex, and virus assembly. Such information will be used for the design of antiviral therapeutics. STEM summer students will learn basic techniques to purify viral proteins and RNA and determine protein-RNA interactions using biochemical and biophysical methods.
Dr. Jonathon Crystal
Email: jcrystal@iu.edu
Neuroscience
Campus location: Bloomington
Research Area: Animal Models of Memory
Research Link: https://compcogn.sitehost.iu.edu/
Research Area keywords: episodic memory, Alzheimer’s disease, animal models
Research Description: Research in our lab focuses on developing animal models of memory. We are particularly interested in human diseases of memory. The big disease of memory is Alzheimer's disease, and the most debilitating aspect of Alzheimer's is a profound impairment in episodic memory. Consequently, we have developed a number of approaches to model episodic memory in rats. Ultimately, our approach may enable the testing of novel therapeutics that specifically target the decline in episodic memory.
Dr. Allison David
Email: allison@iu.edu
Epidemiology & Biostatistics
Campus location: Bloomington
Research Area: Program in Neuroscience
Research Link: https://publichealth.indiana.edu/research/faculty-directory/profile.html?user=allison
Research Area keywords: methods, statistics, mathematics, rigor, transparency
Research Description: Methods, statistics, mathematics, rigor, transparency.
Dr. Amar Flood
Email: aflood@iu.edu
Chemistry
Campus location: Bloomington
Research Area: Solar Energy Harvesting
Research Link: https://smiles.iu.edu/
Research Area keywords: solar energy, crystals, materials, organic molecules
Research Description: We are making materials that can capture light.
Dr. Roger Innes
Email: rinnes@iu.edu
Genomics, Cell and Developmental Biology
Campus location: Bloomington
Research Area: Plant Molecular Biology
Research Link: https://biology.indiana.edu/about/faculty/innes-roger.html
Research Area keywords: plant-microbe interactions
Research Description: We study how plants defend themselves against infection by disease causing organisms.
Dr. Caroline Jarrold
Email: cjarrold@iu.edu
Chemistry
Campus location: Bloomington
Research Area: Physical Chemistry
Research Link: https://jarrold.lab.indiana.edu/
Research Area keywords: negative ion spectroscopy and reactivity
Dr. Lei Jiang
Email: jiang60@iu.edu
Computer Engineering
Campus location: Bloomington
Research Area: Hardware design
Research Link: www.jianglei.org
Research Area keywords: machine learning accelerator
Research Description: Designing low-power hardware accelerators for machine learning applications.
Dr. Blair Johnson
Email: bj33@iu.edu
Exercise Physiology
Campus location: Bloomington
Research Area: Environmental Physiology and Physiological Consequences of Head Trauma
Research Link: https://publichealth.indiana.edu/research/faculty-directory/profile.html?user=bj33
Research Area keywords: cold stress, heat stress, subconcussive head impacts, concussion, autonomic nervous system
Research Description: Our research is focused in two areas: 1) environmental physiology and 2) the physiological consequences of head trauma. Within our environmental physiology focus, we are interested in: 1) improving thermal resilience during extreme cold by activating physiological mechanisms and 2) using environmental stimuli to improve physiological function and health. Within our physiological consequences of head trauma, we are interested in determining: 1) whether subconcussive head impacts influence autonomic regulation of the circulation and cerebral vascular function and 2) whether concussion injuries influence autonomic regulation of the circulation and cerebral vascular function.
Dr. Jay Lennon
Email: lennonj@iu.edu
EEB and Microbiology
Campus location: Bloomington
Research Area: Microbial ecology and evolution
Research Link: https://microbes.sitehost.iu.edu/
Research Area keywords: dormancy, biodiversity, climate change
Dr. Ehren Newman
Email: ehnewman@iu.edu
Neuroscience
Campus location: Bloomington
Research Area: Neurobiology of navigation and memory
Research Link: https://memlab.sitehost.iu.edu/
Research Area keywords: behavior, physiology, health, AI, cognition
Research Description: My lab studies how neural circuits and their physiology enable spatial memory. We use a wide variety of methods including behavioral analysis in rats, electrophysiology, optogenetics, pharmacology, and others.
Dr. Travis O'Brien
Email: obrienta@iu.edu
College of Arts and Sciences
Campus location: Bloomington
Research Area: Extreme Weather and Climate Change
Research Link: https://cascade.lbl.gov/
Research Area keywords: extreme weather, climate change, machine learning
Research Description: The Calibrated and Systematic Characterization, Attribution, and Detection of Extremes (CASCADE; https://cascade.lbl.gov/) project focuses on four questions aimed at ultimately improving confidence in future projections of low-likelihood, high-impact (LLHI) extreme events: 1. How can new approaches –including ML-based emulation of ESMs, new model ensembles, and new experiments – suggest promising ESM development pathways for greater fidelity of simulated LLHIs? 2. How can the observational record be leveraged to improve statistical and physical understanding of LLHIs? 3. What are the sources of LLHI predictability that can provide early warning of LLHIs at seasonal to decadal timescales? 4. What machine learning and computational tools are needed to advance understanding of LLHIs? Students working on CASCADE can expect to learn how analyze extreme weather in climate datasets and use machine learning and dynamical models to simulate extreme weather.
Dr. Heather O'Hagan
Email: hmohagan@iu.edu
Medical Sciences
Campus location: Bloomington
Research Area: Cancer epigenetics
Research Link: https://ohaganlab-iu.mystrikingly.com/
Research Area keywords: epigenetics, chromatin, DNA damage, inflammation, signaling pathways
Research Description: The overall focus of the O'Hagan lab is to determine how epigenetic factors contribute to cancer initiation, progression and therapy response. We study how the acute chromatin response to inflammation and/or DNA damage results in heritable epigenetic changes during carcinogenesis. We are also interested in how altered epigenetic states promote cancer.
Dr. Austin Robinson
Email: ausrobin@iu.edu
Kinesiology
Campus location: Bloomington
Research Area: Human Performance and Physiology
Research Link: TBD
Research Area keywords: dietary salt, hypertension, health behaviors, social determinants, cardiovascular disease prevention, cardiovascular physiology, exercise physiology, nutrition
Research Description: We will accept only one student. Our student would be able to assist with completing assays in the biochemistry laboratory to measure various biomarkers in urine, serum, and plasma samples from this study and other ongoing studies in my laboratory focused on counterstrategies to offset the negative effects of high dietary salt (e.g., administering a ketone monoester supplement. Overall, the student will gain proficiency in nutrient analysis, data entry, basic data visualization (e.g., making high-quality graphs and tables), and performing laboratory assays on human biological samples. We will assist and support the student in presenting data at a scientific meeting.
Dr. Selma Sabanovic
Email: selmas@iu.edu
Informatics, Cognitive Science
Campus location: Bloomington
Research Area: Human-Robot Interaction Research Link: https://luddy.indiana.edu/contact/
Research Area keywords: social robotics, user-centered design, cultural studies of computing, assistive robotics
Research Description: I study the design, use and consequences of social robots in various contexts, including homes, schools, assistive and therapeutic applications, and interpersonal communication. She directs the R-House Laboratory for Human-Robot Interaction (HRI) research at IUB, where faculty and students come together to study the principles of human-robot interaction, and to design and evaluate robots for various applications. My collaborators and I also often work with members of the community, including older adults, caregivers, students and teachers, to identify promising uses and designs for robotic technologies that can benefit users. There are several ongoing projects in the lab. One project involves the design of communication and interaction capabilities for a new robot prototype, Haru (https://spectrum.ieee.org/automaton/robotics/home-robots/honda-research-institute-haru-social-robot), developed by Honda Research Institute in Japan. We are working with Honda to design how the robot might talk to and help people in their homes, how it can be used as a remote presence platform, as well as how it can support intergenerational interaction between adults and children. A second ongoing study involves patients and clinicians working together with researchers to design a socially assistive robot to provide support for, and as an intervention to alleviate the symptoms of, depression. For this project we focus on developing adaptive and personalizable interaction capabilities for Therabot (https://mytherabot.com), an animal type companion robot. The project will allow both patients and clinicians to customize the capabilities and behaviors of the robot in order to improve patient health and well-being. A third project involves develop the QTrobot to assist older adults to reflect on, develop, and maintain their sense of purpose and meaning and life as they age. In this project, we explore how robots can engage older adults in conversations and interactions, develop computer vision and dialogue systems that allow the robots to understand people's feelings and attitudes, and construct models of interaction that help the robots make appropriate suggestions to older adults. Research activities for students on these projects include learning how to work with, program and control robots, recruiting and scheduling participants, running participants for studies in and outside the lab, going to relevant field sites with robots to observe human-robot interaction, collecting and managing textual, audio, and video data, discussing study design, results, and implications, attending regular lab meetings, and working closely with other faculty and students engaged in the project. If you are interested in such topics, we invite you to join us in our studies.
Dr. Patricia Silveyra
Email: psilveyr@iu.edu
Environmental and Occupational Health
Campus location: Bloomington
Research Area: Air pollution effects on lung health
Research Link: http://silveyralab.com/
Research Area keywords: lung disease, lung physiology, e-cigarettes, air pollutants, inhalation toxicology
Research Description: The laboratory of Patricia Silveyra studies the cellular and molecular mechanisms underlying sex differences in lung inflammation and lung disease triggered by various environmental exposures. With an interdisciplinary focus on respiratory physiology, molecular endocrinology, and cellular and molecular immunology, the Silveyra laboratory investigates the effects of air pollutants, cigarette smoke, e-cigarettes, and other environmental exposures in the male and female lung.
Dr. Sara Skrabalak
Email: sskrabal@iu.edu
Materials Chemistry
Campus location: Bloomington
Research Area: Nanoscience
Research Link: https://skrablab.sitehost.iu.edu/ and https://csennd.iu.edu/
Research Area keywords: Nanoscience, Materials Chemistry, Energy, Chemical Sensing, Catalysis
Research Description: Students will participate in the newly formed NSF-sponsored Center for Single-Entity Nanochemistry and Nanocrystal Design, making nanoparticles for catalysis in fuel cell applications and for chemical sensing applications.
Dr. Haixu Tang
Email: hatang@iu.edu
Data Science
Campus location: Bloomington
Research Area: Bioinformatics, security/privacy, artificial intelligence
Research Link: https://luddy.indiana.edu/contact/profile/?Haixu_Tang
Research Area keywords: Computational mass spectrometry, AI security/privacy
Research Description: We are interested on developing AI models for predicting properties of small molecules from their confirmations. We will also apply these models for studying the interactions between small molecules and proteins.
Dr. Claire Walczak
Email: cwalczak@iu.edu
Medical Sciences
Campus location: Bloomington
Research Area: Cell Division and Genome stability
Research Link: https://walczaklab-iu.mystrikingly.com/
Research Area keywords: Genome stability, cancer cell biology, mechanisms to prevent anueploidy
Research Description: Our lab is interested in the fundamental mechanisms that help cells properly segregate their DNA to the daughter cells.
Dr. XiaoFeng Wang
Email: xw7@iu.edu
Security Informatics
Campus location: Bloomington
Research Area: Crosscutting, Artificial Intelligence, Data Science, Security and Privacy
Research Link: https://homes.luddy.indiana.edu/xw7/aboutme/
Research Area keywords: Big-data analytics
Research Description:
- Confidential computing for biomedical data protection: The project focuses on developing a big-data analytics framework built on Trusted Executed Environment (TEE), Intel Software Guard Extensions (SGX) in particular, and applying it to support privacy-preserving, large-scale genomic data analyses and other computing tasks. Based upon the understanding of unique performance impacts of SGX systems, including those incurred by enclave creation, management, trust establishment, cross-enclave communication and others, a new MPI-based cluster computing framework is built to automatically optimize the deployment of computing nodes across enclaves and CPU packages under resource constraints. This new framework supports a set of fundamental genomic computing tasks, ranging from reads-mapping to peptide identification, as well as machine-learning based models. Also, its potential risks, side-channel leaks in particular, are analyzed and effectively controlled to provide high privacy assurance. The work will enable broad sharing of previously inaccessible data and help drive the new insights of individualized health care. IU is taking a leading role in developing TEE-based data-in-use protection, with the recently funded NSF Center for Distributed Confidential Computing (CDCC): https://news.iu.edu/stories/2022/08/iub/releases/04-nsf-cybersecurity-awards-distributed-data-user-privacy.html, the largest NSF investment in the area. The summer intern will work with researchers on this cutting edge research direction and learn the basic technical and research skills that will help make this new innovation possible.
- Intelligent analysis and mitigation of cybercrimes: This project focuses on both criminals' communication with their targets and the underground communications among miscreants. To discover and understand illicit online activities, the research looks for any semantic inconsistency between text content and its context (such as advertisements for selling illegal drugs on an .edu domain) and for inappropriate operations being triggered (such as a malware download). Inconsistencies are captured by the Natural Language Processing (NLP) techniques customized to various security settings. Further, based upon crime-related content discovered, the project will study various machine learning techniques that support automatic extraction and analysis of threat intelligence and criminal activities. The techniques are evaluated using data collected from various sources (public datasets, underground forums and others), and the findings they make are validated through a process that involves manual labeling, communication with affected parties, and collaborations with industry partners. This work will help create in-depth knowledge about underground ecosystems and lead to more effective control of illicit operations of these online businesses. The summer intern working on the project will receive basic training on related machine learning and NLP techniques to help analyze cybercriminal activities, and help innovate the technologies that make the Internet securer.
Dr. Garfield Warren
Email: gtwarren@iu.edu
Physics
Campus location: Bloomington
Research Area: Condensed Matter Physics
Research Link:
Research Area keywords: Material Properties
Research Description: Material Science
Dr. Da Yan
Email: yanda@iu.edu
Computer Science
Campus location: Bloomington
Research Area: Data Science & Artificial Intelligence
Research Link: https://homes.luddy.indiana.edu/yanda
Research Area keywords: geospatial data mining, active learning
Research Description: Our laboratory is currently focused on training highly effective AI models for flood inundation mapping using satellite imagery. A critical initial step in developing robust models is acquiring training datasets that contain precise annotations of flood areas. While abundant data have been collected such as high-resolution optical imagery from satellites and drones (e.g., during natural disasters) and the digital elevation model (DEM) data (e.g., from United States Geological Survey), annotating such data demands significant human effort, making it a time-consuming task. We have developed a browser-based annotation software for annotating satellite images, which renders 3D terrain in real time using the WebGPU technology. Annotators can manipulate the terrain (by shifting, rotation, zoom-in and zoom-out) to locate areas covered by flood to annotate. Given a user-friendly software interface, the annotation process is easy to follow, and annotation accuracy and efficiency can be significantly improved. However, despite the advancements made, manual annotation of each satellite image using our software still requires approximately 1-2 hours per image. This bottleneck significantly limits the amount of annotated data available for training machine learning models. Our upcoming summer research project aims to address this limitation by exploring methods to expedite the data annotation process through the integration of active learning techniques into our existing annotation software. We have already developed a preliminary prototype (available for preview at https://youtu.be/x66zIMdOPkY), which we anticipate will undergo substantial refinement during the summer research project. Additionally, we plan to incorporate recent advancements in AI models tailored for satellite imagery, such as NASA and IBM's Prithvi geo-foundation model, utilizing techniques like prompt tuning and LoRA (Low-Rank Adaptation). This project will also prepare annotated datasets to better validate our machine learning models for flood inundation mapping, These datasets will be made publicly available for use by other researchers, thereby contributing to the broader scientific community.
Dr. Shixiong Zhang
Email: sxzhang@iu.edu
Physics
Campus location: Bloomington
Research Area: Quantum Nanomaterials Physics
Research Link: https://zhanggrp.physics.indiana.edu/
Research Area keywords: nanomaterials, quantum technology, synthesis, and characterizations
Research Description: Develop scanning probe microscopy techniques.
Dr. Chen Zhu
Email: chenzhu@iu.edu
Geochemistry and Hydrogeology
Campus location: Bloomington
Research Area: Climate Change Mitigation
Research Link: https://hydrogeohem.earth.indiana.edu
Research Area keywords: CO2 removal, carbo sequestration
Research Description: Use geochemistry based climate change mitigation to combat global warming. Laboratory based experiments.
Email: hlreynol@iu.edu
Biology
Campus location: Bloomington
Research Area: Ecology
Microbial Interactions and Pathogenesis
Research Description:
Our lab’s broad interests are in plant-environment interactions, with the goals of understanding the mechanisms shaping plant and microbial community composition and diversity, ecosystem functioning, and system responses to abiotic and biotic environmental changes. Within these broad areas, we are especially interested in the importance of plant-soil and plant-microbe relationships and the role of environmental heterogeneity. We work primarily with herbaceous systems (e.g. prairie, old-field, forest floor) using a combination of experimental and observational approaches.
The 21st Century has been dubbed “The Century of the Environment” in recognition of the importance of the world’s diverse ecosystems for the continued health of our society and the increasing threats that human activities pose to this relationship. Thus, we are not only interested in testing and advancing ecological theory, but also in the application of ecological knowledge to restoration and sustainable agriculture, and in educational outreach.
Education and outreach: Service-learning is a form of experiential or active learning (“learning by doing”) that involves partnerships between students and communities. In service-learning, the service is a mechanism by which students can deepen understanding of course content and its application to the “real world,” and explore their own roles and responsibilities as citizens of society. I offer several undergraduate and graduate service-learning courses (see lab website).
Other education and outreach activity includes work with the Biology Club, Volunteers in Sustainability, and the Indiana University Architect’s Office to establish green landscaping with native prairie and woodland species on campus; a research/outreach project with interdisciplinary colleagues focused on invasive species control and native plant restoration in urban woodlands; public presentations on ecological limits, the steady state economy, and the value of ecosystem services; and service on the City of Bloomington Environmental Commission (2001-2010). Promoting understanding of the environmental, social, and economic dimensions of human-environmental interactions is an important focus of my educational activities, and colleagues and I address this literacy in the volume “Teaching Environmental Literacy. Across Campus and Across the Curriculum,” featuring essays by colleagues in Biology and many other campus units.
Email: hahundle@iu.edu
Biology
Campus location: Bloomington
Research Area: Chromatin, Chromosomes, and Genome Integrity
Developmental Mechanisms and Regulation in Eukaryotic Systems
Genomics and Bioinformatics
Research Description:
RNA plays a central role in the expression of genes in all organisms. Understanding how the cell decides which RNAs to express at a given time is a fundamental question in biology. Work in the Hundley lab is centered on a conserved family of proteins, called ADARs, which can affect gene expression through both binding RNA and modifying specific nucleotides (referred to as RNA editing). Both RNA editing and RNA binding are essential functions of human ADARs and dysregulated in over 35 human diseases.
Deciphering the fundamentals of RNA recognition by ADARs: As ADARs can effectively rewrite the genetic code, the recognition of target RNAs must be tightly controlled. Work in the Hundley lab is focused on understanding the in vivo rules that govern ADAR interactions with target RNAs. We use a number of biochemical and genomic techniques to profile both RNAs bound by ADARs as well as those edited by ADARs. Recently, we have also become intrigued by how ADAR recognition of target RNAs can be influenced by changes in the environment to dynamically regulate gene expression and RNA editing.
Regulation of RNA editing: In many diseases and across human tissues during normal development, ADAR expression does not directly correlate with the extent of editing at individual adenosines. Furthermore, spatiotemporal editing patterns vary for individual genes, suggesting that specific factors bind target mRNAs to regulate editing in vivo. To date, we have demonstrated that the editing-deficient members of the ADAR family can influence substrate recognition and editing in both the model organism C. elegans and human glioblastoma (brain cancer) cell lines. Our ongoing work is focused on identifying additional proteins that regulate editing (particularly in a tissue-specific manner) as well as understanding how subcellular localization and other cellular processes (ex. transcription, RNA modification by other enzymes, etc.) alter ADAR function.
Connecting tissue-specific mechanisms of gene regulation to organismal physiology: ADARs play important roles in diversifying the transcriptome. We take advantage of the genetic amenability of the model organism C. elegans to not only monitor ADARs effects on different tissues, but also dissect the molecular mechanisms of how ADARs edit and/or bind RNA uniquely in specific tissues and connect that information to impacts on organismal behavior and/or survival. We have done extensive work on how ADARs bind and edit transcripts in the nervous system and revealed mechanisms that regulate sensing of chemicals and survival to hypoxia (low oxygen). We are also actively exploring how ADARs sense and respond to pathogen infection and impacts of ADARs on other tissues, including the germline.
Oncogenic roles of ADARs: Defects in editing are known to result in misexpression of both tumor suppressors and oncogenes in many cancer types. Our work has focused on the regulation of editing in glioblastoma, a malignant form of brain cancer. We have shown that ADAR3, a deaminase-deficient member of the ADAR family, is a key regulator of RNA editing and expression of ADAR3 is elevated in tissue isolated from glioblastoma patients. Most recently, we have demonstrated that ADAR3 expression results in a gene expression program that provides glioblastoma cells with resistance to irradiation and temozolomide, two standard-of-care therapies. Going forward, we want to understand how ADAR3 expression and activity are regulated and the molecular targets of ADAR3 in glioblastoma.
Email: jcgreave@iu.edu
Environmental Health
Campus location: Bloomington
Research Area: Environmental Microbiology and Virology
Research Description: Our lab studies viral persistence and transport in stagnant and flowing waters. We develop new methods to quantify infectious viruses then use it to understand the risk of infection to the public. Summer students will learn novel viral culture and measurement techniques and perform studies to understand flow of viruses in environmental waters
Research Link:https://publichealth.indiana.edu/research/faculty-directory/profile.html?user=jcgreave
Dr. Paul Sokol
Email:pesokol@iu.edu
Physics
Campus location: Bloomington
Research Area: Condensed Matter Physics
Research Area keywords: Quantum Liquids, Low Dimensional Materials, Neutron and X-ray scattering, Materials Properties, Synthesis and characterization
Research Description: Our work focuses on the study of the structure and dynamics of condensed matter systems under confinement at the nanoscale. Confinement in nanometer size pores or on surfaces can drastically affect the properties of confined systems ranging from classical solids to quantum liquids and can even lead to new phases not present in the bulk. We use neutron and x-ray scattering to probe the microscopic structure and dynamics of these confined systems.