2024 MSI STEM Faculty Mentors
Dr. Heather Bradshaw
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
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
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
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
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
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
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
Chemistry
Campus location: Bloomington
Research Area: Physical Chemistry
Research Link: https://jarrold.lab.indiana.edu/
Research Area keywords: negative ion spectroscopy and reactivity
Research Description:
Dr. Travis Jerde
Pharmacology
Campus location: Indiainapolis-IUPUI
Research Area: Prostate inflammation, BPH Cancer
Research Link: https://medicine.iu.edu/faculty/20950/jerde-travis
Research Area keywords: inflammation, cytokines, BPH, growth, prostate
Research Description: Dr. Jerde's research and professional interests center upon understanding inflammation and how chronic inflammation promotes adult diseases including hyperplasias and cancers. Because inflammation by its nature is regulated by cell-to-cell communication between inflammatory cells and the resident cells of the tissue, Dr. Jerde's expertise resides in the mechanistic study of cellular signal transduction mechanisms. Dr. Jerde's career goals include developing novel therapies for chronic proliferative diseases of the urinary tract including Benign Prostatic Hyperplasia (BPH), prostate cancer, and bladder cancer. Dr. Jerde's teaching efforts similarly center on signal transduction mechanisms and inflammation.
Dr. Lei Jiang
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
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
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
Research Description:
Dr. Bohdan Khomtchouk
BioHealth Informatics
Campus location: Indianapolis
Research Area: Cardiology
Research Link: https://luddy.iupui.ed/contact/profile/bhodan-khomtchouk
Research Area keywords: cardioinformatics, biostatistics, genomics, drug discovery, AI/machine learning
Research Description: Are you passionate about genomics, big data, drug discovery, and AI/machine learning? Interested in advancing cutting-edge multi-omics research to explore genetic and biomolecular mechanisms underlying heart disease, with the ultimate goal of contributing to innovative treatment strategies? Did you know that cardiovascular disease is the leading cause of death worldwide, causing over 17 million deaths per year, with a disproportionally negative impact on racial/ethnic groups historically underrepresented in the US healthcare system? Apply now to work together with computational experts and teams of research scientists to design and implement new approaches to analyzing human biomedical datasets and driving discoveries in public health to uncover novel biological mechanisms and insights into heart health and disease.
Dr. Ehren Newman
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. Kwangsik Nho
Campus location: Indianapolis
Research Area: Integration of multi-omics data with multimodal neuroimaging data for Alzheimer’s disease
Research Link:
https://medicine.iu.edu/radiology/research/neuroimaging
Research Area keywords: human genomics, multi-omics, bioinformatics, Alzheimer’s diseae
Research Description:
To identify functional molecular signatures and pathways that increase the mechanistic understanding of Alzheimer's disease (AD) by bioinformatics approaches in order to analyze multi-omics data (genome, transcriptome, proteome, metabolome) and AD biomarkers measured from multimodal neuroimaging (MRI, PET).
Dr. Travis O'Brien
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
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. Hanxiang Peng
Statistics
Campus location: Indiainapolis-IUPUI
Research Area: Big Data Analysis, High Dimensional Statistical Inference
Research Link: TBD
Research Area keywords: Massive data, high dimension, robust statistics, correlated data
Research Description: I study how to choose a subsample from a massive dataset as a surrogate to conduct the statistical analysis. I also investigate how high dimension affects parameter estimation.
Dr. Austin Robinson
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 have an ongoing study focused on sleep extension and cardiometabolic health in young adults who have poor sleep. We could use assistance with analyzing habitual diet data from 3-day food and fluid diaries and from an ad libitum Chick-fil-A meal collected both before and after the 2-week sleep extension period. Our student will receive training on nutrient analysis software from a registered dietitian. This would be the student's main project: to determine whether sleep extension improves habitual diet choices and appetite regulation. Our student would also 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 1) counterstrategies to offset the negative effects of high dietary salt (e.g., administering a ketone monoester supplement) and 2) the effects of a mitochondrial antioxidant (MitoQ) on cardiovascular health in older adults. 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
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. Titus Schleyer
School of Medicine
Campus location: Indianapolis
Research Area: Biomedical informatics
Research Link: https://medicine.iu.edu/faculty/5163/schleyer-titus
Research Area keywords: Climate, science, health, informatics, public and population health, clinical informatics
Research Description: We are looking to analyze the impact of changes due to global warming on human health. For instance, we will be conducting a study on the effects of the Canadian wildfire smoke (June 2023) on respiratory and other diseases.
Dr. Patricia Silveyra
Environmental 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
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. Yuichiro Takagi
Structural Biology
Campus location: Indiainapolis-IUPUI
Research Area: Structural biology and drug discovery
Research Link: https://twitter.com/LabTakagi
Research Area keywords: cryo-EM, transcription, structural biology, drug discovery
Research Description: Structural biology and drug discovery of molecular machines by cryo-electron microscopy (Cryo-EM).
Dr. Haixu Tang
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
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. Juexin Wang
Bioinformatics
Campus location: Indianapolis
Research Area: Unlocking the Secrets of Disease Developments: Explore Spatial-Temporal Cellular Patterns
Research Link: https://luddy.iupui/edu/contact/profile/juexin-wang
Research Area keywords: spatial omics, machine learning, bioinformatics
Research Description: Emerging spatial omics provide unprecedented cellular and subcellular resolution to track the development of complex diseases such as cancer and Alzheimer’s disease. Modeling the progression of disease development using computational approaches can help to understand the biochemical and biophysical mechanisms underlying these diseases. In this project, students will be coding to analyze the spatial-temporal patterns of disease development. Participants will have an immersive experience in bioinformatics research with cutting-edge data science and biomedical technologies, from data retrieving, data preprocessing, to mathematical modeling, and bioinformatical analyzing.
Dr. XiaoFeng Wang
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
Physics
Campus location: Bloomington
Research Area: Condensed Matter Physics
Research Link:
Research Area keywords: Material Properties
Research Description: Material Science
Dr. Jian Xie
Materials and Energy
Campus location: Indiainapolis-IUPUI
Research Area: advanced battery, fuel cells, carbon capture, and nanomaterilas
Research Link: http://et.engr.iupui.edu/~jianxie/index.htm
Research Area keywords: battery, fuel cell, CO2 emission,
Research Description: Developing new materials, devices and investigate the properties.
Dr. Da Yan
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. Yan Yu
Chemistry
Campus location: Bloomington
Research Area: Biomaterials and immune cells
Research Link: https://yu.lab.indiana.edu/
Research Area keywords: Bioanalytical chemistry, Biomaterials
Research Description: We employ nanotechnology to understand and engineer cell functions. We design novel nanomaterials, use them to elucidate interactions at the nano-bio interface, and then translate the fundamental knowledge into developing new therapeutic materials.
Dr. Shixiong Zhang
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
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.
Dr. Joshua Ziarek
Molecular Life Sciences
Campus location: Bloomington
Research Area: Characterization of G protein-coupled receptors
Research Link: www.ziareklab.com
Research Area keywords: drug discovery, biophysics, structure, G protein-coupled receptors (GPCRs)
Research Description: The majority of elicits substances (marijuana, opiods, cocaine) interact with GPCRs. The goal of our research is to understand the molecular mechanism of these interactions to combat substance abuse as well as develop drugs with improved properties.
External link to partner DataWiz Faculty Mentors:
https://datawiz.iupui.edu/faculty.html