The table below summarizes the research interests of the YPRI 2024 host labs. For the labs you are interested in, please carefully review the prerequisites and detailed project description listed below the table.
Blake Lab | Earth and Planetary Sciences
Prerequisites: Must have completed general chemistry coursework. Prior general chemistry laboratory experience is strongly preferred.
General Lab Description: The Ruth Blake Lab’s primary research interests are related to geochemistry (the chemical composition of natural environments) and geomicrobiology (the role of microbes in geological processes). The lab is particularly interested in the phosphorus cycle as it relates to marine sediments and terrestrial soil properties.
Project Description: The student project would aim to sequentially extract different species of phosphorus from environmental samples to better understand phosphorus release by dissolution of basalt in environmental systems. This is a critical step to uncovering the origin, fate, and cycling of phosphorus. This is important, because it allows us to better understand current and future environmental health issues, as well as look into the past environmental systems which may now be extinct.
Day-to-day Activities: Performing basic laboratory techniques and data analysis. These tasks may include developing a research question, preparing and organizing laboratory materials, performing basic clean laboratory procedures, collecting samples for the experiment, pH and phosphate measurements, centrifugation, decanting supernatant, pipetting, observing reagent preparation, and using Excel for data management and figure making.
Dixit Lab | Biomedical Engineering
Prerequisites: Knowledge of Python/MATLAB or any other programming language. Basics of probability and calculus.
General Lab Description: Our lab works on computational systems biology and biophysics. We have a small project on understanding the role of recombination in the evolution of bacterial species.
Project Description: Modeling the interplay between geographical structure and recombination in bacterial evolution.
Day-to-day Activities: Writing code to simulate a model, analyzing and visualizing model results.
Favuzzi Lab | Neuroscience
Prerequisites: No skills are required but curiosity, motivation, and a strong work ethic (responsible attitude) are needed. Coding ability in any language (especially R) is a plus.
General Lab Description: Our brain and immune system “talk” to each other (think about illnesses like COVID-19, where some patients experience brain-related issues). Our brain is like a city with neighborhoods (regions) and residents (cells) and our team wants to understand which residents are “reading” these messages from the immune system, how, and the “city-wide impact”.
Project Description: In this project, the student will start working with a condition that affects the digestive tract (colitis). Our early work has given us a lead: certain “residents” in the brain ‘light up’ and respond when the colon is upset. The student will (1) watch these brain “residents” closely, using special imaging techniques, to see how they react during colitis, (2) use computers to create a “map” of how these brain parts interact when the immune system sends messages (like plotting the busiest streets during rush hour), and (3) investigate if and how these “residents” change their connections and “conversations” when they receive these messages. This will allow us to understand why we get sick after being stressed, how being sick can affect our feelings and thoughts, or even lead to new treatments for conditions like the “brain fog” experienced in diseases like COVID-19.
Day-to-day Activities: Performing histological experiments (brain sectioning, immunohistochemistry, microscope imaging), and potentially doing some mouse work (breeding, genotyping). These experiments will be followed by analysis of images and data.
He Lab | Applied Physics
Prerequisites: A good understanding of general high school physics, math (solving linear equations), and the ability to use a computer to install software, read software manuals, and make presentation slides.
General Lab Description: We use momentum-resolved spectroscopies (imaging techniques) - photoemission, X-ray scattering, and electron diffraction - to discover, understand, and engineer the physical and structural properties of “quantum materials”.
Project Description: Angle-resolved photoemission spectroscopy (ARPES) is a powerful tool for understanding novel materials. Historically, magnetic fields have been carefully avoided as they are detrimental to the control of photoelectron trajectory during the photoelectron detection process. However, magnetic fields are important for both probing and tuning quantum materials. Recently, our lab has introduced an easily implementable method for creating a tunable magnetic field at the sample position in an ARPES experiment, and we want to analyze magnetic-field-induced artifacts in the ARPES data.
Kalogerias Lab | Electrical Engineering
Prerequisites: Math skills and Python programming (for implementation of machine learning training and testing methods) required.
General Lab Description: Our lab focuses on machine learning, optimization methods, networking and communications.
Project Description: Machine learning methods for resource allocation in wireless communications
Day-to-day Activities: Help primary mentor with experiments (coding) for an ongoing research project related to machine learning for wireless communications.
Lake Lab | Genetics
Prerequisites: Coding skills and experience with programming languages is required. Preference is to have familiarity with R, Python, and/or Bash languages. A beginner level with basic understanding of syntax and ability to write simple code is suitable.
General Lab Description: We study how genetic changes in our DNA influence health and disease. We are especially interested in a special part of our DNA called the ‘mitochondrial genome’.
Project Description: This project aims to compare mitochondrial DNA in humans with that of many other species, identifying both similarities and differences. This study of ‘evolutionary conservation’ can help us understand which genetic changes in the mitochondrial DNA could cause disease in humans.
Day-to-day Activities: This is a computational project that will involve using genetic databases, identifying species to analyze, collecting and comparing genetic data from different species, and writing code to identify similarities and differences between mitochondrial DNA in humans and other species. In addition, the student will make plots or graphs to visualize the data and the results from their analysis.
Libreros Lab | Pathology
Prerequisites: While not a strict requirement, it would be beneficial for the student to possess knowledge of coding, particularly proficiency in R. This would be applied to tasks such as generating heatmaps and conducting network analysis.
General Lab Description: Lipids and lipid mediators play pivotal roles in regulating numerous fundamental human functions. Given their essential functions, it is important to both develop and grasp quantitative methods for the identification of individual lipid species and understanding their dynamics. This knowledge is crucial for identifying their roles in maintaining human health and their implications in disruptions during illness. Our laboratory specializes in the discovery of novel lipids and lipid mediators involved in the resolution of inflammation. We are particularly interested in unraveling new biochemical pathways that regulate lipid metabolism within innate immune cells. To analyze lipid metabolism effectively, we employ a technique called QTRAP Liquid Chromatography Mass Spectrometry (LC-MS-MS). Our lab is one of the few globally equipped to identify novel lipid signaling circuits that contribute to inflammation resolution using LC-MS-MS technology.
Project Description: Leukotriene B4, a significant lipid mediator, is responsible for the excessive infiltration of neutrophils during inflammatory processes. The student will actively participate in the investigation of Leukotriene B4 metabolism in human and murine neutrophils and macrophages. We will employ state-of-the-art mass spectrometry techniques, specifically LC-MS-MS, to conduct this research. The student will conduct experiments that entail isolating both mouse and human neutrophils, incubating these neutrophils with a stimulus, and subsequently conducting LC-MS-MS analyses to investigate the metabolism of Leukotriene B4 (LTB4), a potent proinflammatory mediator.
Day-to-day Activities: The student will be engaged in fundamental laboratory techniques and data analysis. Moreover, they will have the unique opportunity to contribute to the development of a spectral library focusing on the lipid metabolism of LTB4. This will involve working with synthetic compounds to match the profiles of compounds isolated from cells. Specific tasks will include formulating research questions, organizing and preparing laboratory materials, executing standard laboratory protocols, isolating cells, performing lipid extractions, conducting centrifugation, decanting supernatants, precise pipetting, preparing reagents, and managing data using Excel. Furthermore, the student will use ChemDraw for creating chemical structure diagrams and Prism 10 for generating figures.
Prerequisites: Must have a basic understanding of molecular biology
General Lab Description: We are interested in the genetic basis of extreme biology in the immune system. For example, we are investigating why some immune cells do not have a regularly shaped nucleus and the genes involved in this biological process.
Project Description: The project will focus on genes involved in determining nuclear shape. The student will isolate these genes, and express them in the bacteria E coli (a process known as cloning).
Day-to-day Activities: Bacteria culture, and molecular biology techniques such as plasmid preparation, restriction digestion, and gel electrophoresis.
Massilani Lab | Genetics
Prerequisites: Coding in Python and R and some proficiency in the command line is preferred.
General Lab Description: We investigate the evolutionary history of modern and extinct human populations using ancient DNA. Our focus is to retrieve and sequence DNA from archaeological materials to study the peopling of the world (early human migration and settlement), the history of human health and their adaptation to different environments and lifestyle conditions.
Project Description: Our project will focus on a set of genes of the innate immune system, which constitutes the first line of defense against pathogens. We will investigate the variation of these genes across different populations and time.
Day-to-day activities: Different molecular biology techniques such as ancient DNA extraction, polymerase chain reaction (PCR), hybridization capture and library preparation for DNA sequencing. We will also do computational analyses on the sequencing data including variant calling and phylogenetic analyses.
Mayer Lab | Chemistry
Prerequisites: Prior science coursework (preferably chemistry, but not required)
General Lab Description: Research in the Mayer group spans the fields of inorganic, materials, bioinorganic, organometallic, and physical organic chemistry. Our primary focus is on redox reactions (addition or removal of electrons) that involve chemical bond formation and bond cleavage (breaking), in particular the coupled transfers of protons and electrons.
Project Description: How do reactions happen at the surface of materials on the nanoscale? What atoms/electrons are involved and where do they go? These are the questions our lab examines and will closely relate to the student project. The project will examine the conversion of molecules with different nanomaterials and observe how different additives modulate the reactivity (how quickly does it react, what bonds are being broken, etc.). The results of this project will lay a foundation for fundamental reactions at nanomaterial surfaces which could inform the development of future materials relevant for renewable energy applications or electronics.
Day-to-day Activities: Common inorganic techniques including photolysis (addition of electrons by high energy light) of colloidal nanoparticles (NPs) and observation of the reduced species by UV-visible spectroscopy, or the change in color or intensity of the NPs. For example, the NPs change from colorless to dark blue when adding electrons and protons to the material. The number of added electrons can be quantified by the “blueness” of the sample. The student will perform serial dilutions of the NP solutions and titrate them with various molecules to monitor reactivity. For example, student(s) will correlate the change in the NP color with the reactivity of different molecules. Given enough time, student(s) will be given the opportunity to have hands-on experience using stopped flow spectroscopy for reactions that occur too quickly to observe by eye (less than one second).
McDougal Lab | Biostatistics
Prerequisites: Must be able to read and write Python (for writing: comfort with variables, if statements, loops, functions, lists, and dictionaries). Familiarity with reading C or C++ is preferred. Must have an interest in the brain, but no formal neuroscience background is required.
General Lab Description: Our lab develops and studies strategies for using computers to unlock the mysteries of the brain, from simulation to machine learning. We develop methods to computationally represent, analyze and model experimental data from the brain.
Project Description: We’ll examine models from our collection of over 1,800 simulation studies of the brain to better understand how the simulation code connects to the underlying biology. By better understanding this relationship, we can choose the right model components for answering new questions and make better predictions about brain activity.
Day-to-day Activities: Significant amount of reading of both the neuroscience literature and simulation code and making notes about how they relate. Along the way we’ll discuss modeling and work together to write some small Python programs to automatically extract information.
Murray Lab | Pediatrics
Prerequisites: Prior Biology coursework is preferred. Must be able to carefully keep track of and record data from experiments in a laboratory notebook
General Lab Description: The Murray laboratory studies the disinfection of equipment used in the medical setting. Recently virtual reality (VR) equipment has been introduced to distract patients from painful procedures and reduce the anxiety and stress of hospitalization and we are studying how to clean and disinfect it between patient use.
Project Description: This is a small part of a larger CDC project on disinfection of hospital equipment. Keeping patients safe when they are in the hospital is critically important. To help ensure patients are cared for safely, hospital equipment is disinfected to prevent the spread of germs in the hospital.The optimal disinfection method for VR equipment used in healthcare is unknown. We are currently studying whether UV light is an effective disinfection method for VR equipment.
Day-to-day Activities: Daily activities include culturing bacteria and bacteriophage from Virtual Reality equipment before and after disinfection with different UV devices. The student will learn how to disinfect medical equipment and measure how effective disinfection is.
Nwanyanwu Lab | Ophthalmology
Prerequisites: Must be creative and enthusiastic about improving health in New Haven. Successful interns will have great listening skills and excel in communicating findings in written form and through oral presentations.
General Lab Description: The Sight-Saving Engagement and Evaluation in New Haven seeks to decrease preventable blindness from diabetic retinopathy through research and community engagement. Our team employs quantitative and qualitative research methods to address health disparities in diabetic retinopathy. We not only identify and contextualize health disparities; we also design sustainable community-engaged solutions along the path towards equity.
Project Description: We are developing a digital health tool for community members with diabetes. The student will help gather information and engage with community members about interventions that will help them.
Day-to-day Activities: Attending focus groups, evaluating transcripts, and helping design an in-person educational support group for community members.
O’Hern Lab | Mechanical Engineering & Materials Science
Prerequisites: Must have experience coding in Matlab, Python, or C/C++ (familiarity with vectors, operations associated with vectors, and functions). Should have taken or be currently enrolled in Physics, Calculus, and AP Statistics.
General Lab Description: The O’Hern research group carries out theoretical and computational studies of soft and biological materials. Recent work has focused on the glass-forming ability of alloys, clogging of droplets in microfluidic channels, jamming in granular materials, computational protein design and decoy detection, wound healing in epithelia, and breast cancer invasion into adipose tissue.
Project Description: We are interested in understanding how breast tumor cells invade adipose (fat) tissue. Specifically, the primary mentor aims to study how factors such as stiffness of adipocytes (fat cells), spatial distribution of various stiffness adipocytes, and tumor cell activity affect the invasion process. The intern will develop and test a computational model where adipocyte stiffness can be systematically varied.
Day-to-day Activities: Developing molecular dynamics or discrete element method simulations of the physical system and then running the simulations on Yale’s High Performance Computing Facilities. The student would then carry out analyses of the data from the simulations including correlation functions and basic machine learning methods, such as principal component and clustering methods.
Polimanti Lab | Psychiatry
Prerequisites: Strong interest in computational biology and human genetics
General Lab Description: Our overall goal is to understand how molecular and genetic information can be used to improve the healthcare of diverse populations. We are developing and applying computational approaches to investigate the molecular basis of human traits and diseases using large-scale genome-wide datasets and multi-omics information.
Project Description: The project will focus on assessing the genetic predisposition of individuals to psychiatric disorders and evaluating the shared genetic basis and effects among comorbid traits (traits that often coexist with psychiatric disorders in patients).
Day-to-day activities: Analysis of large-scale data using programming languages (e.g. Unix, R, python) and the Yale high-performance computing clusters.
Pahlavan Lab | Mechanical Engineering & Materials Science
Prerequisites: Strong physics and math background is preferred. Coding knowledge is a plus.
General Lab Description: We study how tiny particles (colloids) and bacteria move in different environments, including soil and the ocean. Our focus is on understanding how colloids and bacteria respond to nutrient gradients in these environments.
Project Description: From the spreading of microplastics to bacterial colonization of dissolving organic matter in the oceans or soil, understanding how colloids and bacteria respond to chemical gradients in such complex environments is a necessary step for predicting how processes contribute to the global carbon cycle and impact the Earth’s climate. This project will aim to advance our fundamental understanding of these processes using microfluidic experiments and numerical simulations.
Day-to-day Activities: Performing microfluidic experiments: chip fabrication, pipetting, microscopy, and processing data using MATLAB.
Qiu Lab | Mechanical Engineering & Materials Science
Prerequisites: Some familiarity with Python and the Linux command line is preferred (any level of experience is fine). Chemistry and physics coursework would be helpful.
General Lab Description: We are a computational materials science lab interested in using large scale calculations with supercomputers to predict and understand the properties of materials with applications in energy and quantum information.
Project Description: Halide perovskites are crystals with photosensitive semiconductor properties which can be used to create more efficient solar cells. Currently, we are interested in how perovskites respond to light and how atomic substitutions change the properties of perovskites. Using simulations, the student will compile information and calculate the properties of halide perovskites.
Day-to-day activities: Running simulations of material properties on a supercomputer, analyzing data, and writing data processing scripts.
Prerequisites: Experience coding in Python is preferred, but not required.
General Lab Description: Our aim is to better understand the brain using computational methods. We develop biologically inspired goal- and data- driven artificial intelligence methods to elucidate the neurodynamical basis of behavior, ranging from sensorimotor control to social behavior.
Project Description: To understand how the motor pathways in the brain interact with the body, we build computational models of neuronal networks that interact with a simulated environment of animal behavior. The student project will involve simulating this environment and exploring simulations that achieve a goal, using neural networks.
Day-to-day Activities: The techniques in the lab involve coding (usually in Python, with Jupyter notebooks).
Scassellati Lab | Computer Science
Prerequisites: We minimally expect our student interns to have a working knowledge of computer science fundamentals, be proficient in at least one programming language (preferably C++ or Python), and be able to conduct research (e.g., analyzing data, statistical reporting, professional writing ability).
General Lab Description: Our research focuses on building embodied computational models of human social behavior, especially the developmental progression of early social skills. Our work uses computational modeling and socially interactive robots in different methodological roles to explore questions about social development that are difficult or impossible to study using methods of other disciplines.
Project Description: During this internship, the student will work directly with a graduate student on a selected project. Projects include developing a robot platform that interacts with its users autonomously (focusing on children with allergies going through allergy testing) and planning robot tasks in a kitchen environment.
Day-to-day Activities: Designing a system by assembling hardware and writing code to animate the system, recruiting participants for a human-robot interaction study, collecting and analyzing data on the human-robot interaction, and documenting the interaction outcomes.
Taylor Lab | Psychology
Prerequisites: None required, but animal handling, behavioral research, and/or Python/MATLAB programming experience preferred
General Lab Description: Using rats as a model organism, we are aiming to explore the neural basis of complex social interactive behaviors in a semi-naturalistic setting and understand the neural mechanisms that govern social decision-making, ranging from antisocial to prosocial choices.
Project Description: The student’s project will focus on investigating the impact of specific variables on the social behaviors of rats during interactions that resemble game theory and social inequity scenarios. Two potential questions include: how do rats make social decisions when presented with scenarios that mimic human social dilemmas; and do certain environmental or situational factors influence the rats’ choices on the antisocial to prosocial spectrum?
Day-to-day Activities: Conducting behavioral experiments with the rats, preparing and maintaining the experimental environment to ensure data accuracy, and assisting with rodent colony management. Students with an interest or background in programming will learn to use computer vision and AI tools to analyze video recordings of the animal’s social interactions.
Townsend Lab | Biostatistics
Prerequisites: Fundamental R Studio skills, including installing packages, creating markdown files, and executing commands. Basic background in math and statistics.
General Lab Description: The Townsend Lab’s main focus is on cancer genomics, exploring the disease through the lens of DNA and RNA using evolutionary models and methodologies. While primarily a computational biology lab, it also includes a wet-lab section for conducting experiments on fungal species.
Project Description: The project will involve a detailed analysis of a cancer research paper, utilizing the lab’s innovative computational techniques. The student will analyze specific cancer genomics datasets to estimate selection intensity (why and how particular mutations are selected for in a cancer cell population) and how this gives insight into the development of cancer.
Day-to-day Activities: Studying the selected research paper and other relevant literature, running packages in R studio, interpreting results with the support of the mentor, and engaging in discussions with the mentor about the study design, scientific approach, and topics of interest.
Yale Teen Power Lab | Psychiatry
Prerequisites: An interest in psychology, clinical work, eating disorders or weight; experience with social media, Microsoft Office programs (Word, Excel, PowerPoint)
General Lab Description: We conduct patient-centered research on psychological treatments for teens with eating disorders and/or weight concerns. We also collect data on bullying, parenting (like parent-teen communication) and social media to better understand how these factors affect the development and treatment of eating disorders.
Project Description: The student will design a study about teens and body image that either tests the strength of or challenges the idea of “eating disorder stereotypes.”
Day-to-day Activities: Working on social media posts, recruiting participants with bulimia through pediatricians and other means, and developing/organizing materials for our treatments and health fairs. The student will also work on writing literature reviews (a summary of published work on a particular topic) and other research projects.
Ying Lab | Computer Science
Prerequisites: High proficiency in Python and PyTorch is required. Basic deep learning knowledge and skills are helpful.
General Lab Description: The lab focuses on deep learning that leverages relational reasoning, graphs and knowledge base to solve complex tasks in sciences and industrial AI applications.
Project Description: The project aims to explore a multi-agent system consisting of large language model (LLM) agents. We will simulate complex game environments, and investigate /improve the ability of LLM to reason and perform tasks in an environment with multiple agents, by considering relationships between the agents.
Day-to-day Activities: The project mainly involves coding and prompt engineering to explore multi-agent learning systems.
Zhao Lab | Biostatistics
Prerequisites: Coding experience in R or Python is preferred.
General Lab Description: Our group develops novel statistical and computational methods to address important problems in biology and medicine. We apply our methods to study the biological basis and treatment strategies for many diseases, including lung diseases, cancer, substance dependence, psychiatric disorders (major depression, schizophrenia, bipolar, post-traumatic stress disorder), cardiovascular diseases, autism, congenital heart diseases, aneurysm, hypertension, and others.
Project Description: In this project, we will create an interactive app to explore and understand genomics data from patients with Major Depressive Disorder (MDD) and Post-Traumatic Stress Disorder (PTSD). This app will help show the differences and unique features in the data from these two conditions compared to healthy donors.
Day-to-day Activities: Coding in R or Python to analyze and visualize genomics data (e.g. single-cell RNA-seq data) to interpret the molecular patterns in disorders like MDD and PTSD. The student will also spend time developing an interactive app that contains various visualization tools to allow other scientists to explore the genomics data interactively.
Lin Zhong Lab | Computer Science
Prerequisites: The student should have a GPA>3.8. Must have a strong interest in programming and experience in Python including basic understanding of data structures (such as trees and linked lists) and algorithms (such as sorting).
General Lab Description: We are interested in developing efficient technologies for computing and communication for future mobile systems. Additionally, we are interested in using artificial intelligence (AI) for public safety.
Project Description: Using generative AI models for public safety, especially to help solve school shooting problems by understanding how to detect anomalies before shooting and how to guide survivors to escape after shooting. The student will work with large language models such as GPT to investigate their capabilities in understanding multiple camera video footage and piloting miniature drones.
Day-to-day Activities: Reading papers/documentation, writing code to experiment with cloud-based large-language model services, programming miniature drones, discussing code with other lab members, and presenting research results in lab meetings.
Mingjiang Zhong Lab | Chemical & Environmental Engineering
Prerequisites: Prior organic chemistry laboratory experience is strongly preferred. Should be willing to conduct chemical reactions after appropriate training.
General Lab Description: In our lab, we focus on the innovative design and synthesis of polymer-based soft materials, for applications in soft robotics, biosensing (mixed ion/electron conductivity), and water purification (ion-selective membranes). Our work is driven by a commitment to advancing environmental sustainability and pioneering new technological solutions, underscoring our dedication to creating materials that not only meet current needs but also pave the way for future innovations.
Project Description: The student project focuses on the synthesis of ion-conductive membranes, an essential component in fields like water purification and energy storage. We are interested in how polymer structure determines the efficiency and functionality of ion-conductive membranes. Through this work, students will explore how the manipulation of polymer properties can lead to advancements in critical technologies, contributing to environmental sustainability and innovative engineering solutions.
Day-to-day Activities: Conducting very fundamental organic chemistry reactions for the synthesis of various polymers (polymerization). These polymers will be used for the preparation of ion conductive membranes.