Participating Labs (2025)

The table below summarizes the research interests of the YPRI 2025 host labs. For the labs you are interested in, please carefully review the prerequisites and detailed project description listed below the table.

Lab Name Research Area Research Keywords
Abraham Lab Mechanical Engineering & Robotics Computational Modeling of Robotic Forces, Contact Models
Ben Mamoun Lab Neuroscience & Cell Biology Neurodegeneration, Brain Pathology, Novel Drugs
Blake Lab Chemistry & Geology Geochemistry, Phosphorus Cycling in the Environment
Chandra Lab Neuroscience & Cell Biology Neurodegeneration, Protein Expression in Neurons
Fikrig Lab Microbiology & Cell Biology Mosquito-borne diseases, Dengue Virus
Peijun Guo Lab Physics & Chemistry Energy Storage, Chemical Properties of Materials
Libreros Lab Cell Biology & Biochemistry Lipid Metabolism, Inflammation,  Mass Spectrometry 
Lu Lab Cell Biology Genetic Basis of Nuclear Shape, DNA Cloning
Mandel-Brehm Lab Neuroscience & Cell Biology Autoimmunity against the Brain, Gene Expression
Murray Lab Microbiology Hospital Equipment, Disinfection, Bacterial Culture
Natarajan Lab Astronomy Black Holes, Growth of Galaxies
Pahlavan Lab Mechanical Engineering & Physics Transport of Colloids, Microfluidics, Microplastics
Peters Lab Medical Imaging & Computational Biology  MRI,  Heart Imaging and Tracking 
Saxena Lab Neuroscience & Computational Biology Computational Models of Neuronal Networks, Motor Pathways
Snell Lab Neuroscience & Cell Biology Role of the Cerebellum, Genetic Mutations, Calcium Channels
SPIN Lab Neuroscience & Computational Biology Modeling of Complex Brain Activity, Statistical Physics
Taylor Lab Neuroscience  Social Decision Making, Rat Behavioral Experiments
Wright Lab (Laura Havener) Mechanical Engineering & Physics  High-Energy Particle Collider, Constructing Light Sensors
Ying Lab Computer Science Large Language Models, Generative AI

 

Abraham Lab | Mechanical Engineering and Robotics

Prerequisites: Extensive experience in coding (proficient in data structures and basic algorithms). Python and C++ are the main languages used. 
General Lab Description: The Intelligent Autonomy Lab is led by Prof. Ian Abraham whose research focus is at the intersection of robotics, optimal control, and learning. We focus on developing algorithms that enable robots to explore, learn, and experiment. 
Project Description: The project will be to investigate contact models for robot control. Contact models simulate the contact forces that robots use to grasp and manipulate objects. The student will look at different contact models and quantify how a robot should select which ones to use to improve control.

Day-to-day Activities:  Running experiments with a robot, collecting force data, using code to generate and build upon computational models.


Ben Mamoun Lab | Neuroscience and Cell Biology

General Lab Description: One of the primary research interests of the lab is the discovery of novel anti-fungal compounds against conserved and essential targets. Some of these compounds may also be used to treat other human diseases.
Project Description: In this project, the student will be given the opportunity to explore neuroscience by studying brain tissue from mice with a rare neurodegenerative disease called PKAN. Using special tissue staining techniques, the student will uncover how this disease exerts a pathological effect by visualizing cell death, inflammation, and iron build-up in various brain regions. Furthermore, the student will analyze whether a novel drug can reverse such signs of damage, providing important insights into the potential of this drug to treat the disease.
Day-to-day Activities: Project tasks will include staining of brain tissue slices adhered to microscope slides (with various dyes, antibodies, etc), imaging stained sections with a microscope, and analyzing images using specialized softwares to detect patterns, quantify biomarkers, etc. related to pathology and treatment. The student will also create presentations and posters to report scientific findings.

Blake Lab | Chemistry and Geology 

Prerequisites: An interest in chemistry and geology 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.

Chandra Lab | Neuroscience and Cell Biology

General Lab Description: The goal of the Chandra Lab is to uncover molecular mechanisms and interplay within neurodegenerative diseases, with a focus on synaptic and endolysosomal proteins present in neurons. Diseases we study include include Parkinson’s and a rare, juvenile disorder known as Batten Disease 
Project Description: We are interested in looking at subcellular compartments of the neuron (such as the lysosome and pre-synapse) to uncover changes in proteins that may explain the irregular protein levels (dyshomeostasis) seen in Batten Disease. No treatments exist for the specific subtype we study, and further work remains to be done on how the disease can have 14 different subtypes with similar pathology and symptoms.
Day-to-day Activities: The student will be working with tissue samples isolated from genetically modified mice (gene knock-ins and single/double knockouts) to isolate DNA and genotype the mice via PCR. The student will also run protein isolates via Western blot from cells to probe for changes at various subcellular compartments of the neurons.

Fikrig Lab | Microbiology and Cell Biology

Prerequisites: No skills are required but curiosity, motivation, and a strong work ethic (responsible attitude) are needed. Prior science coursework and coding ability in R and Python are a plus.
General Lab Description: The Fikrig group investigates vector-borne diseases. Studies are directed toward understanding diseases spread by ticks and mosquitoes, such as Lyme disease, flaviviral infections (dengue and West Nile virus), and malaria. We are especially interested in understanding the molecular interactions between pathogens, their arthropod vectors and their mammalian hosts. Finally, we are developing new approaches to prevent ticks and mosquitoes from feeding on a vertebrate host, thereby interfering with pathogen transmission.
Project Description: Mosquitoes deliver viruses while biting mammals to get blood meals. However, not all mosquitoes are able to deliver viruses (ie. competent). The student will test different dengue viruses isolated from different parts of the world to see if our mosquito colony is competent for delivery of those viruses.
Day-to-day Activities: Basic molecular lab techniques such as cloning, PCR, quantitative PCR, and protein purification will be performed routinely. Work with mosquitoes and mice might be added depending on the student’s progress and project needs.

Peijun Guo Lab | Physics and Chemistry

Prerequisites: Intern should have a strong interest in physics and chemistry. 
General Lab Description: Our lab is interested in understanding the functional properties of soft materials that are used for energy conversion, energy storage, and optoelectronics.
Project Description: The student will work on the fabrication of thin films with polymers using solution-based techniques.The physical and chemical properties of the films will be characterized under electrochemical conditions, using optical spectroscopy techniques such as Fourier-Transform Infrared (FTIR) and UV-vis.
Day-to-day Activities: Tasks will include solution processing of thin film samples, optical spectroscopy measurements, and electrochemistry.

Libreros Lab | Cell Biology and Biochemistry

Prerequisites: No specific qualifications; all we ask is a bright attitude, a willingness to learn, and an enthusiasm for making discoveries!
General Lab Description: Lipids and lipid mediators play important 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 lipids and understand their dynamics. This knowledge is crucial for identifying their roles in maintaining human health and the implications of 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 (a type of immune cell) during inflammatory processes. The student will actively participate in the investigation of Leukotriene B4 metabolism in human and mouse immune cells (specifically, 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 learn a variety of experimental techniques, including ELISA kits, flow cytometry, and functional in-vitro assays. They will also gain hands-on experience with the Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) system in the lab, from sample preparation to data acquisition. Additionally, the student will learn to use the mass spectrometry software for peak identification and quantitative data analysis, followed by thorough data analysis and synthesis.In addition to mastering fundamental laboratory techniques and data analysis, the student will have a unique opportunity to contribute to the development of a spectral library focusing on the lipid metabolism of LTB4. This process 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 protocols to isolate cells and extract lipids, and managing data using Excel. Moreover, the student will use ChemDraw to create chemical structure diagrams and Prism 10 to generate figures, gaining a comprehensive skill set to support their scientific development.

Lu Lab | Cell Biology

Prerequisites: A responsible attitude is required. Any prior bench experience will be good but not required. 
General Lab Description: We are interested in decoding the noncoding RNAs in the genome, especially in the setting of immune responses and blood cells. We are investigating the genetic basis of extreme biology in the immune system such as 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 the genetic basis of immune cell structure and function. The student will isolate these genes, and express them in the bacteria E coli (a process known as cloning).  
Day-to-day Activities: The student will use techniques including bacteria culture, and molecular biology techniques such as plasmid preparation, restriction digestion, and gel electrophoresis.

Mandel-Brehm Lab | Neuroscience and Cell Biology

General Lab Description: The lab is interested in the pathology of autoimmune disease targeting the brain. We are investigating the triggers (such as cancer outside the brain) of these autoimmune conditions, as well as the primary pathological process in brain tissue.
Project Description: The student project would involve characterizing the tumor cell lines that are known to trigger autoimmunity against the brain. This will involve investigating protein and gene expression (proteomics and transcriptomics, respectively) of engineered cell lines as well as analysis of their growth behavior.
Day-to-day Activities: The student will use techniques such as cell culture, Western blot (for protein detection), immunofluorescence, and microscopy.

Murray Lab | Microbiology

Prerequisites: Basic microbiology skills helpful but not required.
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: Culturing bacteria and bacteriophages, putting them on the surface of medical equipment, subjecting them to various forms of killing, and counting how many are recovered from the surface to see if the disinfection method worked.

Natarajan Lab | Astronomy

Prerequisites: Some Python coding experience preferred (installing packages, running notebooks, basic command line). No astronomy knowledge required.
General Lab Description: A key interest of our lab is understanding how the supermassive black holes that are found in the hearts of galaxies have formed and grown over cosmic time.
Project Description: The goal is to measure the distances of the galaxies and the masses of their supermassive black holes using established methods. Mass is one of the fundamental properties of black holes that grow as they accrete matter. Once we know the black hole mass, we can compare this to the mass of the stars in the galaxy in order to determine how much the black hole has “grown” over time compared to the galaxy.
Day-to-day Activities: The student will calibrate and analyze spectroscopic data of galaxies with “actively accreting” supermassive black holes that we have obtained from the Palomar and/or Gemini Observatory using python scripts. Day to day tasks will involve downloading data files and Python packages, learning the principles of spectroscopy and calibration, and fitting models to the emission lines in the spectroscopic data.
 

Pahlavan Lab | Mechanical Engineering and Physics

Prerequisites: Familiarity with some programming language and a solid background in Physics/Biology/Chemistry/Math are helpful.
General Lab Description: We study the transport of colloids and bacteria in porous media (soil and rocks) and in the oceans. We use microfluidics and table-top lab setups to study these topics.
Project Description: 
Project 1- The interaction between bacteria and microplastics: microplastics are changing microbial habitats. By studying their interactions, we try to shed light on the environmental/ecological implications of the introduction of microplastics to the environment, from soil to the oceans. 
Project 2- Spreading of microplastics in the oceans: it’s important to understand where the microplastics end up and how far they get transported in the oceans; we use a lab setup to shed light on this problem.
Day-to-day Activities: The student will use techniques including  microscopy, microfluidics, and high-speed imaging. They will also process data using MATLAB. 

Peters Lab | Medical Imaging and Computational Biology

Prerequisites: Interest in math, learning Matlab/Python, interest in medical imaging.
General Lab Description: The lab develops new Magnetic Resonance Imaging (MRI) methods and analysis tools for diagnosing heart disease.
Project Description: This project will involve developing and organizing a data set of movies of the heart, and annotations on these movies, for use to develop a deep learning model tracking the motion of the heart. This model can be used to predict the motion of the heart and to automatically modify the MRI methods to track that motion.
Day-to-day Activities:  Students will learn to use an MRI scanner and analyze MRI data. Students will also learn about heart anatomy and physiology,  develop Matlab or Python code to analyze data sets, and use Excel or jmp to synthesize results.

Saxena Lab | Neuroscience and Computational Biology

Prerequisites: Experience with programming in any language would be beneficial, particularly Python.
General Lab Description: In this lab, we utilize computational methods such as machine learning and control in order to uncover the inner workings of the brain. 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: In collaboration with Amy Orsborn at the University of Washington, we will study how monkeys trained to make arm movements adapt when what they see (their visual sensory input) does not match the movements they make in 3D space. Using machine learning, particularly reinforcement learning, we will model how monkeys respond under such conditions in order to better understand the interplay between movement and sensory processing. Data for this project was collected by the Orsborn lab and utilizes brain computer interfaces (BCIs).
Day-to-day Activities: The student will likely perform simple programming tasks such as running training scripts for machine learning models and keeping track of their progress. Afterwards, analyses of the trained models will be beneficial, if time permits. Other activities would include meetings and general discussion with the Saxena and Orsborn lab, and reading/presenting papers.

Snell Lab | Neuroscience and Cell Biology

General Lab Description: The Snell lab is interested in understanding the contribution of the cerebellum (a part of the brain historically appreciated for its role in motor coordination) to non-motor tasks in health, and in cognitive disorders such as autism and ADHD. We investigate this by assessing expression and function in cell lines and behavior and neuronal function in mouse models.
Project Description:
Project 1: Different mutations in a specific calcium channel (whose activation increases the amount of calcium inside cells resulting in neuronal activity) result in a wide array of patient symptoms, from motor impairment to autism. How can different mutations in the same channel result in such a wide spectrum of symptoms? This student will work with a lab member to isolate and grow the DNA of multiple human mutations in a calcium channel. The student will use imaging analysis to understand possible differences and similarities in channel expression between mutations that result in motor impairment and mutations that result in cognitive impairment. 
 
Project 2: The cerebellum has historically been responsible for motor coordination and motor learning, but has recently been implicated in non-motor tasks such as social interaction and emotional control. Does the cerebellum contribute to motor and non-motor tasks through the same neuronal connectivity and intrinsic activity? This student will work with a lab member to conduct behavior experiments and analyze behavioral experimental data from a mouse model that exhibits both motor and cognitive impairment as a result of a calcium channel mutation present only in the cerebellum.
 
Day-to-day Activities: 
Project 1: The student will perform transformations to produce more DNA of specific mutation, maintain their own cell line to perform transfections (force the cells to express the DNA), and assist in histology and confocal imaging of cells to assess expression. The student will also analyze expression data working closely with a lab member. 
 
Project 2: The student will acclimate mice in the behavior room and help set up behavioral tasks. This student will also help analyze behavioral data/ videos and work closely with a lab member to interpret data. This student will also have the opportunity to conduct histology in cerebellar slices to assess change in expression and cellular morphology in the brains of mice with the calcium channel mutation.

SPIN Lab | Neuroscience and Computational Biology

Prerequisites: Basic coding experience required in Matlab, Python, Mathematica, or any other language. 
General Lab Description: We are interested in understanding how structure and function emerge in complex living systems, particularly the brain. We study how individual neurons interact to form networks; how whole-brain activity orchestrates cognition; and how humans communicate to process information. We approach these problems from a statistical physics perspective: seeking to identify the key minimal ingredients that combine to produce collective macroscopic phenomena.
Project Description: The brain builds maps of the world around us, but how efficient or accurate are these maps? Using recordings of neurons in the mouse brain we can begin to answer this question.
Day-to-day Activities: The student will analyze data from neuroscience experiments. This analysis will involve mathematical ideas from information theory and optimization.

Taylor Lab | Neuroscience 

Prerequisites: This experience will involve on-the-job learning, so while no specific skills are required, we are looking for students who are organized, curious, responsible, and proactive. Coding skills (in Matlab and/or Python) are a plus, and interest in working with rodents is a must.
General Lab Description: What makes some individuals act in a way that harms others (aggression), and others act in a way that benefits others (empathy)? The SNaP Lab is interested in answering these questions from a neuroscience perspective, by investigating the brain regions that interact to influence social behavior.
Project Description: The current project takes a translational approach, which means we use an animal model (in this case, rats) to understand behaviors that are relevant in humans. We are training rats on a task where they have to work together (cooperate) in order to receive a reward (sugar pellets), and the student may be involved in many aspects of this project. Depending on the stage the project is at and the students’ particular interests, responsibilities may range from rodent handling and observing trials, to tracking trial videos and counting active brain cells (neurons) captured in images, to running code that analyzes behavior patterns.
Day-to-day Activities: The student intern will learn how to handle rats and maintain an animal colony, which includes weighing animals, determining appropriate amounts of food, and feeding animals. They will also become proficient in running behavioral experiments, determining the type of trial necessary for the stage of training an animal is at, and setting up the appropriate programs on the lab computer. Students may also gain exposure to wet lab skills, such as mounting sliced brain tissue and performing microscopy.

Prerequisites: Previous coursework in Geometry and Trigonometry and a class in chemistry and/or physics (preferably physics)
General Lab Description: Our research is focused on studying the force that holds the nucleus of an atom together, called the strong nuclear force. We use high-energy particle colliders to smash particles together and break them apart so we can understand how they are put together.
Project Description: We are preparing for a future high-energy particle collider at Brookhaven National Lab (BNL) in Long Island, NY, called the Electron-Ion Collider (EIC) by working on a detector subsystem to be built for measuring particles from EIC collisions. The subsystem’s main goal is to identify types of subatomic particles that are too small to see by eye using a sensor that measures light. This project will involve constructing a light-tight customized enclosure to test these sensors that will eventually be used in the detector.
Day-to-day Activities: The project will involve using computer software to modify the dark box design and eventually order the parts to construct the box. Once the parts arrive, the box will need to be constructed, which will involve modifying some of the pieces and using the Wright Laboratory 3D printer and machine shop to customize additional parts for the enclosure. Finally, the box will be integrated to test the light sensors.

Prerequisites: High proficiency in Python and PyTorch is required. Familiarity with deep learning, generative models (such as diffusion), and an understanding of large language model (LLM) basics (transformer backbone, efficient finetuning, in-context learning).
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 goal is to explore deep generative models involving multiple modalities including text, images, graphs and time series.
Day-to-day Activities: The project mainly involves coding and prompt engineering to explore deep generative models.This includes LLM pre-training; efficient fine-tuning; Transformers; variational autoencoder; diffusion models; potentially hyperbolic representation learning.