Projects
Evolutionary & Functional Interactions Among Proteins
University of Rochester
Project
Posted 61 days ago
12 hours/week
Hybrid
Class of 2026, 2025, 2024
Decision by 07/12/2024
Engineering/ Math/ Computer Science, Natural and Biomedical Sciences
Biological Sciences: Biochemistry, Biological Sciences: Computational Biology, Biological Sciences: Ecology and Evolutionary Biology, Biological Sciences: Molecular Genetics, Data Science
Protein function and evolution: We are utilizing computational and evolutionary approaches to investigate protein-protein interactions. The evolutionary rate correlation (ERC) approach detects proteins that show highly correlated evolutionary rates during mammalian evolution. Such proteins are candidates for biological interactions. For example, we have used an approach called evolutionary rate correlation to identify protein candidates that coevolve with Angiotensin-converting enzyme 2 (ACE2), the protein that SARS-CoV-2 uses to enter human cells (https://peerj.com/articles/12159/) and nuclear-mitochondrial protein interactions (https://academic.oup.com/mbe/article/36/5/1022/5345565). We have expanded the protein database to 15,000 proteins aligned across 202 mammalian species. Protein evolutionary rates across these proteins have been calculated and coevolving protein sets identified, provided a rich set of data for analysis. Our goal is to uncover protein interactions in different biological processes (e.g. development, cellular function, immunity) and disease (e.g. cancer, diabetes, cardiovascular disease), and to study their coevolutionary and functional interactions. We will also develop a website for researchers to explore ERC predicted protein partners, for proteins of interest in their research. We are seeking undergraduate students with interests in computational biology, functional biology and/or evolutionary biology. You will gain experience in network analysis, clustering, protein-protein binding simulations, molecular evolution and/or GUI development.
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Research Groups
AURA Team
University of Rochester
Research Group
Computer Science
Engineering/ Math/ Computer Science
We're on a mission to get every undergraduate involved in research. AURA is a platform that makes research more accessible by providing an easy way to find and apply to on campus research opportunities. We strive to be accessible, convenient, simple and fast, so if you see something that doesn't live up to those values, please let us know by emailing hello@joinaura.us.
Yan Lab
University of Rochester
Research Group
Biological Sciences: Cell and Developmental Biology, Biology
Natural and Biomedical Sciences
Our research interests are in the field of cyclic nucleotide signaling and cardiovascular biology, with a particular focus on cyclic nucleotide phosphodiesterases (PDEs) that catalyze the hydrolysis of cyclic nucleotide second messengers (cAMP and cGMP). cAMP and cGMP regulate a wide variety of cardiac functions, from the short-term effects on myocyte contraction/ relaxation to long-term effects such as gene expression and structural remodeling. To identify the PDE isozymes altered in disease hearts, we have performed initial screening for PDEs that are altered in diseased hearts. The expression of a number of PDE isozymes is changed: some are up-regulated and some are down-regulated. The ongoing and future studies are aimed to determine the role and mechanism of these altered PDEs in cardiac remodeling and dysfunction through genetic and pharmacological approaches. To learn more about our research visit: https://www.urmc.rochester.edu/cardiovascular-research-institute/research/yan.aspx. We are seeking undergraduate students who are interested in cardiovascular biology and molecular biology. The student will have the opportunity to become fully involved with all the steps of research being completed in our laboratory, often working directly with Dr. Vivian Si Chen. The student can attend weekly group zoom meeting.
Active Perception Laboratory
University of Rochester
Research Group
Biological Sciences: Neuroscience, Biomedical Engineering, Brain and Cognitive Sciences, Computer Science, Data Science, Electrical and Computer Engineering, Engineering Science, Optics, Visual Science
Engineering/ Math/ Computer Science, Natural and Biomedical Sciences
A research assistant position is available in the Active Perception Laboratory (https://aplab.bcs.rochester.edu) in the Department Brain and Cognitive Sciences at the university of Rochester. Research in the lab focuses on understanding the interplay between eye movements and vision using a combination of behavioral, computational, high-resolution retinal imaging and evoked potentials (EEG) techniques (https://aplab.bcs.rochester.edu/facilities.html#). Responsibilities will depend on the applicant interests and background. They could include any of the following: experimental data collection with human subjects with eyetracking and/or EEG, implementation of experimental protocols, contribution to the development of novel eyetracking techniques (for candidates with an Optics and /or Engineering background), analysis of behavioral data, collection and analysis of high-resolution retinal images, alignment and calibration of optical devices for eyetracking and retinal imaging (for candidates with an Optics background). Quantitative skills and some computer programming skills are desirable. This position is ideal for someone interested in obtaining experience in vision and neuroscience research, and in improving quantitative and computational skills, with the goal of applying to graduate school.
Johnson Lab
University of Rochester
Research Group
Biological Sciences: Neuroscience
Natural and Biomedical Sciences
The primary focus of Dr. Gail Johnson’s research group is on the molecular mechanisms of neurodegeneration. The lab has a longstanding interest in the pathogenic processes in Alzheimer disease, and more recently in stroke and spinal cord injury (SCI). For their studies they use a wide variety of different approaches from in vitro enzyme assays with purified proteins, to studies in whole animals. This broad-based approach allows them to translate what they learn about a process or signaling pathway at the molecular level to the in vivo situation. Currently all the positions in my lab are filled. However, when positions become available I will post them on AURA.
En-Ability
Rochester Institute of Technology
Research Group
Human Computer Interaction
Engineering/ Math/ Computer Science
The En-Ability Lab is about enabiling, enhancing, and empowering people. Our research areas cover accessibility and HCI, more specifically we investigate topics on design, immersive technologies, and networking. Our lab’s mission is to foster a collaborative environment that values diversity—not only diversity in the topics we research, but also the diversity in our research team, and the communities our research is made to serve.
Porosoff Lab
University of Rochester
Research Group
Chemical Engineering
Engineering/ Math/ Computer Science
The Porosoff group focuses on developing new catalysts for upgrading C1 and C2 resources (CO2, CO, CH4, C2H6) for efficient energy storage and low-cost production of plastics, chemicals and fuels. Understanding the relationships between chemical reactivity and catalyst electronic/structure properties is extremely important for developing catalysts that exploit particular reaction pathways. This approach requires controlled synthesis of catalysts combined with in situ techniques and theoretical calculations. In particular, target areas of research are three types of catalytic reactions for improved shale gas utilization and lowering CO2 emissions: (I) Catalyst development for CO2 hydrogenation, (II) Selective synthesis of light olefins from CO and H2 and (III) Catalytic dehydrogenation of light alkanes to olefins by CO2. Experimental work combines a mix of catalyst synthesis and characterization, reactor studies and in situ spectroscopy.
VIStA (Visual Intelligence & Social Multimedia Analytics)
University of Rochester
Research Group
Computer Science
Engineering/ Math/ Computer Science, Social Sciences, Natural and Biomedical Sciences
[Computer Vision]: recognition of objects, scenes, people, locations, actions, and events from images and videos [Vision and Language]: description and explanation of visual content; language-based search, retrieval, and generation [Social media data mining]: prediction, nowcasting, forecasting, profiling, and recommendation using open-source data [Machine Learning]: learning with large-scale loosely labeled web data, cross-domain learning, few-shot learning [Health informatics]: healthcare and wellness analytics using text and visual data; surgical video analysis [Pervasive computing]: context-aware applications; multimodal inference from multiple sensors [Media experience]: multimodal reliving; aesthetics, emotion, sentiment, and influence of multimedia [Note]: Undergraduate students should seek research opportunities after having done well in the related courses (240/440 Data Mining and/or 249/449 Machine Vision).
Ultrasound Tomography Center
University of Rochester
Research Group
Applied Mathematics, Biomedical Engineering, Computer Science, Electrical and Computer Engineering, Mathematics, Mechanical Engineering, Physics
Engineering/ Math/ Computer Science
We are a multidisciplinary group of scientists, engineers, and physicians working to bring a new ultrasound-based medical imaging platform to the clinic. Most conventional ultrasound systems only use reflected waves to create images of the tissue. This approach can be limited in its capability to quantitatively characterize tissue. Ultrasound tomography uses both the waves reflected by AND transmitted through tissue to fully characterize the material properties of the tissue. Specifically, we observe that these material properties distort the ultrasound wave as it passes through the tissue. These same distortions allow us to interrogate and recover the material properties within the tissue of interest. Our group integrates the latest advances in hardware development and algorithm design to translate these ideas to a clinically relevant imaging modality. We are looking for highly motivated students for both hardware development and algorithm design. Interested students should have a strong interest in some or all of the following categories: acoustics, numerical modeling, signal processing, inverse problems, waveform inversion, computational imaging, and/or imaging hardware design. We expect students to come with a background in MATLAB (or an equivalent language). C/C++ experience (especially CUDA) would be an additional bonus as we also plan to accelerate existing algorithms using GPUs.
MixingLab
University of Rochester
Research Group
Biological Sciences: Neuroscience, Biomedical Engineering, Mechanical Engineering, Physics
Engineering/ Math/ Computer Science
Fluid mixing is both beautiful and devilishly difficult to understand, predict, or control. Our research team, led by Prof. Douglas H. Kelley, studies how flows and the materials they carry change over space and time, primarily with application to cerebrospinal fluid flow in the brain and to liquid metals technologies. Brain cerebrospinal fluid flows through the recently-discovered glymphatic system, which evacuates metabolic wastes to prevent diseases like Alzheimer's, but can also malfunction in situations like stroke or traumatic brain injury. Fluid flow affects the performance of liquid metal batteries, a grid-scale storage technology, and the efficiency of aluminum manufacture, which uses 3% of worldwide electricity. Our research team studies these problems with a combination of experiments, simulations, and theory. Undergraduate researchers work in collaboration with each other and/or with PhD students and postdoctoral researchers, building skills and taking creative ownership of their own efforts. Undergraduate researchers on the team frequently coauthor peer-reviewed journal articles and present at international research conferences. Valuable skills for undergraduate applicants include -- but are not limited to -- coding, machining / fabrication, computer simulation / drawing, and writing. We value interpersonal diversity and encourage all to apply. Students need not be upperclassmen to apply. More information is available on the team website.
Rochester Center for Research on Families and Children
University of Rochester
Research Group
Psychology
Social Sciences
The Rochester Center for Research on Children and Families seeks to better understand children’s adaptation and maladaptation within the context of family relationships and processes. Informed by the developmental psychopathology emphasis on risk and resilience, our work is focused on elucidating the costs and benefits of children’s specific patterns of responding to family processes. The center currently houses several projects, including several large scale, multi-method, multi-level longitudinal research studies funded by the National Institutes of Health.
Le Lab
University of Rochester
Research Group
Psychology
Social Sciences
Psychology lab focused on the study of relationships and well-being.
Montane Forest Dynamics Group
West Virginia University
Research Group
Biological Sciences: Ecology and Evolutionary Biology, Biology
Engineering/ Math/ Computer Science, Social Sciences, Natural and Biomedical Sciences
We do research on past climate, humans, forests using the environmental information stored in tree rings. Our latest project is exploring how the unstable isotope 14C can help us understand past solar storms using the wood stored in ancient trees.
Photoacoustic and Ultrasonic Research & Engineering (PURE)Laboratory
University of Rochester
Research Group
Biomedical Engineering, Computer Science, Data Science, Electrical and Computer Engineering, Mechanical Engineering, Optical Engineering, Optics
Engineering/ Math/ Computer Science, Natural and Biomedical Sciences
The primary focus of the PURE lab at the University of Rochester is to develop novel, hybrid, and ultrasound-based diagnostic methods, and define the clinical utility of the developed technologies as it applies to detection, diagnosis, and therapy of various pathologies. Our ultimate goal is to help physicians and patients by providing more accurate and multi-parametric information about diseases that can help: to detect pathologies at their early stages of development to more accurately locate the diseased tissue to better plan for individualized therapy to monitor the outcome of the therapeutic procedures These developments will serve to improve the diagnosis and treatment guidance of high impact diseases, such as cancer. Almost every project in the lab utilizes ultrasound imaging. Ultrasound imaging (aka sonography) is the most-widely available medical imaging modality in clinical practice due to its notable advantages, including using non-ionizing energy, providing real-time information, portability, and low cost. However, it is limited to imaging tissue morphology and structure, without any functional, cellular, or molecular information. That is why our lab explores a newly born modality known as "Photoacoustic Imaging". Photoacoustic imaging utilizes lasers to complement ultrasound imaging, providing functional and molecular information to the morphological images obtained from ultrasound. Our research team works closely with the School of Medicine. This collaboration has helped us to better identify the real clinical needs and direct our efforts to overcome clinical limitations. We are closely working with several industry-leading imaging companies, such as Verasonics and Siemens, to implement our technologies on existing clinical devices. We believe this could be a key to enable faster clinical translation of the developed methods.
Active Perception Lab
University of Rochester
Research Group
Brain and Cognitive Sciences
Natural and Biomedical Sciences
Paid part-time lab manager position in the Active Perception Lab in the Department of Brain and Cognitive Sciences Typical Duties Managing petty cash: refill the small money bank every day. Once a year, report any taxable payments to the university. Purchasing lab equipment: monitor the purchase log, submit purchase requests to admin, keep track of orders, and physically carry all deliveries to the lab. Research subjects recruitment and advertising: post flyer ads on campus on a regular basis. Connect the prospective subjects to lab personnel. Onboarding: onboarding new lab members. Internal Review Board (IRB): ensure compliance with the IRB and Human Subject Protection Review Board using the ClickIRB platform system. Adding and removing people from the list approved by IRB. Modify IRB documents (study protocol, consent form, screening script) as necessary. Complete a Continuing review that is required every year. Eyetracker maintenance: assist in the execution of maintenance tests on lab experimental equipment. Website and social media: update lab website and twitter. Lab meeting scheduling: organize the lab calendar for weekly lab meetings. Qualifications Proficiency with Microsoft Word and Excel. Ability to log information on various platforms (Notion, ClickIRB, RedCap). Organized, responsible and proactive.
Paid part-time lab manager position in the Active Perception Lab in the Department of Brain and Cognitive Sciences
University of Rochester
Research Group
Brain and Cognitive Sciences
Natural and Biomedical Sciences
Typical Duties Managing petty cash: refill the small money bank every day. Once a year, report any taxable payments to the university. Purchasing lab equipment: monitor the purchase log, submit purchase requests to admin, keep track of orders, and physically carry all deliveries to the lab. Research subjects recruitment and advertising: post flyer ads on campus on a regular basis. Connect the prospective subjects to lab personnel. Onboarding: onboarding new lab members. Internal Review Board (IRB): ensure compliance with the IRB and Human Subject Protection Review Board using the ClickIRB platform system. Adding and removing people from the list approved by IRB. Modify IRB documents (study protocol, consent form, screening script) as necessary. Complete a Continuing review that is required every year. Eyetracker maintenance: assist in the execution of maintenance tests on lab experimental equipment. Website and social media: update lab website and twitter. Lab meeting scheduling: organize the lab calendar for weekly lab meetings. Qualifications Proficiency with Microsoft Word and Excel. Ability to log information on various platforms (Notion, ClickIRB, RedCap). Organized, responsible and proactive.
Laboratory For Laser Energetics (Spring and Summer 2024)
University of Rochester
Research Group
Applied Mathematics, Astronomy, Chemical Engineering, Chemistry, Computer Science, Earth and Planetary Sciences, Electrical and Computer Engineering, Engineering Science, Mathematics, Mechanical Engineering, Optical Engineering, Optics, Physics, Physics and Astronomy
Engineering/ Math/ Computer Science, Natural and Biomedical Sciences
The LLE Undergraduate Education Program enables students to engage in mission-critical science and engineering. The unique work opportunities the LLE has to offer are well suited to provide training, while helping to fill the critical future workforce needs of the National Nuclear Security Administration (NNSA) at all levels, including operators, technicians, engineers and scientists. Undergraduate students pursuing degree programs in related science and engineering fields are welcome to apply. Laboratory for Laser Energetics Internships: Workforce, Research, and Career-Building Opportunities Full-time, Part-Time, Co-Op, REU, and Summer Opportunities Deadline for Summer 2024 Applications: February 15th To Apply: Please send your resume to Laura Kappy, Undergraduate Education Program Director (lkap@lle.rochester.edu) or upload through AURA. Thank you!
Algorithmic Foundation of Data Science
University of Rochester
Research Group
Applied Mathematics, Computer Science, Data Science, Mathematics
Engineering/ Math/ Computer Science
Our group develops the algorithmic foundation of data science. We design, analyze, and implement provably efficient and reliable algorithms for solving a general class of problems in data science. The research scope broadly includes algorithms for optimization, sampling, and games. We aim to apply the algorithms to fascinating areas such as operations research, machine learning, and economics. ************************** ************************** We are looking for a senior student who will graduate in 2024 and seriously considers pursuing a PhD in Fall 2024. ************************** **************************
Computational Social Science
University of Rochester
Research Group
Data Science, Political Science
Engineering/ Math/ Computer Science, Social Sciences
I am looking for undergraduate and graduate students interested in working on various topics related to computational social science and data science. My current interests include emotion detection/quantification, analysis of visual content and videos, analysis of interactions between people/behavioral patterns, social media, political polarization, and developing methods for social sciences. If you are interested in working with me on a research project (e.g., as an independent study student or part-time researcher), please fill out the form in the following link: https://www.cantaycaliskan.net/research-assistance
Libby Lab
University of Rochester
Research Group
Biological Sciences: Cell and Developmental Biology, Biological Sciences: Neuroscience, Biology
Natural and Biomedical Sciences
The primary focus of Dr. Richard Libby’s research group is to understand the molecular mechanisms underlying glaucomatous neurodegeneration. Interests in the lab include investigating how neurons die and investigating how glial cells in the retina contribute to neuronal death. Genetic mouse models allow for questioning into how specific genes in different cell types play a role in neuronal death. Further, techniques such as immunohistochemistry, genotyping, and sectioning are used regularly as cellular outcome measures. All openings are currently filled. Undergraduates interested in joining for future semesters should email graduate student Sarah Yablonski (sarah_yablonski@urmc.rochester.edu). Preference will be given to candidates interested in a long-term research position.
Dye Global Health Lab
University of Rochester
Research Group
Anthropology, Environmental Health, Epidemiology, Gender, Sexuality, and Womens Studies, Health, Behavior, and Society, Human Computer Interaction, International Relations, Latin-American Studies, Medical Anthropology
Social Sciences, Natural and Biomedical Sciences
We prioritize creative engagement with underrepresented and marginalized communities around the world to address health priorities, often through technology and human-centered design. We view humans in their ecological context, understanding that social, biological, environmental, and other factors interact to impact health and illness, and that structural barriers often preclude ethical engagement of indigenous, marginalized, and underrepresented peoples in the scientific enterprise. Our lab values deep inclusion, respect, and liberation among its members and partners; we strive to prioritize the voices of underrepresented and intersectional identities in our work. The work of our lab reflects the integration of qualitative, quantitative, community, and laboratory approaches to science. We are pragmatic, applied, and focused on action. -Global Health, with a special emphasis on Latin America and the Caribbean, Asia and the Pacific, and Global Deaf Health -Perinatal Health, with a special emphasis on social determinants of medical risk in pregnancy and childhood -Technology, in the creation and maintenance of communities of learning, in communication, and to stimulate action Our work crosses boundaries and is transdisciplinary.
University of Rochester Le Lab
University of Rochester
Research Group
Psychology
Social Sciences
Research in our lab is focused on the study of relationships and well-being. We examine how the different ways in which people care and connect with each other impacts personal and relationship well-being. Research assistants' tasks may include the following: behavioral coding of videos, running lab session with participants, and assisting in study construction.
Romanski Lab
University of Rochester
Research Group
Biological Sciences: Neuroscience
Natural and Biomedical Sciences
The Romanski Lab is a neuroscience research lab investigating the brain circuits and neuronal mechanisms that underlie social communication. In particular we are studying how single neurons in the prefrontal cortex bring together face and vocal information when we communicate. This involves neuronal recordings in animal subjects while they look at movies of other animals vocalizing. We are also investigating the anatomy of the prefrontal cortex and determining what brain regions our face-processing neurons receive their information from. We have positions for undergraduate students to assist in these projects. The work will include anatomical circuit tracing on a digitized microscope system, data analysis using excel, MATLAB, and other programs for our neuronal recordings and training of animals in memory tasks. It is possible to sample some time in all three projects if interested. This can be done as a 1 credit research course or as volunteer work. There is the possibility of a full time paid research position after graduation in June 2024.
ADK Climate Project
University of Rochester
Research Group
Dance, Studio Arts, Sustainability
Humanities/ Performance
The ADK Climate Project connects climate change to personal narrative unsing a mobile recording studio that travels through the Adirondack Park. These captured climate narratives are subsequently provided to artists who create artworks in response. The aim is to promote climate action by highlighting our humanity, sharing and reflecting on the local consequences of climate change, as opposed to relying exclusively on scientific data. Because half of the Adirondack Park belongs to all the people of New York State and is constitutionally protected to remain a “forever wild” forest preserve and the remaining half of the park is private land, The Adirondack Park is an ideal location to deconstruct environmental conflict and explore how park residents and visitors are encountering climate change. ADK Climate Project: Audio and Visual Archive The expectation for research students is that you collaborate with faculty mentors and the digital scholarship lab to catalogue and construct an archive of collected stories and art collected as part of the ADK Climate Stories Project. This research is for credit. This project can be done remotely. Questions? Contact: stephanie.ashenfelder@rochester.edu for more information. Weekly meetings with the DSL and faculty members will take place during the semester.
Earth Imaging, Signals and Algorithms
Yale University
Research Group
Data Science, Earth and Planetary Sciences, Electrical and Computer Engineering
Engineering/ Math/ Computer Science, Natural and Biomedical Sciences
The Earth-imaging lab at the UofR investigates the structure and dynamics of the solid Earth using advances in computational imaging, signal processing, and artificially intelligent algorithms
Kennedy Research Group
University of Rochester
Research Group
Chemistry
Natural and Biomedical Sciences
The Kennedy Research Group uses synthetic organic and inorganic chemistry to address challenges in sustainability and human health. We focus on understanding reaction mechanisms that apply terrestrially abundant transition metals as catalysts and use the resulting insights to develop innovative new methods and reactivity strategies. Undergraduates in the group generally participate in a multi-year research experience as they progress from shadowing their research mentors to making independent research contributions culminating in a senior thesis. Researchers are matched with a graduate student mentor to work on projects (ranging from synthetic organic method development, to mechanistic elucidation, to inorganic synthesis and electrochemistry) aligned with their interests and career goals. Students meet regularly with the faculty PI through weekly subgroup meetings, group meetings, and 1:1 quarterly check-in meetings. Expectations for weekly hours in the lab are determined each semester based on the number of credit hours earned (3 hours of in-lab research per credit hour).
FAM&I Lab at The University of Rochester
University of Rochester
Research Group
Psychology, Social and Emotional Development
Social Sciences
Want to do research on the positive development and family assets of racially/ethnically minoritized teens? Join the FAM&I Lab! We investigate how minoritized teens learn to flourish in today’s world in terms of their psychological wellbeing, racial/ethnic and gender identity formation, and academic motivation and achievement. In line with our commitment to diversity, equity, inclusion, and justice, the FAM&I Lab purposefully uses strength-based theories and research approaches to understand the power of racially/ethnically minoritized families and youth. Our new projects include understanding (a) how minoritized adolescents (ages 10-20) form and think about their racial/ethnic, gender, and academic identities in integrated ways; (b) how minoritized families support teens in their identity development, achievement, and overall psychological wellbeing; (c) how emerging adults (ages 18-24) conceptualize what it means to be successful, happy, and thriving; and (d) how developmental assets within minoritized youth and families help protect them from the negative effects of racial discrimination and racism. As a research assistant, you will gain fundamental research skills like conducting interviews and surveys, managing large-scale datasets, as well as professional skills like verbal and written communication and project management. You can also learn about graduate school and possible next steps in your career! We are looking for intellectually curious and responsible research assistants who can commit 10-15 hours per week for a minimum of 2 semesters. Students can earn up to 4 credits per academic semester for their work on this project by enrolling in PSYC 395 (“Independent Research”).
TEST LAB
University of Rochester
Research Group
Biological Sciences: Ecology and Evolutionary Biology
Natural and Biomedical Sciences
*this is a test posting, please disregard*
Bi Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
In eukaryotic organisms chromatin plays a key role in the highly efficient regulation of gene expression. The genome is organized into discrete structural and functional chromatin domains with different potentials for gene expression. Our major goal is to understand the mechanisms underlying the establishment and maintenance of genomic domains in the highly tractably yeast model system. Interests: Epigenetic regulation of eukaryotic gene expression; Structural and functional domains of the genome; Chromatin boundary elements; Gene silencing; DNA damage repair and tolerance
Brisson Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Research in the laboratory investigates the evolution and development of morphology. We’re particularly interested in the interplay of nature and nurture in affecting final adult morphology. We use a variety of approaches including genetics, genomics, and developmental biology. Interests: Evolution of morphology; Molecular basis of phenotypic plasticity; Evolution and development in the pea aphid; The role of epigenetics in polyphenism
Chen Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our research focuses on the genomic basis of contemporary evolution in natural populations. We want to understand the contributions of different evolutionary forces in shaping patterns of variation across the genome through space and time, and to link genetic variation to variation in individual phenotypes, fitness, and eventually population dynamics. We answer these questions by developing genomic resources and statistical tools that combine evolutionary genomics and pedigree data from long-term demographic studies of vertebrates such as the Florida Scrub-Jay. Interests: Population genetics with pedigrees; Contemporary evolution in natural populations; Evolutionary genetics; Conservation genomics; Avian genomics Skills we are looking for: willingness to learn coding and population genetics
Fay Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our research aims to understand the genetic basis of evolutionary change, and specifically how adaptation and constraints shape divergence between species. To achieve this goal we employ computational analyses, field research and wetlab experiments. While our primary experimental system is yeast, we also work on other systems through collaborations. Ultimately, we hope to generate new insights into how species adapt and become different from one another from the molecular to an organism level. Projects: http://labsites.rochester.edu/faylab/research/ Interests: Evolution of gene regulation; Comparative genomics and domestication; Disease consequences of human evolution Skills our lab is looking for: Programming experience (R, Python, etc) for computational projects, but not needed for wetlab projects.
Fry Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
In natural populations of animals and plants, genetic differences among individuals give rise to substantial variation in ability to survive and reproduce, or fitness. This is puzzling, because natural selection would be expected to eliminate fitness-reducing alleles. I investigate the factors maintaining genetic variation for fitness in the fruit fly Drosophila melanogaster. I am also using theory to explore the evolutionary consequences of genetic variation for fitness, especially in the context of sexual selection and mate choice. Interests: Genetics of ecological adaptation in Drosophila; Evolutionary effects of deleterious mutations; Quantitative-genetic theory and methodology
Fu Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our laboratory investigates the cellular roles of nucleic acid modification enzymes in biological processes ranging from neurodevelopment to the cellular stress response. In particular, we focus on discovering the targets and functions of two classes of enzymes: the SAM-dependent methyltransferases and the iron-dependent AlkB dioxygenases. To study the diverse processes modulated by these enzymes, we use an integrated biochemical, molecular and genetic approach in mammalian tissue culture systems as well as mouse knockout models. Through this approach, we have discovered novel targets and functions for enzymes involved in DNA repair, RNA modification and regulated cell death. The pathways and mechanisms identified through our studies provide critical insight into multiple aspects of human health and disease, including anti-cancer chemotherapy, degenerative disorders and aging. Interests: RNA modification and translation regulation; Neurodevelopmental disorders linked to RNA function; Biochemistry and molecular biology
Ghaemmaghami Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our laboratory studies the mechanisms of protein folding and degradation within cells. We investigate how cells maintain a balance between these two processes, and how this homeostasis is affected by disease and aging. The projects in the lab draw on a number of disciplines including protein biochemistry, proteomics and computational biology. Interests: Protein folding and degradation; Neurodegenerative diseases and aging; Prion biology; Proteomics More information can be found at www.ghaemmaghamilab.org Publications can be found at https://www.researchgate.net/profile/Sina_Ghaemmaghami
Glastad Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Ants live in sophisticated societies in which morphologically and behaviorally distinct types of individuals (castes) arise among members of closely-related families (colonies), and because of this, production of such castes is not genetic, but environmentally and epigenetically induced. Importantly, different castes typically exhibit often-extreme differences in behavior, physiology, and lifespan, which can be up to 20-fold longer in queens compared to workers Our lab employs two complementary ant systems as models to understand conserved and novel features governing the regulation of plasticity of behavior and lifespan. Interests: Gene regulation, hormonal signalling, molecular and cellular determinants of aging and lifespan; Mechanisms and evolution of plasticity; Arthropod genomics; Video games
Herrera-Perez
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
The Herrera lab specializes in the study of principles and applications of cellular self-organization. We study both cell-cell and cell-environment dynamic relationships that drive the emergence of structure and function in multicellular systems. We are particularly interested in the role of the cellular microenvironment (mechanical cues and external constraints) as dynamic factors controlling tissue self-organization. We currently perform experiments with cell engineering, molecular biology, advanced confocal microscopy, and cell mechanics in cultured cells and in the developing embryo of the fruit fly. The long-term goal of our research centers in the construction of organized living structures with designed functionalities and three-dimensional forms that can be used to improve tissues models and to develop new engineered biological machines.
Holz Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Current research focuses on teaching effectiveness and use of open educational resources. Research opportunities typically, but not strictly, limited to summer semester. Ability to offer paid position contingent upon securing funding. Interests: Pedagogy; Open educational resources; Equity in education; Physiology, Anatomy, Toxicology Skills our lab is looking for: completion of BIOL204 or BIOL217L course
Lambert Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
We study the cellular and molecular mechanisms underlying animal development, and how these mechanisms can influence evolutionary change. We focus on embryos of molluscs and related animals, because of their large accessible cells, invariant cleavage patterns, informative phylogenetic position in the animal kingdom, and (of course!) their intrinsic beauty. Molluscs are representatives of a large clade of protostome phyla--the Lophotrochozoa--where molecular mechanisms of development are poorly understood. In addition, molluscs typify spiral cleavage, a dominant mode of early development in multiple protostome phyla and a developmental trait with an interesting evolutionary history. These embryos are amenable to a variety of classical embryological manipulations, allowing functional tests of hypotheses about patterning mechanisms. We are pursuing questions about several aspects of early patterning in the snail Ilyanassa, from the mechanisms of asymmetric cell division to signaling by the molluscan embryonic organizer. Our findings are providing new insights into the diversity of developmental mechanisms found in animals, as well as a clearer picture of how such processes evolve. Interests: The evolution of developmental mechanisms; Early patterning in molluscs and related groups; Cytoskeletal basis of asymmetric cell divisions; Evolution of novel phenotypes
Larracuente Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Conflict arises within genomes when genetic elements fail to play by the same rules. Selfish genetic elements (e.g. transposable elements, meiotic drivers, satellite DNAs) create conflict when they gain a transmission advantage to the next generation, often at a cost to the host. The Larracuente lab is interested in the mechanisms used by these selfish genetic elements to cheat and their impacts on the evolution of genomes and gametogenesis. Our focus is on the large blocks of rapidly evolving repeats that comprise most eukaryotic centromeres, telomeres, and sex chromosomes—satellite DNAs (satDNAs). SatDNAs play important roles in chromosome segregation and heterochromatin formation, but they also have the capacity to be selfish in the female germline, where there is an opportunity for centromeres to cheat their way into the egg. Misregulating satDNA is associated with genomic instability, mitotic defects, cancer, and aging phenotypes. We integrate methods in functional genomics, population genetics, and molecular genetics to study selfish repetitive sequences involved in intragenomic conflicts. Interests: Evolutionary genetics and genomics; Intragenomic conflict and the evolution of selfish DNA; Evolutionary and functional genomics of satellite DNA; Sex chromosome and dot chromosome evolution in Drosophila; Centromere organization and evolution Skills our lab is looking for: Genetics, molecular biology, computational biology
Meyer Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our research focuses on understanding and manipulating the conserved pathways used by organisms to defend themselves against damaging environmental agents. We use quantitative techniques in the fields of biophysics, biochemistry and microbiology to study structural dynamics, macromolecular interactions, and physiological responses to environmental stressors. We are also using tools of synthetic biology to engineer novel functions into microorganisms. Our focus is on the production of improved biomaterials and the development of new tools for 3D patterning of bacteria. This approach will lead to tunable fabrication of materials in a simple, environmentally-friendly manner. Interests: Synthetic biology; 3D printing of bacteria; Engineering of bacteria to produce biomaterials; Survival strategies of bacteria; Organization of bacterial DNA
Minckley Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Interests: Ecology and evolution of host breadth in bees; Community structure of desert bees; Conservation biology of pollinators
Murphy Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our lab investigates the mechanisms that activate or silence genes. As cells divide during development, changes in gene expression provide each cell type with a specific identity and function. In a similar sense, when the gene expression patterns of normal adult cells change inappropriately, the cell identity also changes, and this can lead to carcinogenesis. We utilize the zebrafish model in combination with mammalian cell lines to investigate how epigenetic marks control gene expression patterns to drive cell state transitions. This work relies on classic genetics and developmental biology methods, new DNA sequencing technologies, and bioinformatics applications. Interests: Regulation of vertebrate gene transcription in vivo; Epigenetics and chromatin; Zebrafish genetics and genomics; Developmental cell state transitions; Bioinformatics
Peter Lab
University of Rochester
Research Group
Applied Mathematics, Biological Sciences: Computational Biology, Biological Sciences: Ecology and Evolutionary Biology, Biology, Data Science, Statistics
Natural and Biomedical Sciences
We are a computational biology lab, and we work on a wide array of statistical and computational population genetic methods. We are particularly interested in the following topics: - Methods for the analysis of low-coverage ancient DNA - Neandertals, Denisovans, modern humans, and our interactions -Models for complex spatiotemporal population genetic structure - Visualizing genetic data Interests: Population genetics; Evolutionary genetics; Human genetic history; Ancient DNA; Population structure
Portman Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
The Portman laboratory studies the genetic mechanisms that generate sexual dimorphism in development and behavior. Our efforts focus on the powerful nematode model system Caenorhabditis elegans, because of its exceptional tractability and conserved battery of genetic mechanisms. By its nature, our work is fundamentally interdisciplinary, drawing from molecular genetics, developmental biology, molecular/cellular neuroscience, and animal behavior. Understanding sex differences in development and behavior is not only of biological interest; we hope to also understand the genetic basis for the significant sex differences in the incidence of neurological and mental health disorders such as mental retardation and autism. Interests: Genetics of development and behavior in C. elegans; Neural cell fate specification; Sex differences in neural circuit function; Sexual dimorphism in developmental patterning
Presgraves Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
We study the evolution & consequences of selfish genetic elements. Recurrent invasion & innovation by selfish genetic elements and suppression & counter-innovation by hosts are major, if still unappreciated, drivers of genome evolution. Our lab combines classical, molecular, and evolutionary genetics & genomics to study how selfish genetic elements— such as transposons and meiotic drivers— affect speciation, sex chromosome evolution, and meiotic recombination. Interests: Evolutionary genetics ; Speciation genetics; Molecular population genetics; Selfish gene complexes
Seluanov Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our research focus is on understanding the mechanisms of longevity and cancer resistance. Aging is the major cause of death in developed countries. By finding ways to delay aging it will be possible to delay the onset of multiple age-related diseases. Cancer is another major killer in developed world, where 25% of human mortality is caused by cancer. Cancer incidence increases exponentially with age and to achieve long-life species must evolve efficient tumor suppressor mechanisms. Our goal is to understand such mechanisms in mammalian species that are naturally cancer-resistant. Interests: Molecular and cell biology; Tumor suppressor mechanisms in log-lived rodents the Naked Mole-Rat and Eastern Grey Squirrel; Mammalian Sirt proteins in regulation of stress response during aging; Anti-cancer mechanisms in whales
Sterne Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
The overarching goal of the Sterne Lab is to understand the neural circuit mechanisms that generate and shape complex feeding behaviors. To survive, animals must successfully derive energy from their environments. Moment to moment control of feeding requires the synthesis of diverse and sometimes conflicting inputs, including external sensory information, internal state, and experience. The most salient features of these diverse inputs must be translated into neural activity and processed by circuits that select and shape sequenced and rhythmic feeding motor programs. Furthermore, feeding experiences must be remembered to instruct future behavior. While disordered feeding is the cause of many human health conditions, the circuit mechanisms that give rise properly timed, coordinated, and rhythmic feeding behaviors and translate feeding experiences into memory are not well understood.
Albert Uy Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
For nearly two decades, our research has focused on understanding the origin and maintenance of biological diversity in the tropics, the cradle of our planet’s diversity. Our work explores how populations change to adapt to their physical and social environments, and how these changes, in turn, can result in reproductive barriers. To this end, my research group explores two major foci. First, we explore how changes in the ways animals communicate can lead to reproductive barriers between populations — the hallmark of biological species. For instance, we explore how changes in plumage color and song in birds, which are traits used in choosing and competing for mates, can result in premating reproductive barriers between populations. Second, we explore how populations change to more effectively exploit their biotic and abiotic environments, and how these changes can likewise lead to reproductive barriers and the maintenance of species boundaries. We explore, for example, how novel environments, including urbanization, drive changes for more efficient feeding and communication. For both foci, we take advantage of species with populations currently adapting to their environment and/or are on the verge of becoming new species. In these projects, we use an integrative approach to determine the molecular basis and genomic consequences of adaptive change by combining long-term field observations and experiments with cutting-edge approaches in genomics, proteomics, and developmental biology. Interests: Evolutionary Ecology; Behavioral Ecology; Evolutionary Genetics; Speciation; Conservation
Floria Uy Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Our research is focused on understanding the evolution of cooperation and the selective pressures that favor cooperative group living. How do social animals process information from their physical and social environment to make decisions that enhance their survival and reproductive success? In animal societies where group members are constantly interacting, how do these interactions shape brain architecture and function? How can certain social insects persist in broad distributions with different environmental pressures? More recently, we also explore the effect of behavioral manipulation by parasites in these insect societies. We use an integrative approach to investigate the relationship among relatedness, social interactions, behavior cues, environmental factors and brain architecture in group formation and cooperation. Interests: Evolution of sociality; Neuroethology; Host-parasite interactions; Behavioral Ecology; Conservation
Wang Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
The major criterion distinguishing eukaryotes from prokaryotes is the presence of organelles in the former. An organelle is a subcellular structure that has one or more specific jobs to perform in the cell, much like an organ does in the body. Eukaryotic cells can rapidly adjust the abundance, size and shape of their organelles according to physiological needs. This remarkable capacity for adaptation enables cells to maintain homeostasis during stress, differentiation and disease. We are interested in the mechanisms cells use to ensure organelle homeostasis. We study the following two processes: 1) organelle biogenesis, including morphology generation, organelle inheritance during cell division, protein import and lipid transfer during organelle de novo synthesis 2) organelle degradation, particularly through the receptor-mediated selective autophagy pathway. Interests: Cell biology, biochemistry, and molecular genetics; Organelle biogenesis; Organelle degradation through selective autophagy; Organelle aging and neurodegeneration
Welte Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Cells are highly dynamic systems, in which many components are in constant flux: these include molecules, supramolecular complexes, and even entire organelles. They are continually generated, reorganized, relocated, and destroyed. Intracellular trafficking is highly directed in space and carefully controlled in time. The Welte laboratory studies the molecular mechanisms and biological roles of two types of trafficking events: the exchange of proteins between lipid droplets, cytoplasmic fat storage organelles, and the nucleus, as well as the motor-powered transport of various cargoes along microtubules. We employ Drosophila models in which we can combine in vivo visualization with molecular genetics approaches. We dissect the molecular mechanisms of these trafficking events and determine the consequences of disrupted trafficking at the organismal level. Our research is very visual and generates striking images. Currently, we work in three general areas: the role of lipid droplets as sequestration sites for nuclear proteins, the mechanism by which a nesprin family member modulates motor-driven transport, and the temporal regulation of lipid-droplet motion. Interests: Cell and developmental biology; Intracellular trafficking of proteins, RNAs, and organelles; Regulation of motor-driven transport; Cell biology of lipid droplets; Lipid droplets in protein sequestration and innate immunity
Werren Lab
University of Rochester
Research Group
Biology
Natural and Biomedical Sciences
Dr. Werren's area of interest is evolutionary genetics. His research combines genetic, molecular, and population studies to investigate a variety of topics in evolution. Current research topics include: (1) evolution of inherited microorganisms, (2) genetic basis of morphological and behavioral differences between species, and (3) genetic conflict and the evolution of "parasitic" or "selfish" DNA. Interests: Evolutionary genetics, genomics, and proteomics. The unifying theme is how interacting elements shape systems at different levels of biological organization. A current research project focuses on combining computational and molecular evolutionary approaches to investigate protein function and protein-protein interactions relevant to biology and disease. Other research topics include the genetics of speciation, nuclear-mitochondrial coevolution, microbe-host interactions, and parasitism across biological levels.
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