URAP

Reza Abbasi-Asl - Professor, Neuroscience

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: Off Campus

Deep neural networks achieve state-of-the-art performance in many tasks such as computer vision and natural language processing. Interpreting deep networks is essential for applying them to scientific applications such as healthcare. Two prominent approaches to interpret neural networks are saliency methods and network compression. However, both methods...

Reza Abbasi-Asl - Professor, Neuroscience

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: Off Campus

Characterizing the the neural function in the brain and its relationship with connectivity is an eminent question of visual sensory processing. With the recent increase in the amount of the data collected from brain, tools based on machine learning principles play an essential role in understanding the brain function. The...

Reza Abbasi-Asl - Professor, Neuroscience

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: Off Campus

Computational tools based on machine learning principles have shown promising results in analyzing medical images. Deep convolutional neural networks (CNNs) are one of the most successful tools in this domain. While most of the algorithms based on CNNs are supervised and with the increasing amount of un-labeled datasets, it...

Reza Abbasi-Asl - Professor, Neuroscience

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: Off Campus

There is an immense amount of unstructured and uncollated data in neuroscience and bioinformatics that could be used to guide knowledge discovery. Large language models (LLMs) have shown potential in extracting and analyzing unstructured natural language corpora and are promising for semi-automated processing of text into scientific knowledge such...

Rodrigo Almeida - Professor, Environmental Science, Policy and Management

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Grapevine leaf roll disease and red blotch disease are two economically important grape pathogens in California. The diseases are currently not curable, so mitigation efforts including roguing (removing infected plants) are used to reduce disease spread. Roguing requires correctly identifying infected plants, which can be difficult to do visually due...

Rodrigo Almeida - Professor, Environmental Science, Policy and Management

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Xylella fastidiosa is a xylem-limited bacterium associated with several important diseases in a wide range of plants. In California, the bacterium causes Pierce's Disease (PD) of grapevine, which has economic and management implications for the state's wine industry. The range of PD in California is limited by cold winter...

Christopher Ames - Professor, Neurological Surgery

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

At UCSF Spine Center, we have a number of studies related to patient outcomes after surgery. We have studies on frailty, pain and pain medication, personality changes from surgery, surgical complications, analysis of patient-reported outcomes with natural language processing, the effectiveness of a pre-habilitation program, and the effectiveness...

Colette (Coco) Auerswald - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Youth and Allies Against Homelessness (YAAH) is a research team based in i4Y (Innovations for Youth), a Berkeley School of Public Health research center. YAAH is made up of youth community members with lived experience of homelessness and undergraduate and graduate students who have experienced homelessness and/or who have...

Colette (Coco) Auerswald - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Youth and Allies Against Homelessness (YAAH) is a research team based in i4Y (Innovations for Youth), a Berkeley School of Public Health research center. YAAH is made up of youth community members with lived experience of homelessness, undergraduate and graduate students who have experienced homelessness and/or who have demonstrated...

Barbara Baker - Professor, Plant and Microbial Biology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: Off Campus

In eukaryotes, small RNAs (20–30 nt) derived from double stranded RNA precursors direct proteins to regulate chromatin function, transcription, RNA stability, and translation through sequence-targeted mechanisms termed RNA silencing. Two main categories of plant small RNAs, microRNAs (miRNAs) and short interfering RNAs (siRNAs), guide cleavage of mRNA and...

Jeff Belkora - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: Off Campus

STUDENT TESTIMONIALS “This apprenticeship has been the highlight of my time at Berkeley. It has given me a chance to help patients in difficult medical situations, and as a pre-health undergraduate, this is important to me.” “It is a great opportunity to get clinical experience and work with like...

Stefano M. Bertozzi - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Rapid Reviews\Infectious Diseases (RR\ID) [rrid.mitpress.mit.edu], is an initiative of the MIT Press and the University of California, Berkeley. It is an open access, rapid-review overlay journal for the accelerated curation and peer review of COVID-19 and emerging infections disease-related research. RR\ID takes a transdisciplinary...

Stefano M. Bertozzi - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Rapid Reviews\Infectious Diseases (RR\ID) [rrid.mitpress.mit.edu], is an initiative of the MIT Press and the University of California, Berkeley. It is an open access, rapid-review overlay journal for the accelerated curation and peer review of COVID-19 and emerging infections disease-related research. RR\ID takes a transdisciplinary...

Stefano M. Bertozzi - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

Psychiatric disorders including PTSD; and alcohol use disorder and other addictions are responsible for a large portion of both the global burden and US burden of disease. Current therapies help some people suffering from these disorders. Nevertheless, many patients do not respond adequately or cannot tolerate the side-effects accompanying...

Stefano M. Bertozzi - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: Off Campus

The last few decades have seen growing acknowledgement and emphasis on the need to bridge gaps between research and practice. Implementation Science (IS) is the scientific study of methods to promote the systematic uptake of research findings and other evidence-based practices into routine practice. An evolving and interdisciplinary field...

David Bilder - Professor, Molecular and Cell Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Malignant tumors are distinct from benign growths in their ability to hijack and disrupt various processes in the body. Some common examples that most people are familiar with are tumor invasion of adjacent tissues, recruitment vasculature to accelerate growth, and dissemination of metastasizing cells. However, a less well-appreciated fact...

Benjamin Blackman - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

In order to test the function of specific genes or the impact of genetic variants on phenotype, genetic manipulation is required. The aim of the project is to assist with development and implementation of methods for genetic transformation of sunflower and monkeyflower, the two main study systems in the lab...

Benjamin Blackman - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

A major focus of our lab is identifying how genetic and phenotypic variation that has evolved among plant populations adapts plants to their local climates and habitats. Understanding how these adaptations to climate variation across space have evolved will help us understand mechanisms by which plants can evolve to cope...

Benjamin Blackman - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Flowering and reproduction are highly regulated processes in composite plants like sunflower which produce disks that are clusters of many individual flowers. Environmental cues like light and temperature interact with the circadian clock regulate what time of the season buds first start to develop, and the same integration of internal...

Benjamin Blackman - Professor, Plant and Microbial Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

During floral development, patterns of pigment are painted on to the petals of many plants, and these pigments often serve to attract and direct bee pollinators toward pollen and nectar rewards. We have found several natural variants affecting the nectar guide pigmentation patterns of the common monkeyflower in both the...

Mike Boots - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Our research group in the Department of Integrative Biology researches the dynamics of infectious disease evolution and population biology in multiple insect systems, including Lepidopteran hosts (moths and butterflies). We are currently working on two interconnected projects: The first project investigates host heterogeneity by examining how environmental factors (such as...

Mike Boots - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Interactions between infectious diseases and their hosts underpin a vast array of ecological and evolutionary dynamics. These antagonistic biotic interactions may influence processes like why organisms sexually reproduce and migrate and infectious disease evolution is important for many applied problems like antibiotic resistance, disease emergence, and agriculture. Many factors impact...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

We are working on a project to study the adaptation and evolutionary history of hummingbirds and sunbirds. Hummingbirds and sunbirds are two groups of birds that have independently adopted nectar as a major component of their diet and have evolved to be morphologically similar. Our project aims to explore whether...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

My lab is involved with a large collaborative project to study disease transmission within and among species of wild birds. As part of this project, swabs of a variety of bird species are being collected to study their microbial communities (i.e. their microbiome). Lab studies suggest that microbial diversity can...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Students can assist with several ongoing research projects that investigate geographic variation and species limits in birds and integrate these data with quantification of prevalence of disease vectors such as bird malaria and trypanosome infections...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Nest structures are widespread across animals including insects, fish, amphibians, and most conspicuously, birds. Despite their ubiquity, nests remain one of the most understudied components of avian life history. Some of the most remarkable examples of elaborate nest design are within the passerine weaverbirds (family Ploceidae). Weaverbirds are an Old...

Steven Brenner - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

RNA-seq has been widely used in biological and medical research because of its capability to quantify transcriptome changes. Researchers usually use their impressions and experience to choose whether to analyze transcriptome changes in gene expression or alternative splicing levels. A more systematic way to determine whether to focus on...

Steven Brenner - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Genome sequencing identifies a vast number of genetic variants. Predicting these variants’ molecular and clinical effects is one of the preeminent challenges in genetics. Accurate prediction of the impact of genetic variants improves our understanding of how genetic information yields molecular and cellular functions and is an essential step toward...

Steven Brenner - Professor, Plant and Microbial Biology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Proteins often fold into compact structural units, called domains. Protein domains are basic units of protein function and evolution. Delineating domain boundaries is a prerequisite for further analyses of protein structures. However, this process is largely a manual process and the accuracy of these computer programs is still not satisfactory...

Steven Brenner - Professor, Plant and Microbial Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

The field of genome interpretation is essential for our understanding of human biology and the advancement of personalized medicine. However, the rapid accumulation of genomic data far exceeds our capacity for reliable interpretation. Consequently, the majority of variation discovered by next generation sequencing technologies is of unknown significance. These variants...

Charles Briggs - Professor, Latinx Research Center

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Project Title: Documenting Latinx Contributions to Health Care Access and Services “That's what you call solidarity. Everybody pitching in, everybody doing their part. We each one, teach one, each one, reach one!” - Yolanda Chacon- Serna (labor organizer and health advocate) “Health is politics by other means.” Alondra Nelson, author of...

Timothy Brown - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

This project will implement and disseminate the FUTUREPAIN validated questionnaire as a screening device to determine who will benefit from a series of online mind-body interventions (affective self-awareness, mindfulness, and neurobiological education) to treat chronic pain for five chronic pain conditions. This involves developing and testing the online...

Timothy Brown - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Large racial/ethnic disparities exist in medical care. Attenuation or removal of these disparities requires a rigorous understanding of the relevant underlying mechanisms. One such mechanism is high-quality physician-patient relationships. High-quality physician-patient relationships are associated with improved health outcomes and lower costs. However, such relationships appear...

Timothy Brown - Professor, Public Health

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

This project will conduct the first systematic review and meta-analysis to identify the most effective and cost-effective intervention components for universal and targeted (indicated and selected) suicide prevention among college students in a global context. Special attention will be placed on disparities in suicide prevention across sociodemographic subgroups...

Timothy Brown - Professor, Public Health

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

This project will use simulation methods to determine the cost-effectiveness of mind-body interventions using data from randomized controlled trials, national survey data, and other resources. The goal is to publish a peer-reviewed article to help establish the value of these interventions in healthcare. This has not been...

Atul Butte - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: Off Campus

LLMs have demonstrated tremendous potential in various domains, including healthcare. However, evaluating their outputs, especially in clinical settings, presents unique challenges. This project will compare the evaluation metrics obtained from automated methods for assessing free-text outputs generated by LLMs with the assessments from expert clinical judgment. The findings will...

Lu Chen - Professor, Optometry

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Our research focuses on mechanisms and regulation of lymphatic and blood vessel formation and implications in eye diseases, such as glaucoma, inflammation, and transplant rejection. Lymphatic research represents of field of new discovery in recent years. A wide spectrum of in vitro and in vivo techniques are used in our...

John Chorba - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: Off Campus

PCSK9 chaperones the low-density lipoprotein receptor (LDLR) to the lysosome for degradation, thereby raising circulating LDL (i.e. “bad” cholesterol) and accelerating atherosclerosis and heart disease. Despite its validation as a drug target, PCSK9 has proven difficult to drug with small molecules, at least in part because of its single...

John Chorba - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

The LDL receptor clears atherogenic LDL particles from the bloodstream and plays a major role in cholesterol and membrane homeostasis. Through a genome-wide CRISPR interference screen, we identified novel regulators of the LDL receptor as potential therapeutic targets for cholesterol lowering. We have shown that CSDE1 is an RNA...

John Chorba - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: to be negotiated     

A fundamental challenge in drug discovery is that any given therapeutic target requires its own customized strategy. The discovery of a recent compound that binds the human ribosome and inhibits translation in a sequence specific manner offers the potential to “drug” protein targets without the need for a traditional active...

Jan Christoph - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Our group studies heart rhythm disorders, such as ventricular tachycardia or atrial fibrillation, using computer simulations and imaging. Heart rhythm disorders are associated with abnormal electrophysiological excitation wave phenomena in the heart muscle, which can take on complex pattern-forming and self-organizational spatio-temporal dynamics. The excitation triggers intracellular...

Jan Christoph - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Our group develops computational and experimental methods for the imaging of intact, isolated hearts ex vivo. We produce 3D imaging data using fluorescence and ultrasound imaging, see https://arxiv.org/abs/2307.07943, and we combine this data to obtain high-resolution visualizations of beating hearts and heart rhythm disorders...

Jan Christoph - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Are you a computer vision enthusiast and are you interested in applying your skills in biological research? Our group develops computational and experimental methods for the imaging of the heart and heart rhythm disorders. We have developed a novel panoramic high-speed fluorescence imaging setup for the imaging of the...

Jan Christoph - Professor, UC San Francisco

Status: Current Term Now Closed     Weekly Hours: 12 or more hours     Location: On Campus

Our group studies the heart from a complex biological system's perspective und we use computer simulations to study cardiac dynamics during disease and development. In the heart, electrical excitation propagates from cell to cell through ion channels and triggers mechanical contraction and deformation in each cell. This leads to waves...

Susana Chung - Professor, Optometry

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

This research project focuses on the understanding of how the visual system works in people with normal vision, as well as in people with uncorrectable sub-normal vision (visual impairment). Uncorrectable sub-normal vision can occur as a result of an eye disease (e.g. macular degeneration, the leading cause of...

Susana Chung - Professor, Optometry

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

This research project focuses on the understanding of how the visual system responds to the onset of vision loss as a result of eye diseases. By understanding how the visual system responds to vision loss, our ultimate goal is to develop effective rehabilitative strategies to help people with vision loss...

Susana Chung - Professor, Optometry

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

The research project focuses on the understanding of how the visual system recognizes faces and other objects in normally sighted people and people with low vision. Psychophysical methods, retinal imaging and functional brain imaging will be used to answer the research question...

Susana Chung - Professor, Optometry

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Loss of vision in the central visual field brings about dramatic changes to everyday activities (e.g. reading, identifying objects). This research project focuses on identifying how the informative features of objects contribute to overall visual function, with the clinical goal of visual performance improvement by enhancing selected parts of objects...

Carla Cicero - Emeritus Staff Curator, Museum of Vertebrate Zoology

Status: Current Term Now Closed     Weekly Hours: 3-5 hrs     Location: On Campus

UC Berkeley's Museum of Vertebrate Zoology is a major repository for surveyed and/or salvaged North American wildlife, especially California species. We typical have several thousand frozen carcasses at any given time, with a large diversity of amphibians, reptiles, mammals, and birds. These carcasses come from many sources -- wildlife rescue...

Carla Cicero - Emeritus Staff Curator, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 3-5 hrs     Location: On Campus

Students will assist with research projects that investigate geographic variation and species limits in birds. Work may involve morphologic measurements, color measurements, DNA laboratory work, and/or sound analysis. Positions are not available every semester, and students must already have some experience in the MVZ working with specimens and data...