URAP

Bassem Al-Sady - Professor, UC San Francisco

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

Genes in our genome can be kept in active or inactive states in different cell types. Genes coding for opposing cell types are heritably kept inactive. This is possible because a gene repressive structure called heterochromatin can “grow” over regions containing these genes in some, but not other cell types...

Nima Alan - Professor, UC San Francisco

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

Assistant will remotely call patients before and after surgery to collect data and will review medical records for retrospective databases. Assistant will also have the opportunity to shadow in clinic and assist with in-person research tasks...

James Bayrer - Professor, UC San Francisco

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

The intestinal lining undergoes continual renewal, with a near total turnover of epithelial cells occurring every week. Powering this metabolically intense task are the intestinal stem cells that divide and restore the intestine. Understanding how intestinal stem cells can both contribute to normal homeostasis and the repair of damaged tissue...

Jeff Belkora - Professor, UC San Francisco

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

SPECIAL ANNOUNCEMENT: INFORMATION SESSION AUG 28 *** UPDATE 8/21/25: I will host a PSC information session on 8/28 at 6 pm on campus, in person. There's a challenge: I can't reserve a classroom (Berkeley rules for the first weeks of term). So I can't tell you the location yet. Also, the...

Jan Christoph - Professor, UC San Francisco

Status: Full- no new appr needed     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: Full- no new appr needed     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: Full- no new appr needed     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: Full- no new appr needed     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...

Joline Fan - Professor, UC San Francisco

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

Our research focuses on deciphering the network mechanisms underlying the rich relationship between sleep and epilepsy. As human sleep networks have been largely studied using surface EEG with low spatial resolution and PET/fMRI, we employ recording modalities with high spatial-temporal resolution of whole-brain functional activity, e.g. magnetoencephalography...

Trevor Fidler - Professor, UC San Francisco

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

We’re interested in identifying pathways which regulate macrophage function in atherosclerosis. In inflammatory sites like atheromas, macrophages accumulate, phagocytise necrotic cells, and uptake lipids leading to foam cell formation. Recent single-cell RNA sequencing has revealed that within these tissue macrophages can adopt multiple transcriptional states which can promote or...

Trevor Fidler - Professor, UC San Francisco

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

We’re interested in understanding why clonal hematopoiesis is associated with cardiovascular disease. Clonal hematopoiesis is a high prevalent disease in the elderly which occurs when hematopoietic stem cells acquire cancer mutations that promote cell survival. People with clonal hematopoiesis have a 40% increase in mortality. However, rather surprisingly this increase...

Peng He - Professor, UC San Francisco

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

This project focuses on applying and benchmarking state-of-the-art machine learning models—including foundation models like GeneFormer and SCimilarity—for automated cell type annotation using single-cell and spatial genomics data. The goal is to overcome the bottleneck of manual cell type labeling in large-scale datasets by...

Peng He - Professor, UC San Francisco

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

This project centers on the use of human lung organoids—three-dimensional miniature tissue models derived from stem cells—to study how stem cells make fate decisions. In particular, it investigates how stem cells commit to the neuroendocrine lineage, a process with direct relevance to understanding the development of neuroendocrine...

Peng He - Professor, UC San Francisco

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

This project investigates how cells behave and interact in their native environments by analyzing spatial gene expression data. Interns will use Visium and Xenium spatial transcriptomics datasets to identify tissue microenvironments, reconstruct 3D spatial maps, and apply computational tools like NicheFormer...

Peng He - Professor, UC San Francisco

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

This project focuses on building robust and reusable computational pipelines to analyze bulk and single-cell transcriptomics data. Students will contribute to bioinformatics workflows for data processing, integration, and visualization across various tissues and disease contexts, including fibrosis and vascular diseases...

Roland Henry - Professor, UC San Francisco

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

The ability to quantitatively measure changes to the central nervous system is approaching a crucial milestone for neuro-imaging - the ability to measure change on an individual patient level. The Multiple Sclerosis Center at UCSF, in concert with our partners, has prioritized the development of a panoply of neuro-imaging...

Roland Henry - Professor, UC San Francisco

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

UCSF’s Department of Radiology and Biomedical Imaging and Department of Neurology are excited to offer a combined educational and research opportunity for motivated undergraduate students in the medical imaging research team. 3D segmentation of structures in the brain and spinal cord is a problem that deep learning is uniquely equipped...

Roland Henry - Professor, UC San Francisco

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

UCSF’s Department of Neurology has some of the largest clinical neuroimaging datasets in the world. As the director of imaging for the multiple sclerosis group, Dr. Roland Henry’s laboratory is in charge of making sense of this data and applying next generation analytical techniques to translate this raw data into...

Julian Hong - Professor, UC San Francisco

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

The Hong lab is part of the UCSF Department of Radiation Oncology and Bakar Computational Health Sciences Institute. We focus on combining clinical domain knowledge with data science to generate insights from real world data, develop actionable computational tools, and evaluate the benefit of these advances for personalized cancer care...

Guo Huang - Professor, UC San Francisco

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

As shown in our recent publication (Hirose*, Payumo*, et al Science 2019), we aim to understand the divergent regenerative potential in ontogeny and phylogeny. For example, heart regeneration is remarkably robust in adult zebrafish and newborn mice while very limited in adult mammals. We use the heart as a model...

Guo Huang - Professor, UC San Francisco

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

We aim to study whether there are extreme physiological phenomena (1) in individuals with healthy low heart rates (less than 45 beats/min) and (2) among identical twins that can not be explained by any known biological mechanism. We will exploit classical and non-classical model systems to explore these...

Guo Huang - Professor, UC San Francisco

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

Current studies of mouse heart regeneration are largely limited to postmortem analysis of heart tissue to explore cellular activity and molecular mechanisms. We aim to combine a novel imaging window system designed and surgically implanted on the mouse chest by the Huang Lab at UCSF with the free-space angular...

Guo Huang - Professor, UC San Francisco

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

There are emerging AI-trained models that integrate tremendous genomic, genetic and gene expression datasets to successfully predict complex gene networks and functional outcomes after in silico gene perturbation. Now we are exploring these models to understand organ physiology and pathology from developmental and evolutionary perspectives. ------------------------- Publications from previous URAP...

Laurence Huang - Professor, UC San Francisco

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

Chronic obstructive pulmonary disease (COPD) is the most frequent HIV-associated chronic lung disease and its clinical significance is increasing as the HIV+ population ages worldwide. Although both HIV-related and COPD-specific causes are postulated, our understanding of the mechanisms underlying HIV+ COPD is limited. An improved understanding is...

Galateia Kazakia - Professor, UC San Francisco, Electrical Engineering and Computer Science

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

Our research group focuses on advanced imaging techniques for the study of musculoskeletal structure and function (for details please see: http://www.radiology.ucsf.edu/research/kazakia). For this project, we plan to use two recently developed imaging tools to investigate the structure and composition of bone. State-of-the-art micro computed...

Galateia Kazakia - Professor, UC San Francisco, Electrical Engineering and Computer Science

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

Our research group focuses on advanced imaging techniques for the study of musculoskeletal structure and function (for details please see: http://www.radiology.ucsf.edu/research/kazakia). For this project, we will be performing advanced image processing and analysis on high resolution computed tomography (CT) images of the skeleton. These images are being...

John Liu - Professor, UC San Francisco

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

Glioblastoma (GBM) is the most common primary brain cancer. Despite decades of research to better treat this cancer, most patients unfortunately die within 2 years of diagnosis. Surgery followed by radiation therapy and chemotherapy comprise the standard of care for patients with GBM, but resistant to treatment poses a major...

Qihui Lyu - Professor, UC San Francisco

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

This project aims to improve metal artifacts in Computed Tomography (CT) images. In the presence of highly attenuating objects such as dental fillings, spinal screws/rods, hip prostheses, and gold fiducial markers, CT images are often corrupted by streak artifacts, making these images non-diagnostic and impacting the accuracy of...

Qihui Lyu - Professor, UC San Francisco

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

Targeted alpha therapy is a promising treatment technique for late stage cancer patients with metastasis, but its clinical application is limited by the current imaging capabilities. Simultaneous broad-energy imaging is critical, but the current Single-Photon Emission Computed Tomography (SPECT) can only image low energy photons with limited energy...

Qihui Lyu - Professor, UC San Francisco

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

Boron Neutron Capture Therapy (BNCT) is a targeted radiotherapy technique that relies on the preferential accumulation of boron-10 in tumor cells, followed by irradiation with low-energy neutrons to produce high–linear energy transfer alpha particles at the cellular level. Conventional BNCT uses external neutron beams, which results in...

Dengke Ma - Professor, UC San Francisco

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

Life requires a constant supply of energy, yet animals can adapt by slowing down or temporarily shutting off costly processes. One key strategy is ribosomal hibernation, in which ribosomes—the cell’s protein-making machines—pause activity to conserve resources. In the nematode C. elegans, ribosomal hibernation is linked to sleep...

Dengke Ma - Professor, UC San Francisco

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

The nematode C. elegans can be frozen alive, suspend life and revive later virtually any long after freezing, unlike many other multicellular organisms, including flies, fish, mice and humans. How C. elegans achieves this feat remains a fascinating unsolved mystery. This project will use our newly established reporters and assays...

Dengke Ma - Professor, UC San Francisco

Status: Check back for status     

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William Martinez - Professor , UC San Francisco

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

The present study is a randomized control trial to evaluate the efficacy and effectiveness of a school-based group prevention program (Fuerte) in San Francisco Unified School District (SFUSD) Public Schools. Fuerte targets newcomer Latinx immigrant youth (five years or less post arrival in the U.S.) who are at risk...

Marisa Medina - Professor, UC San Francisco

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

There are a limited number of human omics datasets that include menopausal status information for female subjects and include enough premenopausal and postmenopausal women. For instance, multi-omics data has been generated for thousands of Framingham Heart Study (FHS) participants and hundreds of TwinsUK female twin pairs. We will compare...

Marisa Medina - Professor, UC San Francisco

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

A subset of women experience an accelerated rise in certain cardiometabolic risk factors around the time of menopause, increasing their risk for heart disease and other conditions. We would like to discover why some women experience dramatic changes while others are relatively protected...

Julian Motzkin - Professor, UC San Francisco

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

When pain becomes chronic, there can be changes in brain areas involved with processing pain signals. Our research combines fMRI of pain circuits with repetitive transcranial magnetic stimulation (rTMS), a type of non-invasive brain stimulation, to determine how rTMS may alleviate difficult-to-treat pain...

Yuko Oda - Research Staff, UC San Francisco

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

The goal of our research is to identify a mechanism how somatic stem cells determine their cell fate through stage or cell specific transcriptional and epigenetic program. We hypothesized that the vitamin D receptor and its regulator of Mediator is critical for temporal or spatial specific transcription to control epithelial...

Pedro Pinheiro-Chagas - Professor, UC San Francisco

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

The UCSF Memory and Aging Center (MAC) Co-pilot project is an innovative research initiative aimed at revolutionizing the diagnosis of neurodegenerative diseases (NDD), such as Alzheimer's disease and Frontotemporal dementia, through the integration of advanced Large Language Models (LLMs). This project is particularly significant due to the high prevalence...

Pedro Pinheiro-Chagas - Professor, UC San Francisco

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

Alzheimer’s disease and related dementias are neurodegenerative diseases with numbers rapidly increasing and currently no cure. To accurately identify the earliest signs of clinical dementia, there is a critical need for sensitive, low-cost, and high-access cognitive markers in the preclinical phase. Novel cognitive markers can complement biomarker information...

Pedro Pinheiro-Chagas - Professor, UC San Francisco

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

Semantic dementia (SD) presents as a unique neurodegenerative disorder with focal atrophy of the anterior temporal lobes (ATLs). It is comprised of a primarily left-lateralized language syndrome and a right-lateralized behavioral disorder. One current challenge in this disease is in accurately identifying the distant brain regions that are...

Kamalini Ranasinghe - Professor, UC San Francisco

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

The goal of this project is to investigate the associations between anormal protein depositions in the brain and how these may change the neuronal firing in neurodegenerative diseases like Alzheimer’s disease (AD). We use magnetoencephalography (MEG) electroencephalography (EEG) to record the activity of neurons and molecular imaging to quantify amyloid...

Hilde Schjerven - Professor, UC San Francisco

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

The Schjerven Lab at UCSF studies the transcription factor Ikaros (encoded by the Ikzf1 gene) and its different biological roles in immune cell development and disease. In a recent collaborative work, we found that the transcription factor Ikaros is expressed in medullary thymic epithelial cells (mTEC), and important for the...

Hilde Schjerven - Professor, UC San Francisco

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

The Schjerven Lab at UCSF studies the transcription factor Ikaros (encoded by the Ikzf1 gene) and its different biological roles in immune cell development and disease. We have found that the transcription factor Ikaros is important in development of eosinophils, a type of white blood cell that is part of...

Hilde Schjerven - Professor, UC San Francisco

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

The Schjerven Lab at UCSF studies the transcription factor Ikaros (encoded by the Ikzf1 gene) and its different biological roles in immune cell development and disease. Ikaros is an important tumor suppressor in B-cell lineage acute lymphoblastic leukemia, and we have multiple projects in our lab to study how...

Youngho Seo - Professor, UC San Francisco

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

Keywords: cancer, radiopharmaceutical therapy, targeted alpha therapy, alpha particles, image processing, dosimetry, machine learning, digital autoradiography Radiopharmaceutical therapy with alpha-particle emitters (⍺RPT) is an emerging cancer treatment method that has demonstrated high efficacy in clinical trials for several types of cancer. Improvement of these drugs requires thorough pre-clinical...

Youngho Seo - Professor, UC San Francisco

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

Molecular imaging is a powerful method of interrogating biochemical properties of imaging subjects. Particularly in research, we use small animal positron emission tomography (PET) and single photon emission computed tomography (SPECT), which are combined with x-ray computed tomography (CT). More commonly, these imaging modalities are known as microPET/CT...

Youngho Seo - Professor, UC San Francisco

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

Radiotherapy with alpha-emitting nuclides is an extremely promising technique in cancer therapy. The very short range of alpha particles compared to beta particles allows to deliver a much higher therapeutical dose to the lesion, sparing healthy tissue. A fundamental problem with this technique is the inability of current radiation...

Youngho Seo - Professor, UC San Francisco

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

Keywords: image processing, image analysis, segmentation, medical imaging, PET, MRI, cardiac efficiency Myocardial injury causes how the heart muscle consumes energy and converts it to the work required for heart function. This damage could be either localized or global; however, to gain this knowledge, we should compute the local myocardial...

Jae Ho Sohn - Professor, UC San Francisco

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

Radiologists are doctors who specialize in extracting clinically useful information from medical images (such as CT, chest X-ray, and MRIs) and communicating these findings with other doctors. We leverage abstract clinical reasoning and visual pattern recognition skills to extract hidden information in the images that may be important for...