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...

Sergio Arroyo - Professor, UC San Francisco

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

The goal of this project is to investigate the role of cell-type specific inhibition in learning a sensorimotor task. We use calcium imaging and electrophysiological recordings with 'optotagging' to record the activity of specific inhibitory cell tasks as mice learn a cued go task. We aim to understand how...

John Chorba - Professor, UC San Francisco

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

Jennifer Dunn - Professor, UC San Francisco

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

This project will take an interdisciplinary approach to study the phenomenon of health care segregation in the United States through historical and legal research and qualitative methods. Students will have the opportunity to engage in online and archival research, transcribe and analyze audio files of interviews, write literature summaries, and...

Joline Fan - Professor, UC San Francisco

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

We’re interested in identifying pathways which regulate how macrophage behave in atherosclerosis. In inflammatory sites like atheromas, macrophages accumulate. Recent single cell RNA sequencing has revealed that within these tissue macrophages can adopt multiple transcriptional states which can promote or suppress disease. We are currently utilizing CRISPR screening in vivo...

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...

Aaron Fields - Professor, UC San Francisco

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

Many painful pathologies of the spine involve the first sacral (S1) vertebra. For example, damage to the endplates of S1 (in particular, the region near the lumbar intervertebral disc) can cause painful lesions in the vertebral bone marrow—such lesions are relatively common in patients with chronic low back pain...

Aaron Fields - Professor, UC San Francisco

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

Advances in magnetic resonance imaging (MRI) technology enable novel, quantitative, and non-invasive estimation of the biochemical composition of musculoskeletal tissues. The new ability to non-invasively assay tissue composition using MRI has major implications for understanding spinal pathologies related to low back pain, such as intervertebral disc degeneration. Recent...

Aaron Fields - Professor, UC San Francisco

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

The Orthopaedic Biomechanics and Biotransport Laboratory at UCSF conducts research related to structure-function relationships in musculoskeletal tissues, with a particular focus on the mechanisms of nutrient transport in bone and cartilage and harnessing nutrient transport for tissue repair and regeneration. The lab combines engineering and biology approaches for (1...

Aaron Fields - Professor, UC San Francisco

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

The Orthopaedic Biomechanics and Biotransport Laboratory at UCSF conducts research related to structure-function relationships in musculoskeletal tissues, with a particular focus on the mechanisms of nutrient transport in bone and cartilage and harnessing nutrient transport for tissue repair and regeneration. The lab combines engineering and biology approaches for (1...

Peng He - Professor, UC San Francisco

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

This cutting-edge research project focuses on developing and optimizing machine learning tools to automatically identify cell types and states from single-cell genomics data. Single-cell technologies have revolutionized our understanding of cellular diversity, but the manual annotation of cell types remains a significant bottleneck in data analysis. This...

Peng He - Professor, UC San Francisco

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

This project investigates the fascinating world of long non-coding RNAs (lncRNAs) and their crucial role in maintaining stem cell pluripotency. While most RNA molecules are known to encode proteins, lncRNAs represent a mysterious class of RNAs that regulate gene expression through various mechanisms. This research focuses on understanding how...

Peng He - Professor, UC San Francisco

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

This innovative research project aims to uncover the complex organization of tissues by analyzing spatial gene expression patterns. Using cutting-edge spatial transcriptomics technology, we can now measure gene expression while preserving information about where cells are located within a tissue. This project will adapt and apply advanced analytical methods...

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...

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: Current Term Now Closed     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...

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...

Dengke Ma - Professor, UC San Francisco

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

Genome evolution has enabled organisms to live in and adapt to nearly every ecological niche on Earth. Humans live in an oxygen-rich ecosystem and human tissues are susceptible to deprivation of oxygen (hypoxia) under pathological conditions, including ischemic stroke and heart attack. Many organisms, from anaerobic bacteria to hibernating...

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...

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...

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...

Pedro Pinheiro-Chagas - Professor, UC San Francisco

Status: Check back for status     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: Current Term Now Closed     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...

Eva Raphael - Professor, UC San Francisco

Status: Check back for status     Weekly Hours: 6-8 hrs     Location: On Campus

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, particularly among urban-dwelling women. UTIs are primarily caused by Escherichia coli (E. coli). UTIs may cause a range of complications from mild discomfort to severe kidney infections. As antibiotic resistance increases, treatment strategies for UTIs become ineffective...

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

Keywords: deep learning, artificial intelligence, prediction, Alzheimer's disease, positron emission tomography, PET, image processing, FDG, glucose metabolism, amyloid Alzheimer's disease (AD) is the most common type of dementia, and a debilitating condition that affects a large number of aging populations. When symptoms occur, there are a very limited set of...

Steven Seyedin - Professor, UC San Francisco

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

For patients with limited metastatic (stage IV) bladder cancer, high dose, high precision radiation therapy known as stereotactic body radiation therapy (SBRT), to all sites of disease can improve cancer outcomes and extend the time to needing additional therapy. However which patients truly benefit from SBRT is unclear. This study...

Jae Ho Sohn - Professor, UC San Francisco

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

Vasanth Vedantham - Professor, UC San Francisco

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

The heart’s spontaneous rhythmicity has fascinated natural scientists from antiquity to the present. Particularly in the form of the palpable pulse, heart rhythm has always been among the most accessible physiological parameters to physicians, athletes and lay people, and yet the evolution, ontogenesis, and regulation of the heartbeat have remained...

Wendy Yue - Professor, UC San Francisco

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

Spiny mice are among the few mammals capable of shedding and regenerating large areas of skin, a unique adaptation that helps them escape predators. However, this ability comes with a challenge: how do they manage the pain from such severe injuries? This project aims to investigate potential mechanisms that allow...