Research by Faculty
Parnassus/Mt. Zion/Mission Bay
- Mustafa Arain
- Jody Baron
- Kendall Beck
- D. Montgomery Bissell
- Danielle Brandman
- Najwa El-Nachef
- Bilal Hameed
- Priya Kathpalia
- Michael Kattah
- Jennifer Lai
- Sara Lewin
- Susan Lynch
- Averil Ma
- Uma Mahadevan
- Barbara Malynn
- Neil Mehta
- James Ostroff
- Marion Peters
- Jennifer Price
- Jean Publicover
- Monika Sarkar
- Courtney Sherman
- Aparajita Singh
- Jonathan Terdiman
- Norah Terrault
- Bruce Wang
- Michael Whang
- Francis Yao
- Nathan Bass
- Robert Ockner
- Richard Weisiger
Zuckerberg San Francisco General
- Jeffrey Baumgardner
- Laura Bull
- John Cello
- Jennifer Chen
- Sun-Chuan Dai
- Lukejohn Day
- Mandana Khalili
- Jacquelyn Maher
- Melanie Ott (Gladstone Institute)
- Justin Sewell
- Ma Somsouk
- Michele Tana
San Francisco Veterans Affairs
- Christopher Hamerski
- Tonya Kaltenbach
- Kenneth McQuaid
- Alexander Monto
- Andrew Nett
- Robert Owen
- James Ryan
- Amandeep Shergill
Parnassus/Mt Zion/Mission Bay
Dr. Baron’s research focuses on the immune response to hepatitis B infection. She has successfully modeled the immune response that follows primary HBV infection using specialized transgenic mouse systems. She recently uncovered age-dependent differences in the immune response to hepatitis B that mimic differences seen in humans (young individuals tend to develop persistent infection, whereas adults tend to clear the virus). Her lab is working to identify factors that contribute to age-related differences in the immune response to HBV.
Dr. Beck's interests include general gastroenterology, as well as inflammatory conditions of the bowel with a focus on short bowel syndrome and intestinal rehabilitation.
Dr. Bissell is an expert in cell and extracellular matrix biology with a focus on the liver. He has made seminal contributions to hepatology research including the development of methods for primary hepatocyte culture and the identification of stellate cells as the principal collagen producers in the liver. He also studied the involvement of hepatic progenitor cells in the process of tissue replacement and remodeling, and identified an important role for the TNF-like cytokine TWEAK as a trophic factor for hepatic progenitor cells. Dr. Bissell also studies hepatic porphyrias, and is a member of a national Rare Disease Clinical Research Consortium for these diseases. The purpose of the network is to integrate translational studies of the porphyrias with clinical trials testing new therapeutics.
Dr. Brandman engages in outcomes-based research involving nonalcoholic fatty liver disease (NAFLD). She is one of the investigators on the NIH-funded NASH clinical research network. She works on several clinical trials involving investigative medications to treat NAFLD and liver fibrosis. She has a special interest in NAFLD and liver transplantation: the post-transplant outcomes of patients with NAFLD, selection of patients with NAFLD for transplant, recurrence of NAFLD following transplant, new-onset NAFLD after liver transplantation for other causes of liver disease, and the closely related condition, post-transplant metabolic syndrome. She is also evaluating the impact of pre-transplant predictors of post-transplant kidney function as the site PI for the NIH-funded study, Models for Optimal Liver Transplant Outcomes (MOLTO).
Dr. El-Nachef’s interests include Celiac Disease, Women’s Health, General Gastroenterology and Inflammatory Bowel Disease.
Dr. Hameed investigates the epidemiology and management of non-alcoholic fatty liver disease and sleep apnea in fatty liver disease. He is also engaged in modeling outcomes in advanced liver disease and liver transplantation.
Dr. Kathpalia specializes in motility disorders of the GI tract in addition to general gastroenterology. Her interests include esophageal disorders, swallowing disorders including achalasia, eosinophilic esophagitis, and scleroderma.
As an Assistant Adjunct Professor in the Division of GI at UCSF, Dr.Kattah is interested in the molecular underpinnings of intestinal inflammation and Inflammatory Bowel Disease (IBD). His team employ various tools to study intracellular signaling proteins involved in cell death and inflammation. Currently, they are using chemical screening and proteomics to try and develop novel therapies for IBD and other autoimmune diseases. They are also performing translational studies on mucosal biopsies from IBD patients, including generating and testing intestinal organoids.
Dr. Jennifer C. Lai is a general and transplant hepatologist who specializes in caring for patients with chronic viral hepatitis, autoimmune disorders, and cirrhosis, particularly those awaiting liver transplantation. She is also actively engaged in patient-oriented clinical research within three major areas: integrating core principles of geriatrics (e.g., frailty, disability, palliative care, multi-morbidity) to patients with cirrhosis, investigating disparities in organ allocation and distribution as well as assessing the impact of liver donor quality on outcomes. As the principal investigator for the NIH-funded Functional Assessment in Liver Transplantation (FrAILT) study, Lai aims to apply measures of frailty and functional status to patients with end-stage liver disease awaiting liver transplantation. Her research lays the groundwork for therapeutic interventions aimed at "pre-habilitating" patients awaiting liver transplantation to improve their outcomes and quality of life.
Dr. Lynch’s human microbiome research program focuses on the gastrointestinal and airway microbiomes and their influence on the development and maintenance of chronic inflammatory disease. She studies the early-life origins of chronic inflammatory disease and has demonstrated a role for the neonatal gut microbiome and its metabolic products as a predictor of allergic asthma development in childhood. She is also interested in established inflammatory conditions and has shown that distinct microbiota exist in adults with IBD, chronic sinusitus or HIV-infection, which relate to immunologically and pathologically distinct disease endotypes. Her group has pioneered the application of newly developed statistical approaches to the multi-dimensional microbiome data sets developed by next generation sequencing approaches. They have developed and made publicly available custom scripts and novel tools to facilitate such analyses. In addition, they have developed novel ex vivo assays to assess the capacity of human microbiota, specific microbial species or their products to elicit host immune responses ex vivo, providing an objective assessment of their immunomodulatory capacity. Dr. Lynch founded and directed the Microbiome Research Core, and is the Associate Director of the Microbiome in Inflammatory Bowel Disease Research Program at UCSF. She has also co-founded and served as a board member of Siolta Therapeutics, a start-up company at QB3 that focuses on translating bench-based human microbiome findings into effective therapeutics for prevention or treatment of immune disorders.
Dr. Averil Ma is Director of the UCSF IBD Center. He oversees translational and basic research in IBD and other inflammatory diseases.
Basic research in the laboratory studies molecular mechanisms that preserve tissue health and prevent inflammation. These include host-commensal interactions at mucosal interfaces as well as other potential triggers of cell stress. We have focused upon a subset of proteins that regulate ubiquitin dependent signaling pathways, as these proteins: (1) prevent inflammatory diseases and cancer in human patients; (2) prevent inflammation in experimental mice; (3) restrict NFkB signaling and immune cell activation; (4) prevent cell death; and (5) preserve tissue integrity. Two potent regulators of ubiquitination are A20 and its binding partner, ABIN-1 (A20 Binding Inhibitor of NFkB). Ongoing studies utilize genetic engineering, signaling, and mass spectrometry techniques to unravel the cellular and biochemical mechanisms by which A20, ABIN-1 and related proteins restrict ubiquitin dependent signals and intestinal immune homeostasis. They are capitalizing on these molecules to pursue novel approaches of preventing inflammatory diseases. Translational research in the laboratory seeks to convert insights from biochemical and mouse based biology toward the biology of human tissues. The lab is also studying human immune cells and intestinal epithelial cells in efforts to better characterize disease subtypes as well as to optimize treatments.
Dr. Mahadevan specializes in the treatment of inflammatory bowel disease (IBD) which includes ulcerative colitis, Crohn’s disease, pouchitis and microscopic colitis. She has a particular interest in pregnancy and fertility in IBD, as well as in clinical trials of experimental therapy for both ulcerative colitis and Crohn’s disease. Her current projects include the PIANO Registry - a national prospective registry of pregnancy outcomes and drug safety in 1000 women with IBD and the effects of IBD medications on newborns with IBD. She also studies the role of the environment, diet and microbiome in the development of IBD in people of South Asian descent. Finally, she conducts multiple trials of novel therapy for IBD as well optimizing the use of currently available therapy.
Dr. Mehta’s research focus is on outcomes for patients with HCC both in those awaiting liver transplant and also following liver transplant. He is also actively studying outcomes on the practice of “down-staging” HCC prior to liver transplantation. Dr. Mehta is also studying the risk of HCC recurrence post-transplant based on transplant waiting times, tumor markers, and explant pathology and has recently created and validated an HCC recurrence risk score termed RETREAT (Risk Estimation of Tumor Recurrence After Transplant) to enhance post-transplant surveillance strategies and determine who may benefit from neoadjuvant therapies.
Dr. Peters studies viral hepatitis in the context of HIV infection. She has led the Hepatitis Working Group within the Women’s Interagency HIV Study (WIHS) since 2005. She recently completed a study evaluating two mathematical algorithms, the aminotransferase/platelet ratio index (APRI) and fibrosis-4 (FIB-4), as predictors of death in WIHS participants with HCV infection. She is also is examining the impact of gender and hormonal status on liver disease progression in HIV/HCV co-infection, as well as other co-factors that influence liver disease progression in co-infected patients such as alcohol and cannabis use. Through her work with the AIDS Clinical Trials Group, Dr. Peters develops protocols for treatment of hepatitis B and C in co-infected patient cohorts.
Dr. Jennifer Price is a gastroenterologist and liver expert, or hepatologist, who specializes in treating patients who are awaiting liver transplants. In her research, she addresses liver disease in HIV infection, treatment of viral hepatitis and nonalcoholic fatty liver disease.
Dr. Monika Sarkar is a transplant hepatologist with a particular research interest in women's health, including the role of sex hormones in the progression of liver disease and liver disease in pregnancy. She earned her medical degree at the University of California, San Francisco (UCSF) and completed internal medicine residency at the University of Pennsylvania. She then completed fellowships in gastroenterology and transplant hepatology, as well as her Masters in Clinical Research at UCSF. Dr. Sarkar supervises the training of medicine residents and both gastroenterology and liver transplant fellows. She has funding from the NIH to study the role of sex hormones in women with nonalcoholic fatty liver disease (NAFLD), including women with polycystic ovarian syndrome given their increased risk of NAFLD and early onset of liver scarring.
Dr. Aparajita Singh is the Director of Quality Improvement for the Division of Gastroenterology and her research interests are improving quality and safety of patient care and implementing tools for measuring and improving quality indicators.
As Associate Director for the Gastrointestinal Clinic Cancer Prevention Clinic she is interested in managing patients with hereditary gastrointestinal cancers like Lynch Syndrome and Familial Adenomatous Polyposis. Her research interests includes improving quality of care for Lynch syndrome patients, understanding multi-gene panel testing for gastrointestinal cancer patients and use of web based tools to improve care of this patient population.
Dr. Terrault's research focuses on the epidemiology and natural history of hepatitis C and hepatitis B, particularly in special populations such as those undergoing liver transplantation. She monitors the impact of numerous variables on pre- and post-transplant outcomes, including race, gender and hepatic steatosis. With collaborators she is working to develop new models that predict fibrosis progression in HCV-infected populations. Dr. Terrault is UCSF site PI for the NASH CRN and Co-PI for the HBV CRN. She is Co-Investigator on the Solid Organ Transplantation in HIV study and the A2ALL Living Donor Liver Transplantation cohort. She is also contributing to the Bay Area Hepatitis C Cooperative Research Center by developing retrospective and prospective cohorts of patients with hepatitis C for immunological study.
Dr. Terdiman's research interests are related to GI cancer prevention and inflammatory bowel disease. Ongoing research projects are investigating the optimal provision of genetic counseling and testing for hereditary cancer syndromes and cancer risk mitigation through chemoprevention and endoscopic surveillance. Dr Terdiman also is engaged in research examining new therapies for inflammatory bowel disease, including therapies to manipulate the microbiome such as fecal transplant.
Dr. Wang’s lab studies how the different cell types in the liver, in particular the hepatocyte, are generated during development, patterned and maintained during adulthood, and regenerate after injury. The long-term goals of the lab are to improve the understanding of liver disease pathophysiology and develop novel methods of treatment for liver diseases, including cell replacement therapy. Currently, the lab has two major research focuses:
Dr. Wang also studies hepatic porphyrias. He is a member of the Porphyrias Consortium, a NIH sponsored Rare Disease Clinical Research Consortium. The purpose of the network is to integrate translational studies of the porphyrias with clinical trials testing new therapeutics.
Dr.Whang is interested in how ubiquitination regulates autoimmune diseases. A20 is a ubiquitin binding and modifying enzyme that is linked to various autoimmune diseases, including inflammatory bowel disease. His research is focused on the mechanism by which A20 regulates inflammation by controlling ubiquitin chain stability.
Dr. Yao’s research focus is on patient outcomes following liver transplantation for HCC. With local colleagues he developed the “UCSF Criteria” for liver transplantation, which have been widely adopted by transplant programs. He is also actively studying outcomes on the practice of “down-staging” HCC prior to liver transplantation and the strategy of “ablate and wait” for patients who may not come immediately to liver transplantation for HCC.
Zuckerberg San Francisco General
Dr. Bull studies the genetics of cholestatic liver disease. She works on the proteins FIC1 (familial intrahepatic cholestasis-1) and BSEP (bile salt export protein), transporters that are mutated in hereditary cholestatic disorders. She is also searching for new genes responsible for inherited cholestatic disorders. Dr. Bull has generated a mouse carrying one of the principal mutations in FIC1 in humans and is investigating the mechanism of liver disease in FIC1 mutants; studies to date indicate different phenotypes in different mouse strains, suggesting the presence of modifier genes. Dr. Bull collaborates nationally and internationally with adult and pediatric hepatologists. She participates in the Childhood Liver Disease Research and Education Network (ChiLDREN).
Dr. Cello is engaged in clinical research on the following topics
Dr. Day directs the endoscopy center and clinical activities at the San Francisco General Hospital. His research interests center on organizational design and development of efficiency models for health care system delivery to vulnerable patient populations. Specifically, he focuses on the delivery of healthcare through the endoscopy center including increasing access to colorectal cancer screening. Dr. Day has been actively involved in advancements in colorectal cancer screening as demonstrated by his published research examining colorectal cancer screening rates among American Indians/Alaskan Natives in the U.S. and expanding colorectal cancer screening services to vulnerable patients at the San Francisco General Hospital.
Dr. Khalili's research is focused on viral hepatitis natural history, treatment, and disease complications. Dr. Khalili studies insulin resistance as a consequence of hepatitis C infection. She measures insulin sensitivity and insulin secretion directly in HCV-infected patients using regulated glucose and insulin infusions. Her research location at SFGH enables her to study consequences of hepatitis and factors influencing health disparity in an ethnically diverse population including studies of patient and provider knowledge, attitudes, and barriers to hepatitis B and hepatitis C management and care coordination. Dr. Khalili is also a Co-Principal Investigator for the UCSF site of the Hepatitis B Clinical Research Network. Within the network she is leading studies of abnormalities in glucose metabolism, as well as studies of HBV-HIV co-infection. Dr. Khalili is also a participant in the Bay Area Hepatitis C Cooperative, where she recruits HCV-infected individuals receiving therapy for immunologic studies.
Dr. Maher directs the UCSF Liver Center and supervises its Cell Biology Core. She also Program Director for the UCSF Postoctoral Research Training Program in Hepatology (T32 DK060414). Dr. Maher studies the pathogenesis of steatohepatitis; research in her laboratory addresses the effects of dietary macronutrients (sugars and fats) on liver outcome in mouse models of fatty liver disease, as well as the relationship between endoplasmic reticulum stress and fatty liver disease. Her studies emphasize the hepatotoxic potential of dietary sugar and the synergistic adverse effect of dietary sugar and saturated on the liver. Additional work in Dr. Maher’s laboratory focuses on the mechanism by which saturated fatty acids, produced in the liver from dietary sugar, induce hepatocellular damage.
Melanie Ott is a physician scientist and molecular virologist with a longstanding interest in host:pathogen interactions. She studies how to eradicate HIV from infected individuals, how liver viruses manipulate lipids and how Zika virus causes neuropathology. She recently developed a new interest in using human organoids for studies of human pathogenic viruses.
Dr. Justin Sewell performs medical education research related to workplace learning, endoscopic skills training, and cognitive load theory. He also has experience and expertise in health services and clinical research.
Dr. Somsouk’s research program embraces health information system and technology to develop effective and economical solutions that improve patient health outcomes. One major area focuses on improving population-level screening for colorectal cancer and managing high-risk individuals with abnormal screening tests. Another translational research area utilizes samples from patients with gastrointestinal disorders to understand disease etiology, progression, and response to therapy. Patient samples are used to develop intestinal organoids, profile immune cells, and microbiota in the setting of inflammatory bowel disease, HIV, and other health conditions.
San Francisco Veterans Affairs
Dr. Monto performs patient-oriented research related to hepatitis C infection, cirrhosis and hepatocellular cancer. He directs the Hepatitis C Resource Center (HCRC) at the SFVAMC, which is one of only 4 HCRC’s nationally whose goals are to develop best practices in hepatitis C prevention, clinical care, and education of patients and providers. His investigative interest is in the progression of viral hepatitis to cirrhosis, portal hypertension and cancer based on age, disease stage, and co-morbidities such as HIV. Dr. Monto is also analyzing outcomes of patients treated (or not) for HCV, to determine the impact of treatment and treatment response on disease progression. He is a participant in the Bay Area Hepatitis C Cooperative Research group.
Dr. Owen’s research has involved delineation of the structure and function of Peyer's patches and other mucosal lymphoid organs, using ultrastructure, immunohistology, morphometric analysis, and FACS analysis in immunocompetent and immunodeficient animal models. Clinical research interests include diarrhea and intestinal infections, identifying the role of opportunistic pathogens including Giardia, Cryptosporidia, Microsporidia and Mycobacterium avium.
Dr. Ryan’s primary research program is focused on the fundamental roles of innate host defenses against viruses such as HCV. In collaboration with other UCSF investigators, he is currently engaged in a comprehensive analysis of innate immune receptors as they correlate with divergent clinical outcomes of HCV. Immunophenotyping of patients is being facilitated by the Liver Center’s Liver Immunology and Cell Analysis Core. Studies to date show that NK cell receptors of the KIR family play a major role in HCV immunity.
They suggest that NK cells likely play an important role in the interface between innate and adaptive immunity to this virus. Moreover, these studies implicate KIR as prognostic markers for divergent HCV outcomes and as attractive targets for future immunotherapies. In addition to his work with HCV, Dr. Ryan is exploring immune cross-talk between the liver and adipose tissue in the pathogenesis of fatty liver disease. He is particularly interested in macrophage polarization during diet-induced obesity and its implications for the liver.
Dr. Shergill’s research concentrates on the following topics:
- understanding the biology of adult hepatocyte stem cells and
- developing a liver cell atlas.
- Randomized sham-controlled trial of transoral gastroplasty for morbid obesity.
- Randomized, controlled clinical trial of ERCP plus laparoscopic cholecystectomy vs. laparoscopic cholecystectomy plus bile duct exploration. Predictors of CBD stones.
- Maturation of brush border enzymes in the jejunum following gastric bypass for morbid obesity.
- Nutrient absorption before and following gastric bypass surgery.
- ERCP in patients with pancreatic trauma and ductal injury.
- Healthcare delivery for patients with inflammatory bowel disease in the safety net healthcare system
- The effects of race/ethnicity and socioeconomic status on the course and outcomes of inflammatory bowel disease
- Developing and testing innovations to increase quality of gastroenterological care and to improve coordination between primary and specialty care
- Gastrointestinal tract as a reservoir and site of HIV pathogenesis. Dr. Somsouk studies the impact of HIV in the gut, answering questions related to viral persistence, immune activation, epithelial barrier dysfunction, and their relationship to systemic inflammation, aging, and cancer using observational studies and interventional trials.
- Prevention of colorectal cancer. The SFGH population often presents with late-stage cancer, particularly among Asians and blacks, with low rates of colorectal cancer screening and late utilization of health care services. Dr. Somsouk identifies barriers to access healthcare/colorectal cancer screening in the safety-net population. In addition to cohort studies, he uses mathematical simulation models to identify challenges and best practices for colorectal cancer screening/surveillance.
- Optimizing ergonomics of gastrointestinal endoscopy
- Colon cancer screening
- Inflammatory Bowel Disease