Research by Faculty
- Christian Mathy
- Kenneth McQuaid
- Alexander Monto
- James Ostroff
- Melanie Ott (Gladstone Institute)
- Robert Owen
- Marion Peters
- Catherine Rongey
- James Ryan
- Justin Sewell
- Janak Shah
- Amandeep Shergill
- Ma Somsouk
- Norah Terrault
- Jonathan Terdiman
- Fernando Velayos
- Holger Willenbring (UCSF Stem Cell Institute)
- Francis Yao
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. Bhat has clinical research interests in the areas of pancreaticobiliary endoscopy, endoscopic ultrasound, interventional endoscopy, endoscopic mucosal resection and endoscopic treatment of esophageal diseases.
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 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, and new-onset NAFLD after liver transplantation for other causes of liver disease. She is also interested in the post-transplant metabolic syndrome.
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:
- 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.
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. 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. 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.
The primary objective of Dr. Korn’s research is the rational design of targeted combination therapies for GI cancer. His projects exploring the systems biology of cancer and have a strongly translational angle. He utilizes cutting edge technologies and collaborates with leading scientists to design novel cancer therapies based on an in-depth understanding of cancer signal transduction networks. Specific studies fall into two major categories: (a) the analysis and prediction of pathway responses to targeted inhibition of the EGF receptor pathway in esophageal and breast cancer, and (b) the regulation and function of the human coxsackie-adenovirus receptor CAR, which is which is mission-critical for the success of adenovirus-based cancer treatments.
Dr. Lai is engaged in research investigating clinical outcomes in patients with chronic liver disease. Her research focuses on three main areas:
- Understanding the impact of functional status and physiologic reserve (i.e., frailty) in patients with cirrhosis awaiting liver transplantation,
- Evaluating the association between chronic hepatitis C and systemic inflammation with Vitamin D status and bone mineral density, and
- Characterizing patterns of liver allocation and distribution and their association with liver transplant outcomes (both pre- and post-transplant) on a national level
Dr. Lynch directs the Colitis and Crohn’s Disease Microbiome Research Core. Her microbiome-focused studies examine the complex microbial-host interactions that contribute to chronic inflammatory diseases including inflammatory bowel disease and respiratory conditions. Her previous work has led to the identification of a specific gastrointestinal species that promotes proliferation of Th17 cells, a novel microbiome-based etiology for chronic rhinosinusitus, and some of the first studies defining alterations in airway microbiome composition related to declining pulmonary status or bronchial hyper-responsiveness in cystic fibrosis and asthmatic patients respectively. On-going investigations, both in human populations and murine models, examine environmental microbial exposures, diet and gastrointestinal microbiome manipulation, on various aspects of ulcerative colitis, asthma and cystic fibrosis disease processes. The Lynch Lab website can be visited HERE.
Dr. Ma is Director of the UCSF IBD Center and Director of the UCSF Postdoctoral Research Training Program in Gastroenterology. His laboratory studies ubiquitin modifying enzymes that regulate inflammation. A20 is a remarkable de-ubiquitinating enzyme that also exhibits E3 ligase activity and non-catalytic ubiquitin binding functions. ABIN-1 is a ubiquitin binding protein that also binds A20. Their lab helped link A20 and ABIN-1 (A20 Binding Inhibitor of NFkB) genes to human rheumatoid arthritis, SLE, psoriasis, celiac disease and IBD. They have generated multiple lines of gene targeted mice bearing global or lineage specific deletions of these enzymes, as well as fine point mutations. Hence, ongoing studies focus on the cellular and biochemical mechanisms by which A20 and ABIN-1 (and related proteins) restrict ubiquitin dependent inflammatory signals, and on novel approaches of modifying the functions of these proteins for therapeutic benefit.
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. 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.
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. 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. Rongey is a health service and implementation science researcher dedicated towards informing health systems’ efforts to improve access to specialty liver and gastroenterology care with a particular focus on health information technologies (HIT). She is the director of the San Francisco Veterans Affairs SCAN-ECHO program, a telemedicine based program that provides liver, inflammatory bowel disease, HIV, pharmacy and epilepsy care to veterans in California, Nevada and Hawaii. She is partnered with several Veterans Affairs central office divisions in D.C. Previously funded by the American Gastroenterology Association, she is currently funded by the UCSF KL2 award program examining innovative ways in which HIT can be leveraged to improve specialty care access and quality. She is also a member HIV/Hepatitis Quality Enhancement Research Initiative, a collaborative of health services, health outcomes, implementation science and health economics researchers within the Veterans Affairs.
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. Sewell’s research focuses on the following topics:
- 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
Dr. Shah’s research interests are in the areas of pancreaticobiliary endoscopy, endoscopic ultrasound, interventional endoscopy and endoscopic mucosal resection
Dr. Shergill’s research concentrates on the following topics:
- Optimizing ergonomics of gastrointestinal endoscopy
- Colon cancer screening
- Inflammatory Bowel Disease
Dr. Somsouk focuses on the following topics:
- 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.
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 clinical and translational research in the areas of colorectal cancer prevention, especially among individuals at high risk for cancer, such as those with hereditary cancer syndromes or those with longstanding inflammatory bowel disease. Particular areas of interest include the optimal provision of genetic counseling and testing, cancer risk factor identification and risk mitigation by interventions such as drugs (chemoprevention) and colonoscopy. He also studies the use of genetic and genomic markers to determine cancer risk and prognosis and prediction of response to therapy among those already diagnosed with cancer. He is interested in projects related to biomarkers of prognosis and prediction of response to therapies in patients with inflammatory bowel disease.
Dr. Velayos’ research focuses on the following topics:
- Chemoprevention for IBD-related colorectal cancer
- Molecular markers of dysplasia and progression in IBD
- Adherence to surveillance colonoscopy in IBD
- Natural history of dysplasia in IBD
- Surgical volume and outcomes in IBD
- Predictors of outcomes in IBD
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.