Sean D. Mooney, PhD
Professor, Biomedical Informatics and Medical Education
Chief Research Information Officer (CRIO) of UW Medicine
Principal Investigator

Education-MooneyCrop.2Professor Mooney has spent his career as a researcher and group leader in biomedical informatics. He now leads research IT for UW Medicine and is leading efforts to support and building clinical informatic platforms as it’s first Chief Research Information Officer (CRIO) and as a professor in the Department of Biomedical Informatics and Medical Education at the University of Washington.  Previous to his CRIO role, he was an Associate Professor and Director of Bioinformatics at the Buck Institute for Research on Aging. As an Assistant Professor, he was appointed in Medical and Molecular Genetics at Indiana University School of Medicine and was founder and director of the Indiana University School of Medicine Bioinformatics Core. In 1997, he received his B.S. with Distinction in Biochemistry and Molecular Biology from the University of Wisconsin at Madison. Then receiving a Ph.D. in 2001 at the University of California in San Francisco, and then an American Cancer Society John Peter Hoffman Fellowship at Stanford University.

Tim Bergquist
Research Associate

Born and raised in Seattle, Tim Bergquist has spent his undergraduate career earning his B.S. in Biochemistry from Grove City College in Pennsylvannia. A recent addition to the Mooney Lab this summer, Tim works on the Autism project and researches gene prioritization methods, hoping to find a means to predict Autistic individuals from sequenced exomes of patients. Tim also is part of the team involved in the CAGI (Critical Assessment of Genome Interpretation) competition and is applying methods developed in the Autism project to predict results. He spends his free time hiking, swimming, and occasionally jumping out of airplanes.

Christian Bock
International VISIT Student

Christian_BockChristian joined the mooney group to finish his master's thesis in the field of protein structure prediction. While assessing predicted protein structures, he is interested in whether predicted protein structures can be used to predict pathogenicity of genetic mutations. He earned his B.S in medical informatics from Heidelberg University in 2014 where he worked on the visualization of sensor data in smart homes for the elderly. He developed a strong interest in bioinformatics while he was working at SAP to build a web based, interactive genome browser for several academic partners. Besides being interested in data visualization and genomics, his research interests lie in the field of machine learning and clinical informatics. For more information about Christian visit his website at www.christianbock.info.

Binghuang Cai, PhD
Senior Fellow

Dr. Cai is a Senior Fellow in the lab, working on knowledge discovery of EMR data based on machine learning. Before joining the lab, he was a Postdoctoral Associate in the Department of Biomedical Informatics at the University of Pittsburgh from October 2012 to May 2015, and a Research Fellow in the Centre for Autonomous Systems at the University of Technology, Sydney from September 2010 to May 2012. Dr. Cai received his Ph.D. in Information Systems from Sun Yat-sen University in 2010, his M.S. degree in Signal and Information Processing from Shantou University (STU) in 2007, and his B.S. degree in Electronic Information Engineering also from STU in 2004. His research interests include biomedical informatics, machine learning, artificial neural networks, optimization, robotics and image processing.

Nikhil Gopal
PhD Candidate

Nikhil earned a B.S. in Biotechnology--Bioinformatics from UC Davis with a focus on algorithms. After graduating, he worked for Affymetrix as a Data Analyst and Illumina as an Associate Bioinformatics Scientist. While working in the biotechnology industry, Nikhil was completing graduate courses in the BMI program at Stanford and contributed to open source biology projects. Since joining the PhD program at the University of Washington, Nikhil has been studying biological data visualizations and biological networks. Outside of research and open source, Nikhil spends his time hiking, rock climbing, traveling, and watching indie films. Since Nikhil has a adventurous approach to hobbies, he is generally trying his hand at some new skill every few months. You can reach him via twitter @NikhilGopal or visit his website: http://www.nikhilgopal.com.

Chethan Jujjavarapu
BIME PhD Student

ChethanChethan is a computational biologist and PhD student in the Biomedical and Health Informatics Department. He graduated from UC Santa Cruz with a focus in Immunology, but transitioned to computational biology and data science at UC San Francisco, where he spent almost 2 years working on different projects to build and hone his computational skills. He’s now focused on leveraging the wealth of knowledge in the UW EHR to improve diagnosis and treatments for autoimmune patients.

willWill Kearns
BIME PhD Student

Will is an National Library of Medicine Predoctoral Fellow working toward the completion of the Biomedical and Health Informatics Ph.D. Program within the University of Washington School of Medicine. His research interests include clinical decision support, information retrieval, and dialog systems. He previously worked on CHAI (Communication History and Analysis Interface) a data visualization and clustering tool for the exploration of patient-provider and caretaker-provider chat logs. In addition to his research, Will serves as Research Coordinator for the High Performance Computing Club, an RSO that manages the Student Technology Fee allocation on the Hyak supercomputer, and as a mentor for undergraduate students interested in bioinformatics and computational linguistics.

More info at: kearnsw.com

Vikas Pejaver
eScience Fellow

VikasVikas Rao Pejaver is a Moore-Sloan and Washington Research Foundation post-doctoral fellow in the Mooney lab and the eScience Institute. He is interested in the development and application of machine learning methods for translational research, with a particular emphasis on the integration of heterogeneous data from disparate sources, such as genomic, proteomic and health data sets. The use of computational methods in the health and life sciences first excited Vikas at the People’s Education Society Institute of Technology, where he received his B.E. in Biotechnology in 2008. This motivated him to pursue an M.S. in Bioinformatics at Indiana University, Bloomington, where he worked on comparative genomics problems in bacterial genomes. Upon completion in 2010, he stayed on at Indiana to pursue doctoral studies in Dr. Predrag Radivojac’s research group. In 2016, he received a Ph.D. in Informatics with a dissertation that focused on the sequence-based prediction of over 50 different types of structurally and functionally important sites in proteins, and their integration into the prediction of disease-associated missense variants. In the Mooney lab, he continues to think about machine learning in human health and disease, but with a greater focus on electronic health records.

Jimmy Phuong
PhD Candidate

Jimmy_PhuongJimmy is a computational scientist and PhD student in the UW Biomedical and Health Informatics program. His research is focused on data integration and analytics, currently applied in the biology of Aging and the geospatial informatics of environmental health. Jimmy received his bachelors of science in Molecular Toxicology from UC Berkeley in 2010, and his Masters in Science in Public Health from UNC Chapel Hill in 2014. Prior to joining Mooney Lab, Jimmy worked at the US EPA ToxCast and Tox21 toxicity testing programs in bioassay annotation and integration as well as a number of Public Health projects pertaining to environmental toxicants and computational prediction. In his free time, Jimmy likes long walks on the beach, hiking, and exploring through music and movie archives.

Abhishek(Abhi) Pratap
Graduate Student  & Research Consultant

Abhi is a computational biologist with 7 years of professional experience in the analysis of high-throughput genomics and proteomics datasets and biological data visualization. He has worked on analyzing data from  various sequencing technologies such as Illumina, Roche-454 and Pacific Biosciences developing end-to-end integrated analysis pipelines for genome assembly, variant calling, differential expression etc. Currently at Sage Bionetworks, he is leading the data analysis and management in two consortium based  projects working in Neurofibromatosis – II and Acute Myeloid Leukemia. These involve careful data access management, providing researchers with protected workspaces for sharing results and provenance enabled statistical analysis. He also builds interactive data dashboards to share his analysis thereby enabling biologists, clinicians explore multidimensional biomedical data. Currently as a first year graduate student in Biomedical Health Informatics, Abhi is exploring research areas in use of mobile health technologies specially in low income groups. His long term interests is in developing solutions to help patients take control of their own health and working with their healthcare provider for better overall outcomes. 

Sicheng Song
PhD Candidate

Sicheng_SongGraduated from biological science in Sichuan University, Sicheng is now a PhD student in Biomedical Health Informatics program. During his research internships with the state key laboratory of biotherapy and cancer center in China with publishing 5 research papers (total IF=17.45), he has developed an interest in translational bioinformatics and systems biology, such as personalized medicine and cancer genomics. Outside of the lab, he loves kendo, hiking, soccer, skiing and archery.

Don Smith
BIME PhD Student

Xiyao Yang
Master's Candidate

Xiyao_YangXiyao, graduated from Huazhong University of Science and Technology(HUST), Wuhan, China, is now a second year master student in Biomedical Health Informatics program in UW. She joined the lab firstly for research in clinical data natural language processing. During the internship in Institute of Translational Health Sciences(ITHS) in 2016 summer, she was committed to development of a self-service clinical data query application called Leaf. Xiyao is doing her master thesis on data visualization of clinical information through Leaf now. Her research interests include clinical informatics, natural language processing, web application development, machine learning and data visualization.

Samir Yhann
Undergraduate Student

SamirSamir is a sophomore undergrad at the University of Washington working on a degree in engineering and physics. He joined the group in the fall of 2016 to work with databases and data visualization. In his free time Samir plays with the Husky Marching Band, explores the wilderness, and programs small apps for fun.