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Project Team and Advisors

Project Team

Maryann Martone, dkNET PI

Dr. Martone has a BA from Wellesley College in biological psychology and a Ph. D. in neuroscience from the University of California, San Diego, where she is currently a Professor in the Department of Neuroscience. Her background is in neuroanatomy, particularly light and electron microscopy, but she spends most of her time now in the field of neuroinformatics. She is the principal investigator of the Neuroinformatics Framework project, a national project to establish a uniform resource description framework for neuroscience. Her recent work has focused on building ontologies for neuroscience for data integration. She heads the International Neuroinformatics Coordinating Facility (INCF) program on ontologies. She is the president of FORCE11, an organization dedicated to advancing scholarly communication and e-scholarship.

Jeffrey Grethe, dkNET PI

Dr. Grethe has a BS from the University of California Irvine in Applied Mathematics and a Ph.D. in Neuroscience, with a focus on bioinformatics, from the University of Southern California. Throughout his career, his primary focus has been on enabling collaborative research, data sharing and discovery through the application of advanced informatics approaches. Before coming to UCSD he was one of the core members responsible for bringing the fMRI Data Center online, the first publicly accessible repository of peer-reviewed fMRI studies. He is currently leading a number of large scale biological and biomedical informatics projects (i.e. PI for the NIDDK Interconnectivity Network Coordinating Center, co-PI for the Neuroscience Information Framework, and Technical Lead for the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis) in the Center for Research in Biological Systems at the University of California, San Diego.

Ko-Wei Lin, Project Manager

Dr. Lin has a DVM from National Taiwan University and a PhD in Comparative Biomedical Sciences, focusing on Cell Biology, from North Carolina State University. Her post-doctoral training at University of California San Diego were both in Biomedical Sciences focusing on inflammatory and immune pathways, and in Biomedical Informatics. She also has extensive experience in bridging the biomedical sciences and informatics -e.g. through information model development and validation, user outreach, and user requirement analysis for developing information retrieval tools.

Sean Penticoff, Systems Support

Sean is a systems engineer working for the Center for Research in Biological Systems at the University of California, San Diego. He has 10+ years of experience working on system integration and configuration management.

Burak Ibrahim Ozyurt, Nature Language Processing (NLP) Engineer

Chun-Nan Hsu, Associate Professor, Nature Language Processing (NLP)

Dr. Hsu earned his PhD in Computer Science from USC and was Assistant Professor in Computer Science & Engineering at Arizona State University before he joined Academia Sinica, Taiwan (1998-2014). He joined UCSD in 2013 and has been leading teaching and research in biomedical text mining since then. He was awarded Senior Member of Association of Computing Machinery (ACM) in 2011 and the IBM Faculty Award for his distinguished contributions to biomedical text mining in 2012.

Stephanie Hagstrom, Outreach Coordinator

Xiaohui (Vicky) Guo, Web Developer

Xiaohui (Vicky) has a BS in telecommunication engineering. She previously worked as a programmer in the bioinformatics core in Sanford Burnham Prebys Medical Discovery Institute focusing on developing pipelines for various bioinformatics analyese and web-based bioinformatics tool. She joined UCSD in 2018 and was in charge of web interface development.

James Go, Alumni, Web Developer

James has a BS in Cell and Molecular Biology from Cal State Northridge. He previously worked as a researcher and web developer at UCLA where he analyzed epigenetic and proteomic data and created web interfaces for collaborating researchers to access their data. James has gone back to UCLA to pursue an advanced degree in bioinformatics.

Collaborators - Signaling Pathways Project (SPP)

Neil McKenna, Ph.D., SPP PI

Scott A. Ochsner, Ph.D., Biocuration Lead

NIH NIDDK Program Staff

Silva Corinne, Ph.D., Project Scientist

As Program Director of Signaling and Nutrient Sensing, I oversee a portfolio of grants that are focusedon elucidating the role of nutrient sensing signaling pathways in the development and/or progression of insulin resistance, type 2 diabetes, obesity, and metabolic disease. Studies involve the identification of regulators, interacting partners, and substrates to elucidate modes of signal transmission, including circadian regulation, that impact physiological systems and result in metabolic dysfunction. A particular focus is on the nuclear hormone receptor superfamily, a unique class of proteins that regulate an array of molecular functions including metabolic homeostasis. In addition, I oversee a growing portfolio of research grants that focuses on the role of the intrauterine environment in metabolic disease of the offspring. These grants include both basic and translational studies that investigate the mechanisms by which the intrauterine environment alters metabolic responses in the offspring including, but not limited to, intracellular signaling pathways, inflammatory cytokines, nutrient sensing pathways, and epigenetic imprinting. The ultimate goal of this research is to identify molecular targets that could be used therapeutically to prevent metabolic disease.

Xujing Wang, Ph.D., Program Director

As the program director for data science and computational biomodelling, I manage a research portfolio of projects that develop methods and tools that enable the utilization of data science in, that utilize high-throughput (Big) data in, and that develop computational, or joint computational and laboratory approaches to model biological processes relevant to, diabetes and metabolic disease research, or any other area of disease or biology of relevance to the DEM mission. I am also the program director for HIRN-CBDS, HIRN-HPAP, dkNET, and co-program director for TEDDY.

NIH NIDDK Ad Hoc Advisors

Kristin Abraham, Ph.D.

My portfolio includes research grants focused on the role of inflammation in diabetes and projects developing animal models to enhance basic and preclinical research in diabetes, endocrinology, and metabolic diseases. I also play an active role in the Mouse Metabolic Phenotyping Centers Program, the Diabetic Complications Consortium, and in the second phase of the KOMP2 Knockout Mouse Project. In addition, I am a member of the Common Fund High-Risk High-Reward working group that assists with oversight of the NIH Director's HRHR portfolio including the Pioneer, New Innovator, Early Investigator, and Transformative R01 programs

Arthur Castle, Ph.D.

I direct programs that study metabolomics and informatics. As such, I manage a research portfolio that applies technology to measure the large-scale integrated metabolism of cells, tissues, and organ systems. These studies measure and identify many metabolites within multiple pathways and aim to discover new relationships between metabolite profile changes and the pathology of specific metabolic diseases or syndromes. I am a co-coordinator of the Common Fund Metabolomics Initiative. The NIH Common Fund addresses key roadblocks in biomedical research that impede basic scientific discovery and its translation into improved human health. As director of the training program, I manage a research portfolio of fellowships and institutional training grants in diabetes, endocrinology, and metabolism. These fellowships and training appointments provide stipend support for predoctoral and postdoctoral students and fellows doing research in NIDDK mission-related fields. As the informatics director, I manage a research portfolio of bioinformatics and modeling grants and serve on committees related to bioinformatics.

External Scientific Advisory Panel (2019-)

Mark A. Musen, M.D., Ph.D., Professor, Medicine (Biomedical Informatics) and Biomedical Data Science, Stanford University School of Medicine

Dr. Musen is Professor of Biomedical Informatics and of Biomedical Data Science at Stanford University, where he is Director of the Stanford Center for Biomedical Informatics Research. Dr. Musen conducts research related to open science, intelligent systems, computational ontologies, and biomedical decision support. His group developed Protégé, the world’s most widely used technology for building and managing terminologies and ontologies. He served as principal investigator of the National Center for Biomedical Ontology, one of the original National Centers for Biomedical Computing created by the U.S. National Institutes of Heath (NIH). He is principal investigator of the Center for Expanded Data Annotation and Retrieval (CEDAR), supported by the NIH Big Data to Knowledge Initiative. CEDAR develops semantic technology to ease the authoring and management of biomedical experimental metadata. Dr. Musen directs the World Health Organization Collaborating Center for Classification, Terminology, and Standards at Stanford University, which has developed much of the information infrastructure for the authoring and management of the 11th edition of the International Classification of Diseases (ICD-11).

Dr. Musen was the recipient of the Donald A. B. Lindberg Award for Innovation in Informatics from the American Medical Informatics Association in 2006. He has been elected to the American College of Medical Informatics, the Association of American Physicians, the International Academy of Health Sciences Informatics, and the National Academy of Medicine.

Susanna-Assunta Sansone, Ph.D., Group Leader and Principal Investigator, Associate Director, Oxford e-Research Centre, University of Oxford; Associate Professor, Department of Engineering Science, University of Oxford

Dr. Sansone's group researches and develops methods and tools to improve data reuse. They work towards improving data transparency, research integrity and the overall evolution of scholarly publishing. Dr. Sansone is the founding Honorary Academic Editor of Springer Nature's Scientific Data open access journal, and one of the co-authors of the FAIR Principles.

Dr. Sansone holds a PhD in Molecular Biology from the Imperial College of Science, Technology and Medicine in London. Before joining the University of Oxford in 2010, she was a Team Coordinator at the EMBL-EBI for almost 9 years, and previously a Senior Scientist in vaccine research in an Imperial spin off.

Andrew Su, Ph.D., Professor, Department of Integrative, Structural and Computational Biology, The Scripps Research Institute

Dr. Su is a Professor at the Scripps Research Institute in the Department of Integrative, Structural and Computational Biology (ISCB). His research focuses on building and applying bioinformatics infrastructure for biomedical discovery. His research has a particular emphasis on leveraging crowdsourcing for genetics and genomics. Representative projects include the Gene Wiki, BioGPS, MyGene.Info, and Mark2Cure, each of which engages the crowd to help organize biomedical knowledge. These resources are collectively used millions of times every month by members of the research community, by students, and by the general public.

Wei Wang, Ph.D., Leonard Kleinrock Chair Professor, Department of Computer Science, University of California, Los Angeles; Director, the Scalable Analytics Instiutue (ScAi)

Dr. Wang is the Leonard Kleinrock Chair Professor in Computer Science and Computational Medicine at the University of California, Los Angeles and the director of the Scalable Analytics Institute (ScAi). She is also a member of the UCLA Jonsson Comprehensive Cancer Center, Institute for Quantitative and Computational Biology, and Bioinformatics Interdepartmental Graduate Program. She received her PhD degree in Computer Science from the University of California, Los Angeles in 1999. She was a professor in Computer Science and a member of the Carolina Center for Genomic Sciences and Lineberger Comprehensive Cancer Center at the University of North Carolina at Chapel Hill from 2002 to 2012, and was a research staff member at the IBM T. J. Watson Research Center between 1999 and 2002. Dr. Wang's research interests include big data analytics, data mining, database systems, natural language processing, bioinformatics and computational biology, and computational medicine. She has filed seven patents, and has published one monograph and more than two hundred research papers in international journals and major peer-reviewed conference proceedings.

Dr. Wang received the IBM Invention Achievement Awards in 2000 and 2001. She was the recipient of a UNC Junior Faculty Development Award in 2003 and an NSF Faculty Early Career Development (CAREER) Award in 2005. She was named a Microsoft Research New Faculty Fellow in 2005. She was honored with the 2007 Phillip and Ruth Hettleman Prize for Artistic and Scholarly Achievement at UNC. She was recognized with an IEEE ICDM Outstanding Service Award in 2012, an Okawa Foundation Research Award in 2013, and an ACM SIGKDD Service Award in 2016. Dr. Wang has been an associate editor of the IEEE Transactions on Knowledge and Data Engineering, IEEE Transactions on Big Data, ACM Transactions on Knowledge Discovery in Data, Journal of Knowledge and Information Systems, Data Mining and Knowledge Discovery, Journal of Computational Biology, IEEE/ACM Transactions on Computational Biology and Bioinformatics, International Journal of Knowledge Discovery in Bioinformatics, and an editorial board member of the International Journal of Data Mining and Bioinformatics and the Open Artificial Intelligence Journal. She serves on the organization and program committees of international conferences including ACM SIGMOD, ACM SIGKDD, ACM BCB, VLDB, ICDE, EDBT, ACM CIKM, IEEE ICDM, SIAM DM, SSDBM, ISMB, RECOMB, BIBM. She was elected to the Board of Directors of the ACM Special Interest Group on Bioinformatics, Computational Biology, and Biomedical Informatics (SIGBio) in 2015.

External Scientific Advisory Panel

Director of Biomedical Informatics & Alliances, Clinical Data Interchange Standards Consortium (CDISC), and Assistant Professor, Baylor College of Medicine
Department of Obstetrics and Gynecology, UT Southwestern Medical Center
Associate Director, Center for Biotechnology and Genomic Medicine, Augusta University

Andrea de Souza, Ph.D.

Director, Informatics & Data AnalysisBroad Institute, Broad Institute

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