BMIR Labs and Staff
Mete Ugur Akdogan
Mete received his B.Sc. from Istanbul Technical University, M.Sc. and Ph.D. in Computer Engineering from Dokuz Eylul University, Izmir, Turkey. He worked as a Research Assistant at Dokuz Eylul University and in the Laboratory of Quantitative Imaging at Stanford University before joining the Mussen Lab. His main research subjects are big data analytics, parallel algorithms, biomedical imaging and informatics.
Yan Cao
Yan holds two MS degrees - one in Computer Science from Georgia Institute of Technology and another in Food Science from the University of Minnesota. She joined the Musen Lab as a Software Developer I after graduating from Georgia Tech. Her passion lies in software development for the Bioscience fields, and she had been contributing to the CEDAR project since joining the team and now working on RADx (Rapid Acceleration of Diagnostics for Covid) project.
Michael Dorf
Misha Dorf has been the Chief Software Architect at the Stanford Center for Biomedical Informatics Research for more than 10 years. Misha has an extensive software development background in both industrial and academic environments. He has played the principle role in devising the architecture of the BioPortal and OntoPortal technologies and has extensive experience in Web-based application development with a heavy focus on back-end frameworks and programming languages. He also contributes to RADx (Rapid Acceleration of Diagnostics for Covid) project.
Attila L. Egyedi
Attila is a full-stack software developer. He received his MS in Computer Science (Machine Learning) from Georgia Tech after his BS from the Technical University of Cluj-Napoca, Romania. He worked at several companies in Romania, Hungary, previously he was part of the CEDAR team for five years. After 1.5 years of AWS experience, he returned to continue the work on CEDAR and other projects of the Musen Lab.
Josef Hardi
Josef is a senior software developer at Stanford University with over 12 years' experience developing software and managing complex data. His interest in Ontology and Semantic Web Technologies began during his first job at a data lab where the team was doing a research and development in relational databases and ontologies where they discovered a novel method to connect both. Later this knowledge and skill set eventually led him to Musen Lab at Stanford University where he began working on developing modules for Protégé, an ontology editor software known widely by the semantic web communities. Subsequently, he became more involved in bigger projects such as CEDAR and FAIRware, which focus on addressing challenges in metadata management in biomedicine. Currently, he is part of a multi-institutional team working towards the creation of a human atlas at cellular level, called HuBMAP, and is responsible for shaping the reporting guidelines for cell research datasets.
Josef earned a Master's degree from the European Masters Programme in Software Engineering (EMSE), which he completed in Italy and Sweden.
Matthew Horridge
Matthew is a research software engineer in the Musen Lab. He works on the Protégé suite of tools for ontology engineering.
Christian Kindermann
Christian is interested in helping scientist manage their data with semantic technologies (ontologies, knowledge graphs, automated reasoning). He earned a PhD from the University of Manchester, England, where he developed a range of novel pattern-based ontology engineering techniques. He continued his research as a postdoc at the University of Oslo, Norway, before joining the Musen Lab at Stanford as a postdoctoral scholar, where he will apply his techniques in data integration efforts.
Marcos MartÃnez-Romero
Marcos MartÃnez-Romero is an experienced Research Software Engineer with a strong background in Knowledge Engineering and Semantic Technology. He earned his B.Sc., M.Sc., and Ph.D. in Computer Science and Artificial Intelligence from the University of A Coruña, Spain. Marcos started his journey with BMIR in 2013 and contributed to various projects, including BioPortal and CEDAR. After serving as an Ontology and Knowledge Engineer at Acubed, Airbus’ Innovation Center in Silicon Valley, Marcos returned to BMIR, currently focusing on the RADx project among other key initiatives.
Martin O'Connor
With over two decades of experience as a research software engineer, Martin O'Connor specializes in constructing tools that facilitate the integration of semantic technologies into software systems. Currently, his primary emphasis lies in enhancing metadata representations by incorporating rich semantic content through the use of ontologies. Martin played a pivotal role in architecting and overseeing the development of CEDAR, a web-based platform designed for the management of metadata related to scientific experiments.
Alex Skrenchuk
Alex is an experienced Linux Systems/DevOps Engineer specializing on High Performance computing, configuration management frameworks, CI/CD pipelines and support of in-house developed web applications.
Sowmya S Sundaram
Sowmya is a postdoctoral scholar, working with Prof. Mark Musen at the Center for Biomedical Informatics Research. She was previously working as a postdoc at the intersection of natural language processing and biomedical project at L3S Research Centre, Hannover. During that phase, she worked with real medical datasets and interacted with doctors and clinicians from MHH, Hannover, for dental implants and cochlear implants. She earned her PhD from Indian Institute of Technology, Madras, India, which was on different representations for NLP problems for the use case of school level word problems. At the Musen Lab, she will be the NLP expert for devising algorithms that clean up ontology metadata and enhance user experience.
Jennifer Vendetti
Jennifer is a senior software engineer at the Stanford Center for Biomedical Informatics Research in the Musen Lab. Her focus is developing the BioPortal software for accessing and sharing biomedical ontologies. She additionally holds the role of the primary Stanford representative within the OntoPortal Alliance, an international consortium comprised of research teams dedicated to promoting and collaboratively advancing the OntoPortal open-source software.