MIND Informatics develops and applies integrative computational methods in biomedical and brain research, working with leading clinicians and researchers to understand and cure neurological disorders.

People

MIND Informatics personnel.

Tim Clark

Tim Clark, Ph.D., is a researcher in biomedical informatics with over 24 years of experience in the field. He is Director of Informatics at the MassGeneral Institute for Neurodegenerative Disease; Assistant Professor of Neurology at Harvard Medical School; directs the MGH Biomedical Informatics Core; and co-directs the Data and Statistics Core at the Massachusetts Alzheimer Disease Research Center. Dr. Clark is also a Founding Editorial Board member of the journal Briefings in Bioinformatics, and an Advisory Board member for F1000 Research. Before coming to Harvard, Tim was Vice President of Informatics at Millennium Pharmaceuticals, where his team built one of the first integrated bio- and chemi-informatics software platforms in the pharmaceutical industry. He began his career in life science informatics at the NCBI/NIH, where he led the database development team for NCBI GenBank. Tim's core research group is based in the Neurology Research Department of the Massachusetts General Hospital (MGH), where it works in the areas of neuroinformatics, semantic web, and social computing. Dr. Clark’s academic training is in Computer Science. He earned his M.S. at Johns Hopkins University; and his Ph.D. at the University of Manchester (UK) under Professor Carole Goble, with a dissertation on the sociotechnical architecture and computational semantics of biomedical communications.

Sudeshna Das

Sudeshna Das is Instructor in Neurology at the Harvard Medical School, Assistant in Neuroscience at the Mass Genral Hospital, Affiliate faculty of the Harvard Stem Cell Institute and Associate Director of the MGH Biomedical Informatics Core. She holds a Ph.D. in biomedical engineering from Boston University. She has worked in bioinformatics and computational biology for over 10 years. As a graduate student, she developed novel methods for protein domain and function identification using graph-theoretic approaches and probability models. After graduate school, she worked at a leading biopharmaceutical company directing computational and software development projects. There she and her colleagues developed novel approaches for statistical analysis of drug-discovery and pre-clinical data as well as large-scale software for drug discovery and development. Her current research interests include development of scientific communities, semantic web technologies, neuro-informatics and computational analysis of complex biomedical data using statistical and data-mining techniques.

Nathan A. Bihlmeyer

Nathan A. Bihlmeyer is a Postdoctoral Fellow in Neurology with a joint appointment at Massachusetts General Hospital and Harvard Medical School. He holds a Ph.D. in Human Genetics from Johns Hopkins University School of Medicine focused on the genetics of electrical conduction in the heart, investigating the role of both rare and common genetic variants in humans. As a part of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium EKG working group, he was the junior project lead supporting 23 analysts working with the Illumina ExomeChip towards finding genes that effect cardiac repolarization, and by extension risk for Sudden Cardiac Death (SCD), in a meta-analysis involving over 95,000 human subjects. Nathan is currently working on integrating multi-omic data in an effort to discover novel molecular targets in Alzheimer disease therapeutics as a part of the MassCATS project.

Paolo Ciccarese

Paolo Ciccarese is Assistant Professor of Neurology at Harvard Medical School and Assistant in Neurology at the Mass General Hospital. He holds a M.S. in Computer Science and he started his career as freelance consultant in knowledge management software development. Soon after, Paolo received a PhD in Bioengineering and Bioinformatics from the University of Pavia, Italy, where he was also a teaching assistant for five years in courses on the subjects of artificial intelligence in medicine and object oriented programming. After completing his PhD, he became a research fellow in neurology at the Mass General Hospital/Harvard Medical School as well as a research fellow in medical informatics at the University of Pavia. He has been involved in the design and development of data/knowledge management systems for rare pathologies. Paolo co-developed the rdf visualizer Welkin for the SIMILE project and founded the JDPF (Java Data Processing Framework) project, a modular and extendable open source infrastructure for processing big quantities of heterogeneus data. Paolo currently works on the DOMEO and Open Annotation projects.

M. Emily Merrill

Emily Merrill is a bioinformatician and software developer at MIND Informatics. She has a Bachelor's degree in Biochemistry from Oberlin College and a Master's in Bioinformatics from Northeastern. Between degrees, she served as a Peace Corps Volunteer in Guyana, South America, where she worked with the Region 6 Department of Education to integrate educational technology into local schools. Her primary work is on eXframe, a Drupal-based re-usable software platform that allows researchers to store, share, and analyze their experiment data. eXframe is also the underlying software for the experimental repository of the Stem Cell Commons. There, Emily has dual roles as both bioinformatics software developer and curator. She has worked at MIND Informatics since 2010.

Marco Ocana

Marco Ocana is a senior Java, AJAX and semantic web software architect for bioinformatics applications, with eleven years bioinformatics and cheminformatics experience and almost twenty years total in software engineering. In addition to leading SWAN architecture development he has led and participated in other significant projects at: Massachusetts General Hospital, Sention Pharmaceuticals, Biogen Idec Inc., and Millennium Pharmaceuticals. Marco holds an MS in Computer Science from Worcester Polytechnic Institute.

Alumni

Samuel Brin

Sam Brin is a recent graduate of the University of Maryland, College Park, where he studied Computer Science and Physics. Sam joins MIND Informatics as an engineer for The Science Collaboration Framework (SCF). Prior to coming on full-time, he developed a JavaScript image annotation tool for PD Online Research, an SCF site. Sam is excited to contribute to the open source Drupal content management system while building semantically enabled biomedical web communities.

Stéphane Corlosquet

Stéphane Corlosquet has been the driving force in getting Semantic Web capabilities into Drupal 7. His work in making RDF and RDFa part of Drupal core's DNA is a natural extension of his leading work bringing Semantic Web technologies to Drupal in the contributed code space, such as with the RDF CCK, evoc, and Neologism modules. Stéphane started out as a fledgling Electronic Engineer. His interests soon diverted to Web Development and his love of open source solutions led him inevitably to Drupal and the community therein 2 years ago. He is member of the security team and the documentation team. Stéphane completed his master's degree in Semantic Web at the Digital Enterprise Research Institute (DERI), National University of Ireland, Galway. He has been working in the field of IT and web development since 2003.

Timothy Danford

Timothy Danford is a Bioinformatics Engineer at Mass General Hospital. He graduated from Dartmouth College and holds an M.S. in Computer Science from the Massachusetts Institute of Technology. At MIT he worked under David Gifford, developing computational analyses of microarray expression, ChIP-chip, and high-throughput sequencing data in yeast, mice, and human. He helped develop an integrated Java system for the spatial anlaysis of genomic datasets, the Genomic Spatial Events (GSE) database. His interests include the application of machine learning techniques and Semantic Web modeling languages to assist and enhance biological investigations and data curation.

Gabriele Fariello

Gabriele Fariello is Assistant Dean for Computing at the Harvard School of Engineering and Applied Sciences, and Director of Clinical Research Informatics at Massachusetts General Hospital. He was a member of our team during its first few years of existence, working on development of a clinical research database for brain imaging studies in collaboration with Hans Breiter, Gregory Gasic and Bruce Rosen at the Martinos Center for Biomedical Imaging. He then went on to work as head of Randy Buckner's neuroinformatics team in the Harvard Department of Psychology and at the Mass General.

Gabriele trained in Molecular Biology at University of Wisconsin, Madison and is fluent in English, French and Italian. 

Nicholas Maloney

Nick Maloney is a software developer at the MassGeneral Institute for Neurodegenerative Disease (MIND). Nick has over a decade of experience developing and managing software projects in finance, higher-ed and health care. His primary area of expertise is leveraging open source technologies such as Drupal to solve complex content management needs. Nick earned his BS in Computer Information Systems from Bentley University.