Explore This Lab

Overview

Our group, formerly called MIND Informatics, uses both high-dimensional molecular -omics datasets and healthcare big-data to advance Alzheimer’s research using statistical inference and machine learning. We frequently apply bioinformatics techniques to study the mechanistic basis of human disease with a focus on Alzheimer’s and other neurodegenerative disorders.

Research Projects

Data Core of the Massachusetts Alzheimer Disease Research Center (MADRC)

Dr. Das leads the data core of the Massachusetts Alzheimer Disease Research Center (MADRC) along with Dr. Lori Chibnik. We provide end-to-end data solutions from process optimization, data capture and storage to querying and reporting for the Clinical, Imaging, Biomarker and Neuropathology Cores of the MADRC. Using open source solutions, we have developed a linkage database, nLINQUE, that integrates data across the cores for use by all MADRC researchers. We also assist MADRC investigators with their various data needs.

Alzheimer DataLENS

Alzheimer DataLENS is a project of the Massachusetts Center for Alzheimer Therapeutics Science (MassCATS), which is a public-private partnership to discover new treatments for Alzheimer's disease, organized through the Massachusetts Life Sciences Center. Alzheimer DataLENS provides information on hypothesis-driven and data driven research, allowing neuroscientists to share, browse and visualize comprehensive results from bioinformatics analysis of public omics datasets. It also serves as a tool to organize and share results from MassCATS investigations.

EHR Data Mining

We are investigating the use of real-world data, such as Electronic Health Records (EHR), for dementia research. Using EHR, we are collaborating on a project to emulate trials to repurpose FDA approved drugs that may reduce the risk of dementia or slow cognitive decline (Dr. Mark Albers, PI). We are applying a causal inference, competing risk framework to estimate the risk of dementia in drugs of interest. We are also exploring the use of Natural Language Processing (NLP) to assess and stage dementia in these data.

AD Bioinformatics

We have applied integrative bioinformatics analysis to several public genomics and transcriptomics datasets to understand, for example, the role of calcium signaling genes, the effect on angiogenesis-related or oxidative stress gene expression in Alzheimer’s pathology. We have conducted meta-analysis to generate signatures of astrocyte activation. We are investigating the role of APOE ε4, the biggest genetic risk factor for Alzheimer’s disease, in microglial activation as well as using multiple cohorts to understand potential differential risks of the APOE ε4 allele across populations and haplotypes.

MGH Biomedical Informatics Core

Our laboratory is an official Research Core for Partners Healthcare (MGH Biomedical Informatics Core) and provides free initial consultation on problems in computational biology, research data management, web development, ontology development and use, as well as general scientific software engineering. We are funded by research grants and contracts from government, private philanthropies and industry. We provide consultation and software engineering to members of the Partners Healthcare consortium, academia and industry, on a monthly-invoiced time and materials basis.

Scientific Community Websites

We have developed and continue to support several scientific community websites: notably an IOS press journal website for Alzheimer’s Disease with over 7000 registered researchers, a globally recognized site for informing and engaging patients with small-fiber neuropathy (SFN), a pain research forum to foster discussion and collaboration among neuropathic pain researchers and a similar forum for multiple sclerosis investigators.

Team

Principal Investigator

Sudeshna Das, PhD

Current Lab Members

Emily Merrill, MSc, Bioinformatics Specialist
Aziz M. Mezlini, PhD, Post-Doctoral Fellow
Colin Magdamo, BSc, Data scientist
Zhaozhi Li, BSc, Bioinformatics Intern

Alumni:

Timothy W. Clark, PhD, former Principal Investigator
Nate A. Bihlmeyer, PhD, Post-Doctoral Fellow
Max Levinson, BSc, Data Science
Paolo Ciccarese, PhD, Asst. Professor of Neurology
Marco Ocana, MSc, Software Engineer
Samuel Brin, BSc, Software Engineer
Stéphane Corlosquet, MSc, Software Engineer
Timothy Danford, MSc, Biomedical Engineer
Nicholas Maloney, BSc, Software Engineer