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About Me

👋 Hi, I’m Vivek Das

👀 I work on finding therapeutic targets or biomarkers (prognostic/predictive) for multiple cardiometabolic (e.g. Chronic Kidney, Atherosclerosis, Diabetes, Liver, Neurodegenerative, etc.) diseases combining data-driven and knowledge-driven avenues by leveraging the integration of bulk and single-cell multi-omics data alongside clinical data from human observational cohorts and clinical trials

🌱 I currently collaborate, mentor PhD/PostDocs/Data Scientists, lead studies/projects and a team of exceptional clinical data scientists and bioinformaticians involving single-cell transcriptomics, spatial transcriptomics, proteomics, metabolomics, multi-omics data integration, clinical data integration to achieve the above

💻 I also worked on omics projects involving preclinical data with interventional designs e.g. knockout or drug-treated at single cell or bulk multi-omics level

💞️ I also collaborate on developing applied machine learning models using publicly available data with curious students or researchers and contribute to open science and open source modeling. I am fascinated by the potential of high-dimensional and high-throughput biomedical data.

Publications

📚 To read more about our published works kindly check out my Google Scholar page

Experience

• Lead Data Scientist in Novo Nordisk A/S - 2023 - Present - Clinical Trial Omics & Precision Medicine in Clinical Development, Soborg, Denmark

  Lead, design, build, deploy, & implement integrative multi-omics strategies, in-silico analytical frameworks & interpretability in Late-Stage Clinical Trial (CardioRenal and neuronal) settings.

• Senior Research Scientist in Novo Nordisk A/S - 2021-2023 - Early Drug Discovery, Malov, Denmark

  In-silico Target and Biomarker discovery using high dimensional bulk/single-cell multi-Omics data, analysis, visualization and integration with clinical phenotypic measurements using advanced statistics and ML.

• Post Doctoral Scientist in Novo Nordisk A/S - 2018-2021 - Early Research in Seattle, USA

  Industrial research for biomarkers and target discovery in T1D, Immunology, and Kidney Research Unit through integrative systems medicine approach as a part of IMI delivery. Special focus on Diabetes and Chronic Kidney Diseases(currently End-Stage) as a part of integrating multi-omics discovery(NGS, Microarray, targeted NanoString Panels and Clinical data) from varied tissue sources extracted from patients/model organisms to deliver new research insights for therapies.

• Post Doctoral Scientist in European Institute of Oncology - 2017-2018 - Early Oncology Research in Milan, Italy

  Post PhD project follow-ups, transition and closure in both the cancer models (Glioblastoma recurrence and Ovarian Cancer) that I have worked on during PhD years using NGS technologies for Omics integration (from patients to gene networks).

• Programmer Analyst in Cognizant - 2010-2012 - Database management, Programming in PERL, Java & SQL in Kolkata, India

  Experienced in algorithm development, Software Development, deployment, and unit testing for both business and scientific innovation. In this organization I worked both as a Software Developer and an IT infrastructure maintenance consultant within Retail and Life Sciences vertical as a part of Master Data Management (MDM) horizontal in a matrix setting. My final project was that of a Support Programmer Analyst maintaining and enhancing a Life Science Database using Oracle (SQL programming) for a leading pharmaceutical company where I handled critical issues, performed bug analysis and system integration via programmatic solution.

Education

• PhD in Molecular Medicine (Curriculum Computational Systems Biology) from European School of Molecular Medicine, SEMM, Milan, Italy 2012-2017

• Masters in Science in Bioinformatics from Birla Institute of Technology, Mesra, India 2008-2010

• Bachelor in Biotechnology (Chemistry, Mathematics & Zoology) from PESIAS, Bangalore, India 2005-2008

Consortium and Collaborations

I have collaborated with a few biotech, pharmaceutical companies in pre-competitive space, universities, and hospitals within and outside my current job across projects, leading work packages, team, supervision of PhD and Post-Doctorial researchers.

Consortium and collaborations I have been part of:

• IMI BEAt-DKD

• Renal Pre-competitive consortia

• Karolinkska Institute - Novo Nordisk A/S collaboration

• Danish Diabetes Endocrine Society Scholarship with Rinschen Lab Aarhus University with co-funding from Novo Nordisk A/S

• novoSTAR Post-Doctoral collaboration between NN A/S and RWTH Aachen University with Kramman Lab and Hayat lab

• Prof. Rajat K. De lab, Machine Intelligence Unit, Indian Statistical Institute, ISI, Kolkata, India

• Michigan Kidney Translational Medicine Center

• Transformative Research In DiabEtic NephropaThy, or TRIDENT

Open source projects

• Multiomics Feature Extraction model using Autoencoders multOmicsIntegration

• Single Cell Multiomics integration model UMINT

• Single Cell type Annotation modeling CASSL

• Single Cell Multiomics integration and feature selection UMINT-FS

• Metabolomics feature selection plantmetaBolGCMS

Board Member

• Scientific Advisory Board Member at Pythia Biosciences - 2024-Present - Remote

Scientific advice and suggestions on the utility of current and potential features of the bioinformatics software and solutions, focusing on algorithms, statistical methods, and user experience.

Talks, Interviews and Podcasts (Selected)

• Transition from PhD to Industry

• EASD 2023 oral presentation on Multiomics, clinical data integration in T2D ASCVD patients

• Vivek Das Novo Nordisk KGDD4

• From omics to insights in early drug discovery and late-stage clinical development

• Podcast Being a Bioinformatician : Dr. Vivek Das

• Computational Biologist Interview

Certifications and Awards

• Machine Learning for Single Cell Analysis (Issued 2020) - Yale Genetics and Yale SEASYale Genetics and Yale SEAS

• GATK variant analysis (Issued 2017) - GATK Team Broad Institute

• Workshop in Systems Biology by EPIGEN in TIGEM, Naples (Issued 2013) - National Research Council of Italy

• AIRC-FIRC Fellowship - Recipient of the 3-year AIRC-FIRC cancer research fellowship to carry independent research in the field of cancer biology between 2014-2017

• FEBS Travel grant award at ENABLE 2017 symposium for poster presentation - Recipient of Travel grant award for the poster presented at ENABLE 2017 symposium in Barcelona

How to reach out

• 📫 vivekdas.0687@gmail.com
• LinkedIn

Technical blogging

• Biostars

General blogging

• Medium
• ResearchGate
• Quora

Topic of interest

• Leadership
• Applied Statistics and Applied Machine Learning
• Multi omics and clinical data integration
• Drug Target Identification
• Biomarker Discovery and Development
• Late-stage Drug development
• Big Data in Omics and Healthcare
• Start-up advisory and consulting
• Applied LLM in Biology and drug development
• Clinical Trial Design
• Single-cell and multi-omics predictive modeling
• Cardiometabolic diseases (Diabetes, Chronic Kidney Disease, Cardiovascular Disease, Liver Disease, Solid Cancers)
• Digital Strategy
• Software products
• Team building
• Mentorship
• Open-source project