Academic Career

Instructor (January 2021 - Present), 

Postdoctoral researcher (April 2017 - December 2020)

Centers for Autoimmunity, Inflammation, and Cancer Immunotherapy, La Jolla Institute for Immunology, La Jolla, CA 92037, USA

Supervisors: Dr. Ferhat Ay and Dr. Pandurangan Vijayanand

Research areas 

1. Computational biology, epigenomics, 3D genome, gene regulation

   • Predictive modeling of 3D chromatin structures and gene regulatory mechanism

   • Novel algorithms and statistical methods applied on next-generation sequencing (NGS) epigenomic and chromatin conformation capture (3C) datasets

2. Human genetics: Prediction of putative functional (causal) genetic variants (SNPs) utilizing GWAS, QTL, epigenomic data and 3D chromatin assays, for various diseases and cell types

   • Statistical and algorithmic techniques to prioritize putatively causal genetic variants for context-specific gene regulation

3. Deep learning based modeling of gene-regulatory landscape.

4. Single cell and multi-omic data analysis for modeling disease-specific genes and regulatory regions.

Ph.D. (July 2012 — August 2017)

Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India

Supervisor: Dr. Jayanta Mukhopadhyay

Research area: Algorithms in Computational phylogenetics and molecular evolution. 

4. • Resolving the conflict of evolutionary information among a group of species, due to the difference in individual genetic lineages.

Thesis title: Couplet based Analysis of Phylogenetic Trees

Master of Science (M.S.) by research (July 2009—July 2012)

Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India

Supervisors: Dr. Jayanta Mukhopadhyay and Dr. Arun Kumar Majumdar

Research area: Machine learning based detection of epileptic seizure patterns using neonatal electroencephalogram (EEG) signal and video.

Thesis title: Analysis of newborn video-EEG for epileptic seizure detection

Bachelor in Engineering (B.E) (June 2002—June 2006) 

Department of Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal 700032, India

Research Grants

• NIH R-03 grant 1R03OD034494-01 (Using Common Fund datasets for prioritization of disease-associated genetic variants): Assisted my supervisor Dr. Ferhat Ay in preparing the grant proposal, initial results, and currently supervising graduate students in preparing a HiChIP database. (link)

• D - Challenge 2021: Our team (Joaquin Reyna, Sourya Bhattacharyya, Nikhil Rao, Abhijit Chakraborty and Ferhat Ay) obtained a grant of $20,000 for research in Type 1 Diabetes (T1D), from SugarScience (https://thesugarscience.org/). For details, check http://info.thesugarscience.org/dknet-21-d-challenge

Awards / Fellowship / Travel Grants / Recognitions

• JULY 2022: Conference travel fellowship from ISMB 2022.

• MARCH 2022: Our work on single-cell eQTL in immune cells is featured in various scientific news articles.

• NOVEMBER 2021: Our work on Functional variants of COVID-19 in immune cells is featured in various scientific news articles.

• JANUARY 2021: Our work on promoter interacting eQTL is highlighted in various scientific news articles.

• JUNE 2019: Our work Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer is featured in various scientific news articles. 

• JUNE 2015: Conference Travel fellowship from the Organizing Committee of ISBRA 2015.

• MAY 2015: Conference Travel fellowship from the Department of Science and Technology (DST), India, for attending conference ISBRA 2015.

• APRIL 2013: Ph.D. fellowship from Tata Consultancy Services (TCS) 

• JULY 2012: Ph.D. fellowship from Indian Institute of Technology, Kharagpur (until March 2013).

Previous Work Experiences

1. Research Software Engineer in ST Microelectronics Private Limited, Greater Noida, India (July 2006 - July 2009)

Division: AST (Advanced System & Technology) group (R&D section)

Projects: 

1. Video transcoding between formats  H.264, MPEG-4, and MPEG-2, along with the bit rate control mechanism, for supporting low bandwidth.

   • Target Application: Integrated in STMicroelectronics implemented DBS (Dynamic Bitstream Shaper) transcoding library (integrated into STm71xx product family).

2. Integration of A/V codecs in  OpenMAX (Open Media Acceleration) and MPLAYER (version 1.0pre8) multimedia libraries.

2. Sponsored Research and Industrial Consultancy (SRIC), IIT Kharagpur (July 2009 - July 2012)

Project: To design a framework for the analysis of newborn video-EEG to detect epileptic seizures. Included data collection, data annotation, and project report.

Collaborators: 

1) Department of Neonatology, Institute of Post Graduate Medical Education and Research (IPGMER), Seth Sukhlal Karnani Memorial (SSKM) Hospital, Kolkata 700020 

2) West Bengal Electronics Industry Development Corporation Limited (WEBEL), Kolkata, India. 

Funding: Department of Information Technology (DIT) and Ministry of Communications and Information Technology (MCIT), Govt of India (currently named as Department of Electronics and Information Technology (DeitY))

Teaching experience

Department of CSE, Indian Institute of Technology Kharagpur, India

(for * marked courses, designed course materials, and teaching slides as well)

1. Computational Phylogenetics and Molecular Evolution *  (Theory course as a teaching assistant of  Prof. Jayanta Mukhopadhyay): Spring 2015-16, Spring 2014-15.

2. Algorithms in Bioinformatics *  (Theory course as a teaching assistant of  Prof. Jayanta Mukhopadhyay): Autumn 2015-16, Autumn 2014-15, Autumn 2013-14.

3. Computational Biophysics: Algorithms to Applications (Theory course as a teaching assistant of Dr. Pralay Mitra): Spring 2013-2014.

4. Advanced Digital Image Processing and Computer Vision (Theory course as a teaching assistant of Prof. Jayanta Mukhopadhyay and Dr. Rajiv Ranjan Sahay):  Spring 2012-13.

5. Programming and Data Structures Lab (as a teaching assistant of  Prof. Jayanta Mukhopadhyay): Autumn 2010-11, Autumn 2011-12, Spring 2011-12, Autumn 2012-13.

6. Programming and Data Structures Lab (as a teaching assistant of Prof. Sudebkumar Prashant Pal): Spring 2010-11.