About Me
As a Scientific Researcher with 4+ years of experience in Computational Biology and 4+ years experience in experimental Biochemistry, I strive to make biological systems more quantitative, holistic, predictable, and eventually controllable. My enthusiasm for theoretical and experimental biology drives me to be truly discipline-agnostic and to come up with ideas from multiple paradigms to aid my scientific research.
Things I currently have the most experience with can be broadly classified into: Biochemistry, TIRF Microscopy and Computational Biology. However, I am always eager to explore new ideas and concepts, which helps me grow both personally and professionally. I enjoy staying adaptable and open-minded in the face of new challenges and opportunities.
Research Experience
Max Planck Institute of Molecular Physiology
Ph.D. Candidate
July 2019 - Present | Peter Bieling Lab
mpi-dortmund.mpg.de
Regulating Actin Dynamics and Branched Network Nucleation for Force Generation during Cell Protrusions.
When cells move, they extend their membranes into flat protrusions, which are formed as a result of forces generated by an orchestrated process that creates a branched network of actin filaments. My goal is to understand the spatial and temporal mechanisms that regulate this process.
Supervisor: Dr. Peter Bieling
Indian Institute of Science Education and Research
Research Fellow
August 2016 - May 2019 | COSPI Lab
cospi.iiserpune.ac.in
Knowledge-Based Prediction of Protein-Protein Interactions.
Protein-protein interactions are ubiquitous in cells and are responsible for a variety of biological functions, ranging from signal transduction to force generation. However, experimental methods for predicting interacting surfaces and characterising the whole interactome are time consuming, cost prohibitive, and unscalable. In this project, I designed a computational algorithm for predicting protein-protein interactions.
Supervisor: Prof. M.S. Madhusudhan
Indian Institute of Science Education and Research
Master's Dissertation Student
August 2015 - July 2016 | COSPI Lab
cospi.iiserpune.ac.in
Protein Structure Modelling of Entire Proteome.
Modelled the protein structures of 53% of the Plutella xylostella proteome (~11,000 proteins) using a custom built automated pipeline for template matching and homology modelling with MODELLER.
Supervisor: Prof. M.S. Madhusudhan
Institute of Bioinformatics and Biotechnology
Project Student
July 2013 - August 2014 | Smita Zinjarde Lab
unipune.ac.in
Characterization of Bioactive Peptide from Soil Bacteria.
Isolated, cloned and characterised a gene encoding an antimicrobial protein BLDZ1 from Bacillus licheniformis D1.
Supervisor: Prof. Smita Zinjarde
Publications
Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments
doi.org/10.1038/s41594-023-01101-9W Oosterheert, FEC Blanc, A Roy, A Belyy, O Hofnagel, G Hummer, P Bieling, S Raunser | Nature Structural & Molecular Biology | September 2023
P Sanghavi, P Kumar, A Roy, MS Madhusudhan, R Mallik | Proceedings of the National Academy of Sciences | April 2021
A knowledge-based scoring function to assess quaternary associations of proteins
doi.org/10.1093/bioinformatics/btaa207AS Dhawanjewar*, AA Roy*, MS Madhusudhan | Bioinformatics | June 2020
N Sen*, TR Kanitkar*, AA Roy*, N Soni, K Amritkar, S Supekar, S Nair, G Singh, MS Madhusudhan | PLoS Neglected Tropical Diseases | December 2019
Structural insights of a cellobiose dehydrogenase enzyme from the basidiomycetes fungus Termitomyces clypeatus
doi.org/10.1016/j.compbiolchem.2019.05.013S Banerjee, A Roy, MS Madhusudhan, HR Bairagya, A Roy | Computational Biology and Chemistry | October 2019
Protein Interaction Z Score Assessment (PIZSA) - an empirical scoring scheme for evaluation of protein–protein interactions
doi.org/10.1093/nar/gkz368AA Roy*, AS Dhawanjewar*, P Sharma, G Singh, MS Madhusudhan | Nucleic Acids Research | July 2019
A Roy*, S Nair*, N Sen, N Soni, MS Madhusudhan | Methods | December 2017
AR Agnihotri, AA Roy, RS Joshi | Insect Molecular Biology | May 2016
* indicates equal contribution
Education
Institute of Bioinformatics and Biotechnology
M.Sc. Biotechnology
2011 - 2016
5 year integrated Master's degree at Savitribai Phule Pune University (formerly known as University of Pune).
Multidisciplinary course with subjects including Physics, Chemistry, Biology, Mathematics and Computer Science.
Learning Centre
Biology
2009 - 2011
Learning how to learn!
I had the opportunity to be mentored by Mr. S.L. Acharya, who instilled in me a deep passion for Science and a desire to never stop learning.
Certifications
Deep Neural Networks
Differential Equations | Gradients | Gradient Descent | Hessian
Linear Regression | Logistic Regression | Artificial Neural Networks | Decision Trees | Clustering | Anomaly Detection | Recommender Systems | Reinforcement Learning
Clustering | Anomaly Detection | Recommender Systems | Collaborative Filtering | Content-based Filtering | Reinforcement Learning
Artificial Neural Networks | Decision Trees | Random Forest | XGBoost
Linear Algebra | Machine Learning | Eigenvalues and Eigenvectors
Machine Learning | Linear Regression | Logistic Regression
Convolutional Neural Networks | Semantic Segmentation | Computer Vision
Galaxy | Genomic Analysis
Python | Biopython | Bioinformatics | Genomics
Next Generation Sequencing | Bioinformatics | Statistics
When I'm not in the lab
Alongside my interests in research some of my other interests and hobbies are:
- Sports: Weight Training, Bouldering, Football, Cricket
- Reading: Popular Science, Technology, Productivity
- Teaching: Programming, Algorithms
- Science and Technology: Synthetic Biology, Artificial Intelligence, Fusion Power, Space Exploration, Renewable Energy