Soumen Roy
Professor
Soumen Roy
Professor, Physical Sciences
PhD: Homi Bhabha National Institute, 2007
Previous appointments:
Institute for Genomics and Systems Biology, The University of Chicago
Center for Computational Science and Engineering, University of California, Davis
Research interests:
Recently published and ongoing projects are in the areas of:
- Complex systems, Networks, and, Statistical physics
- Networks and information theory
- Quantum entanglement on networks
- Networks and game theory
- New measures in networks and their implications
- Innovative
applications of networks, e.g. in Information retrieval, image
processing,
and non-invasive diagnostics, mutagenesis, phage resistance
etc.
- Phase transitions and critical phenomena
- Communication, competition and co-operation in Microbial systems (Theory and Experiments)
- Antimicrobial resistance
- Phage-bacteria interactions and dynamics
- Computational Systems Biology
- Structure, function and dynamics of biological macromolecules
- Microbial systems
- Further details on Group website
Contact:
| Address: |
Physical Sciences Unified Academic Campus Bose Institute EN-80, Sector V Bidhan Nagar Kolkata - 700 091, India |
| E-Mail: | soumen[at]jcbose.ac.in |
| Phone: | +91-33-25693232 |
Research:
For more details please visit our Lab website
Our interdisciplinary lab in the Dept. of physical sciences and has been associated with institutional research programmes in: (i) complex systems, (ii) physical and environmental sciences, and, (iii) systems and synthetic biology.
We study various physical and biological systems by applying tools from statistical physics, network science, non-linear dynamics and game theory. We also design and conduct experiments in parallel with mathematical modelling to achieve a better understanding of biological systems. Recently published and ongoing projects are listed here.
Recent work by students of our lab has been published in interdisciplinary, physics and life science journals like Bioinformatics (Oxford), Europhysics Letters (EPL), Physical Review E (APS), Applied and Environmental Microbiology (ASM), Scientific Reports (Nature), and Frontiers in Physics (Frontiers). Our invited contributions have appeared in publications like Methods in Molecular Biology and Advances in Applied Microbiology.
Publications:
Patents granted as Principal Inventor:
A system and method
for analyzing videos of application or function for feature identification of
the videos and related application or function [ Patent No. 472279 (2023) ]
Soumen Roy et al.
Software
for analyzing videos of application or function for feature
identification of the videos and related application or function Registration
number: [ SW-10052 (2018) ]
Soumen Roy et al.
Papers/preprints:
*Corresponding / Co-corresponding author
Foreword: special issue on statistical physics and complex systems
Indian Journal of Physics (Springer), 98, 3753-3755 (2024)
Deepak Dhar and Soumen Roy
An ab initio information-theoretic approach to proteins and protein-ligand interactions (2024)
Deep Nath, Rajdeep Kaur Grewal, Devrani Mitra* and Soumen Roy*
Assessing combinatorial diversity of Aureochrome bZIPs through genome-wide screening (2024)
Madhurima Khamaru, Deep Nath, Devrani Mitra* and Soumen Roy*
Mutations, mathematics, and medicine: Probing phages (Invited review, submitted)
Swati Sharma, Akash Gupta and Soumen Roy*
Modeling plaque formation: Phages on bacteria (Invited article, submitted)
Deep Nath, Swati Sharma and Soumen Roy*
Network approach to mutagenesis sheds insight on phage resistance in mycobacteria
Bioinformatics [Oxford], 37, 213-220 (2021) PDF
Saptarshi Sinha, Sourabh Samaddar, Sujoy Das Gupta and Soumen Roy*
Summary Popular Coverage at Research Matters Popular Coverage at Daily Hunt
Scale-free networks may not necessarily witness cooperation
Euro Physics Letters [EPL], 134, 60002 (2021) arXiv:2101.01167
Deep Nath, Saptarshi Sinha and Soumen Roy*
Topology dependent payoffs can lead to escape from prisoner’s dilemma
European Physical Journal B, 94, 80 (2021) arXiv:2006.14593
Saptarshi Sinha, Deep Nath and Soumen Roy*
Mass testing and proactiveness affect epidemic spreading [Invited]
Special issue on "Emerging Trends in Modeling and Analysis of Complex Systems"
Journal of the Indian Institute of Science, 101, 371-380 (2021) arXiv:2008.10387
Saptarshi Sinha, Deep Nath and Soumen Roy*
Modeling phage-bacteria dynamics
Methods in Molecular Biology, 2131, 309-327 (2020) [Springer]
Saptarshi Sinha, Rajdeep Kaur Grewal and Soumen Roy*
Residue interaction dynamics in Vaucheria aureochrome1 light-oxygen-voltage: Bridging theory and experiments
Proteins: Structure, Function, and Bioinformatics [Wiley], 88, 1660-1674 (2020)
Anwesha Deb, Rajdeep Kaur Grewal, Soumen Roy* and Devrani Mitra*
A pedestrian review of games on structured populations [Invited review] PDF
International Journal of Advances in Engineering Sciences
and Applied Mathematics [Springer], 11, 138-152 (2019)
Saptarshi Sinha, Susanta Ghosh and Soumen Roy*
Role of a 19S proteasome subunit -
PSMD10 Gankyrin in neurogenesis of human neuronal progenitor cells
International Journal of Stem Cells, 12, 463-473,
(2019)
Indrajit Sahu, Padma Nanaware, Minal Mane, Soumen Roy* and Prasanna Venkatraman*
Topologically inspired walks on
randomly connected landscapes with correlated fitness
Frontiers in Physics [Frontiers], 6: 138 (2018)
Rajdeep Kaur Grewal, Saptarshi Sinha and Soumen Roy*
Modeling bacteria-phage interactions
and implications for phage therapy
Advances in Applied Microbiology [Academic Press], 103,
103-141 (2018)
Saptarshi Sinha, Rajdeep Kaur Grewal and Soumen Roy*
Dynamics of
Mycobacteriophage-Mycobacterial host interaction - evidence for secondary
mechanisms for host lethality
Applied and Environmental Microbiology [ASM], 82, 124-133
(2016) PDF Supplementary Information
Sourabh Samaddar, RK Grewal, S Sinha, S Ghosh, Soumen Roy* and Sujoy Das Gupta*
Selected as an article of significant interest by the Editors for AEM Spotlight
Using complex networks towards information retrieval and diagnostics in
multidimensional imaging
Scientific Reports [Nature] 5: 17271 (2015) arxiv:1506.02602 PDF Supplementary Information
Soumya Jyoti Banerjee, Mohammad Azharuddin, Debanjan Sen, Smruti Savale, Himadri Datta, Anjan Dasgupta and Soumen Roy*
Slow poisoning and destruction of networks: Edge proximity and
its implications for biological and infrastructure networks
Physical Review E [APS] 91 022807 (2015) arxiv:1409.8268 PDF
Soumya Jyoti Banerjee, Saptarshi Sinha and Soumen Roy*
Mapping networks of light-dark transition in LOV
photoreceptors
Bioinformatics [Oxford] 31 3608-3616 (2015) Supplementary Information
Rajdeep Kaur Grewal, Devrani Mitra and Soumen Roy*
Modeling proteins as residue interaction networks [Invited
review]
Protein & peptide letters 22 923-933 (2015)
Rajdeep Kaur Grewal and Soumen Roy*
Perspectives in systems biology
Editorial for special issue
Systems and Synthetic Biology [Springer] (2014) 8: 1-2 PDF
Soumen Roy*
Efficient scheduling using complex networks
arxiv:1206.2866
Osamu Yamaguchi, Soumen Roy* and Raissa
M. D'Souza
Systems biology beyond degree, hubs and scale-free networks: the
case for multiple metrics in complex networks
Systems and Synthetic Biology [Springer] (2012) 6: 31-34 arxiv:1205.2318 PDF
Soumen Roy*
Analysis
of early host responses for asymptomatic disease detection and management
of speciality crops
Critical Reviews in Immunology 30 277-289 (2010)
A. M. Dandekar et. al.
Resilience
and rewiring of the passenger airline networks in the United States
Physical Review E 82 056101 (2010) arxiv:0901.0774
PDF
Daniel R. Wuellner, Soumen Roy* and Raissa M. D'Souza
Strong associations between microbe phenotypes and their network
architecture
Physical Review E (Rapid) 80 040902(R) (2009) arxiv:0901.0775
PDF
Soumen Roy* and Vladimir Filkov
Modeling and verifying a broad array of network properties
Europhysics Letters 86 (2009) 28003 arxiv:0805.1489 PDF
Vladimir Filkov, Zachary M. Saul, Soumen Roy, Raissa
M. D'Souza and Prem Devanbu
"Graphlet arrival model" has been covered in the book: An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks (Chapman & Hall/CRC Computational Biology Series)
Network growth with feedback
Physical Review E (Rapid) 78 045101(R) (2008) arxiv:0805.4020 PDF
Raissa M. D'Souza and Soumen Roy*
Motion of a random walker in a quenched power law correlated
velocity field
Physical Review E 73 026106 (2006) cond-mat/0511008 PDF
Soumen Roy* and Dibyendu Das
Giant coherence in driven systems
J. Stat. Mech. (2006) P09012 cond-mat/0511519 PDF
Soumen Roy*, Debasis Dan and A. M. Jayannavar
Is small-world network disordered?
Physics Letters A 352 13 (2006) cond-mat/0409012 PDF
Soumen Roy* and Somendra
M. Bhattacharjee
Enhanced Thermodynamic efficiency in time asymmetric ratchets
J. Stat. Mech. (2005) P04012
cond-mat/0412303 PDF
Raishma Krishnan, Soumen Roy* and A. M. Jayannavar
Invited book chapters:
"Allostery and networks" in "Advances in Biology"
Nova, New York, USA (2023)
Swati Sharma, Deep Nath, and Soumen Roy*
"Systems biology in plant cells and their
organelles" in "Plant cells and their organelles"
John Wiley & Sons Ltd., UK (2017). Editors: Dashek and Miglani
Rajdeep Kaur Grewal, Saptarshi Sinha and Soumen Roy*
[Book
Review: "Perhaps the most important chapter in this book ...",
Elizabeth Friar, Crop Science (2017) 57
3360-3361 ]
"Complex networks and systems biology" in "Systems and Synthetic Biology"
Springer Netherlands (2015). Editors: Singh and Dhar
Ushasi Roy, Rajdeep Kaur Grewal and Soumen Roy*
"Networks, metrics and systems biology" in "A systems theoretic approach to
systems and synthetic biology I: models and system characterizations"
Springer Netherlands (2014). Editors: Kulkarni, Stan and Raman
Soumen Roy*
Contributed book chapters:
"The network route to
biological complexity" in BIOMAT 2015 - Proceedings of the 15'th
International Symposium on Mathematical and Computational Biology - IIT Roorkee
World
Scientific (2016). Editor: Mondaini
Soumya Jyoti Banerjee, Rajdeep Kaur Grewal, Saptarshi Sinha and Soumen Roy*
Recognition:
- Guest Editor, Special Issue on Statistical physics and complex systems, Indian Journal of Physics (Springer), 2024
- Reviewer, (Mathematics & Computer Science Panel), National Research, Development and Innovation Office, Hungary, Since 2022
- Academic Editor, PLOS ONE, 2018--present
- Regular Associate, International Centre for Theoretical Physics (UNESCO), Trieste, Italy, 2017--present
- Editor, Special Issue, Systems and Synthetic Biology (Springer), 2014
- Hon. Assoc. Editor, Indian Journal of Physics (Springer), 2012--present
- Member, Planning Commission Task Force on Systems and Synthetic Biology, Govt of India, 2011
Teaching:
Statistical analysis
Ph.D. 2024
Statistical physics
Ph.D. 2023
Computer programming with python
Ph.D. 2023
Research ideology and research ethics
Ph.D. 2024, 2023, 2022
Numerical methods
Ph.D. 2022
Computational and Systems Biology (609)
Integrated Ph.D. in Life Sciences 2020-2021
Statistical Physics - II
Integrated Ph.D. in Physical Sciences 2019-2020
Statistical Physics - I
Integrated Ph.D. in Physical Sciences 2017-2018
Integrated Ph.D. in Physical Sciences 2016-2017
Integrated Ph.D. in Physical Sciences 2015-2016
Computation and numerical techniques - I
Integrated Ph.D. in Physical Sciences 2014-2015
Integrated Ph.D. in Physical Sciences 2013-2014
Dynamical systems (Tools of systems biology - II)
Integrated Ph.D. in Life Sciences (Bose Institute) 2014-2015
Integrated Ph.D. in Life Sciences (Bose Institute) 2013-2014
Networks (Computational and systems biology)
Integrated Ph.D. in Life Sciences 2014-2015
Integrated Ph.D. in Life Sciences 2013-2014
Concepts of approximations (Tools of systems biology - I)
Integrated Ph.D. in Life Sciences 2014-2015
Integrated Ph.D. in Life Sciences 2013-2014
Integrated Ph.D. in Life Sciences 2012-2013
Students:
| Image | Name | Designation | Department | Campus | Contact number | |
|---|---|---|---|---|---|---|
 |
Arijit Roy | Junior Research Fellow | Physics | Unified | arijitroy@jcbose.ac.in | |
 |
Ramnarayan Bera | Junior Research Fellow | Physics | Unified | ramnarayan97@jcbose.ac.in | |
 |
Swati Sharma | Junior Research Fellow | Physics | Unified | swatisharma@jcbose.ac.in |
Former:
Former Doctoral Fellows:
Ph. D. Registration [ Theoretical physics ] University of Calcutta
Dr. Saptarshi Sinha -- Current / next affiliation: University of California, San Diego, USA
Ph. D. [ Microbiology (Systems Biology) ] University of Calcutta
Dr. Rajdeep Kaur Grewal -- Current / next affiliation: Ohio State University, USA
Ph. D. [ Applied Mathematics (Networks) ] University of Calcutta
Ph.D. Thesis Title: Studies on Biological Networks
Group News:
For more details please visit our Group website
Special Issue on "Statistical Physics and Complex Systems"
Indian Journal of Physics (Springer)
Guest Editors: Deepak Dhar and Soumen Roy