Soumen Roy - Publications

List of publications and preprints:

https://orcid.org/0000-0002-0417-5751

* Corresponding / Co-corresponding author

General concurrence percolation on quantum networks
arXiv:2501.11004 [quant-ph] (2025)

Deep Nath* and Soumen Roy*

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)
bioRxiv 2024.03.06.583646
Deep Nath, Rajdeep Kaur Grewal, Devrani Mitra and Soumen Roy*

Assessing combinatorial diversity of Aureochrome bZIPs through genome-wide screening
Cells Tissues Organs [Karger], 213, 133-146 (2024) [Invited]    bioRxiv 2022.06.05.494858
Madhurima Khamaru, Deep Nath, Devrani Mitra* 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 in: Research Matters        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*

Residue interaction dynamics in Vaucheria aureochrome1 light-oxygen-voltage: Bridging theory and experiments
Proteins [Wiley], 88, 1660-1674 (2020)
Anwesha Deb, Rajdeep Kaur Grewal, Soumen Roy* and Devrani Mitra*

Modeling phage-bacteria dynamics
Methods in Molecular Biology, 2131, 309-327 (2020) [Springer]
Saptarshi Sinha, Rajdeep Kaur Grewal and Soumen Roy*

A pedestrian review of games on structured populations [Invited review]

International Journal of Advances in Engineering Sciences and Applied Mathematics [Springer], 11, 138-152 (2019)       PDF
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*, Prasanna Venkatraman*

Topologically inspired walks on randomly connected landscapes with correlated fitness
Frontiers in Physics [Frontiers] 6: 138 (2018)    PDF
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 article of significant interest by Editors for AEM Spotlight

Using complex networks towards information retrieval and diagnostics in multidimension- al 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 Bio [Springer] (2012) 6: 31-34 arxiv:1205.2318     PDF
Soumen Roy*

Analysis of early host responses for asymptomatic disease detection and management of specialty 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

Cited in:
(A) "Networks", Mark Newman, Oxford University Press, UK (2018)
(B) AS 63 [Ref. 16], First Report of Session 2013-14 (Vol 1), House of Commons Transport Committee on Aviation Strategy, Parliament of UK.

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 also 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*