Publications (Systems Biology)

Systems / Computational / Quantitative Biology and Biophysics:

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

* Corresponding / Co-corresponding author

Mutations, mathematics, and medicine: Probing phages (Invited review, submitted)

Modeling plaque formation: Phages on bacteria ( and Soumen Roy* Assessing combinatorial diversity of Aureochrome bZIPs through genome-wide screening
Cells Tissues Organs [Karger] (2022) [Invited] Biorxiv: 2022.06.05.494858 (2022)
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

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*

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*

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 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*

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*

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 specialty crops

Critical Reviews in Immunology 30 277-289 (2010)

A. M. Dandekar et. al.

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

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*