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 Soumen Roy
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Systems Biology

Systems Biology

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Network science / Complex networks:
 
* Corresponding / Co-corresponding  author

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

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: 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*, 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*

Using complex networks towards information retrieval and diagnostics in multidimensional imaging
Scientific Reports [Nature] 5: 17271 (2015)     arxiv:1506.02602     PDF    
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 specialty crops
Critical Reviews in Immunology  30 277-289 (2010)

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*


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:


Soumen Roy