citations_google_scholar.bib

@article{banerjee2009hybrid,
  title={A hybrid agent based and differential equation model of body size effects on pathogen replication and immune system response},
  author={Banerjee, Soumya and Moses, Melanie},
  journal={Artificial Immune Systems},
  pages={14--18},
  year={2009},
  publisher={Springer}
}

@article{banerjee2010scale,
  title={Scale invariance of immune system response rates and times: perspectives on immune system architecture and implications for artificial immune systems},
  author={Banerjee, Soumya and Moses, Melanie},
  journal={Swarm Intelligence},
  volume={4},
  number={4},
  pages={301--318},
  year={2010},
  publisher={Springer}
}

@article{banerjee2010modular,
  title={Modular RADAR: An immune system inspired search and response strategy for distributed systems},
  author={Banerjee, Soumya and Moses, Melanie},
  journal={Artificial Immune Systems},
  pages={116--129},
  year={2010},
  publisher={Springer}
}

@article{banerjee2011value,
  title={The Value of Inflammatory Signals in Adaptive Immune Responses},
  author={Banerjee, Soumya and Levin, Drew and Moses, Melanie and Koster, Frederick and Forrest, Stephanie},
  journal={Artificial Immune Systems},
  pages={1--14},
  year={2011},
  publisher={Springer}
}

@inproceedings{moses2010biologically,
  title={Biologically Inspired Design Principles for Scalable, Robust, Adaptive, Decentralized Search and Automated Response (RADAR)},
  author={Moses, Melanie and Banerjee, Soumya},
  booktitle={2011 IEEE Symposium on Artificial Life (ALIFE), Paris, France},
  year={2010}
}

@phdthesis{banerjee2013scaling,
  title={Scaling in the Immune System},
  author={Banerjee, Soumya},
  year={2013},
  school={University of New Mexico}
}

@article{liu2014bioorthogonal,
  title={A Bioorthogonal Small-Molecule-Switch System for Controlling Protein Function in Live Cells},
  author={Liu, Peng and Calderon, Abram and Konstantinidis, Georgios and Hou, Jian and Voss, Stephanie and Chen, Xi and Li, Fu and Banerjee, Soumya and Hoffmann, Jan-Erik and Theiss, Christiane and others},
  journal={Angewandte Chemie},
  volume={126},
  number={38},
  pages={10213--10219},
  year={2014},
  publisher={WILEY-VCH Verlag}
}

@article{banerjee2011comparing,
  title={Comparing immune response times and pathogen replication rates across vertebrate host species: a case study in West Nile Virus},
  author={Banerjee, Soumya and Moses, Melanie},
  journal={The Journal of Immunology},
  volume={186},
  number={(Meeting Abstracts 1)},
  pages={170--17},
  year={2011}
}

@article{curt2014science,
  title={Science and technology consortia in US biomedical research: A paradigm shift in response to unsustainable academic growth},
  author={Curt Balch, Hugo Arias-Pulido, Soumya Banerjee, Alex K. Lancaster, Kevin B. Clark, Michael Perilstein, Brian Hawkins, John Rhodes, Piotr Sliz, Jon Wilkins, Thomas W. Chittenden},
  journal={BioEssays},
  volume={37},
  number={2},
  pages={119--122},
  year={2014}
}

@article{banerjee2015competitive,
  title={Competitive dynamics between criminals and law enforcement explains the super-linear scaling of crime in cities},
  author={Banerjee, Soumya and Hentenryck, Pascal Van and Cebrian, Manuel},
  journal={Palgrave Communications},
  volume={1},
  number={15022},
  year={2015}
}

@inproceedings{banerjee2015multi,
  title={A Multi-Agent System Approach to Load-Balancing and Resource Allocation for Distributed Computing},
  author={Banerjee, Soumya and Hecker, Joshua},
  booktitle={Complex Systems Digital Campus 2015 -- World e-Conference, Conference on Complex Systems},
  year={2015},
  organization={http://arxiv.org/abs/1509.06420}
}

@inproceedings{banerjee2015analysis,
  title={Analysis of a Planetary Scale Scientific Collaboration Dataset Reveals Novel Patterns},
  author={Banerjee, Soumya},
  booktitle={Complex Systems Digital Campus 2015 -- World e-Conference, Conference on Complex Systems},
  year={2015},
  organization={http://arxiv.org/abs/1509.07313v2}
}

@article{banerjee2016biologically,
  title={A Biologically Inspired Model of Distributed Online Communication Supporting Efficient Search and Diffusion of Innovation},
  author={Banerjee, Soumya},
  journal={Interdisciplinary Description of Complex Systems},
  volume={14},
  number={1},
  pages={10--22},
  year={2016},
  publisher={10.7906/indecs.14.1.2}
}

@article{drew2016spatial,
  title={A spatial model of the efficiency of T cell search in the influenza-infected lung},
  author={Drew, Levin and Stephanie, Forrest and Soumya, Banerjee and Candice, Clay and Judy, Cannon and Melanie, Moses and Frederick, Koster},
  journal={Journal of Theoretical Biology},
  volume={398},
  number={7},
  pages={52--63},
  year={2016},
  publisher={Elsevier}
}

@article{banerjee2016estimating,
  title={Estimating biologically relevant parameters under uncertainty for experimental within-host murine West Nile virus infection},
  author={Banerjee, Soumya and Guedj, Jeremie and Ribeiro, Ruy and Moses, Melanie and Perelson, Alan},
  journal={Journal of the Royal Society Interface},
  volume={13},
  number={117},
  year={2016},
  publisher={http://rsif.royalsocietypublishing.org/content/13/117/20160130}
}

@article{banerjee2016roadmap,
  title={A Roadmap for a Computational Theory of the Value of Information in Origin of Life Questions},
  author={Banerjee, Soumya},
  journal={Interdisciplinary Description of Complex Systems},
  volume={14},
  number={3},
  pages={314--321},
  year={2016},
  publisher={https://www.researchgate.net/publication~…}
}

@article{banerjee2017immune,
  title={An Immune System Inspired Theory for Crime and Violence in Cities},
  author={Banerjee, Soumya},
  journal={Interdisciplinary Description of Complex Systems},
  volume={15},
  number={2},
  pages={133--143},
  year={2017},
  publisher={http://indecs.eu/2017/indecs2017-pp133-143.pdf}
}

@incollection{garcia2018analysis,
  title={Analysis of Demand and Operations of Inter-modal Terminals},
  author={Garc{\'\i}a-Flores, Rodolfo and Banerjee, Soumya and Mathews, George and Vacher, Blandine and Thorne, Brian and Borhan, Nazanin and Aracena, Claudio and Tyshetskiy, Yuriy},
  booktitle={Data and Decision Sciences in Action},
  pages={27--41},
  year={2018},
  publisher={Springer}
}

@inproceedings{2016analysis,
  title={Analysis of Demand and Operations of Intermodal Terminals},
  booktitle={Proceedings of the 24th National Conference of the Australian Society for Operations Research (2016)},
  year={2016}
}

@article{melanie2017excitable,
  title={An excitable Rho GTPase signaling network generates dynamic subcellular contraction patterns},
  author={Melanie Graessl, Johannes Koch, Abram Calderon, Dominic Kamps, Soumya Banerjee, Tom{\'a}{\v{s}} Mazel, Nina Schulze, Jana Kathrin Jungkurth, Rutuja Patwardhan, Djamschid Solouk, Nico Hampe, Bernd Hoffmann, Leif Dehmelt, Perihan Nalbant},
  journal={Journal of Cell Biology},
  volume={216},
  number={12},
  pages={4271--4285},
  year={2017},
  publisher={Rockefeller University Press}
}

@article{banerjee2017modelling,
  title={Modelling the effects of phylogeny and body size on within-host pathogen replication and immune response},
  author={Banerjee, Soumya and Perelson, Alan and Moses, Melanie},
  journal={Journal of the Royal Society Interface},
  volume={14},
  number={136},
  year={2017},
  publisher={http://rsif.royalsocietypublishing.org/content/14/136/20170479}
}

@article{banerjee2018citizen,
  title={Citizen Data Science for Social Good in Complex Systems},
  author={Banerjee, Soumya},
  journal={Interdisciplinary Description of Complex Systems},
  volume={16},
  number={1},
  pages={88--91},
  year={2018},
  publisher={http://indecs.eu/index.php?s=x\&y=2018\&p=88-91}
}

@article{banerjee2018influence,
  title={Influence of correlated antigen presentation on T cell negative selection in the thymus},
  author={Banerjee, Soumya and Chapman, S Jonathan},
  journal={Journal of the Royal Society Interface},
  volume={15},
  number={48},
  year={2018},
  publisher={http://rsif.royalsocietypublishing.org/content/15/148/20180311}
}

@inproceedings{tyshetskiy2016forecasting,
  title={Forecasting Australian port throughput: Lessons and Pitfalls in the era of Big Data},
  author={Tyshetskiy, Yuriy and Banerjee, Soumya and Mathews, George and Vitsounis, Thomas},
  booktitle={Proceedings of the Annual Conference of the International Association of Maritime Economists},
  pages={https--osf},
  year={2016}
}

@incollection{garcia2017using,
  title={Using Optimisation and Machine Learning to Validate the Value of Infrastructure Investments},
  author={Garc{\i}a-Flores, Rodolfo and Banerjee, Soumya and Mathews, George},
  booktitle={In: Tiryaki, G.F.; Mota dos Santos, A.L., editors. Infrastructure Investments: Politics, Barriers and Economic Consequences.},
  year={2017},
  publisher={https://osf.io/g6mah/}
}

@article{mallick2019predictive,
  title={Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences},
  author={Mallick, Himel and Franzosa, Eric A and Mclver, Lauren J and Banerjee, Soumya and Sirota-Madi, Alexandra and Kostic, Aleksandar D and Clish, Clary B and Vlamakis, Hera and Xavier, Ramnik J and Huttenhower, Curtis},
  journal={Nature communications},
  volume={10},
  number={1},
  pages={1--11},
  year={2019},
  publisher={Nature Publishing Group}
}

@inproceedings{banerjee2016computationally,
  title={Computationally simulating intermodal terminal attractiveness and demand},
  author={Banerjee, S and Mathews, G and Aracena, C and Thorne, B and Tyshetskiy, Y and Vitsounis, T},
  booktitle={Proceedings of the 23rd Intelligent Transport Systems World Congress, Melbourne, Australia},
  year={2016}
}

@article{banerjee2020hydroxychloroquine,
  title={Hydroxychloroquine: balancing the needs of LMICs during the COVID-19 pandemic},
  author={Banerjee, Soumya},
  journal={The Lancet Rheumatology},
  volume={2},
  number={7},
  year={2020},
  publisher={Elsevier}
}

@article{chen2020early,
  title={The early impact of COVID-19 on mental health and community physical health services and their patients’ mortality in Cambridgeshire and Peterborough, UK},
  author={Chen, Shanquan and Jones, Peter B and Underwood, Benjamin R and Moore, Anna and Bullmore, Edward T and Banerjee, Soumya and Osimo, Emanuele F and Deakin, Julia B and Hatfield, Catherine F and Thompson, Fiona J and others},
  journal={Journal of Psychiatric Research},
  volume={131},
  pages={244--254},
  year={2020},
  publisher={Pergamon}
}

@article{aschenbrenner2020deconvolution,
  title={Deconvolution of monocyte responses in inflammatory bowel disease reveals an IL-1 cytokine network that regulates IL-23 in genetic and acquired IL-10 resistance},
  author={Aschenbrenner, Dominik and Quaranta, Maria and Banerjee, Soumya and Ilott, Nicholas and Jansen, Joanneke and Steere, B and Chen, Yin-Huai and Ho, Stephen and Cox, Karen and Arancibia, C and others},
  journal={Gut},
  volume={10},
  year={2020},
  publisher={BMJ}
}

@article{kamps2020optogenetic,
  title={Optogenetic Tuning Reveals Rho Amplification-Dependent Dynamics of a Cell Contraction Signal Network},
  author={Kamps, Dominic and Koch, Johannes and Juma, Victor O and Campillo-Funollet, Eduard and Graessl, Melanie and Banerjee, Soumya and Mazel, Tom{\'a}{\v{s}} and Chen, Xi and Wu, Yao-Wen and Portet, Stephanie and others},
  journal={Cell Reports},
  volume={33},
  number={9},
  pages={108467},
  year={2020},
  publisher={Elsevier}
}

@misc{banerjeereply,
  title={reply: balancing human liberties with saving lives},
  author={Banerjee, Soumya},
  journal={https://science.sciencemag.org/content/rebalancing-human-liberties-saving-lives-updated},
  number={https://science.sciencemag.org/content/r}
}

@article{cardinal2021simulating,
  title={Simulating a community mental health service during the COVID-19 pandemic: effects of clinician--clinician encounters, clinician--patient--family encounters, symptom-triggered protective behaviour, and household clustering},
  author={Cardinal, Rudolf N and Meiser-Stedman, Caroline E and Christmas, David M and Price, Annabel C and Denman, Chess and Underwood, Benjamin R and Chen, Shanquan and Banerjee, Soumya and White, Simon R and Su, Li and others},
  journal={Frontiers in Psychiatry},
  volume={12},
  pages={196},
  year={2021},
  publisher={Frontiers}
}