Cellular Engineering Lab       


Cellular Engineering Lab - Papers

Selected recent publications

  1. Chang, C., Bianco, S., Acevedo, A., Tang, C., and Andino, R. Genetic interactions shaping evolutionary trajectories in an RNA virus population. https://www.biorxiv.org/content/10.1101/2020.01.16.908129v1. (pdf)
  2. Chadwick, WL., Biswas, SK., Bianco, S. and Chan, YHM. Non random distribution of vacuoles in S. pombe, under review on Physical Biology.
  3. Pastore, VP.,  Megiddo, N., Bianco, S. An anomaly detection approach for plankton species discovery, submitted to ISBI.
  4. Ferguson, P., Zimmerman, T., Bianco, S. High Throughput Device for Screening Chemical Sensitivit­­y of Plankton Samples, under review on ScienceMatters.
  5. Bianco, S., Chan, MYH., Marshall, WF. Towards computer aided design of cellular structure, perspective, Physical Biology, in press. (pdf)
  6. Pastore, VP., Zimmerman, T., Biswas, S, and Bianco, S. Annotation-free Learning of Plankton for Classification and Anomaly Detection. bioRxiv 856815; doi: https://doi.org/10.1101/856815
  7. Kaufman, J. H., Elkins, C. A., Davis, M., Weis, A. M., Huang, B. C., Mammel, M. K., Bianco, S. and Weimer, B. (2019). Insular Microbiogeography: Three Pathogens as Exemplars. Current issues in molecular biology, 36, 89-108. (pdf) 
  8. Rousseau, E., Bonneault, M., Fabre, F., Moury, B., Mailleret, L., & Grognard, F. (2019). Virus epidemics, plant-controlled population  bottlenecks and the durability of plant resistance. Philosophical Transactions of the Royal Society B. https://doi.org/10.1098/RSTB.2018.0263
  9. Biswas, SK., Zimmerman, T., Maini, L., Adebiyi, A., Bozano, L., Brown, C., Pastore, VP. & Bianco, S. (2019, February). High throughput analysis of plankton morphology and dynamic. In Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVI (Vol. 10881, p. 1088109). International Society for Optics and Photonics.
  10. Pastore, VP., Zimmerman, T., Biswas, SK. & Bianco, S. (2019, February). Establishing the baseline for using plankton as biosensorIn Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVI (Vol. 10881, p. 108810H). International Society for Optics and Photonics.
  11. Zimmerman, T., Antipa, N., Elnatan, D., Murru, A., Biswas, S., Pastore, V., ... & Bianco, S. (2019, February). Stereo in-line holographic digital microscope. In Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVI (Vol. 10883, p. 1088315). International Society for Optics and Photonics.
  12. Shirogane, Y., Rousseau, E., Voznica, J., Rouzine, I., Bianco, S., & Andino, R. (2019). Experimental and mathematical insights on the competition between poliovirus and a defective interfering genome. BioRxiv, 519751.
  13. Park, N. H., Cheng, W., Lai, F., Yang, C., Florez de Sessions, P., Periaswamy, B., ..., Bianco, S & Chen, Q. (2018). Addressing drug resistance in cancer with macromolecular chemotherapeutic agents. Journal of the American Chemical Society140(12), 4244-4252.
  14. Chin, W., Zhong, G., Pu, Q., Yang, C., Lou, W., De Sessions, P. F., ..., Bianco, S. & Gao, S. (2018). A macromolecular approach to eradicate multidrug resistant bacterial infections while mitigating drug resistance onset. Nature communications9(1), 917.
  15. Chowdhury, A., Biswas, S. K., Bianco, S. (2017). "Active deep learning reduces annotation burden in automatic cell segmentation",
  16. Worden, L.,  Schwartz, I. B., Bianco, S., Ackley, S.,  Lietman, T.M., and Porco, T. (2017). "Hamiltonian analysis of subcritical stochastic epidemic dynamics", Computational and Mathematical Methods in Medicine, in press. (pdf)
  17. Hughes, A., Mornin, J. D., Biswas, S. K., Bauer, D. P., Bianco, S., Gartner, Z. J. (2018). "Quantius: a tool for rapid, flexible, crowd-sourced based annotation", Nature Methods 15, 587-590, https://www.nature.com/articles/s41592-018-0069-0 (open biorxiv link: http://www.biorxiv.org/content/early/2017/07/15/164087.) (pdf)
  18. Tamisier, L., Rousseau, E., Barraille, S., Nemouchi, G., Szadkowski, M., Mailleret, L., Grognard, F., Fabre, F., Moury, B., Palloix A. (2017). "Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation", Journal of General Virology, http://10.1099/jgv.0.000835.
  19. Biswas, S. K., Milanfar, P. (2017). "Linear Support Tensor Machine with LSK Channels: Pedestrian Detection in Thermal Infrared Images," in IEEE Transactions on Image Processing , vol.PP, no.99, pp.1-1, http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7931588&isnumber=4358840. (pdf)
  20. Kaufman, J. H., Elkins, C. A., Davis, M., Weis, A. M., Huang, B. C., Mammel, M. K., ... Bianco, S., & Weimer, B. C. (2017). Insular microbiogeography. http://arxiv.org/abs/1703.07454. (pdf)
  21. Nieddu, G. T., Billings, L., Kaufman, J. H., Forgoston, E., & Bianco, S. (2017). Extinction pathways and outbreak vulnerability in a stochastic Ebola model, Journal of The Royal Society Interface, http://dx.doi.org/10.1098/rsif.2016.0847. (pdf)
  22. Xiao, Y., Rouzine, I. M., Bianco, S., Acevedo, A., Goldstein, E. F., Farkov, M., … Andino, R. (2016). RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence. Cell Host & Microbe, 19(4), 493–503. http://doi.org/10.1016/j.chom.2016.03.009. (pdf)
  23. Jones, B. A., Lessler, J., Bianco, S., & Kaufman, J. H. (2015). Statistical Mechanics and Thermodynamics of Viral Evolution. PLOS ONE, 10(9), e0137482. Populations and Evolution. http://doi.org/10.1371/journal.pone.0137482.
  24. Hu, K., Bianco, S., Edlund, S., & Kaufman, J. (2015). The Impact of Human Behavioral Changes in 2014 West Africa Ebola Outbreak. In Social Computing, Behavioral-Cultural Modeling, and Prediction (Vol. 9021, pp. 75–84). http://doi.org/10.1007/978-3-319-16268-3_8
  25. Stern, A., Bianco, S., Yeh, M. Te, Wright, C., Butcher, K., Tang, C., … Andino, R. (2014). Costs and Benefits of Mutational Robustness in RNA Viruses. Cell Reports, 1–11. http://doi.org/10.1016/j.celrep.2014.07.011
  26. Li, Z., Bianco, S., Zhang, Z., & Tang, C. (2014). Generic properties of random gene regulatory networks. Quantitative Biology, 1(4), 253–260. http://doi.org/10.1007/s40484-014-0026-6
  27. Hu, K., Thoens, C., Bianco, S., Edlund, S., Davis, M., Douglas, J., & Kaufman, J. H. (2013). The effect of antibody-dependent enhancement, cross immunity, and vector population on the dynamics of dengue fever. Journal of Theoretical Biology, 319, 62–74. http://doi.org/10.1016/j.jtbi.2012.11.021
  28. Forgoston, E., Bianco, S., Shaw, L. B., & Schwartz, I. B. (2011). Maximal sensitive dependence and the optimal path to epidemic extinction. Bulletin of Mathematical Biology, 73(3), 495–514.
  29. Schwartz, I. B., Forgoston, E., Bianco, S., & Shaw, L. B. (2011). Converging towards the optimal path to extinction. Journal of The Royal Society Interface, 8(65), 1699–1707. http://doi.org/10.1098/rsif.2011.0159
  30. Bianco, S., & Shaw, L. B. (2011). Asymmetry in the presence of migration stabilizes multistrain disease outbreaks. Bulletin of Mathematical Biology, 73(1), 248–60. http://doi.org/10.1007/s11538-010-9541-4
  31. Bianco, S., Shaw, L. B., & Schwartz, I. B. (2009). Epidemics with multistrain interactions: The interplay between cross immunity and antibody-dependent enhancement. Chaos, 19(4). http://doi.org/10.1063/1.3270261



Recent news


Elsa Rousseau publishes a new paper on plant resistance to viruses and population bottlenecks. (link).


New paper out on Nature Methods on Quanti.us, a novel platform for crowdsourced annotation. The paper contains our new AI algorithm, which is able to efficiently generalize from noisy annotation. (link).


New paper coming out on the Journal of the American Chemical Society, which describes a new synthetic polymer that is able to kill drug resistant cancer cells (link).


Simone publishes a paper on Nature Communications describing a new polymer that is able to kill antimicrobial resistance bacteria (link).

(press release)


Welcome to Cellular Engineering interns Amanda Paulson and Jacob Kimmel!


Congrats to Elsa Rousseau for her recent publication on the Journal of General Virology! (link).


Elsa Rousseau presents her recent work on defective viral particles at the 2017 Ecology and Evolution of Infectious Disease meeting, in Santa Barbara.


Congrats to Sujoy Biswas for his recent publication on the IEEE Transactions on Image Processing! (link).


Simone speaks about viral dynamic at the SIAM Symposium on applications of Dynamical Systems (DS 2017) (abstract here).


Simone publishes an article about Cellular Engineering on www.01net.it (in Italian).


Press release about recent paper about the role of the animal reservoir on the spread of the Ebola virus.

See also:

Healtcare IT News
Clinical Innovation + Technology


Article about Cellular Engineering (and other projects at IBM Almaden) on the Italian newspaper Il Foglio (pdf, in Italian).