Cellular Engineering Lab     

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Cellular Engineering Lab - Papers


Selected recent publications

  1. Daniels, K. G., Wang, S., Simic, M. S., Bhargava, H. K., Capponi, S., Tonia, Y., Yu, W., Bianco, S., Lim, W. A. (2022). Decoding CAR T cell phenotype using combinatorial signaling motif libraries and machine learning. Science 378, 1194-1200 https://www.science.org/doi/pdf/10.1126/science.abq0225
  2. Wang, S.,  Capponi, S., Bianco, S. (2022). Inferring conditional probability distributions of noisy gene expression from limited observations by deep learning. GENBiotech, 1 (6) https://www.liebertpub.com/doi/abs/10.1089/genbio.2022.0030?journalCode=genbio 
  3. Agarwal, A., ...,  Capponi, S., Bianco, S., ..., Mukherjee, V., Kaufman, J. H. (2022). Predicting epitope candidates for SARS-CoV-2. Viruses 2022, 14(8), 1837 https://www.mdpi.com/1999-4915/14/8/1837
  4. Chen, Y., M. Sotomayor, S. Capponi, B. Hariharan, I. D. Sahu, M. Haase, G. A. Lorigan, A. Kuhn, S. H. White, R. Dalbey. A hydrophilic microenvironment in the substrate-translocating groove of the YidC membrane insertase is essential for enzyme function. Journal of Biological Chemistry (2022) 298(3) 101690-. https://www.jbc.org/article/S0021-9258(22)00130-2/fulltext
  5. Zimmerman, T., Doung, K. B. J., Dean, Z., Bianco, S., Esquerra, R.,  Evaluating Automated reconstruction Methods for Digital Inline Holographic Images of Plankton.  Proc. SPIE Photonics West 2022 on Demands (2022)
  6. Bianco, S., Capponi, S. Face masks are essential to prevent the spread of airborne diseases like COVID-19 (2021). XRDS: Crossroads, The ACM Magazine for Students, 28(2), 40-45 https://dl.acm.org/doi/10.1145/3495260
  7.  Clabough, E. B. D., Kaplan, E., Hermeyer, D., Zimmerman, T., Chamberlin, J., Wantman, S. The secret life of baby turtles: A novel system to predict hatchling emergence, detect infertile nests, and remotely monitor sea turtle nest events. (2022) PLoS One. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0275088 
  8. Xiao, Y., Lidsky, P. V., Shirogane, Y., ..., Rousseau, E., Capponi, S., Bianco, S., Nakamura, R, Jackson, P. K., Frydman, J., Andino, R . (2021). A defective vital genome strategy elicits broad protective immunity against respiratory viruses. Cell  184(25), 6037-6051. e14  https://www.sciencedirect.com/science/article/pii/S0092867421013386
  9. Shirogane, Y., Rousseau, E., Voznica, J., Xiao, Y., Su, W., Catching, B., Shitfield, Z. J. W. Rouzine, I., Bianco, S., & Andino, R. (2019). Experimental and mathematical insights on the interactions between poliovirus and a defective interfering genome. PLoS Pathogens (2021). https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009277
  10. Beck, K.L, Seabolt, E., Agarwal, A., Nayar, G., Bianco, S., Krishnareddy, H., Ngo, T. A., Kunitomi, M., Mukherjee, V., Kaufman, J. H. (2021). Semi-supervised pipeline for Autonomous Annotations of SARS-CoV-2 genomes. Viruses 13(12), 2426 (2021) https://www.mdpi.com/1999-4915/13/12/2426
  11. Wang, S., Bianco, S. (2021). Multiscale simulations: Linking the length scales. Nature Machine Intelligence https://www.nature.com/articles/s42256-021-00351-w
  12. Zimmerman, T.G., Park, A.,  Bianco, S  (2021). Evaluating autofocusing metrics for plankton holographic microscope image reconstruction, Proc. SPIE 11710, Practical Holography XXXV: Displays, Materials, and Applications, 117100A; https://doi.org/10.1117/12.2582798
  13. Capponi, S., Wang, S., Navarro, E. J., and Bianco, S. (2021) AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations. The European Physical Journal E 44 (10), 1-17 https://link.springer.com/article/10.1140/epje/s10189-021-00119-5
  14. Capponi, S., Wang, S., and Bianco, S. (2021) Machine learning methods to predict binding of SARS-CoV-2. Accepted on AAAI Syn Bio 2021.
  15. Hindes, J., Bianco, S., & Schwartz, I. B. (2021). Optimal periodic closure for minimizing risk in emerging disease outbreaks. Plos one, 16(1), e0244706.
  16. Zimmerman, T. G., Bianco, S., McGillivary, R. M., & Marshall, W. F. (2020). U.S. Patent No. 10,810,759. Washington, DC: U.S. Patent and Trademark Office.
  17. Gopalakrishnan, V., Pethe, S., Kefayati, S., Srinivasan, R., Hake, P., Deshpande, A., ... Bianco, S. & Kaufman, J. H. (2021). Globally Local: Hyper-local Modeling for Accurate Forecast of COVID-19. Epidemics, 37, 100510 https://www.sciencedirect.com/science/article/pii/S175543652100058X?via%3Dihub
  18. Shah, D. H., Biswas, S. K., Martin, A. M., Bianco, S., & Denetclaw, W. F. (2020). Endoderm Nitric Oxide Signals to Regulate Nascent Development of Cardiac Progenitors in Chicken Embryos. https://www.biorxiv.org/content/10.1101/2020.08.29.272989v2
  19. Chowdhury, A., Biswas, S. K., Bianco, S. (2020). Active deep learning reduces annotation burden in automatic cell segmentation, Proc SPIE, forthcoming. https://www.biorxiv.org/content/early/2017/11/01/211060. (pdf)
  20. Zimmerman, T.,  Barrera-Velasquez, A., Cisneros, R., Martin, A., Samperio, D.E., Sanchez, A., Antipa, N., Elnatan, D., Waller, L., Phillips, M., Esquerra, R.M., Chan, M. (2020). Direct in-line Holographic Video Microscope, American Journal of Physics, under review.
  21. Capponi, S., Alvarez, F., Racko, D. (2020). Free Volume in a PVME Polymer-Water Solution, Macoromolecules, 53, 12. https://pubs.acs.org/doi/abs/10.1021/acs.macromol.0c00472
  22. Yeh, M.T., Capponi, S., Catching, A., Bianco, S., Andino, R (2020). Mapping Attenuation Determinants in Enterovirus-D68. Viruses, 12, 867. https://doi.org/10.3390/v12080867
  23. Catching, A., Capponi, S., Te Yeh, M., Bianco, S., & Andino, R. (2020). Examining the interplay of face mask usage, asymptomatic transmission, and social distance on the spread of COVID-19. https://www.nature.com/articles/s41598-021-94960-5
  24. Pastore, V. P., Zimmerman, T., Bisvas, S. K., & Bianco, S. (2020). Monitoring Water Quality Using Plankton as Biosensor. JDREAM. Journal of interDisciplinary REsearch Applied to Medicine, 4(1), 15-20.
  25. Pastore, VP., Zimmerman, T., Biswas, S, and Bianco, S. (2020) Annotation-free Learning of Plankton for Classification and Anomaly Detection. Sci Rep, 10, 12142. https://doi.org/10.1038/s41598-020-68662-3; bioRxiv 856815; doi: https://doi.org/10.1101/856815
  26. Ferguson, P., Zimmerman, T., Bianco, S. (2020) High Throughput Device for Screening Chemical Sensitivit­­y of Plankton Samples, Matters, (ISSN: 2297-8240). http://sosjournals.s3.amazonaws.com/jqJieRusm9yLMatz.pdf
  27. Zimmerman, T, Pastore, VP, Biswas, SK, and Bianco, SB. Embedded System to Detect, Track and Classify Plankton Using a Lensless Video Microscope. arXiv https://arxiv.org/abs/2005.13064v1
  28. Schwartz, IB, Kaufman, JH, Hu, K and Bianco, S. Predicting the impact of asymptomatic transmission, non-pharmaceutical intervention and testing on the spread of COVID19. medRxiv 2020.04.16.20068387; doi: https://doi.org/10.1101/2020.04.16.20068387.
  29. 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
  30. Chadwick, WL., Biswas, SK., Bianco, S. and Chan, YHM. Non random distribution of vacuoles in S. pombe, Physical Biology, 17(6), 065004. https://doi.org/10.1088/1478-3975/aba510
  31. Pastore, VP.,  Megiddo, N., Bianco, S. An anomaly detection approach for plankton species discovery, submitted to ISBI.
  32. Bianco, S., Chan, MYH., Marshall, WF. (2020) Towards computer aided design of cellular structure, perspective, Physical Biology, 17(2) (pdf)
  33. 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) 
  34. 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
  35. 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.
  36. 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.
  37. 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.
  38. Kaufman, J. H., Elkins, C. A., Davis, M., Weis, A. M., Huang, B. C., Mammel, M. K., ... Bianco, S., Kunitomi, M, Weimer, B. C. (2019). Insular microbiogeography: three pathogens as exemplars. Curr. Issues Mol. Biol 36(1) 89-108 https://www.mdpi.com/1467-3045/36/1/89
  39. Park, N. H., Cheng, W., Lai, F., Yang, C., Florez de Sessions, P., Periaswamy, B., ..., Bianco, S, ..., Hedrick, J. L. (2018). Addressing drug resistance in cancer with macromolecular chemotherapeutic agents. Journal of the American Chemical Society, 140(12), 4244-4252.
  40. Chin, W., Zhong, G., Pu, Q., Yang, C., Lou, W., De Sessions, P. F., ..., Bianco, S., ..., Yang, Y. Y. (2018). A macromolecular approach to eradicate multidrug resistant bacterial infections while mitigating drug resistance onset. Nature communications, 9(1), 917.
  41. Hedrick, J. L., Bianco, S., Kunitomi, M., Yang, Y. Y., Ding, X., Yang, C., ... & Periaswamy, B. (2020). U.S. Patent Application No. 16/144,040.
  42. 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)
  43. 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)
  44. 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.
  45. 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)
  46. 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)
  47. 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)
  48. 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.
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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.
  54. 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
  55. 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
  56. 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