For a complete list, please visit Babak's Google Scholar profile.

Biology

(*equal contribution)

M. Zaccaria*, Luigi Genovese*, B. E. Lawhorn, W. Dawson, A. S. Joyal, J. Hu, P. Autissier, T. Nakajima, W. E. Johnson, I. Fofana, M. Farzan, and B. Momeni . Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling. Journal of the Royal Society Interface 21, 20230614. doi: 10.1098/rsif.2023.0614 (2024)

N. Sandlin and B. Momeni . Starch can expedite the screening for bacterial aflatoxin degraders . bioRxiv. doi: 10.1101/2023.09.27.559811 (2023)

N. Sandlin, J. Lee, M. Zaccaria, M. Domin, and B. Momeni . Weakly alkaline conditions degrade aflatoxins through lactone ring opening. bioRxiv. doi: 10.1101/2023.10.31.564999 (2023)

M. Zaccaria, W. Dawson, D. Russel Kish, M. Reverberi, M. C. Bonaccorsi di Patti, M. Domin, V. Cristiglio, B. Chan, L. Dellafiora, F. Gabel, T. Nakajima, L. Genovese & B. Momeni. Experimental–theoretical study of laccase as a detoxifier of aflatoxins. Scientific Reports 13, 860. doi: 10.1038/s41598-023-27519-1 (2023)

S. Dedrick, V. Warrier, K. P. Lemon, and B. Momeni. When does a Lotka-Volterra model represent microbial interactions? Insights from in-vitro nasal bacterial communities. mSystems 8, e00757-22. doi: 10.1128/msystems.00757-22 (2023)

A Lobanov*, S Dyckman*, H Kurkjian, B Momeni. Spatial structure favors microbial coexistence except when slower mediator diffusion weakens interactions. eLife 12, e82504. doi: 10.7554/eLife.82504 (2023)

M. Beccaccioli, N. Pucci, M. Salustri, M. Scortichini, M. Zaccaria, B. Momeni, S. Loreti, M. Reverberi, and V. Scala. . Fungal and bacterial oxylipins are signals for intra- and inter-cellular communication within plant disease. Frontiers in Plant Science 13, 823233. doi: 10.3389/fpls.2022.823233 (2022)

M. Zaccaria, N. Sandlin, Y. Soen, and B. Momeni. Partner-assisted artificial selection of a secondary function for efficient bioremediation. iScience 26, 107632. doi: 10.1016/j.isci.2023.107632 (2023)

N Sandlin, D Russell Kish, J Kim, M Zaccaria, B Momeni. Current and emerging tools of computational biology to improve the detoxification of mycotoxins. Applied and Environmental Microbiology 88, e02102-21. doi: 10.1128/AEM.02102-21 (2022)

Zaccaria*, M., Genovese*, L., Farzan, M., Dawson, W., Nakajima, T., Johnson, W.E. & Momeni, B. Probing the mutational landscape of the SARS-CoV-2 spike protein via quantum mechanical modeling of crystallographic structures. PNAS Nexus, 2022. https://doi.org/10.1093/pnasnexus/pgac180 (2021)

K. Lee-Sarwar*, S. Dedrick, B. Momeni, R.S. Kelly, R.S. Zeiger, G.T. O’Connor, M.T. Sandel, L.B. Bacharier, A. Beigelman, N. Laranjo, D.R. Gold, J. Lasky-Su, A.A. Litonjua, Y.-Y. Liu, & S.T. Weiss. Association of the Gut Microbiome and Metabolome with Wheeze Frequency in Childhood Asthma. Journal of Allergy and Clinical Immunology. https://doi.org/10.1016/j.jaci.2022.02.005 (2022)

Finotti, E., A. Parroni, M. Zaccaria, M. Domin, B. Momeni, C. Fanelli, and M. Reverberi, Aflatoxins are natural scavengers of reactive oxygen species. Scientific Reports 11, 16024 (2021).

Dedrick, S., M.J. Akbari, S. Dyckman, N.Zhao, Y.-Y. Liu, and B. Momeni, Impact of temporal pH fluctuations on the coexistence of nasal bacteria in an in silico community. Frontiers in Microbiology (2021).

Kurkjian, H., M.J. Akbari, and B. Momeni, The impact of interactions on invasion and colonization resistance in microbial communities. PLOS Computational Biology, 17:e1008643 (2021).

V. Scala, N. Pucci, M. Salustri, V. Modesti, A. L’Aurora, M. Scortichini, M. Zaccaria, B. Momeni, M. Reverberi, and S. Loreti, Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and vice versa. PLoS One 15, e0233013 (2020).

Dedrick, S., B. Sundaresh, Q. Huang, C. Brady, T. Yoo, C. Cronin, C. Rudnicki, M. Flood, B. Momeni, J. Ludvigsson, and E. Altindis, The role of gut microbiota and environmental factors in type 1 diabetes pathogenesis. Frontiers in Endocrinology 11, 78 (2020).

Scala, V., C. Pietricola, V. Farina, M. Beccaccioli, S. Zjalic, F. Quaranta, M. Fornara, M. Zaccaria, B. Momeni, M. Reverberi, and A. Iori, Tramesan elicits durum wheat defense against the septoria disease complex. Biomolecules 10, 608 (2020).

Zaccaria, M., W. Dawson, V. Cristiglio, M. Reverberi, L.E. Ratcliff, T. Nakajima, L. Genovese, and B. Momeni, Designing a bioremediator: mechanistic models guide cellular and molecular specialization. Current Opinion in Biotechnology 62, 98-105 (2020).

Niehaus, L., I. Boland, M. Liu, K. Chen, D. Fu, C. Henckel, K. Chaung, S. Espinoza Miranda, S. Dyckman, M. Crum, S. Dedrick, W. Shou, and B. Momeni, Microbial coexistence through chemical-mediated interactions. Nature Communications 10, 2052 (2019). 

Hart, S.F.M., H. Mi, R. Green, L. Xie, J.M.B. Pineda, B. Momeni, and W. Shou. Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells. PLoS Biology 17, e3000135 (2019).

Momeni, B., Division of Labor: How Microbes Split Their Responsibility. Current Biology 28, R697-R699 (2018)

Fan Y., Y. Xiao, B. Momeni, and Y.-Y. Liu. Horizontal gene transfer can help maintain the equilibrium of microbial communities. J. Theor. Biol. 454, 53-59 (2018).

Zaccaria M., S. Dedrick, and B. Momeni. Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists. Processes. 2017 September 25; 5(4):53. doi:10.3390/pr5040053

Momeni, B., L. Xie, and W. Shou, Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions. Elife. e25051 (2017)

Widder, S., R. Allen, T. Pfeiffer, T. Curtis, C. Wiuf, W. Sloan, O. Cordero, S. Brown, B. Momeni, W. Shou, H. Kettle, H. Flint, A. Haas, B. Laroche, J.-U. Kreft, P. Rainey, S. Freilich, S. Schuster, K. Milferstedt, J. Roelof Van der Meer, T. Grosskopf, J. Huisman, A. Free, C. Picioreanu, C. Quince, I. Klapper, S. Labarthe, B. Smets, H. Wang, Isaac Newton Institute Fellows, O. Soyer. 2016. Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME J 10, 2557 (2016).

Kang, S., S. Kahan, and B. Momeni, Simulating Microbial Community Patterning Using Biocellion. Methods in Molecular Biology, 1151: 233–53. doi:10.1007/978-1-4939-0554-6_16 (2014).

Momeni, B., A. Waite, and W. Shou, Spatial Self-Organization Favors Heterotypic Cooperation over Cheating. eLife 2: e00960 (2013).

Momeni, B., K. Brileya, M. Fields, and W. Shou, Strong Inter-Population Cooperation Leads to Partner Intermixing in Microbial Communities. eLife, 2: e00230 (2013).

Momeni, B., and W. Shou, Cryosectioning Yeast Communities for Examining Fluorescence Patterns. Journal of Visual Experimentation, 70: e50101 (2012)

Momeni, B., C.–C. Chen, K. Hillesland, A. Waite, and W. Shou, Using Artificial Systems to Explore the Ecology and Evolution of Symbioses. Cellular and Molecular Life Sciences 68 (8): 1353–68 (2011)

Technology

B. Momeni, M. Askari, E. Shah Hosseini, A. Atabaki, and A. Adibi. 2010. An on-Chip Silicon Grating Spectrometer Using a Photonic Crystal Reflector. Journal of Optics 12, 035501. doi: 10.1088/2040-8978/12/3/035501.

M. Chamanzar, M. Soltani, B. Momeni, S. Yegnanarayanan, and A. Adibi. 2010. Hybrid Photonic Surface-Plasmon-Polariton Ring Resonators for Sensing Applications. Applied Physics B 101, 263. doi: 10.1007/s00340-010-4034-6.

B. Momeni, E. Shah Hosseini, M. Askari, M. Soltani, and A. Adibi. 2009. Integrated Photonic Crystal Spectrometers for Sensing Applications. Optics Communications 282 (15): 3168–71. doi: 10.1016/j.optcom.2009.04.052.

B. Momeni, E. Shah Hosseini, and A. Adibi. 2009. Planar Photonic Crystal Microspectrometers in Silicon-Nitride for the Visible Range. Optics Express 17 (19): 17060–69. doi: 10.1364/OE.17.017060.

B. Momeni, S. Yegnanarayanan, M. Soltani, A. A. Eftekhar, E. Shah Hosseini, and A. Adibi. 2009. Silicon Nanophotonic Devices for Integrated Sensing. Journal of Nanophotonics 3, 031001. doi: 10.1117/1.3122986.

Momeni, B., M. Chamanzar, E. Shah Hosseini, M. Askari, M. Soltani, and A. Adibi. 2008. Strong Angular Dispersion Using Higher Bands of Planar Silicon Photonic Crystals. Optics Express 16 (18): 14213–20. doi:10.1364/OE.16.014213.

Momeni, B., A. A. Eftekhar, and A. Adibi. 2007. Effective Impedance Model for Analysis of Reflection at the Interfaces of Photonic Crystals. Optics Letters 32 (7): 778–80. doi:10.1364/OL.32.000778.

Tay, S., J. Thomas, B. Momeni, M. Askari, A. Adibi, P. J. Hotchkiss, S. C. Jones, S. R. Marder, R. A. Norwood, and N. Peyghambarian. 2007. Planar Photonic Crystals Infiltrated with Nanoparticle/polymer Composites. Applied Physics Letters 91 (22): 221109–221109 – 3. doi:10.1063/1.2817964.

Momeni, B., J. Huang, M. Soltani, M. Askari, S. Mohammadi, M. Rakhshandehroo, and A. Adibi. 2006. Compact Wavelength Demultiplexing Using Focusing Negative Index Photonic Crystal Superprisms. Optics Express 14 (6): 2413–22. doi:10.1364/OE.14.002413.

Momeni, B., and A. Adibi. 2005. An Approximate Effective Index Model for Efficient Analysis and Control of Beam Propagation Effects in Photonic Crystals. Journal of Lightwave Technology 23 (3): 1522.

Momeni, B., and A. Adibi. 2005. Adiabatic Matching Stage for Coupling of Light to Extended Bloch Modes of Photonic Crystals. Applied Physics Letters 87 (17): 171104. doi:10.1063/1.2115081.

Momeni, B., and A. Adibi. 2003. Optimization of Photonic Crystal Demultiplexers Based on the Superprism Effect. Applied Physics B: Lasers and Optics 77 (6-7): 555–60. doi:10.1007/s00340-003-1287-3.