Silveira, Cynthia B., Antoni Luque, and Forest Rohwer. "The landscape of lysogeny across microbial community density, diversity, and energetics." Environmental Microbiology (2021). doi.org/10.1111/1462-2920.15640
A. Luque, J. Mullinix, M. Anderson, K.S. Williams, and J. Bowers, "Aligning calculus with life sciences disciplines: the argument for integrating statistical reasoning," PRIMUS, 05 Feb, 2021: www.tandfonline.com/doi/full/10.1080/10511970.2021.1881847.
A. Luque, S. Benler, D. Lee, C. Brown, and S. White, "The missing tailed phages: prediction of small capsid candidates," Microorganisms, 8:1944, 2020: doi.org/10.3390/microorganisms8121944. The initial version of the manuscript prior to peer-review is available in Preprints.org: www.preprints.org/manuscript/202011.0024/v1.
A. Luque and C.B. Silveira, "Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles," mSystems, 5:e00353-20, 2020: https://doi.org/10.1128/mSystems.00353-20. Initial pre-print in bioRxiv, April 24, 2020: https://www.biorxiv.org/content/10.1101/2020.04.22.056689v1.
A. Cobarrubia, J. Tall, A. Crispin-Smith, and A. Luque, "Unifying framework for the diffusion of microscopic particles in mucus," bioRxiv, July 26, 2020: https://www.biorxiv.org/content/10.1101/2020.04.22.056689v1
M. Anthenelli, E. Jasien, R.A. Edwards, B. Bailey, B. Felts, P. Katira, J. Nulton, F. Rohwer, C.B. Silveira, and A. Luque, "Phage and bacteria diversification through a prophage acquisition ratchet," bioRxiv, April 9, 2020
https://www.biorxiv.org/content/10.1101/2020.04.08.028340v1
J. Bowers, K. Williams, A. Luque, D. Quick, M. Beisiegel, J. Sorensen, J. Kunz, D. Smith, and L. Kayes, "Paradigms for creating activities that integrate mathematics and science topics," Journal of Mathematics and Science: Collaborative Explorations, 16: Article 6, 2020: doi.org/10.25891/14f6-by82.
C.B. Silveira, F.H. Coutinho, G.S. Cavalcanti, S. Benler, M.P. Doane, E.A. Dinsdale, R.A. Edwards, R.B. Francini-Filho, C.C. Thompson, A. Luque, F.L. Rohwer, and F. Thompson, "Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes," BMC Genomics, 21:126, 2020: https://doi.org/10.1186/s12864-020-6523-2.
C.B. Silveira, A. Luque, T.N.F. Roach, H. Villela, A. Barno, K. Green, B. Reyes, E. Rubio-Portillo, T. Le, S. Mead, M. Hatay, M.J.A. Vermeij, Y. Takeshita, A. Haas, B. Bailey, and F. Rohwer, "Biophysical and physiological processes causing oxygen loss from coral reefs," eLife, 8:e49114, 2019: elifesciences.org/articles/49114. eLife Digest: "Starving corals of oxygen", elifesciences.org/digests/49114/starving-corals-of-oxygen.
K. Joiner, A. Baljon, J. Barr, F. Rohwer, and A. Luque, "Impact of bacteria motility in the encounter rates with bacteriophage in mucus," Scientific Reports, 9:16427, 2019: doi.org/10.1038/s41598-019-52794-2.
R. Twarock and A. Luque, "Structural puzzles in virology solved with an overarching icosahedral design principle," Nature Communications, 10:4414, 2019: https://doi.org/10.1038/s41467-019-12367-3. Press releases: "Geometry goes viral" (link) and "Why viruses like Herpes and Zika will need to be reclassified" (link).
E.E. George, J. Mullinix, F. Meng, B. Bailey, C. Edwards, B. Felts, A. Haas, A.C. Hartmann, B. Mueller, J. Nulton, T.N.F. Roach, P. Salamon, C.B. Silveira, M.J.A. Vermeij, F.L. Rohwer, and A. Luque, "Relevance of coral geometry in the outcomes of the coral-algal benthic war," bioRxiv, doi: https://doi.org/10.1101/327031 (2018).
S. Nguyen, K. Baker, B.S. Padman, R. Patwa, R.A. Dunstan, T.A. Weston, K. Schlosser, B. Bailey, T. Lithgow, M. Lazarou, A. Luque, F. Rohwer, R.S. Blumberg, and J.J. Barr, "Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers," mBio 8:e01874–17, 2017: link. Press release in Science: "Does a sea of viruses inside our body help keep us healthy?: link.
B. Knowles, B. Bailey, L. Boling, M. Breitbart, A. Cobian-Guemes, J. del Campo, R. Edwards, B. Felts, J. Grasis, A.F. Haas, P. Katira, L. Wegley-Kelly, A. Luque, J. Nulton, L. Paul, G. Peters, N. Robinett, S. Sandin, A. Segall, C. Silveira, M. Youle, and F. Rohwer, "Variability and host density independence in inductions-based estimates of environmental lysogeny," Nature Microbiol. 2:17064, 2017 link.
B. Knowles, C.B. Silveira, B.A. Bailey, K. Barott, V.A. Cantu, A.G. Cobian-Guemes, F.H. Coutinho, E.A. Dinsdale, B. Felts, K.A. Furby, E.E. George, K.T. Green, G.B. Gregoracci, A.F. Haas, J.M. Haggerty, E.R. Hester, N. Hisakawa, L.W. Kelly, Y.W. Lim, A. Luque, T. McDole-Somera, K. McNair, L.S. de Oliveira, S.D. Quistad, N.L. Robinett, E. Sala, P. Salamon, S.E. Sanchez, S. Sandin, G.G.Z. Silva, J. Smith, C. Sullivan, C. Thompson, M.J.A. Vermeij, M. Youle, C. Young, B. Zgliczynski, R. Brainard, R.A. Edwards, J. Nulton, F. Thompson, and F. Rohwer, “Lytic to temperate switching of viral communities," Nature 531:466-470, 2016 link. Press note.
A. Luque, G. Ozer, and T. Schlick, "Correlation among DNA linker length, linker histone concentration, and histone tails in chromatin," Biophys. J. 110:2309-2319, 2016 link.
G. Ozer, A. Luque, and T. Schlick, “The chromatin fiber: multiscale problems and approaches," Curr. Opin. Struct. Biol. 31:124-139, 2015 link.
A. Luque, R. Collepardo-Guevara, S. Grigoryev, and T. Schlick, “Dynamic condensation of linker histone C-terminal domain regulates chromatin structure," Nucleic Acids Res. 42:7553–7560, 2014 link.
M. Hernando-Pérez, M. Aznar, E. Pascual Vega, A. Ionel, J.R. Castón, A. Luque, J.R. Carrascosa, D. Reguera, and and P.J. de Pablo, “The interplay between mechanics and stability of viral cages," Nanoscale 6:2702–2709, 2014 link.
A. Luque and D. Reguera, “Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses," in M.G. Mateo, editor, Structure and Physics of Viruses, Springer, 2013 link.
A. Luque, D. Reguera, A. Morozov, J. Rudnick, and R. Bruinsma, “The assembly of spherical shells: Line energy, implosion, and closure catastrophe," J. Chem. Phys. 136:184507, 2012 link.
M. Aznar, A. Luque, and D. Reguera, “Relevance of capsid structure in the buckling and maturation of spherical viruses," Phys. Biol. 9:036003, 2012 link.
D. Reguera, A. Luque, P. S. Burada, G. Schmid, J. M. Rubí, and P. Hänggi, “Entropic splitter for particle separation," Phys. Rev. Lett. 108:020604, 2012 link. This paper was highlighted as “Editor’s choice” in the APS journal Physics: link. Press note.
C. Carrasco, A. Luque, M. Hernando-Pérez, R. Miranda, J. L. Carrascosa, P. A. Serena, M. de Ridder, A. Raman, J. Gómez-Herrero, I. A. T. Schaap, D. Reguera, and P. J. de Pablo, “Built-in mechanical stress in viral shells," Biophys. J. 100:1100–1108, 2011 link. Press note.
A. Luque and D. Reguera, “The structure of elongated viral capsids," Biophys. J. 98:2993–3003, 2010 link. Press note.
A. Luque, R. Zandi, and D. Reguera, “Optimal architectures of elongated viruses," Proc. Nat. Acad. Sci. USA 107:5323-5328, 2010 link. Press note.
A. Luque and D. Reguera, “Physical origin of the structure of viruses” (Origen fisic de l‘estructura dels virus), Omnis Cellula (Catalan magazine), 16:9, 2008.
A. Luque, J. Mullinix, M. Anderson, K.S. Williams, and J. Bowers, "Aligning calculus with life sciences disciplines: the argument for integrating statistical reasoning," PRIMUS, 05 Feb, 2021: www.tandfonline.com/doi/full/10.1080/10511970.2021.1881847.
A. Luque, S. Benler, D. Lee, C. Brown, and S. White, "The missing tailed phages: prediction of small capsid candidates," Microorganisms, 8:1944, 2020: doi.org/10.3390/microorganisms8121944. The initial version of the manuscript prior to peer-review is available in Preprints.org: www.preprints.org/manuscript/202011.0024/v1.
A. Luque and C.B. Silveira, "Quantification of lysogeny caused by phage coinfections in microbial communities from biophysical principles," mSystems, 5:e00353-20, 2020: https://doi.org/10.1128/mSystems.00353-20. Initial pre-print in bioRxiv, April 24, 2020: https://www.biorxiv.org/content/10.1101/2020.04.22.056689v1.
A. Cobarrubia, J. Tall, A. Crispin-Smith, and A. Luque, "Unifying framework for the diffusion of microscopic particles in mucus," bioRxiv, July 26, 2020: https://www.biorxiv.org/content/10.1101/2020.04.22.056689v1
M. Anthenelli, E. Jasien, R.A. Edwards, B. Bailey, B. Felts, P. Katira, J. Nulton, F. Rohwer, C.B. Silveira, and A. Luque, "Phage and bacteria diversification through a prophage acquisition ratchet," bioRxiv, April 9, 2020
https://www.biorxiv.org/content/10.1101/2020.04.08.028340v1
J. Bowers, K. Williams, A. Luque, D. Quick, M. Beisiegel, J. Sorensen, J. Kunz, D. Smith, and L. Kayes, "Paradigms for creating activities that integrate mathematics and science topics," Journal of Mathematics and Science: Collaborative Explorations, 16: Article 6, 2020: doi.org/10.25891/14f6-by82.
C.B. Silveira, F.H. Coutinho, G.S. Cavalcanti, S. Benler, M.P. Doane, E.A. Dinsdale, R.A. Edwards, R.B. Francini-Filho, C.C. Thompson, A. Luque, F.L. Rohwer, and F. Thompson, "Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes," BMC Genomics, 21:126, 2020: https://doi.org/10.1186/s12864-020-6523-2.
C.B. Silveira, A. Luque, T.N.F. Roach, H. Villela, A. Barno, K. Green, B. Reyes, E. Rubio-Portillo, T. Le, S. Mead, M. Hatay, M.J.A. Vermeij, Y. Takeshita, A. Haas, B. Bailey, and F. Rohwer, "Biophysical and physiological processes causing oxygen loss from coral reefs," eLife, 8:e49114, 2019: elifesciences.org/articles/49114. eLife Digest: "Starving corals of oxygen", elifesciences.org/digests/49114/starving-corals-of-oxygen.
K. Joiner, A. Baljon, J. Barr, F. Rohwer, and A. Luque, "Impact of bacteria motility in the encounter rates with bacteriophage in mucus," Scientific Reports, 9:16427, 2019: doi.org/10.1038/s41598-019-52794-2.
R. Twarock and A. Luque, "Structural puzzles in virology solved with an overarching icosahedral design principle," Nature Communications, 10:4414, 2019: https://doi.org/10.1038/s41467-019-12367-3. Press releases: "Geometry goes viral" (link) and "Why viruses like Herpes and Zika will need to be reclassified" (link).
E.E. George, J. Mullinix, F. Meng, B. Bailey, C. Edwards, B. Felts, A. Haas, A.C. Hartmann, B. Mueller, J. Nulton, T.N.F. Roach, P. Salamon, C.B. Silveira, M.J.A. Vermeij, F.L. Rohwer, and A. Luque, "Relevance of coral geometry in the outcomes of the coral-algal benthic war," bioRxiv, doi: https://doi.org/10.1101/327031 (2018).
S. Nguyen, K. Baker, B.S. Padman, R. Patwa, R.A. Dunstan, T.A. Weston, K. Schlosser, B. Bailey, T. Lithgow, M. Lazarou, A. Luque, F. Rohwer, R.S. Blumberg, and J.J. Barr, "Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers," mBio 8:e01874–17, 2017: link. Press release in Science: "Does a sea of viruses inside our body help keep us healthy?: link.
B. Knowles, B. Bailey, L. Boling, M. Breitbart, A. Cobian-Guemes, J. del Campo, R. Edwards, B. Felts, J. Grasis, A.F. Haas, P. Katira, L. Wegley-Kelly, A. Luque, J. Nulton, L. Paul, G. Peters, N. Robinett, S. Sandin, A. Segall, C. Silveira, M. Youle, and F. Rohwer, "Variability and host density independence in inductions-based estimates of environmental lysogeny," Nature Microbiol. 2:17064, 2017 link.
B. Knowles, C.B. Silveira, B.A. Bailey, K. Barott, V.A. Cantu, A.G. Cobian-Guemes, F.H. Coutinho, E.A. Dinsdale, B. Felts, K.A. Furby, E.E. George, K.T. Green, G.B. Gregoracci, A.F. Haas, J.M. Haggerty, E.R. Hester, N. Hisakawa, L.W. Kelly, Y.W. Lim, A. Luque, T. McDole-Somera, K. McNair, L.S. de Oliveira, S.D. Quistad, N.L. Robinett, E. Sala, P. Salamon, S.E. Sanchez, S. Sandin, G.G.Z. Silva, J. Smith, C. Sullivan, C. Thompson, M.J.A. Vermeij, M. Youle, C. Young, B. Zgliczynski, R. Brainard, R.A. Edwards, J. Nulton, F. Thompson, and F. Rohwer, “Lytic to temperate switching of viral communities," Nature 531:466-470, 2016 link. Press note.
A. Luque, G. Ozer, and T. Schlick, "Correlation among DNA linker length, linker histone concentration, and histone tails in chromatin," Biophys. J. 110:2309-2319, 2016 link.
G. Ozer, A. Luque, and T. Schlick, “The chromatin fiber: multiscale problems and approaches," Curr. Opin. Struct. Biol. 31:124-139, 2015 link.
A. Luque, R. Collepardo-Guevara, S. Grigoryev, and T. Schlick, “Dynamic condensation of linker histone C-terminal domain regulates chromatin structure," Nucleic Acids Res. 42:7553–7560, 2014 link.
M. Hernando-Pérez, M. Aznar, E. Pascual Vega, A. Ionel, J.R. Castón, A. Luque, J.R. Carrascosa, D. Reguera, and and P.J. de Pablo, “The interplay between mechanics and stability of viral cages," Nanoscale 6:2702–2709, 2014 link.
A. Luque and D. Reguera, “Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses," in M.G. Mateo, editor, Structure and Physics of Viruses, Springer, 2013 link.
A. Luque, D. Reguera, A. Morozov, J. Rudnick, and R. Bruinsma, “The assembly of spherical shells: Line energy, implosion, and closure catastrophe," J. Chem. Phys. 136:184507, 2012 link.
M. Aznar, A. Luque, and D. Reguera, “Relevance of capsid structure in the buckling and maturation of spherical viruses," Phys. Biol. 9:036003, 2012 link.
D. Reguera, A. Luque, P. S. Burada, G. Schmid, J. M. Rubí, and P. Hänggi, “Entropic splitter for particle separation," Phys. Rev. Lett. 108:020604, 2012 link. This paper was highlighted as “Editor’s choice” in the APS journal Physics: link. Press note.
C. Carrasco, A. Luque, M. Hernando-Pérez, R. Miranda, J. L. Carrascosa, P. A. Serena, M. de Ridder, A. Raman, J. Gómez-Herrero, I. A. T. Schaap, D. Reguera, and P. J. de Pablo, “Built-in mechanical stress in viral shells," Biophys. J. 100:1100–1108, 2011 link. Press note.
A. Luque and D. Reguera, “The structure of elongated viral capsids," Biophys. J. 98:2993–3003, 2010 link. Press note.
A. Luque, R. Zandi, and D. Reguera, “Optimal architectures of elongated viruses," Proc. Nat. Acad. Sci. USA 107:5323-5328, 2010 link. Press note.
A. Luque and D. Reguera, “Physical origin of the structure of viruses” (Origen fisic de l‘estructura dels virus), Omnis Cellula (Catalan magazine), 16:9, 2008.