A. Luque, S. Benler, D. Lee, C. Brown, and S. White, "The missing tailed phages: prediction of small capsid candidates," Preprints, 2020110024, 2020: http://doi.org/10.20944/preprints202011.0024.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 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).