Publications

SUMMARY

The lab has published 34 articles, receiving 1824 citations as of January 16, 2024. You can receive notifications of any new publication via the Principal Investigator’s Google Scholar.

LIST OF PUBLICATIONS

The names in bold highlight the researchers who have contributed to publications as part of the Luque lab.

  1. Brown, Colin, Anuradha Agarwal, and Antoni Luque. “pyCapsid: Identifying dominant dynamics and quasi-rigid mechanical units in protein shells.” Bioinformatics, 40(1), btad761, 2024. https://doi.org/10.1093/bioinformatics/btad761

  2. Cobo-López, Sergio, Matthew Witt, Forest L. Rohwer, Antoni Luque. “Emerging dynamic regimes and tipping points from finite empirical principles.” bioRxiv, December 27, 2023. https://doi.org/10.1101/2023.12.27.573307

  3. Papudeshi, Bhavya, Alejandro A. Vega, Cole Souza, Sarah K. Giles, Vijini Mallawaarachchi, Michael J. Roach, Michelle An, Nicole Jacobson, Katelyn McNair, Maria Fernanda Mora, Karina Pastrana, Christopher Leigh, Clarice Cram, Will S. Plewa, Susanna R. Grigson, George Bouras, Przemysław Decewicz, Antoni Luque, Lindsay Droit, Scott A. Handley, Anca M. Segall, Elizabeth A. Dinsdale, Robert A. Edwards. “Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2.” Microbial Genomics, 9(9), 001100, 2023. https://doi.org/10.1099/mgen.0.001100

  4. Silveira, Cynthia B., Antoni Luque, Andreas F. Haas, Ty NF Roach, Emma E. George, Ben Knowles, Mark Little, Christopher J. Sullivan, Natascha S. Varona, Linda Wegley Kelly, Russel Brainard, Forest Rohwer, Barbara Bailey. “Viral predation pressure on coral reefs.” BMC Biology 21, no. 1 2023: 1-13. https://doi.org/10.1186/s12915-023-01571-9

  5. Podgorski, Jennifer .M., Joshua Podgorski, Lawrence Abad, Deborah Jacobs-Sera, Krista G. Freeman, Colin Brown, Graham Hatfull, Antoni Luque, Simon J. White. “A novel stabilization mechanism accommodating genome length variation in evolutionarily related viral capsids.” bioRxiv, November 3, 2023. https://doi.org/10.1101/2023.11.03.565530

  6. Varona, Natascha, Poppy Hesketh-Best, Alexandra Stiffler, Sofia Garcia, Yun Scholten, Andreas Haas, Mark Little, Felipe Hernandes Coutinho, Mark Vermeij, Antoni Luque, Cynthia Silveira. “Productive viral infections in oligotrophic marine waters.” Research Square, June 14, 2023. https://doi.org/10.21203/rs.3.rs-3040647/v1

  7. McKerral, Jody C., Bhavya Nalagampalli Papudeshi, Laura K. Inglis, Michael J. Roach, Przemyslaw Decewicz, Katelyn McNair, Antoni Luque, Elizabeth A. Dinsdale, and Robert A. Edwards. “The Promise and Pitfalls of Prophages.” bioRxiv, 2023: 2023-04. https://doi.org/10.1101/2023.04.20.537752

  8. Hufsky, Franziska, Denis Beslic, Dimitri Boeckaerts, Sebastian Duchene, Enrique González-Tortuero, Andreas J. Gruber, Jiarong Guo, Daan Jansen, John Juma, Kunaphas Kongkitimanon, Antoni Luque, Muriel Ritsch, Gabriel Lencioni Lovate, Luca Nishimura, Celia Pas, Esteban Domingo, Emma Hodcroft, Philippe Lemey, Matthew B. Sullivan, Friedemann Webber, Fernando González-Candelas, Sarah Krautwurst, Alba Pérez-Cataluña, Walter Randazzo, Gloria Sánchez, Manja Marz. “The International Virus Bioinformatics Meeting 2022.” Viruses 14, no. 5:973, 2022. https://doi.org/10.3390/v14050973

  9. Lee, Diana Y., Caitlin Bartels, Katelyn McNair, Robert A. Edwards, Manal A. Swairjo, and Antoni Luque. “Predicting the capsid architecture of phages from metagenomic data.” Computational and Structural Biotechnology Journal, 20:721-732, 2022. https://doi.org/10.1016/j.csbj.2021.12.032. Press release: “Math is Magical.”

  10. Silveira, Cynthia B., Antoni Luque, Forest Rohwer. “The landscape of lysogeny across microbial community density, diversity and energetics.” Environmental Microbiology, 23:4098-4111, 2021. https://doi.org/10.1111/1462-2920.15640

  11. George, Emma E., James A. Mullinix, Fanwei Meng, Barbara A. Bailey, Clinton Edwards, Ben Felts, Andreas F. Haas, Aaron C. Hartmann, Benjamin Mueller, Ty NF. Roach, Peter Salamon, Cynthia Silveira, Mark J.A. Vermeij, Forest Rohwer, Antoni Luque. “Space-filling and benthic competition on coral reefs.” Peerj, 9:e11213, 2021. https://doi.org/10.7717/peerj.11213. Video abstract and interviews. The data is available at https://doi.org/10.5683/SP2/HQMPKC and the code is available on GitHub.

  12. Luque, Antoni, James Mullinix, Matt Anderson, Kathy S. Williams, Janet Bowers. “Aligning Calculus with Life Sciences Disciplines: The Argument for Integrating Statistical Reasoning.” Primus, 1-19, 2021. https://doi.org/10.1080/10511970.2021.1881847

  13. Cobarrubia, Antonio, Jarod Tall, Austin Crispin-Smith, and Antoni Luque. “Empirical and theoretical analysis of particle diffusion in mucus.” Frontiers in Physics, 9:594306, 2021. https://doi.org/10.3389/fphy.2021.594306. Press release: “Alumni publish capstone project findings on particle flow in mucus.”

  14. ​Luque, Antoni, Sean Benler, Diana Y. Lee, Colin Brown, Simon White. “The missing tailed phages: prediction of small capsid candidates.” Microorganisms, 8:1944, 2020. https://doi.org/10.3390/microorganisms8121944

  15. Luque, Antoni, Cynthia 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

  16. Anthenelli, Maxwell, Emily Jasien, Robert Edwards, Barbara Bailey, Ben Felts, Parag Katira, James Nulton, Peter Salamon, Forest Rohwer, Cynthia B. Silveira, Antoni Luque. “Phage and bacteria diversification through a prophage acquisition ratchet.” bioRxiv, 2020. https://doi.org/10.1101/2020.04.08.028340

  17. Silveira, Cynthia B., Felipe H. Coutinho, Giselle S. Cavalcanti, Sean Benler, Michael P. Doane, Elizabeth A. Dinsdale, Robert A. Edwards, Ronaldo B. Francini-Filho, Cristiane C. Thompson, Antoni Luque. “Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes.” BMC Genomics, 21:1-11, 2020. https://doi.org/10.1186/s12864-020-6523-2

  18. Bowers, Janet, Kathy Williams, Antoni Luque, Devon Quick, Mary Beisiegel, Jody Sorensen, Joan Kunz, Diane Smith, Lori Kayes. “Paradigms for creating activities that integrate mathematics and science topics.” Journal of Mathematics and Science: Collaborative Explorations, 16:6, 2020. https://doi.org/10.25891/14f6-by82.

  19. Silveira, Cynthia B., Antoni Luque, Ty NF Roach, Helena Villela, Adam Barno, Kevin Green, Brandon Reyes, Esther Rubio-Portillo, Tram Le, Spencer Mead, Mark Hatay, Mark JA Vermeij, Yuichiro Takeshita, Andreas Haas, Barbara Bailey, Forest Rohwer. “Biophysical and physiological processes causing oxygen loss from coral reefs,” eLife, 8: e49114, 2019. https://doi.org/10.7554/eLife.49114. ELife Digest: [“Starving corals of oxygen,”](elifesciences.org/digests/49114/starving-corals-of-oxygen](https://elifesciences.org/digests/49114/starving-corals-of-oxygen).

  20. Joiner, Kevin L., Arlette Baljon, Jeremy Barr, Forest Rohwer, Antoni Luque. “Impact of bacteria motility in the encounter rates with bacteriophage in mucus.” Scientific Reports, 9:16427, 2019: https://doi.org/10.1038/s41598-019-52794-2

  21. Twarock, Reidun, Antoni 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” and “Why viruses like Herpes and Zika will need to be reclassified”.

  22. Nguyen, Sophie, Kristi Baker, Benjamin S. Padman, Ruzeen Patwa, Rhys A. Dunstan, Thomas A. Weston, Kyle Schlosser, Barbara Bailey, Trevor Lithgow, Michael Lazarou, Antoni Luque, Forest Rohwer, Richard S. Blumberg, Jeremy J. Barr. “Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers.” mBio, 8:e01874-17, 2017. https://doi.org/10.1128/mBio.01874-17. Press release in Science: “Does a sea of viruses inside our body help keep us healthy?

  23. Knowles, Ben, Barbara Bailey, Lance Boling, Mya Breitbart, Ana Cobian-Guemes, Javier Del Campo, Rob Edwards, Ben Felts, Juris Grasis, Andreas F. Haas, Parag Katira, Linda Wegley Kelly, Antoni Luque, Jim Nulton, Lauren Paul, Gregory Peters, Nate Robinett, Stuart Sandin, Anca Segall, Cynthia Silveira, Merry Youle, Forest Rohwer. “Variability and host density independence in inductions-based estimates of environmental lysogeny.” Nature Microbiology, 2:17064, 2017. https://doi.org/10.1038/nmicrobiol.2017.64

  24. Luque, Antoni, Gungor Ozer, Tamar Schlick. “Correlation among DNA linker length, linker histone concentration, and histone tails in chromatin.” Biophysical Journal, 110:2309-2319, 2016. https://doi.org/10.1016/j.bpj.2016.04.024

  25. Knowles, B., Cynthia 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, M. Little, 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, F. Rohwer. “Lytic to temperate switching of viral communities.” Nature, 531:466-470, 2016. https://doi.org/10.1038/nature17193. Press note.

  26. Ozer, Gungor, Antoni Luque, Tamar Schlick. “The chromatin fiber: multiscale problems and approaches.” Current Opinion In Structural Biology, 31:124-139, 2015. 2015. https://doi.org/10.1016/j.sbi.2015.04.002

  27. Luque, Antoni, Rosana Collepardo-Guevara, Sergei Grigoryev, Tamar Schlick. “Dynamic condensation of linker histone C-terminal domain regulates chromatin structure.” Nucleic Acids Research, 42:7553-7560, 2014. https://doi.org/10.1093/nar/gku491

  28. Hernando-Pérez, Mercedes, Elena Pascual, María Aznar, Alina Ionel, José R. Castón, Antoni Luque, José L. Carrascosa, David Reguera, and Pedro J. de Pablo. “The interplay between mechanics and stability of viral cages.” Nanoscale 6, 5: 2702-2709, 2014. https://doi.org/10.1039/C3NR05763A

  29. Luque, Antoni, David Reguera. “Theoretical studies on assembly, physical stability and dynamics of viruses.” Structure And Physics Of Viruses, Springer, 553–595, 2013. https://doi.org/10.1007/978-94-007-6552-8_19

  30. Luque, Antoni, David Reguera, Alexander Morozov, Joseph Rudnick, Robijn Bruinsma. “Physics of shell assembly: Line tension, hole implosion, and closure catastrophe.” The Journal of Chemical Physics, 136,18:184507, 2012. https://doi.org/10.1063/1.4712304

  31. Aznar, Maria, Antoni Luque, David Reguera. “Relevance of capsid structure in the buckling and maturation of spherical viruses.” Physical Biology, 9:036003, 2012. https://doi.org/10.1088/1478-3975/9/3/036003

  32. Reguera, David, Antoni Luque, Poornachandra Sekhar Burada, Gerhard Schmid, J. Miguel Rubi, Peter Hänggi. “Entropic splitter for particle separation.” Physical Review Letters, 108, 2: 020604, 2012. https://doi.org/10.1103/PhysRevLett.108.020604

  33. Carrasco, Carolina, Antoni Luque, Mercedes Hernando-Pérez, Roberto Miranda, José L. Carrascosa, P. A. Serena, M. De Ridder, A. Raman, J. Gómez-Herrero, I.A.T. Schaap, D. Reguera, and Pedro J. de Pablo. “Built-in mechanical stress in viral shells.” Biophysical Journal, 100, 4: 1100-1108, 2011. https://doi.org/10.1016/j.bpj.2011.01.008. Press note.

  34. Luque, Antoni, David Reguera. “The structure of elongated viral capsids.” Biophysical Journal, 98:2993–3003, 2010. https://doi.org/10.1016/j.bpj.2010.02.051. Press note.

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