Writing | Keymer Lab

Scientific Papers

Wetherington MT, P. Galajda, JE. Keymer Editorial: Spatial ecology of cells living in micro-structured environments Front. Ecol. Evol., Sec. Biogeography and Macroecology Volume 11, 14 November (2023). https://doi.org/10.3389/fevo.2023.1325165

Simpson K., L’Homme A., Keymer JE., F. Federici Spatial biology of Ising-like synthetic genetic networks BMC Biology 21, 185 (2023). https://doi.org/10.1186/s12915-023-01681-4

Wetherington MT, Nagy K, L Dér, Á Ábrahám, J Noorlag, P. Galajda, and JE Keymer Ecological succession and the competition-colonization trade-off in microbial communities BMC Biology 20, 262 (2022). https://doi.org/10.1186/s12915-022-01462-5

Wetherington MT, Nagy K, L Dér, J Noorlag, P. Galajda, and JE Keymer Variance in Landscape Connectivity Shifts Microbial Population Scaling Frontiers in Microbiology 13:831790. doi: 10.3389/fmicb.2022.831790, 2022

Nagy K, B Dukic, O Hodula, Á Ábrahám, E Czakvarig, L Dér, MT Wetherington, J Noorlag, JE Keymer, and P. Galajda Emergence of Resistant Escherichia coli Mutants in Microfluidic On-Chip Antibiotic Gradients, Frontiers in Microbiology 13:820738. doi: 10.3389/fmicb.2022.820738, 2022

Castillo S, JE Keymer, and PA Marquet Do microenvironmental changes disrupt multicellular organisation with ageing, enacting and favouring the cancer cell phenotype? BioEssays, 00, e2000126, 2020

Wetherington MT, and JE Keymer Expansion, Exploitation and Extinction: Niche Construction in Ephemeral Landscapes Scientific Reports, 10:10067, 2020

Nagy K, Á Ábrahám, JE Keymer and P Galajda Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial Frontiers in Microbiology: microbial symbioses, 20 March 2018

Nuñez I, T Matute, R Herrera, JE Keymer, T Marzullo, T Rudge , and F Federici Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering PLoS ONE November 15, 2017 12(11):e0187163

Wetherington MT, and JE Keymer What does not kill you makes you stronger. Trends in Microbiology, August 2017, 25(8):605-607

Hol FJH, B. Hubert, C. Dekker, and JE Keymer Density-dependent adaptive resistance allows swimming bacteria to colonize an antibiotic gradient. The ISME Journal 10, 30-38, 2016. Featured on phys.org.

Hol FJH, P Galajda, R. Woolthuis, C. Dekker, and JE Keymer The idiosyncrasy of spatial structure in bacterial competition. BMC Research Notes, 2015, BMC Research Notes 2015, 8:245

Wu F., B. van Schie, JE Keymer, and C Dekker Symmetry and scale orient Min protein patterns in shaped bacterial sculptures. Nature Nanotechnology 10, 719-726, June 22, 2015. Featured on the Issue’s cover.

Wu F, E. van Rijn, BGC van Schie, JE Keymer, and C. Dekker Multicolor imaging of bacterial cell division with blue, orange and near-infrared fluorescent proteins Frontiers in Microbiology: microbial physiology and metabolism, June 17, 2015,6:607.

Hol FJH, MJ Voges, C Dekker, JE Keymer Nutrient-responsive regulation determines biodiversity in a colicin-mediated bacterial community.BMC Biology, August 27, 2014, 12:68.

Van Vliet S, FJH Hol, T Weenink, P Galajda, and JE Keymer The Effects of Chemical Interactions and Culture History on the Colonization of Structured Habitats by Competing Bacterial Populations.BMC Microbiology, May 7, 2014 Vol. 14:116 doi:10.1186/1471-2180-14-116. Highly Accessed paper.

Chen P, L Xu, J Liu, FJH Hol, JE Keymer, F Taddei, D Han, and AB Lindner Nanoscale Probing the Kinetics of Oriented Bacterial Cell Growth Using Atomic Force Microscopy Small, April 6th 2014. doi: 10.1002/smll.201303724

Hol, FJH, P Galajda, K. Nagy, R. Woolthuis, C. Dekker, and JE Keymer Spatial structure facilitates cooperation in a social dilemma: empirical evidence from a bacterial community Plos One, October 22, 2013, Vol. 8 No. 10 e77042

Männik J., F. Wu, FJH Hol, P. Bissichia, D. Sherratt, JE Keymer, and C. Dekker Robustness and accuracy of cell division in Escherichia coli in diverse cell shapes. PNAS, April 6, 2012, Vol. 109 No. 18, p. 6957-6962.

Hol FJ., X Wang, and JE Keymer Population Structure Increases the Evolvability of Genetic Algotrithms. Complexity May/June 2012, Vol. 17 No.5, p.58-64.

Keymer JE, Fuentes M, and Marquet P. Diversity Emerging: From Competitive Exclusion to Neutral Coexistence in Ecosystems Theoretical Ecology, 2012, Vol.5 No.3, p. 457-463.

Männik J. , Driessen R, Galajda P,Keymer JE, and C Dekker Bacterial growth and motility in submicron constrictions. PNAS September 1, 2009 Vol. 106(35) 14861-14866. Featured on the Issue’s cover.

Keymer JE, Galajda P, Lambert G, Liao D, and Austin RH Computation of mutual fitness by competing bacteria. PNAS December 23, 2008 Vol. 105(51) 20269-20273.

Galajda P, Keymer JE, Dalland J, Park S, Kou S, and Austin RH. Funnel Ratchets in Biology at Low Reynolds Number: Choanotaxis. Journal of Modern Optics, November, 2008 , Vol. 55, Issue 19 & 20pages 3413 – 3422.

Galajda P, Keymer JE, Chaikin P, Austin R A wall of funnels concentrates swimming bacteria. Journal of Bacteriology, December 2007, Vol. 189, No. 23, p. 8704-8707.

Keymer JE,Endres RG, Skoge M, Meir Y, Wingreen N Chemosensing in Escherichia coli: two regimes of two-state receptors. PNAS February 7, 2006 Vol. 103(6) 1786-1791. Commented in textbook “Physical Biology of the Cell”. Paperback: 978-0-8153-4450.6

Keymer JE, Galajda P, Muldoon C, Park S, Austin R Bacterial metapopulations in nanofabricated landscapes. PNAS November 14, 2006 Vol 103(46) 17290-17295. Commented in Nature Research highlights, Nature 444:126-127 and also in Nature materials nanozone news, Novembre 2006.

Dobson A, Lodge D, Alder J, Cumming GS, Keymer JE, McGlade J, Mooney H, Rusak JA, Sala O, Wolters V, Wall D, Winfree R, and Xenopoulos MA Habitat loss, trophic collapse, and the decline of ecosystem services. August 2006, Ecology Vol. 87(8) 1915-1924

Muller-Landau HC, Levin SA, and Keymer JE Theoretical perspectives on evolution of long-distance dispersal and the example of specialized pests. August 2003, Ecology Vol. 84 (8) 1957-1967.

Dushoff J, Worden L, Keymer JE, and Levin SA. Metapopulations, community assembly, and scale invariance in aspect space. December 2002, Theoretical Population Biology Vol. 62 (4) 329-338.

Levin SA, Dushoff J,and Keymer JE Community assembly and the emergence of ecosystem pattern. 2001, Scientia Marina 65: 171-179 Suppl. 2.

Keymer JE, Marquet PA, Velasco-Hernandez JX, and Levin SA. Extinction thresholds and metapopulation persistence in dynamic landscapes. November 2000, The American Naturalist Vol. 156 (5) 478-494. Commented in Trends in Ecology and Evolution 16:225-226 (2001) and Awarded the prize “Outstanding paper in landscape ecology” from US-IALE in 2001.

Lima M, Keymer JE, and Jaksic FM El Nino-southern oscillation-driven rainfall variability and delayed density dependence cause rodent outbreaks in western South America: Linking demography and population dynamics. May 1999, The American Naturalist 153 (5) 476-491.

Keymer JE, Gaete J, Kameid G, and Alvarez J Acetylcholinesterase and inhibitors: effects upon normal and regenerating nerves of the rat. March 1999, European Journal of Neuroscience Vol. 11 (3) 1049-1057.

Keymer JE, Marquet PA, and Johnson AR Pattern formation in a patch occupancy metapopulation model: A cellular automata approach. September 1998, Journal of Theoretical Biology 194 (1) 79-90.

Book Chapters

JE Keymer and PA Marquet (2014) The complexity of cancer ecosystems. In: In Frontiers in Ecology and Complexity. M. Benites, O. Miramontes A. Valiente (Editors) CopIt arXives, Mexico. ISBN: 978-1-938128-05-9.

Austin R., Galajda P, and Keymer JE (2007)Guided Evolution in Interacting Microchemostat arrays for optimization of photobacterial hydrogen production. In: S. Luryi, J. Xu, A. Zaslavsky (eds) Future trends in microelectronics: up the nano creek. Wiley-IEEE Press.

Kareiva P., Agard JBR, Alder J, Bennett E, Butler C, Carpenter S, Cheung WWL, Cumming GS, Defries R, de Vries B, Dickinson RE, Dobson A, Foley JA, Geoghegan J, Holland B, Kabat P, Keymer JE, Kleidon A, Lodge D, Manson SM, McGlade J, Mooney H, Parma AM, Pascual MA, Pereira HM, Rosegrant M, Ringler C, Sala OE, Turner BL, van Vuuren D, Wall DH, Wilkinson P, & Wolters V. (2006) State of the Art in Simulating Future Changes in Ecosystem Services. Chapter 4, Vol. 2. In: Reid R, Scheffer M, & Alonso A (rev. eds.), Millennium Ecosystem Assessment.

Marquet PA, Abades S, Keymer JE, and Zeballos H (2006) Discontinuities in body size distributions: a view from the top. In: C.R Allen and C.S. Holling (eds). Cross-scale structure & discontinuities in ecosystems & other complex systems. Columbia University Press.

Marquet PA, Keymer JE, and Cofre H (2004) Breaking the stick in space: niche models, metacommunities, and patterns in the relative abundance of species. In: T.M. Blackburn & K.J. Gaston (eds). Macroecology: concepts and consequences. Blackwell.

Marquet PA,Velasco-Hernandez JX, and Keymer JE (2003) Patch dynamics, habitat fragmentation and space in metapopulations. In: Bradshaw, GA, Marquet PA (eds) How Landscapes Change: Human Disturbance and Ecosystem Fragmentation in the Americas. Springer.

Conference Proceedings

F. Wu, FJH Hol, B. van Schie, E. van Rijn, JE Keymer, and C. Dekker Symmetry Breaking and Plasticity of Min Protein Oscillators in Living Bacteria Sculptured into Defined Geometries. January 28, 2014, Biophysical Journal Vol.106 No.2 Issue 1. p.188a.

Männik J., F. Wu, FJH Hol, JE Keymer, and C. Dekker Localization of the Escherichia Coli divisome by nucleoid occlusion and membrane curvature. January 31, 2012, Biophysical Journal Vol.102 No.3 p.475a.

Männik J., F. Wu, FJH Hol, JE Keymer,and C. Dekker Chromatin distribution guides cell division in E. coli. February 2, 2011, Biophysical Journal Vol. 100 No. 3, p. 192a-193a.

Männik J., F. Sekhavati, JE Keymer, and C. Dekker Bacteria in submicron channels and microvalves. October 3-7, 2010, Proc. μTAS2010, p. 1376-1378 .

Männik J., P. Galajda, JE Keymer, and C. Dekker Morphogenesis and cell division of E. coli under mechanical confinement. January 1, 2010, Biophysical Journal Vol. 98 No. 3, p. 416a-417a.