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Jump to: Australian Research Council (ARC) | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC) | Carlsbergfondet (Copenhagen, Denmark) [Carlsberg foundation] | Carnegie-Mellon University. School of Computer Science | Centre national de la recherche scientifique (France) (CNRS) | Comissionat per Universitats i Recerca de la Generalitat de Catalunya (CURGC) | Defence Science and Technology Laboratory (Great Britain) | Engineering and Physical Sciences Research Council (EPSRC) | Fondo per gli Investimenti della Ricerca di Base (FIRB) | France. Agence nationale de la recherche (ANR) | France. Ministère de l'enseignement supérieur et de la recherche | Horizon 2020 (European Commission) (H2020) | Isaac Newton Institute for Mathematical Sciences | Italy. Ministero dell'istruzione, dell'università e della ricerca (MIUR) | Los Alamos National Laboratory (LANL) | Lundbeck Foundation | Microsoft Research | National Institute for Health Research (Great Britain) (NIHR) | National Institutes of Health (U.S.) (NIH) | National Science Foundation (U.S.) (NSF) | Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung [Swiss National Science Foundation] (SNSF) | Scottish Universities Life Sciences Alliance | Seventh Framework Programme (European Commission) (FP7) | Society in Science : The Branco Weiss Fellowship (SSBWF) | Spain. Cortes Generales | Spain. Ministerio de Economía y Competitividad | Statens samfundsvidenskabelige forskningsråd (Denmark) | United States. Army Research Office (ARO) | United States. Beacon Center for the Study of Evolution in Action | University of Exeter | University of Exeter (UoE) | University of Sydney | University of Warwick. School of Life Sciences | Université Grenoble | Wellcome Trust (London, England) | Wissenschaft Kollege zu Berlin (WIKO)
Number of items: 61.
Australian Research Council (ARC)
Soyer, Orkun S. and O'Malley, Maureen A. (2013) Evolutionary systems biology : what it is and why it matters. BioEssays, Volume 35 (Number 8). pp. 696-705. doi:10.1002/bies.201300029 ISSN 0265-9247.
Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC)
Cavaliere, Matteo, Feng, Song, Soyer, Orkun S. and Jiménez, José I. (2017) Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology, 19 (8). pp. 2949-2963. doi:10.1111/1462-2920.13767 ISSN 1462-2912.
Großkopf, Tobias, Zenobi, Simone, Alston, Mark, Folkes, Leighton, Swarbreck, David and Soyer, Orkun S. (2016) A stable genetic polymorphism underpinning microbial syntrophy. The ISME Journal, 10 . pp. 2844-2853. doi:10.1038/ismej.2016.80 ISSN 1751-7362.
Widder, Stefanie, Allen, Rosalind, Pfeiffer, Thomas, Curtis, Thomas P., Wiuf, Carsten, Sloan, William T., Cordero, Otto X., Brown, Sam P., Momeni, Babak, Shou, Wenying et al.
(2016)
Challenges in microbial ecology : building predictive understanding of community function and dynamics.
The ISME Journal, 2016
(10).
pp. 2557-2568.
doi:10.1038/ismej.2016.45
ISSN 1751-7362.
Großkopf, Tobias and Soyer, Orkun S. (2016) Microbial diversity arising from thermodynamic constraints. The ISME Journal, 10 . pp. 2725-2733. doi:10.1038/ismej.2016.49 ISSN 1751-7362.
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
Hemsley, Claudia M., Luo, Jamie X., Andreae, Clio A., Butler, Clive S., Soyer, Orkun S. and Titball, Richard W. (2014) Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation but not anaerobic respiration. Antimicrobial Agents and Chemotherapy, Volume 58 (Number 10). pp. 5775-5783. doi:10.1128/AAC.02793-14 ISSN 0066-4804.
Großkopf, Tobias and Soyer, Orkun S. (2014) Synthetic microbial communities. Current Opinion in Microbiology, Volume 18 . pp. 72-77. doi:10.1016/j.mib.2014.02.002 ISSN 1369-5274.
Carlsbergfondet (Copenhagen, Denmark) [Carlsberg foundation]
Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca and Soyer, Orkun S. (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, Volume 9 (Number 11). Article number e1003322. doi:10.1371/journal.pcbi.1003322 ISSN 1553-7358.
Carnegie-Mellon University. School of Computer Science
Kuwahara, Hiroyuki and Soyer, Orkun S. (2012) Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology, Volume 8 (Number 564). Article no. 564. doi:10.1038/msb.2011.98 ISSN 1744-4292.
Centre national de la recherche scientifique (France) (CNRS)
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
Comissionat per Universitats i Recerca de la Generalitat de Catalunya (CURGC)
Kothamachu, Varun B., Feliu, Elisenda, Cardelli, Luca and Soyer, Orkun S. (2015) Unlimited multistability and Boolean logic in microbial signalling. Journal of The Royal Society Interface, Volume 12 (Number 108). pp. 1-9. Article number 20150234. doi:10.1098/rsif.2015.0234 ISSN 1742-5689.
Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca and Soyer, Orkun S. (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, Volume 9 (Number 11). Article number e1003322. doi:10.1371/journal.pcbi.1003322 ISSN 1553-7358.
Defence Science and Technology Laboratory (Great Britain)
Senior, Nicola J., Sasidharan, Kalesh, Saint, Richard J., Scott, Andrew E., Sarkar-Tyson, Mitali, Ireland, Philip M., Bullifent, Helen L, Rong Yang, Z., Moore, Karen, Oyston, Petra C. F., Atkins, Timothy P., Atkins, Helen S., Soyer, Orkun S. and Titball, Richard W. (2017) An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions. BMC Microbiology, 17 (1). 163. doi:10.1186/s12866-017-1073-8 ISSN 1471-2180.
Cizmeci, Deniz, Dempster, Emma L., Champion, Olivia L., Wagley, Sariqa, Akman, Ozgur E., Prior, Joann L., Soyer, Orkun S., Mill, Jonathan and Titball, Richard W. (2016) Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection. Scientific Reports, 6 . 30861. doi:10.1038/srep30861 ISSN 2045-2322.
Engineering and Physical Sciences Research Council (EPSRC)
Cavaliere, Matteo, Feng, Song, Soyer, Orkun S. and Jiménez, José I. (2017) Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology, 19 (8). pp. 2949-2963. doi:10.1111/1462-2920.13767 ISSN 1462-2912.
Montefusco, Francesco, Akman, Ozgur E., Soyer, Orkun S. and Bates, Declan (2016) Ultrasensitive negative feedback control : a natural approach for the design of synthetic controllers. PLoS One, 11 (8). e0161605. doi:10.1371/journal.pone.0161605 ISSN 1932-6203.
Feng, Song, Sáez, Meritxell, Wiuf, Carsten, Feliu, Elisenda and Soyer, Orkun S. (2016) Core signalling motif displaying multistability through multi-state enzymes. Journal of The Royal Society Interface, 13 (123). 20160524. doi:10.1098/rsif.2016.0524 ISSN 1742-5689.
Feng, Song, Ollivier, Julien F. and Soyer, Orkun S. (2016) Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks. PLoS Computational Biology, 12 (5). e1004918. doi:10.1371/journal.pcbi.1004918 ISSN 1553-7358.
Steinacher, Arno, Bates, Declan, Akman, Ozgur E. and Soyer, Orkun S. (2016) Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels. PLoS One, 11 (4). e0153295. doi:10.1371/journal.pone.0153295 ISSN 1932-6203.
Feng, Song, Ollivier, Julien F., Swain, Peter S. and Soyer, Orkun S. (2015) BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Research, 43 (19). e123. doi:10.1093/nar/gkv595 ISSN 0305-1048.
Kothamachu, Varun B., Feliu, Elisenda, Cardelli, Luca and Soyer, Orkun S. (2015) Unlimited multistability and Boolean logic in microbial signalling. Journal of The Royal Society Interface, Volume 12 (Number 108). pp. 1-9. Article number 20150234. doi:10.1098/rsif.2015.0234 ISSN 1742-5689.
O’Malley, Maureen A., Soyer, Orkun S. and Siegal, Mark L. (2015) A philosophical perspective on evolutionary systems biology. Biological Theory, Volume 10 (Number 1). pp. 6-17. doi:10.1007/s13752-015-0202-6 ISSN 1555-5542.
Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca and Soyer, Orkun S. (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, Volume 9 (Number 11). Article number e1003322. doi:10.1371/journal.pcbi.1003322 ISSN 1553-7358.
Fondo per gli Investimenti della Ricerca di Base (FIRB)
Csikasz-Nagy, A., Cardelli, L. and Soyer, Orkun S. (2010) Response dynamics of phosphorelays suggest their potential utility in cell signalling. Journal of The Royal Society Interface, 8 (57). pp. 480-488. doi:10.1098/rsif.2010.0336 ISSN 1742-5689.
France. Agence nationale de la recherche (ANR)
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
France. Ministère de l'enseignement supérieur et de la recherche
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
Horizon 2020 (European Commission) (H2020)
Cavaliere, Matteo, Feng, Song, Soyer, Orkun S. and Jiménez, José I. (2017) Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology, 19 (8). pp. 2949-2963. doi:10.1111/1462-2920.13767 ISSN 1462-2912.
Isaac Newton Institute for Mathematical Sciences
Großkopf, Tobias and Soyer, Orkun S. (2016) Microbial diversity arising from thermodynamic constraints. The ISME Journal, 10 . pp. 2725-2733. doi:10.1038/ismej.2016.49 ISSN 1751-7362.
Italy. Ministero dell'istruzione, dell'università e della ricerca (MIUR)
Salathé, Marcel and Soyer, Orkun S. (2008) Parasites lead to evolution of robustness against gene loss in host signaling networks. Molecular Systems Biology, Volume 4 . Article no. 202. doi:10.1038/msb.2008.44 ISSN 1744-4292.
Los Alamos National Laboratory (LANL)
Cavaliere, Matteo, Feng, Song, Soyer, Orkun S. and Jiménez, José I. (2017) Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology, 19 (8). pp. 2949-2963. doi:10.1111/1462-2920.13767 ISSN 1462-2912.
Lundbeck Foundation
Feng, Song, Sáez, Meritxell, Wiuf, Carsten, Feliu, Elisenda and Soyer, Orkun S. (2016) Core signalling motif displaying multistability through multi-state enzymes. Journal of The Royal Society Interface, 13 (123). 20160524. doi:10.1098/rsif.2016.0524 ISSN 1742-5689.
Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca and Soyer, Orkun S. (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, Volume 9 (Number 11). Article number e1003322. doi:10.1371/journal.pcbi.1003322 ISSN 1553-7358.
Microsoft Research
Kothamachu, Varun B., Feliu, Elisenda, Cardelli, Luca and Soyer, Orkun S. (2015) Unlimited multistability and Boolean logic in microbial signalling. Journal of The Royal Society Interface, Volume 12 (Number 108). pp. 1-9. Article number 20150234. doi:10.1098/rsif.2015.0234 ISSN 1742-5689.
Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca and Soyer, Orkun S. (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, Volume 9 (Number 11). Article number e1003322. doi:10.1371/journal.pcbi.1003322 ISSN 1553-7358.
National Institute for Health Research (Great Britain) (NIHR)
Soyer, Orkun S. and Goldstein, Richard A. (2011) Evolution of response dynamics underlying bacterial chemotaxis. BMC Evolutionary Biology, 11 (1). 240. doi:10.1186/1471-2148-11-240 ISSN 1471-2148.
National Institutes of Health (U.S.) (NIH)
O’Malley, Maureen A., Soyer, Orkun S. and Siegal, Mark L. (2015) A philosophical perspective on evolutionary systems biology. Biological Theory, Volume 10 (Number 1). pp. 6-17. doi:10.1007/s13752-015-0202-6 ISSN 1555-5542.
National Science Foundation (U.S.) (NSF)
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
O’Malley, Maureen A., Soyer, Orkun S. and Siegal, Mark L. (2015) A philosophical perspective on evolutionary systems biology. Biological Theory, Volume 10 (Number 1). pp. 6-17. doi:10.1007/s13752-015-0202-6 ISSN 1555-5542.
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung [Swiss National Science Foundation] (SNSF)
Salathé, Marcel and Soyer, Orkun S. (2008) Parasites lead to evolution of robustness against gene loss in host signaling networks. Molecular Systems Biology, Volume 4 . Article no. 202. doi:10.1038/msb.2008.44 ISSN 1744-4292.
Scottish Universities Life Sciences Alliance
Feng, Song, Ollivier, Julien F., Swain, Peter S. and Soyer, Orkun S. (2015) BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Research, 43 (19). e123. doi:10.1093/nar/gkv595 ISSN 0305-1048.
Seventh Framework Programme (European Commission) (FP7)
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
Society in Science : The Branco Weiss Fellowship (SSBWF)
Soyer, Orkun S. and Pfeiffer, Thomas (2010) Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Computational Biology, Volume 6 (Number 8). Article no. e1000907. doi:10.1371/journal.pcbi.1000907 ISSN 1553-7358.
Spain. Cortes Generales
Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca and Soyer, Orkun S. (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, Volume 9 (Number 11). Article number e1003322. doi:10.1371/journal.pcbi.1003322 ISSN 1553-7358.
Spain. Ministerio de Economía y Competitividad
Kothamachu, Varun B., Feliu, Elisenda, Cardelli, Luca and Soyer, Orkun S. (2015) Unlimited multistability and Boolean logic in microbial signalling. Journal of The Royal Society Interface, Volume 12 (Number 108). pp. 1-9. Article number 20150234. doi:10.1098/rsif.2015.0234 ISSN 1742-5689.
Statens samfundsvidenskabelige forskningsråd (Denmark)
Feng, Song, Sáez, Meritxell, Wiuf, Carsten, Feliu, Elisenda and Soyer, Orkun S. (2016) Core signalling motif displaying multistability through multi-state enzymes. Journal of The Royal Society Interface, 13 (123). 20160524. doi:10.1098/rsif.2016.0524 ISSN 1742-5689.
United States. Army Research Office (ARO)
Widder, Stefanie, Allen, Rosalind, Pfeiffer, Thomas, Curtis, Thomas P., Wiuf, Carsten, Sloan, William T., Cordero, Otto X., Brown, Sam P., Momeni, Babak, Shou, Wenying et al.
(2016)
Challenges in microbial ecology : building predictive understanding of community function and dynamics.
The ISME Journal, 2016
(10).
pp. 2557-2568.
doi:10.1038/ismej.2016.45
ISSN 1751-7362.
United States. Beacon Center for the Study of Evolution in Action
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
University of Exeter
Kuwahara, Hiroyuki and Soyer, Orkun S. (2012) Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology, Volume 8 (Number 564). Article no. 564. doi:10.1038/msb.2011.98 ISSN 1744-4292.
Soyer, Orkun S. and Pfeiffer, Thomas (2010) Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Computational Biology, Volume 6 (Number 8). Article no. e1000907. doi:10.1371/journal.pcbi.1000907 ISSN 1553-7358.
University of Exeter (UoE)
Feng, Song, Ollivier, Julien F., Swain, Peter S. and Soyer, Orkun S. (2015) BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Research, 43 (19). e123. doi:10.1093/nar/gkv595 ISSN 0305-1048.
Amin, Munia, Kothamachu, Varun B., Feliu, Elisenda, Scharf, Birgit E., Porter, Steven L. and Soyer, Orkun S. (2014) Phosphate sink containing two-component signaling systems as tunable threshold devices. PLoS Computational Biology, Volume 10 (Number 10). Article number e1003890. doi:10.1371/journal.pcbi.1003890 ISSN 1553-7358.
Soyer, Orkun S. and Goldstein, Richard A. (2011) Evolution of response dynamics underlying bacterial chemotaxis. BMC Evolutionary Biology, 11 (1). 240. doi:10.1186/1471-2148-11-240 ISSN 1471-2148.
Csikasz-Nagy, A., Cardelli, L. and Soyer, Orkun S. (2010) Response dynamics of phosphorelays suggest their potential utility in cell signalling. Journal of The Royal Society Interface, 8 (57). pp. 480-488. doi:10.1098/rsif.2010.0336 ISSN 1742-5689.
University of Sydney
Soyer, Orkun S. and O'Malley, Maureen A. (2013) Evolutionary systems biology : what it is and why it matters. BioEssays, Volume 35 (Number 8). pp. 696-705. doi:10.1002/bies.201300029 ISSN 0265-9247.
University of Warwick. School of Life Sciences
Feng, Song, Sáez, Meritxell, Wiuf, Carsten, Feliu, Elisenda and Soyer, Orkun S. (2016) Core signalling motif displaying multistability through multi-state enzymes. Journal of The Royal Society Interface, 13 (123). 20160524. doi:10.1098/rsif.2016.0524 ISSN 1742-5689.
Feng, Song, Ollivier, Julien F. and Soyer, Orkun S. (2016) Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks. PLoS Computational Biology, 12 (5). e1004918. doi:10.1371/journal.pcbi.1004918 ISSN 1553-7358.
Feng, Song, Ollivier, Julien F., Swain, Peter S. and Soyer, Orkun S. (2015) BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Research, 43 (19). e123. doi:10.1093/nar/gkv595 ISSN 0305-1048.
Université Grenoble
Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.
Wellcome Trust (London, England)
Hemsley, Claudia M., Luo, Jamie X., Andreae, Clio A., Butler, Clive S., Soyer, Orkun S. and Titball, Richard W. (2014) Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation but not anaerobic respiration. Antimicrobial Agents and Chemotherapy, Volume 58 (Number 10). pp. 5775-5783. doi:10.1128/AAC.02793-14 ISSN 0066-4804.
Wissenschaft Kollege zu Berlin (WIKO)
Großkopf, Tobias and Soyer, Orkun S. (2016) Microbial diversity arising from thermodynamic constraints. The ISME Journal, 10 . pp. 2725-2733. doi:10.1038/ismej.2016.49 ISSN 1751-7362.
This list was generated on Tue Apr 23 12:05:27 2024 BST.