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Items: 1 to 50 of 55

1.

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer.

Chen J, Wade MJ, Dolfing J, Soyer OS.

J R Soc Interface. 2019 May 31;16(154):20190129. doi: 10.1098/rsif.2019.0129.

2.

Interrogating metabolism as an electron flow system.

Zerfaß C, Asally M, Soyer OS.

Curr Opin Syst Biol. 2019 Feb;13:59-67. doi: 10.1016/j.coisb.2018.10.001. Review.

3.

In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics.

Feng S, Soyer OS.

Methods Mol Biol. 2019;1945:315-339. doi: 10.1007/978-1-4939-9102-0_15.

PMID:
30945254
4.

Manganese Oxide Biomineralization Provides Protection against Nitrite Toxicity in a Cell-Density-Dependent Manner.

Zerfaß C, Christie-Oleza JA, Soyer OS.

Appl Environ Microbiol. 2019 Jan 9;85(2). pii: e02129-18. doi: 10.1128/AEM.02129-18. Print 2019 Jan 15.

5.

Biodiversity-function relationships in methanogenic communities.

Sierocinski P, Bayer F, Yvon-Durocher G, Burdon M, Großkopf T, Alston M, Swarbreck D, Hobbs PJ, Soyer OS, Buckling A.

Mol Ecol. 2018 Nov;27(22):4641-4651. doi: 10.1111/mec.14895. Epub 2018 Nov 22.

6.

Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses.

Aller S, Scott A, Sarkar-Tyson M, Soyer OS.

J R Soc Interface. 2018 Sep 12;15(146). pii: 20180125. doi: 10.1098/rsif.2018.0125.

7.

MetQy-an R package to query metabolic functions of genes and genomes.

Martinez-Vernon AS, Farrell F, Soyer OS.

Bioinformatics. 2018 Dec 1;34(23):4134-4137. doi: 10.1093/bioinformatics/bty447.

8.

Impact of spatial organization on a novel auxotrophic interaction among soil microbes.

Jiang X, Zerfaß C, Feng S, Eichmann R, Asally M, Schäfer P, Soyer OS.

ISME J. 2018 Jun;12(6):1443-1456. doi: 10.1038/s41396-018-0095-z. Epub 2018 Mar 23.

9.

Engineering microbial communities using thermodynamic principles and electrical interfaces.

Zerfaß C, Chen J, Soyer OS.

Curr Opin Biotechnol. 2018 Apr;50:121-127. doi: 10.1016/j.copbio.2017.12.004. Epub 2017 Dec 18. Review.

10.

A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities.

Sierocinski P, Milferstedt K, Bayer F, Großkopf T, Alston M, Bastkowski S, Swarbreck D, Hobbs PJ, Soyer OS, Hamelin J, Buckling A.

Curr Biol. 2017 Nov 6;27(21):3390-3395.e4. doi: 10.1016/j.cub.2017.09.056. Epub 2017 Oct 26.

11.

An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions.

Senior NJ, Sasidharan K, Saint RJ, Scott AE, Sarkar-Tyson M, Ireland PM, Bullifent HL, Rong Yang Z, Moore K, Oyston PCF, Atkins TP, Atkins HS, Soyer OS, Titball RW.

BMC Microbiol. 2017 Jul 21;17(1):163. doi: 10.1186/s12866-017-1073-8.

12.

Cooperation in microbial communities and their biotechnological applications.

Cavaliere M, Feng S, Soyer OS, Jiménez JI.

Environ Microbiol. 2017 Aug;19(8):2949-2963. doi: 10.1111/1462-2920.13767. Epub 2017 May 29. Review.

13.

Microbial diversity arising from thermodynamic constraints.

Großkopf T, Soyer OS.

ISME J. 2016 Nov;10(11):2725-2733. doi: 10.1038/ismej.2016.49. Epub 2016 Apr 1.

14.

Challenges in microbial ecology: building predictive understanding of community function and dynamics.

Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS.

ISME J. 2016 Nov;10(11):2557-2568. doi: 10.1038/ismej.2016.45. Epub 2016 Mar 29. Review.

15.

Core signalling motif displaying multistability through multi-state enzymes.

Feng S, Sáez M, Wiuf C, Feliu E, Soyer OS.

J R Soc Interface. 2016 Oct;13(123). pii: 20160524.

16.

Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

Großkopf T, Consuegra J, Gaffé J, Willison JC, Lenski RE, Soyer OS, Schneider D.

BMC Evol Biol. 2016 Aug 20;16(1):163. doi: 10.1186/s12862-016-0733-x.

17.

Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers.

Montefusco F, Akman OE, Soyer OS, Bates DG.

PLoS One. 2016 Aug 18;11(8):e0161605. doi: 10.1371/journal.pone.0161605. eCollection 2016.

18.

Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection.

Cizmeci D, Dempster EL, Champion OL, Wagley S, Akman OE, Prior JL, Soyer OS, Mill J, Titball RW.

Sci Rep. 2016 Aug 3;6:30861. doi: 10.1038/srep30861.

19.

A stable genetic polymorphism underpinning microbial syntrophy.

Großkopf T, Zenobi S, Alston M, Folkes L, Swarbreck D, Soyer OS.

ISME J. 2016 Dec;10(12):2844-2853. doi: 10.1038/ismej.2016.80. Epub 2016 Jun 3.

20.

Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks.

Feng S, Ollivier JF, Soyer OS.

PLoS Comput Biol. 2016 May 10;12(5):e1004918. doi: 10.1371/journal.pcbi.1004918. eCollection 2016 May.

21.

Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.

Steinacher A, Bates DG, Akman OE, Soyer OS.

PLoS One. 2016 Apr 15;11(4):e0153295. doi: 10.1371/journal.pone.0153295. eCollection 2016.

22.

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.

Feng S, Ollivier JF, Swain PS, Soyer OS.

Nucleic Acids Res. 2015 Oct 30;43(19):e123. doi: 10.1093/nar/gkv595. Epub 2015 Jun 22.

23.

Engineering and Biology: Counsel for a Continued Relationship.

Calcott B, Levy A, Siegal ML, Soyer OS, Wagner A.

Biol Theory. 2015 Mar;10(1):50-59.

24.

A Philosophical Perspective on Evolutionary Systems Biology.

O'Malley MA, Soyer OS, Siegal ML.

Biol Theory. 2015 Mar 1;10:6-17.

25.

Unlimited multistability and Boolean logic in microbial signalling.

Kothamachu VB, Feliu E, Cardelli L, Soyer OS.

J R Soc Interface. 2015 Jul 6;12(108):20150234. doi: 10.1098/rsif.2015.0234.

26.

Phosphate sink containing two-component signaling systems as tunable threshold devices.

Amin M, Kothamachu VB, Feliu E, Scharf BE, Porter SL, Soyer OS.

PLoS Comput Biol. 2014 Oct 30;10(10):e1003890. doi: 10.1371/journal.pcbi.1003890. eCollection 2014 Oct.

27.

Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation but not anaerobic respiration.

Hemsley CM, Luo JX, Andreae CA, Butler CS, Soyer OS, Titball RW.

Antimicrob Agents Chemother. 2014 Oct;58(10):5775-83. doi: 10.1128/AAC.02793-14. Epub 2014 Jul 21.

28.

Synthetic microbial communities.

Grosskopf T, Soyer OS.

Curr Opin Microbiol. 2014 Apr;18:72-7. doi: 10.1016/j.mib.2014.02.002. Epub 2014 Mar 14. Review.

29.

Phosphorelays provide tunable signal processing capabilities for the cell.

Kothamachu VB, Feliu E, Wiuf C, Cardelli L, Soyer OS.

PLoS Comput Biol. 2013;9(11):e1003322. doi: 10.1371/journal.pcbi.1003322. Epub 2013 Nov 7.

30.

Systems and synthetic biology underpinning biotechnology.

Soyer OS, Swain PS.

Curr Opin Biotechnol. 2013 Aug;24(4):735-6. doi: 10.1016/j.copbio.2013.06.002. Epub 2013 Jun 27. No abstract available.

PMID:
23810372
31.

Evolutionary systems biology: what it is and why it matters.

Soyer OS, O'Malley MA.

Bioessays. 2013 Aug;35(8):696-705. doi: 10.1002/bies.201300029. Epub 2013 May 16. Review.

PMID:
23681824
32.

Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways.

McClymont K, Soyer OS.

Nucleic Acids Res. 2013 Jun;41(11):e113. doi: 10.1093/nar/gkt234. Epub 2013 Apr 10.

33.

Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks.

Amin M, Porter SL, Soyer OS.

PLoS Comput Biol. 2013;9(3):e1002949. doi: 10.1371/journal.pcbi.1002949. Epub 2013 Mar 7.

34.

Evolutionary principles underlying structure and response dynamics of cellular networks.

Steinacher A, Soyer OS.

Adv Exp Med Biol. 2012;751:225-47. doi: 10.1007/978-1-4614-3567-9_11. Review.

PMID:
22821461
35.

The roles of integration in molecular systems biology.

O'Malley MA, Soyer OS.

Stud Hist Philos Biol Biomed Sci. 2012 Mar;43(1):58-68. doi: 10.1016/j.shpsc.2011.10.006. Epub 2011 Nov 1.

PMID:
22326073
36.

Bistability in feedback circuits as a byproduct of evolution of evolvability.

Kuwahara H, Soyer OS.

Mol Syst Biol. 2012 Jan 17;8:564. doi: 10.1038/msb.2011.98.

37.

Evolution of response dynamics underlying bacterial chemotaxis.

Soyer OS, Goldstein RA.

BMC Evol Biol. 2011 Aug 16;11:240. doi: 10.1186/1471-2148-11-240.

38.

Evolution under fluctuating environments explains observed robustness in metabolic networks.

Soyer OS, Pfeiffer T.

PLoS Comput Biol. 2010 Aug 26;6(8). pii: e1000907. doi: 10.1371/journal.pcbi.1000907.

39.

Duplicate retention in signalling proteins and constraints from network dynamics.

Soyer OS, Creevey CJ.

J Evol Biol. 2010 Nov;23(11):2410-21. doi: 10.1111/j.1420-9101.2010.02101.x. Epub 2010 Sep 6.

40.

Response dynamics of phosphorelays suggest their potential utility in cell signalling.

Csikász-Nagy A, Cardelli L, Soyer OS.

J R Soc Interface. 2011 Apr 6;8(57):480-8. doi: 10.1098/rsif.2010.0336. Epub 2010 Aug 11.

41.

The promise of evolutionary systems biology: lessons from bacterial chemotaxis.

Soyer OS.

Sci Signal. 2010 Jun 29;3(128):pe23. doi: 10.1126/scisignal.3128pe23.

PMID:
20587804
42.

Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses.

Soyer OS, Kuwahara H, Csikász-Nagy A.

FEBS J. 2009 Jun;276(12):3290-8. doi: 10.1111/j.1742-4658.2009.07054.x. Epub 2009 May 5.

43.

Parasites lead to evolution of robustness against gene loss in host signaling networks.

Salathé M, Soyer OS.

Mol Syst Biol. 2008;4:202. doi: 10.1038/msb.2008.44. Epub 2008 Jul 15.

44.

Evolution of taxis responses in virtual bacteria: non-adaptive dynamics.

Goldstein RA, Soyer OS.

PLoS Comput Biol. 2008 May 23;4(5):e1000084. doi: 10.1371/journal.pcbi.1000084.

45.

Adaptive dynamics with a single two-state protein.

Csikász-Nagy A, Soyer OS.

J R Soc Interface. 2008 Aug 6;5 Suppl 1:S41-7. doi: 10.1098/rsif.2008.0099.focus.

46.
47.

Evolution of complexity in signaling pathways.

Soyer OS, Bonhoeffer S.

Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16337-42. Epub 2006 Oct 23.

48.

Simulating the evolution of signal transduction pathways.

Soyer OS, Pfeiffer T, Bonhoeffer S.

J Theor Biol. 2006 Jul 21;241(2):223-32. Epub 2006 Jan 5.

PMID:
16403533
49.

Signal transduction networks: topology, response and biochemical processes.

Soyer OS, Salathé M, Bonhoeffer S.

J Theor Biol. 2006 Jan 21;238(2):416-25. Epub 2005 Jul 20.

PMID:
16045939
50.

The evolution of connectivity in metabolic networks.

Pfeiffer T, Soyer OS, Bonhoeffer S.

PLoS Biol. 2005 Jul;3(7):e228. Epub 2005 Jun 28.

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