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Items: 1 to 20 of 34

1.

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.

2.

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.

PMID:
26085824
3.

A Philosophical Perspective on Evolutionary Systems Biology.

O'Malley MA, Soyer OS, Siegal ML.

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

PMID:
26085823
4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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
10.

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
11.

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.

12.

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.

13.

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
14.

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
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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
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