Publications

Quick links:

Articles | Pre Prints | Books

Articles

65. STRONG: metagenomics strain resolution on assembly graphs Quince, C., Nurk, S., Raguideau, S., James R., Soyer OS., Summers JK., Limasset A., Eren AM., Chikhi R & Darling A. Genome Biol 22, 214 (2021) \| Link
64. Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteria Kelsey Cremin, Bryn Jones, James Teahan, Gabriel N. Meloni, David Perry, Christian Zerfass, Munehiro Asally, Orkun S. Soyer, Patrick R. UnwinAnalytical Chemistry (2020) \| LinkLink opens in a new window \| Featured in Bioelectricity BuzzLink opens in a new window
63. Inhibiting the reproduction of COVID-19-causing SARS-CoV-2 through perturbations in human cell metabolic network Hadrien Delattre, Kalesh Sasidharan, Orkun Soyer Life Science Alliance (2020) 4(1): published online November 24 2020 \| LinkLink opens in a new window \| SBML model \| GitHub - FBAhv
62. Campylobacter jejuni 11168H exposed to penicillin forms persister cells and cells with altered redox protein activity Helen Morcrette, Andrea Kovacs-Simon, Richard Kenneth Tennant, John Love, Sariqa Wagley, Zheng R Yang, David J. Studholme, Orkun S Soyer, Olivia L Champion, Clive S Butler, Richard Titball Frontiers in Cellular and Infection Microbiology, (2020) 10:583. LinkLink opens in a new window
61. Bioelectrical understanding and engineering of cell biology Zoe Schofield, Gabriel N. Meloni, Peter Tran, Christian Zerfass, Giovanni Sena, Yoshikatsu Hayashi, Murray Grant, Sonia A. Contera, Shelley D. Minteer, Minsu Kim, Arthur Prindle, Paulo Rocha, Mustafa B. A. Djamgoz,Teuta Pilizota, Patrick R. Unwin, Munehiro Asally and Orkun S. Soyer Journal of the Royal Society Interface (2020) 17:20200013. LinkLink opens in a new window
60. Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis Hadrien Delattre, Jing Chen, Matthew Wade, Orkun S Soyer Journal of the Royal Society Interface (2020) 17:20200053. LinkLink opens in a new window \| GitHub - MicodymoraLink opens in a new window
59. Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulphate reducer Jing Chen, Matthew J Wade, Jan Dolfing, Orkun S Soyer Journal of the Royal Society Interface 16: 20190129 (2019) LinkLink opens in a new window
58. In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics Song Feng, Orkun S Soyer Methods in Molecular Biology 1945:315-339 (2019) LinkLink opens in a new window
57. Manganese oxide biomineralization provides protection against nitrite toxicity in a cell density dependent manner Christian Zerfass, Joseph-Christie Oleza, Orkun S Soyer Applied and Environmental Microbiology 85(2). pii: e02129-18 (2019). LinkLink opens in a new window
56. Interrogating metabolism as an electron flow system Christian Zerfass, Munehiro Asally, Orkun S Soyer Current Opinion in Systems Biology 13: 59-67 (2019). LinkLink opens in a new window
55. Biodiversity function relationships in methanogenic communities Pawel Sierocinski, Florian Bayer, Gabriel Yvon Durocher, Melia Burdon, Tobias Großkopf, Mark Alston, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Angus Buckling Molecular Ecology 27(22):4641-4651 (2018). LinkLink opens in a new window
54. MetQy an R package to query metabolic functions of genes and genomes Andrea Martinez-Vernon, Frederick Farrell, Orkun S Soyer Bioinformatics 34(23):4134-4137 (2018). LinkLink opens in a new window \| GitHub - MetQyLink opens in a new window
53. Integrated Human-Virus Metabolic Stoichiometric Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses Sean Aller, Andrew E Scott, Mitali Sarkar-Tyson, Orkun S Soyer Royal Society Interface 12;15:146 (2018). LinkLink opens in a new window \| Resource 13 (ViraNet)Link opens in a new window
52. Impact of spatial organization on a novel auxotrophic interaction among soil microbes Xue Jiang, Christian Zerfass, Song Feng, Ruth Eichmann, Munehiro Asally, Patrick Schaefer, Orkun S Soyer The ISME Journal 12(6):1443-1456 (2018). LinkLink opens in a new window \|
51. Engineering microbial communities using thermodynamic principles and electrical interfaces. Christian Zerfass, Jing Chen, Orkun S Soyer, Current Opinion in Biotechnology 50:121-127 (2017). LinkLink opens in a new window
50. A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities. Pawel Sierocinski, Kim Milferstedt, Florian Bayer, Tobias Großkopf, Mark Alston, Sarah Bastkowski, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Jerome Hamelin, Angus Buckling Current Biology 27(21):3390-3395 (2017). LinkLink opens in a new window \| CommentaryLink opens in a new window
49. Cooperation in microbial communities and their biotechnological applications. Matteo Cavaliere, Song Feng, Orkun S. Soyer, Jose I. Jimenez Environmental Microbiology 19:8 (2017). LinkLink opens in a new window
48. An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions. Nicola J. Senior, Kalesh Sasidharan, et al, Orkun S. Soyer and Richard W. Titball BMC Microbiology 17:163 (2017). LinkLink opens in a new window
47. Metabolic modelling in an evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. Tobias Grosskopf, Jessika Consuegra, Joel Gaffe, John C. Willison, Richard E. Lenski, Orkun S. Soyer, and Dominique Schneider BMC Evolutionary Biology 16(1):163 (2016). LinkLink opens in a new window \| Resource 12 (evoFBA)Link opens in a new window
46. A stable genetic polymorphism underpinning microbial syntrophy. Tobias Großkopf, Simone Zenobi, Mark Alston, Leighton Folkes, David Swarbreck, and Orkun S Soyer The ISME Journal 10:12 (2016). LinkLink opens in a new window \| Sequence DataLink opens in a new window \|
45. Core signalling motif displaying multistability through multi-state enzymes. Song Feng, Meritxell Sez, Carsten Wiuf, Elisenda Feliu, and Orkun S. Soyer Royal Society Interface 13:123 (2016). LinkLink opens in a new window
44. Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks Song Feng, Julien F. Ollivier, and Orkun S. Soyer PLoS Computational Biology 12(5):e1004918 (2016). LinkLink opens in a new window \| Resource 11Link opens in a new window
43. Microbial diversity arising from thermodynamic constraints. Tobias Großkopf and Orkun S. Soyer The ISME Journal 10:11 (2016). LinkLink opens in a new window \| Resource 10Link opens in a new window
42. Challenges in microbial ecology: building predictive understanding of community function and dynamics. Stefanie Widder, Rosalind Allen, et al, and Orkun S. Soyer The ISME Journal 10:11 (2016). LinkLink opens in a new window \| In "top download list" at ISME website.
41. Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers. Francesco Montefusco, Ozgur E. Akman, Orkun S. Soyer, and Declan Bates PLoS One 18;11(8):e0161605 (2016). LinkLink opens in a new window
40. Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection. Deniz Cizmeci, Emma L. Dempster, Olivia L. Champion, Sariqa Wagley, Ozgur E. Akman, Joann L. Prior, Orkun S. Soyer, Jonathan Mill, and Richard W. Titball Scientific Reports 6:30861 (2016). LinkLink opens in a new window
39. Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels Arno Steinacher, Declan G. Bates, Ozgur E. Akman, and Orkun S. Soyer PLoS One 11(4):e0153295 (2016). LinkLink opens in a new window
38. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling Song Feng, Julien Ollivier, Peter S. Swain, and Orkun S. Soyer Nucleic Acid Research 43(19):e123 (2015). LinkLink opens in a new window \| GitHub - BioJazzLink opens in a new window
37. Unlimited multistability and Boolean logic in microbial signaling Varun B. Kothamachu, Elisenda Feliu, Luca Cardelli, and Orkun S. Soyer Royal Society Interface 12:108 (2015). LinkLink opens in a new window
36. Engineering and biology: Counsel for a continued relationship Brett Calcott, Arnon Levy, Mark L. Siegal, Orkun S. Soyer, and Andreas Wagner. Biological Theory 10(1):50-59 (2015) PDFLink opens in a new window
35. A philosophical perspective on evolutionary systems biology. Maureen A. O'Malley, Orkun S. Soyer, and Mark L. Siegal. Biological Theory 10(1):6-17 (2015). PDFLink opens in a new window
34. Phosphate sink containing two-component signaling systems as tunable threshold devices. Munia Amin, Varun B. Kothamachu, Elisenda Feliu, Birgit E. Scharf, Steven L. Porter, and Orkun S. Soyer PLoS Computational Biology 10(10):e1003890 (2014). PDFLink opens in a new window
33. Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation, but not anaerobic respiration. Claudia M. Hemsley, Jamie X. Luo, Clio A. Andreae, Clive S. Butler, Orkun S. Soyer, and Richard W. Titball Antimicrobial Agents and Chemotherapy 58(10):5775-83 (2014). PDFLink opens in a new window
32. Synthetic microbial communities. Tobias Grosskopf and Orkun S. Soyer Current Opinion in Microbiology 18:72-77 (2014). Link \| In "top download list" at Current Opinion in Microbiology website.
31. Phosphorelays provide tunable signal processing capabilities for the cell. Varun B. Kothamachu, Elisenda Feliu, Carsten Wuif, Luca Cardelli, and Orkun S. Soyer PLoS Computational Biology 9(11):e1003322 (2013). PDFLink opens in a new window
30. Systems and synthetic biology underpinning biotechnology. Orkun S. Soyer and Peter Swain Current Opinion Biotechnology 24(4):735-6 (2013).
29. Evolutionary Systems Biology: What it is and why it matters. Maureen O'Malley and Orkun S Soyer BioEssays 35(8):696-705 (2013).
28. Metabolic Tinker: An online tool for guiding the design of synthetic metabolic pathways. Kent McClymont and Orkun S. Soyer Nucleic Acid Research 41(11):e113 (2013). PDFLink opens in a new window \| Resource 8Link opens in a new window
27. Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks. Amin Munia, Steve Porter, and Orkun S. Soyer PLoS Computational Biology 9(3): e1002949 (2013). PDFLink opens in a new window \|
26. Bistability in feedback circuits as a byproduct of evolution of evolvability. Hiroaki Kuwahara and Orkun S Soyer Molecular Systems Biology 8:564 (2012). PDFLink opens in a new window \| Resource 7Link opens in a new window \| In "top download list" at Nature MSB website.
25. Evolutionary principles underlying structure and response dynamics of cellular networks. Arno Steinacher and Orkun Soyer Advances in Experimental Medicine and Biology 751 (2012).
24. The roles of integration in molecular systems biology. Maureen A. O'Malley and Orkun S. Soyer Studies in History and Philosophy of Biological and Biomedical Sciences 43:1 (2012). Link \| In "top download list" at ScienceDirect subject website.
23. Evolution of response dynamics underlying bacterial chemotaxis. Orkun S. Soyer and Richard A. Goldstein BMC Evolutionary Biology 11:240 (2011). PDFLink opens in a new window
22. The promise of evolutionary systems biology: Lessons from bacterial chemotaxis. Orkun S. Soyer Science Signaling 3:128, pe23 (2010). Abstract
21. Duplicate retention in signaling proteins and constraints from network dynamics. Chris J. Creevey and Orkun S. Soyer Journal of Evolutionary Biology 23:11 (2010). LinkLink opens in a new window \| Resource 6Link opens in a new window
20. Response dynamics of phosphorelays suggest their potential utility in cell signaling. Attila Csiksz-Nagy, Luca Cardelli, and Orkun S. Soyer Journal of Royal Society Interface 8:57 (2010). PDFLink opens in a new window \| Resource 5Link opens in a new window
19. Evolution under fluctuating environments explains observed robustness in metabolic networks. Orkun S. Soyer and Thomas Pfeiffer PLoS Computational Biology 6(8): e1000907 (2010). PDFLink opens in a new window
18. Fate of a duplicate gene in a network context. Orkun S. Soyer Invited chapter in "Evolution After Gene Duplication", Dittmar K., Liberles D.A. (eds.) Wiley and Sons, ISBN: 978-0-470-59382-0, October 2010. Book DescriptionLink opens in a new window
17. Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses. Orkun S. Soyer, Hiroaki Kuwahara, and Attila Csiksz-Nagy FEBS Journal, 276:12 (2009). LinkLink opens in a new window
16. Evolution of taxis responses in bacteria: nonadaptive dynamics. Richard A. Goldstein and Orkun S. Soyer PLoS Computational Biology, 4:5, e1000084 (2008). LinkLink opens in a new window \| Resource 3, 4Link opens in a new window
15. Parasites lead to evolution of robustness against gene loss in host signaling networks. Marcel Salathe and Orkun S. Soyer Molecular Systems Biology, 4:202 (2008). LinkLink opens in a new window \| Resource 2Link opens in a new window \| Featured in NatureLink opens in a new window \| Top ten download at Nature MSB website.
14. Adaptive dynamics with a single two state protein. Attila Csiksz-Nagy and Orkun S. Soyer Royal Society Interface, 5:Suppl 1, S41-7 (2008). LinkLink opens in a new window
13. Evolving BlenX programs to simulate the evolution of biological networks. Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer Theoretical Computer Science, 408:1 (2008).
12. Emergence and maintenance of functional modules in signaling pathways. Orkun S Soyer BMC Evolutionary Biology, 7:205 (2007). LinkLink opens in a new window
11. A formal and integrated framework to simulate evolution of biological pathways. Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer Proceedings of the Fifth International Conference on Computational Methods in Systems Biology (CMSB) 106-120 (2007).
10. Evolution of complexity in signaling pathways. Orkun S. Soyer and Sebastian Bonhoeffer Proc. Natl. Acad. Sci. USA (PNAS), 103:44 (2006). LinkLink opens in a new window
9. Simulating the evolution of signal transduction pathways. Orkun S Soyer, Thomas Pfeiffer, and Sebastian Bonhoeffer Journal of Theoretical Biology, 241:2 (2006).
8. Signal transduction networks: topology, response, and biochemical reactions. Orkun S. Soyer Marcel Salathe, and Sebastian Bonhoeffer Journal of Theoretical Biology, 238:2 (2006). Resource 1Link opens in a new window
7. Evolution of connectivity in metabolic networks. Thomas Pfeiffer, Orkun S. Soyer, and Sebastian Bonhoeffer PLoS Biology, 3:7 (2005). LinkLink opens in a new window \| Featured in Journal of Cell BiologyLink opens in a new window
6. Predicting functional sites in proteins: Site specific evolutionary models and their application to neurotransmitter transporters. Orkun S. Soyer and Richard A. Goldstein Journal of Molecular Biology, 339:1 (2004).
5. Probing conformational changes in neurotransmitter transporters in a structural context. Naomi R. Goldberg, Thijs Beuming, Orkun S. Soyer, Richard A. Goldstein, Harel Weinstein, and Jonathan A. Javitch European Journal of Pharmacology, 479:1-3 (2003).
4. Dimerization in aminergic G-protein coupled receptors: Application of a hidden site-class model of protein evolution. Orkun S. Soyer, Matt W. Dimmic, Richard R. Neubig, and Richard A. Goldstein Biochemistry, 42:49 (2003).
3. Depict a proteins two faces: Using phylogenetic tree based HMMs for G-protein coupled receptor classification. Bin Qian, Orkun S. Soyer, Richard R. Neubig, and Richard A. Goldstein FEBS Letters, 554:1-2 (2003).
2. NMR Structure of the second intracellular loop of the alpha2a adrenergic receptor: Evidence for a novel cytoplasmic helix. Duane A. Chung, Erik R. P. Zuiderweg, Carol B. Fowler, Orkun S. Soyer, Henry I. Mosberg, and Richard R. Neubig Biochemistry, 41:11 (2002).
1. Using evolutionary methods to study G-protein coupled receptors. Orkun S. Soyer, Matt W. Dimmic, Richard R. Neubig, and Richard A. Golstein Pacific Symposium on Biocomputing (PSB) 625-36 (2002).

Pre Prints

Listed here are currently unpublished manuscripts deposited at biorxiv or Authorea. Previous manuscripted deposited at biorxiv/Authorea which were then published in a peer-reviewed journal are now listed under Articles.

6. ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks Connah G. M. Johnson, Alexander G. Fletcher, Orkun S. Soyer Posted October 22, 2021 \| bioRxiv link
5. Thioflavin T indicates membrane potential in mammalian cells and can affect it in a blue light dependent manner Emily Skates, Hadrien Delattre, Zoe Schofield, Munehiro Asally, Orkun S. SoyerPosted October 22, 2021 \| bioRxiv linkLink opens in a new window
4. Novel microbial syntrophies identified by longitudinal metagenomics Sebastien Raguideau, Anna Trego, Fred Farrell, Gavin Collins, Christopher Quince, Orkun S SoyerPosted July 05, 2021 \| bioRxiv linkLink opens in a new window
3. Multi-site enzymes as a mechanism for bistability in reaction networks Clarmyra Hayes, Elisenda Feliu, Orkun S Soyer Posted May 07, 2021 \| bioRxiv linkLink opens in a new window
2. A low-cost DIY device for high resolution, continuous measurement of microbial growth dynamics. Kalesh Sasidharan, Andrea S Martinez-Vernon, Jing Chen, Tiantian Fu, Orkun Soyer Posted Sept 04, 2018 \| bioRxiv linkLink opens in a new window
1. Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes. Fred Farrell, Orkun S Soyer, Christopher Quince Posted April 25, 2018 \| bioRxiv linkLink opens in a new window

Books

4. An evolutionary systems biology view on metabolic system structure and dynamics Johnson C, Delattre H, Hayes C and Soyer, OS (2021). In: Crombach, Anton, (ed.) Evolutionary Systems Biology : Advances, Questions, and Opportunities. Springer-Nature. (In Press) Chapter Link
3. In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics Feng S and Soyer OS (2019) In: Hlavacek W. S. (ed.) Methods in Molecular Biology: Modeling Biomolecular Site Dynamics. Springer (2019) Series InfoLink opens in a new window
2. Evolutionary Principles Underlying Structure and Response Dynamics of Cellular Networks Steinacher A and Soyer OS (2012) In Soyer O.S. (ed.). Evolutionary Systems Biology: Adv. in Exp. Medicine and Biology. Springer, (2012) Book InfoLink opens in a new window
1. Fate of a Duplicate in a Network Context Soyer OS (2011) In: Dittmar K. and Liberles D. (eds.). Evolution after Gene Duplication. Wiley-Blackwell, (2011) Book InfoLink opens in a new window

Quick links:

Articles | Pre Prints | Books

Articles

65. STRONG: metagenomics strain resolution on assembly graphs

64. Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteria

63. Inhibiting the reproduction of COVID-19-causing SARS-CoV-2 through perturbations in human cell metabolic network

62. Campylobacter jejuni 11168H exposed to penicillin forms persister cells and cells with altered redox protein activity

61. Bioelectrical understanding and engineering of cell biology

60. Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

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

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

57. Manganese oxide biomineralization provides protection against nitrite toxicity in a cell density dependent manner

56. Interrogating metabolism as an electron flow system

55. Biodiversity function relationships in methanogenic communities

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

53. Integrated Human-Virus Metabolic Stoichiometric Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses

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

51. Engineering microbial communities using thermodynamic principles and electrical interfaces.

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

49. Cooperation in microbial communities and their biotechnological applications.

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

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

46. A stable genetic polymorphism underpinning microbial syntrophy.

45. Core signalling motif displaying multistability through multi-state enzymes.

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

43. Microbial diversity arising from thermodynamic constraints.

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

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

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

39. Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels

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

37. Unlimited multistability and Boolean logic in microbial signaling

36. Engineering and biology: Counsel for a continued relationship

35. A philosophical perspective on evolutionary systems biology.

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

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

32. Synthetic microbial communities.

31. Phosphorelays provide tunable signal processing capabilities for the cell.

30. Systems and synthetic biology underpinning biotechnology.

29. Evolutionary Systems Biology: What it is and why it matters.

28. Metabolic Tinker: An online tool for guiding the design of synthetic metabolic pathways.

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

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

25. Evolutionary principles underlying structure and response dynamics of cellular networks.

24. The roles of integration in molecular systems biology.

23. Evolution of response dynamics underlying bacterial chemotaxis.

22. The promise of evolutionary systems biology: Lessons from bacterial chemotaxis.

21. Duplicate retention in signaling proteins and constraints from network dynamics.

20. Response dynamics of phosphorelays suggest their potential utility in cell signaling.

19. Evolution under fluctuating environments explains observed robustness in metabolic networks.

18. Fate of a duplicate gene in a network context.

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

16. Evolution of taxis responses in bacteria: nonadaptive dynamics.

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

14. Adaptive dynamics with a single two state protein.

13. Evolving BlenX programs to simulate the evolution of biological networks.

12. Emergence and maintenance of functional modules in signaling pathways.

11. A formal and integrated framework to simulate evolution of biological pathways.

10. Evolution of complexity in signaling pathways.

9. Simulating the evolution of signal transduction pathways.

8. Signal transduction networks: topology, response, and biochemical reactions.

7. Evolution of connectivity in metabolic networks.

6. Predicting functional sites in proteins: Site specific evolutionary models and their application to neurotransmitter transporters.

5. Probing conformational changes in neurotransmitter transporters in a structural context.

4. Dimerization in aminergic G-protein coupled receptors: Application of a hidden site-class model of protein evolution.

3. Depict a proteins two faces: Using phylogenetic tree based HMMs for G-protein coupled receptor classification.

2. NMR Structure of the second intracellular loop of the alpha2a adrenergic receptor: Evidence for a novel cytoplasmic helix.

1. Using evolutionary methods to study G-protein coupled receptors.

Pre Prints

6. ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks

5. Thioflavin T indicates membrane potential in mammalian cells and can affect it in a blue light dependent manner

4. Novel microbial syntrophies identified by longitudinal metagenomics

3. Multi-site enzymes as a mechanism for bistability in reaction networks

2. A low-cost DIY device for high resolution, continuous measurement of microbial growth dynamics.

1. Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes.

Books

4. An evolutionary systems biology view on metabolic system structure and dynamics

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

2. Evolutionary Principles Underlying Structure and Response Dynamics of Cellular Networks

1. Fate of a Duplicate in a Network Context