Cognitive Constraints Shape Public Debate on the Risks of Synthetic Biology
L. Swiney, D. G. Bates, J. D. Coley
Trends in Biotechnology
October 08, 2018
Manganese oxide biomineralization is a social trait protecting against nitrite toxicity
C. Zerfaß, J. A. Christie-Olezaa, O. S. Soyer
bioRxiv
April 04, 2018
Computationally Efficient Modelling of Stochastic Spatio-Temporal Dynamics in Biomolecular Networks
J. Kim, M. Foo, D. G. Bates
Scientific Reports
February 22, 2018
Biosynthesis: Reprogramming assembly lines
B. R. K. Menon, M. Jenner
Nature Chemistry
February 20, 2018
Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery
F. Alberti, D. J. Leng, I. Wilkening, L. Song, M. Tosin, C. Corre
bioRxiv
February 15, 2018
Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes
A. P. S. Darlington, J. Kim, J. I. Jiménez, D. G. Bates
Nature Communications
February 15, 2018
Modelling and Control of Gene Regulatory Networks for Perturbation Mitigation
M. Foo, J. Kim, D. G. Bates
IEEE/ACM Transactions on Computational Biology and Bioinformatics
January 11, 2018
Mechanism of intersubunit ketosynthase–dehydratase interaction in polyketide synthases
M. Jenner, S. Kosol, D. Griffiths, P. Prasongpholchai, L. Manzi, A. S. Barrow, J. E. Moses, N. J. Oldham, J. R. Lewandowski, G. L. Challis
Nature Chemical Biology
January 08, 2018
Engineering microbial communities using thermodynamic principles and electrical interfaces
C. Zerfaß, J. Chen, O. S. Soyer
Current Opinion in Biotechnology
December 18, 2017
Human Adenosine A2A Receptor: Molecular Mechanism of Ligand Binding and Activation
B. Carpenter, G. Lebon
Frontiers in Pharmacology
December 14, 2017
clusterTools: Proximity Searches For Functional Elements To Identify Putative Biosynthetic Gene Clusters
E. LC. de los Santos, G. L. Challis
BioRxiv
December 12, 2017
In Vitro Biosynthetic Studies of Bottromycin Expand the Enzymatic Capabilities of the YcaO Superfamily
C. J. Schwalen, G. A. Hudson, S. Kosol, N. Mahanta, G. L. Challis, D. A. Mitchell
Journal of the American Chemical Society
December 04, 2017
Engineering of biomolecules by bacteriophage directed evolution
A. Jaramillo, A. K Brödel, M. Isalan
Current Opinion in Biotechnology
November 22, 2017
Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture
L. Walker, C. Boddington, D. Jenkins, Y. Wang, J. T. Grønlund, J. Hulsmans, S. Kumar, D. Patel, J. D. Moore, A. Carter, S. Samavedam, G. Bonomo, D. S. Hersh, G. M. Coruzzi, N. J. Burroughs, M. L. Gifford
The Plant Cell
November 10, 2017
Permeable Protein-Loaded Polymersome Cascade Nanoreactors by Polymerization-Induced Self-Assembly
L. D. Blackman, S. Varlas, M. C. Arno, A. Fayter, M. I. Gibson, R. K. O’Reilly
ACS Macro Letters
October 31, 2017
Modeling the architecture of the regulatory system controlling methylenomycin production in Streptomyces coelicolor
J. E. Bowyer, E. LC. de los Santos, K. M. Styles, A. Fullwood, C. Corre, D. G. Bates
Journal of Biological Engineering
October 03, 2017
Impact of spatial organization on a novel auxotrophic interaction among soil microbes
X. Jiang, C. Zerfaß, R. Eichmann, M. Asally, P. Schaefer, O. Soyer
bioRxiv
September 28, 2017
Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication
A. K Brödel, A. Jaramillo, M. Isalan
Nature Protocols
August 10, 2017
System identification of gene regulatory networks for perturbation mitigation via feedback control
M. Foo, D. G. Bates, J. Kim
International Conference on Networking, Sensing and Control
August 03, 2017
Essentialism, moral reasoning, and evaluations of synthetic biology
L. Swiney
Cognitive Science Society
August 01, 2017
Model-based design of RNA hybridization networks implemented in living cells
G. Rodrigo, S. Prakash, S. Shen, E. Majer, J. Daròs, A. Jaramillo
Nucleic Acids Research
August 01, 2017
Symposium on Intuitive Biology and Global Challenges
L. Swiney
Convener, Cognitive Science Society Annual Conference
July 29, 2017
Commentary: Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet-Induced Metabolic Syndrome
B. O. Anonye
Frontiers in Immunology
July 27, 2017
Mechanistic modelling of a recombinase-based two-input temporal logic gate
J. E. Bowyer, V. Hsiao, W. W. Wong, D. G. Bates
Engineering Biology
July 27, 2017
Synthetic biology : Engineered stable ecosystems
A. Jaramillo
Nature Microbiology
July 25, 2017
An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions
N. J. Senior, K. Sasidharan, R. J. Saint, A. E. Scott, M. Sarkar-Tyson, P. M. Ireland, H. L Bullifent, Z. Rong Yang, K. Moore, P. C. F. Oyston, T. P. Atkins, H. S. Atkins, O. S. Soyer, R. W. Titball
BMC Microbiology
July 21, 2017
Control Strategies for Mitigating the Effect of External Perturbations on Gene Regulatory Networks
M. Foo, I. Gherman, K. Denby, D. G. Bates
20th World Congress of the International Federation of Automatic Control
July 14, 2017
Nutrient recycling facilitates long-term stability of marine microbial phototroph–heterotroph interactions
J. A. Christie-Oleza, D. Sousoni, M. Lloyd, J. Armengaud, D. J. Scanlan
Nature Microbiology
June 26, 2017
Regulation of Angiopoietin Signalling by Soluble Tie2 Ectodomain and Engineered Ligand Trap
D. O. A. Alawo, T. A. Tahir, M. Fischer, D. G. Bates, S. R. Amirova, N. P. J. Brindle
Scientific Reports
June 16, 2017
Phototaxis beyond turning: persistent accumulation and response acclimation of the microalga Chlamydomonas reinhardtii
J. Arrieta, A. Barreira, M. Chioccioli, M. Polin, I. Tuval
Scientific Reports
June 14, 2017
Discovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis
L. Song, M. Jenner, J. Masschelein, C. Jones, M. J. Bull, S. R. Harris, R. C. Hartkoorn, A. Vocat, I. Romero-Canelon, P. Coupland, G. Webster, M. Dunn, R. Weiser, C. Paisey, S. T. Cole, J. Parkhill, E. Mahenthiralingam, G. L. Challis
Journal of the American Chemical Society
May 22, 2017
Translation initiation events on structured eukaryotic mRNAs generate gene expression noise
E. Dacheux, N. Malys, X. Meng, V. Ramachandran, P. Mendes, J. E. G. McCarthy
Nucleic Acids Research
May 17, 2017
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
K. Blin, T. Wolf, M. G. Chevrette, X. Lu, C. J. Schwalen, S. A. Kautsar, H. G. Suarez Duran, E. L. C. de los Santos, H. Uk Kim, M. Nave, J. S. Dickschat, D. A. Mitchell, E. Shelest, R. Breitling, E. Takano, S. Yup Lee, T. Weber, M. H. Medema
Nucleic Acids Research
April 28, 2017
Cooperation in microbial communities and their biotechnological applications
M. Cavaliere, S. Feng, O. S. Soyer, J. I. Jiménez
Environmental Microbiology
April 26, 2017
Evidence for the formation of ScbR/ScbR2 heterodimers and identification of one of the regulatory targets in Streptomyces coelicolor
X. Li, J. Wang, M. Shi, W. Wang, C. Corre, K. Yang
Applied Microbiology and Biotechnology
April 24, 2017
Identification of the anti‐mycobacterial functional properties of piperidinol derivatives
C. S. Guy, E. Tichauer, G. L. Kay, D. J. Phillips, T. L. Bailey, J. Harrison, C. M. Furze, A. D. Millard, M. I. Gibson, M. J. Pallen, E. Fullam
British Journal of Pharmacology
March 23, 2017
Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway
I. Lidbury, M. A Mausz, D. J Scanlan, Y. Chen
The ISME Journal
March 17, 2017
Enhanced processing in arrays of optimally tuned nonlinear biomimetic sensors: A coupling-mediated Ringelmann effect and its dynamical mitigation
A. P. Nikitin, A. R. Bulsara, N. G. Stocks
Physical Review E
March 13, 2017
Methylamine as a nitrogen source for microorganisms from a coastal marine environment
M. Taubert, C. Grob, A. M. Howat, O. J. Burns, J. Pratscher, N. Jehmlich, M. von Bergen, H. H. Richnow, Y. Chen, J. Colin Murrell
Environmental Microbiology
February 28, 2017
Watasemycin biosynthesis in Streptomyces venezuelae: thiazoline C-methylation by a type B radical-SAM methylase homologue
Y. Inahashi, S. Zhou, M. J. Bibb, L. Song, M. M. Al-Bassam, M. J. Bibb, G. L. Challis
Chemical Science
January 19, 2017
Design of an embedded inverse-feedforward biomolecular tracking controller for enzymatic reaction processes
M. Foo, J. Kim, R. Sawlekar, D. G. Bates
Computers & Chemical Engineering
January 17, 2017
Biomolecular implementation of nonlinear system theoretic operators
M. Foo, R. Sawlekar, J. Kim, D. G. Bates, G. Stan, V. Kulkarni
European Control Conference
January 09, 2017
Proportional–Integral Degradation Control Allows Accurate Tracking of Biomolecular Concentrations With Fewer Chemical Reactions
M. Foo, J. Kim, J. Kim, D. G. Bates
IEEE Life Sciences Letters
December 23, 2016
JAZ2 controls stomata dynamics during bacterial invasion
S. Gimenez-Ibanez, M. Boter, A. Ortigosa, G. García-Casado, A. Chini, M. G. Lewsey, J. R. Ecker, V. Ntoukakis, R. Solano
New Phytol
December 22, 2016
A crotonyl-CoA reductase-carboxylase independent pathway for assembly of unusual alkylmalonyl-CoA polyketide synthase extender units
L. Ray, T. R. Valentic, T. Miyazawa, D. M. Withall, L. Song, J. C. Milligan, H. Osada, S. Takahashi, S. Tsai, G. L. Challis
Nature Communications
December 21, 2016
Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N‐oxide
Y. Chen, et al.
Molecular Microbiology
December 20, 2016
Engineering orthogonal dual transcription factors for multi-input synthetic promoters
A. K. Brödel, A. Jaramillo, M. Isalan
Nature Communications
December 16, 2016
Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis
X. Meng, H. Firczuk, P. Pietroni, R. Westbrook, E. Dacheux, P. Mendes, J. E. G. McCarthy
Nucleic Acids Research
December 07, 2016
DNA-, RNA-, and protein-based stable-isotope probing for high-throughput biomarker analysis of active microorganisms
E. Jameson, M. Taubert, S. Coyotzi, Y. Chen, O. Eyice, H. Schäfer, J. Colin Murrell, J. D. Neufeld, M. G. Dumont
Metagenomics : methods and protocols
November 30, 2016
Exploiting the dynamic properties of covalent modification cycle for the design of synthetic analog biomolecular circuitry
M. Foo, R. Sawlekar, D. G. Bates
Journal of Biological Engineering
November 14, 2016
Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways
N. Archer, M. D. Walsh, V. Shahrezaei, D. Hebenstreit
Cell Systems
November 10, 2016
The Proteasome Acts as a Hub for Plant Immunity and Is Targeted by Pseudomonas Type III Effectors
S. Üstün, A. Sheikh, S. Gimenez-Ibanez, A. Jones, V. Ntoukakis, F. Börnke
Plant Physiology
November 04, 2016
Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions
M. Foo, R. Sawlekar, V. V. Kulkarni, D. G. Bates
38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society
October 18, 2016
Discovery of Unusual Biaryl Polyketides by Activation of a Silent Streptomyces venezuelae Biosynthetic Gene Cluster
A. Thanapipatsiri, J. Pablo Gomez-Escribano, L. Song, M. J. Bibb, M. Al-Bassam, G. Chandra, A. Thamchaipenet, G. L. Challis, M. J. Bibb
Chembiochem
October 13, 2016
Predicting the Dynamics and Heterogeneity of Genomic DNA Content within Bacterial Populations across Variable Growth Regimes
M. du Lac, A. H. Scarpelli, A. K. D. Younger, D. G. Bates, J. N. Leonard
ACS Synthetic Biology
September 30, 2016
O2‐independent demethylation of trimethylamine N‐oxide by Tdm of Methylocella silvestris
Y. Zhu, A. Z. Ksibe, H. Schäfer, C. A. Blindauer, T. D. H. Bugg, Y. Chen
FEBS Journal
September 19, 2016
Mechanistic insights into class B radical-S-adenosylmethionine methylases: ubiquitous tailoring enzymes in natural product biosynthesis
S. Zhou, L. M. Alkhalaf, E. LC. de los Santos, G. L. Challis
Current Opinion in Chemical Biology
September 12, 2016
Discrete-time L1 adaptive controller to regulate in vivo protein expressions
V. V. Kulkarni, F. Islam
QSP-UK 1st Exchange Workshop
September 05, 2016

Gene drive responses to Zika: A case of the Anthropocene predicament?

N. Lee
4S/EASST Annual Conference
August 31, 2016

Human germline editing: Global governance challenges

A. Rosemann
4S/EASST Annual Conference
August 31, 2016

Session on gene editing in context

N. Lee, A. Rosemann
Conveners, 4S/EASST Annual Conference
August 31, 2016
Thioester reduction and aldehyde transamination are universal steps in actinobacterial polyketide alkaloid biosynthesis
U. R. Awodi, J. L. Ronan, J. Masschelein, E. L. C. de los Santos, G. L. Challis
Chemical Science
August 22, 2016
Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers
F. Montefusco, O. E. Akman, O. S. Soyer, D. G. Bates
PLoS One
August 18, 2016
Host-aware modelling of a synthetic genetic oscillator
A. Darlington, D. G. Bates
38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society
August 08, 2016
The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1
D. Couto, R. Niebergall, X. Liang, C. A. Bücherl, J. Sklenar, A. P. Macho, V. Ntoukakis, P. Derbyshire, D. Altenbach, D. Maclean, S. Robatzek, J. Uhrig, F. Menke, J. Zhou, C. Zipfel
PLOS Pathogens
August 05, 2016
Parasitic plants—A CuRe for what ails thee
V. Ntoukakis, S. Gimenez-Ibanez
Science
July 29, 2016
WISB: Warwick Integrative Synthetic Biology Centre
J. McCarthy
Biochemical Society Transactions
June 09, 2016
Mechanistic Modeling of a Rewritable Recombinase Addressable Data Module
J. Bowyer, J. Zhao, P. Subsoontorn, W. Wong, S. Rosser, D. G. Bates
IEEE Transactions on Biomedical Circuits and Systems
May 24, 2016
Overproduction and identification of butyrolactones SCB1-8 in the antibiotic production superhost Streptomyces M1152
J. D. Sidda, V. Poon, L. Song, W. Wang, K. Yang, C. Corre
Organic & Biomolecular Chemistry
May 10, 2016
Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions
R. Sawlekar, F. Montefusco, V. V. Kulkarni, D. G. Bates
IEEE Transactions on NanoBioscience
April 29, 2016
Development of a Synthetic Oxytetracycline-Inducible Expression System for Streptomycetes Using de Novo Characterized Genetic Parts
W. Wang, T. Yang, Y. Li, S. Li, S. Yin, K. Styles, C. Corre, K. Yang
ACS Synthetic Biology
April 21, 2016
Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels
A. Steinacher, D. G. Bates, O. E. Akman, O. S. Soyer
PLoS ONE
April 15, 2016
Biological insights from synthetic biology
J. Garcia-Ojalvo, A. S. Khalil, J. McCarthy
Integrative Biology
April 11, 2016
Microbial diversity arising from thermodynamic constraints
T. Großkopf, O. S Soyer
The ISME Journal
April 01, 2016
Using RNA as Molecular Code for Programming Cellular Function
M. Kushwaha, W. Rostain, S. Prakash, J. N. Duncan, A. Jaramillo
ACS Synthetic Biology
March 21, 2016
A Flavin-Dependent Decarboxylase–Dehydrogenase–Monooxygenase Assembles the Warhead of α,β-Epoxyketone Proteasome Inhibitors
D. Zabala, J. W. Cartwright, D. M. Roberts, B. J. C. Law, L. Song, M. Samborskyy, P. F. Leadlay, J. Micklefield, G. L. Challis
Journal of the American Chemical Society
March 21, 2016
Genetically modified bacteriophages
A. P. Sagona, A. M. Grigonyte, P. R. MacDonald, A. Jaramillo
Integrative Biology
February 15, 2016
Plant root-microbe communication in shaping root microbiomes
A. Lareen, F. Burton, P. Schäfer
Plant Molecular Biology
January 04, 2016
Functionalization of an Antisense Small RNA
G. Rodrigo, S. Prakash, T. Cordero, M. Kushwaha, A. Jaramillo
Journal of Molecular Biology
January 04, 2016
Biomolecular Implementation of a Quasi Sliding Mode Feedback Controller based on DNA Strand Displacement Reactions
R. Sawlekar, F. Montefusco, V. V. Kulkarni, D. G. Bates
Proceedings of the 37th IEEE Engineering in Medicine and Biology Conference
December 01, 2015
Anaerobic choline metabolism in microcompartments promotes growth and swarming of P roteus mirabilis
E. Jameson, T. Fu, I. R. Brown, K. Paszkiewicz, K. J. Purdy, S. Frank, Y. Chen
Environmental Microbiology
November 03, 2015

Playing God and Fighting Wars: Refreshing Synthetic Biology and AMR

N. Lee
4S/EASST Annual Conference
November 01, 2015
Ion channels enable electrical communication in bacterial communities
A. Prindle, J. Liu, M. Asally, J. Garcia-Ojalvo, G. M. Süel
Nature
October 21, 2015
Unique post-translational oxime formation in the biosynthesis of the azolemycin complex of novel ribosomal peptides from Streptomyces sp. FXJ1.264
N. Liu, L. Song, M. Liu, F. Shang, Z. Anderson, D. J. Fox, G. L. Challis, Y. Huang
Chemical Science
October 06, 2015
Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells
G. Rodrigo, E. Majer, S. Prakash, J. Daròs, A. Jaramillo, J. F. Poyatos
Biophysical Journal
September 01, 2015
Engineering Transcriptional Regulator Effector Specificity Using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor
E. L. C. de los Santos, J. T. Meyerowitz, S. L. Mayo, R. M. Murray
ACS Synthetic Biology
August 11, 2015
Constraint-Based Genetic Compilation
C. Ladroue, S. Kalvala
Lecture Notes in Bioinformatics
August 05, 2015
Characterization of para-Nitrophenol-Degrading Bacterial Communities in River Water by Using Functional Markers and Stable Isotope Probing
A. Kowalczyk, O. Eyice, H. Schäfer, O. R. Price, C. J. Finnegan, R. A. van Egmond, L. J. Shaw, G. Barrett, G. D. Bending
Appl Environ Microbiol.
July 24, 2015
Metabolic co-dependence gives rise to collective oscillations within biofilms
J. Liu, A. Prindle, J. Humphries, M. Gabalda-Sagarra, M. Asally, D. D. Lee, S. Ly, J. Garcia-Ojalvo, G. M. Süel
Nature
July 22, 2015
Growth versus immunity — a redirection of the cell cycle?
R. Eichmann, P. Schäfer
Current Opinion in Plant Biology
July 17, 2015
Standards for plant synthetic biology: a common syntax for exchange of DNA parts
N. J. Patron, D. Orzaez, S. Marillonnet, H. Warzecha, C. Matthewman, M. Youles, O. Raitskin, A. Leveau, G. Farré, C. Rogers, A. Smith, J. Hibberd, A. A. R. Webb, J. Locke, S. Schornack, J. Ajioka, D. C. Baulcombe, C. Zipfel, S. Kamoun, J. D. G. Jones, H. Kuhn, S. Robatzek, H. Peter Van Esse, D. Sanders, G. Oldroyd, C. Martin, R. Field, S. O'Connor, S. Fox, B. Wulff, B. Miller, A. Breakspear, G. Radhakrishnan, P. Delaux, D. Loqué, A. Granell, A. Tissier, P. Shih, T. P. Brutnell, W. Paul Quick, H. Rischer, P. D. Fraser, A. Aharoni, C. Raines, P. F. South, J. Ané, B. R. Hamberger, J. Langdale, J. Stougaard, H. Bouwmeester, M. Udvardi, J. A. H. Murray, V. Ntoukakis, P. Schäfer, K. Denby, K. J. Edwards, A. Osbourn, J. Haseloff
New Phytologist
July 14, 2015
Spatial dissection of the Arabidopsis thaliana transcriptional response to downy mildew using Fluorescence Activated Cell Sorting
T. L. R. Coker, V. Cevik, J. L. Beynon, M. L. Gifford
Front. Plant Sci.
July 10, 2015
Discovery of microbial natural products by activation of silent biosynthetic gene clusters
P. J. Rutledge, G. L. Challis
Nature Reviews Microbiology
June 29, 2015
Stereochemistry and Mechanism of Undecylprodigiosin Oxidative Carbocyclization to Streptorubin B by the Rieske Oxygenase RedG
D. M. Withall, S. W. Haynes, G. L. Challis
Journal of the American Chemical Society
May 29, 2015
Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression
S. Shen, G. Rodrigo, S. Prakash, E. Majer, T. E. Landrain, B. Kirov, J. Daròs, A. Jaramillo
Nucleic Acids Research
April 27, 2015

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