PUBLICATIONS

DNA synthesis technologies to close the gene writing gap.

Hoose A, Vellacott R, Storch M, Freemont PS, Ryadnov MG

Nat Rev Chem. 2023;7(3):144-161. doi: 10.1038/s41570-022-00456-9.

CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery.

Benns HJ, Storch M, Falco JA, Fisher FR, Tamaki F, Alves E, Wincott CJ, Milne R, Wiedemar N, Craven G, Baragaña B, Wyllie S, Baum J, Baldwin GS, Weerapana E, Tate EW, Child MA.

Nat Microbiol 7, 1891–1905 (2022). https://doi.org/10.1038/s41564-022-01249-y

basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method.

Matthew C Haines, Benedict Carling, James Marshall, Vasily A Shenshin, Geoff S Baldwin, Paul Freemont, Marko Storch

Synthetic Biology, ysac023, doi: 10.1093/synbio/ysac023

Transmission of SARS-CoV-2 by children to contacts in schools and households: a prospective cohort and environmental sampling study in London.

Cordery R, Reeves L, Zhou J, Rowan A, Watber P, Rosadas C, Crone M, Storch M, Freemont P, Mosscrop L, Cowley A, Zelent G, Bisset K, Le Blond H, Regmi S, Buckingham C, Junaideen R, Abdulla N, Eliahoo J, Mindlin M, Lamagni T, Barclay W, Taylor GP, Sriskandan S.

Lancet Microbe. 2022 Aug 24:S2666-5247(22)00124-0. doi: 10.1016/S2666-5247(22)00124-0.

Synthetic biology and bioelectrochemical tools for electrogenetic system engineering.

Lawrence JM, Yin Y, Bombelli P, Scarampi A, Storch M, Wey LT, Climent-Catala A; PixCell iGEM Team, Baldwin GS, O'Hare D, Howe CJ, Zhang JZ, Ouldridge TE, Ledesma-Amaro R.

Sci Adv. 2022 May 6;8(18):eabm5091. doi: 10.1126/sciadv.abm5091.

Pandemic preparedness: synthetic biology and publicly funded biofoundries can rapidly accelerate response time.

Vickers CE, Freemont PS.

Nat Commun. 2022 Jan 21;13(1):453. doi: 10.1038/s41467-022-28103-3. PMID: 35064129

A high-throughput pipeline for scalable kit-free RNA extraction.

Han P, Go MK, Chow JY, Xue B, Lim YP, Crone MA, Storch M, Freemont PS, Yew WS.

Sci Rep. 2021 Dec 1;11(1):23260. doi: 10.1038/s41598-021-02742-w.

SARS-CoV-2 whole-genome sequencing using reverse complement PCR: For easy, fast and accurate outbreak and variant analysis.

Coolen JPM, Wolters F, Tostmann A, van Groningen LFJ, Bleeker-Rovers CP, Tan ECTH, van der Geest-Blankert N, Hautvast JLA, Hopman J, Wertheim HFL, Rahamat-Langendoen JC, Storch M, Melchers WJG.

J Clin Virol. 2021 Nov;144:104993. doi: 10.1016/j.jcv.2021.104993. PMID: 34619382

Community transmission and viral load kinetics of the SARS-CoV-2 delta (B.1.617.2) variant in vaccinated and unvaccinated individuals in the UK: a prospective, longitudinal, cohort study.

Singanayagam A, Hakki S, Dunning J, Madon KJ, Crone MA, Koycheva A, Derqui-Fernandez N, Barnett JL, Whitfield MG, Varro R, Charlett A, Kundu R, Fenn J, Cutajar J, Quinn V, Conibear E, Barclay W, Freemont PS, Taylor GP, Ahmad S, Zambon M, Ferguson NM, Lalvani A; ATACCC Study Investigators.

Lancet Infect Dis. 2021 Oct 29:S1473-3099(21)00648-4. doi: 10.1016/S1473-3099(21)00648-4.

Optimized protocol for a quantitative SARS-CoV-2 duplex RT-qPCR assay with internal human sample sufficiency control.

Rowan AG, May P, Badhan A, Herrera C, Watber P, Penn R, Crone MA, Storch M, Garson JA, McClure M, Freemont PS, Madona P, Randell P, Taylor GP.

J Virol Methods. 2021 Aug;294:114174. doi: 10.1016/j.jviromet.2021.114174. Epub 2021 May 10. PMID: 33984396

Refactoring of a synthetic raspberry ketone pathway with EcoFlex.

Moore SJ, Hleba YB, Bischoff S, Bell D, Polizzi KM, Freemont PS.

Microb Cell Fact. 2021 Jun 10;20(1):116. doi: 10.1186/s12934-021-01604-4.PMID: 34112158

Biofoundries are a nucleating hub for industrial translation.

Farzaneh T, Freemont PS.

Synth Biol (Oxf). 2021 Jun 23;6(1):ysab013. doi: 10.1093/synbio/ysab013. PMID: 34712838

Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs.

Beal J, Baldwin GS, Farny NG, Gershater M, Haddock-Angelli T, Buckley-Taylor R, Dwijayanti A, Kiga D, Lizarazo M, Marken J, de Mora K, Rettberg R, Sanchania V, Selvarajah V, Sison A, Storch M, Workman CT; iGEM Interlab Study Contributors.

PLoS One. 2021 Jun 7;16(6):e0252263. doi: 10.1371/journal.pone.0252263. PMID: 34097703

Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly.

Young R, Haines M, Storch M ,Freemont PS.

Metab Eng. 2021;63:81-101. doi:10.1016/j.ymben.2020.12.001

Engineered RNA-Interacting CRISPR Guide RNAs for Genetic Sensing and Diagnostics.

Galizi R, Duncan JN, Rostain W, Quinn CM, Storch M, Kushwaha M, Jaramillo A.

CRISPR J. 2020 Oct;3(5):398-408. doi: 10.1089/crispr.2020.0029. PMID: 33095053.

A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics.

Crone MA, Priestman M, Ciechonska M, Jensen K, Sharp DJ, Anand A, Randell P, Storch M, Freemont PS.

Nat Commun. 2020 Sep 8;11(1):4464. doi: 10.1038/s41467-020-18130-3. PMID: 32900994

SARS-CoV-2 infection, clinical features and outcome of COVID-19 in United Kingdom nursing homes.

Graham NSN, Junghans C, Downes R, Sendall C, Lai H, McKirdy A, Elliott P, Howard R, Wingfield D, Priestman M, Ciechonska M, Cameron L, Storch M, Crone MA, Freemont PS, Randell P, McLaren R, Lang N, Ladhani S, Sanderson F, Sharp DJ.

J Infect. 2020 Sep;81(3):411-419. doi: 10.1016/j.jinf.2020.05.073. Epub 2020 Jun 3. PMID: 32504743.

DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology.

Storch M, Haines MC, Baldwin GS.

Synth Biol (Oxf). 2020 Jul 9;5(1):ysaa010. doi: 10.1093/synbio/ysaa010. eCollection 2020. PMID: 32995552

BASIC: A Simple and Accurate Modular DNA Assembly Method.

Storch M, Dwijayanti A, Mallick H, Haines MC, Baldwin GS.

Methods Mol Biol. 2020;2205:239-253. doi: 10.1007/978- 1-0716-0908-8_14. PMID: 32809203

Biological Materials: The Next Frontier for Cell-Free Synthetic Biology.

Kelwick RJR, Webb AJ, Freemont PS.

Front Bioeng Biotechnol. 2020 May 12;8:399. doi: 10.3389/fbioe.2020.00399. eCollection 2020.

The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise?

Beal J, Goñi-Moreno A, Myers C, Hecht A, de Vicente MDC, Parco M, Schmidt M, Timmis K, Baldwin G, Friedrichs S, Freemont P, Kiga D, Ordozgoiti E, Rennig M, Rios L, Tanner K, de Lorenzo V, Porcar M.

EMBO Rep. 2020 May 6;21(5):e50521. doi: 10.15252/embr.202050521. Epub 2020 Apr 26.

Cell-Free Protein Synthesis as a Prototyping Platform for Mammalian Synthetic Biology.

Kopniczky MB, Canavan C, McClymont DW, Crone MA, Suckling L, Goetzmann B, Siciliano V, MacDonald JT, Jensen K, Freemont PS.

ACS Synth Biol. 2020 Jan 17;9(1):144-156. doi: 10.1021/acssynbio.9b00437. Epub 2020 Jan 3.

Building a global alliance of biofoundries.

Hillson N, Caddick M, Cai Y, Carrasco JA, Chang MW, Curach NC, Bell DJ, Le Feuvre R, Friedman DC, Fu X, Gold ND, Herrgård MJ, Holowko MB, Johnson JR, Johnson RA, Keasling JD, Kitney RI, Kondo A, Liu C, Martin VJJ, Menolascina F, Ogino C, Patron NJ, Pavan M, Poh CL, Pretorius IS, Rosser SJ, Scrutton NS, Storch M, Tekotte H, Travnik E, Vickers CE, Yew WS, Yuan Y, Zhao H, Freemont PS.

Nat Commun. 2019 May 9;10(1):2040. doi: 10.1038/s41467-019-10079-2.

Engineering a Model Cell for Rational Tuning of GPCR Signaling.

Shaw WM, Yamauchi H, Mead J, Gowers GF, Bell DJ, Öling D, Larsson N, Wigglesworth M, Ladds G, Ellis T.  Cell. 2019 Apr 18;177(3):782-796.e27. doi:10.1016/j.cell.2019.02.023. Epub 2019 Apr 4. PubMed PMID: 30955892; PubMed Central PMCID: PMC6476273.

Enabling the Advanced Bioeconomy through Public Policy Supporting Biofoundries and Engineering Biology.

Kitney R, Adeogun M, Fujishima Y, Goñi-Moreno Á, Johnson R, Maxon M, Steedman S, Ward S, Winickoff D, Philp J. Trends Biotechnol. 2019 Apr 26. pii: S0167-7799(19)30076-9. doi: 10.1016/j.tibtech.2019.03.017. [Epubahead of print] PubMed PMID: 31036350.

Miniaturisation of high-throughput plasmid DNA library preparation
for next-generation sequencing using multifactorial optimisation.

Suckling L, McFarlane C, Sawyer C, Chambers SP, Kitney RI, McClymont DW,
Freemont PS.  Synth Syst Biotechnol. 2019 Jan 22;4(1):57-66. doi: 10.1016/j.synbio.2019.01.002.

eCollection 2019 Mar. PubMed PMID: 30723818; PubMed Central PMCID: PMC6352296.

Utilising datasheets for the informed automated design and build of a
synthetic metabolic pathway.

Exley K, Reynolds CR, Suckling L, Chee SM, Tsipa A, Freemont PS, McClymont D,
Kitney RI. J Biol Eng. 2019 Jan 18;13:8. doi:10.1186/s13036-019-0141-z. eCollection 2019. PubMed PMID: 30675181; PubMed Central PMCID: PMC6339355.

Rapid acquisition and model-based analysis of cell-free transcription-translation reactions from nonmodel bacteria.

 Moore SJ, MacDonald JT, Wienecke S, Ishwarbhai A, Tsipa A, Aw R, Kylilis N, Bell DJ, McClymont DW, Jensen K, Polizzi KM, Biedendieck R, Freemont PS. Proc Natl Acad Sci U S A. 2018 May 8;115(19):E4340-E4349. doi: 10.1073/pnas.1715806115. Epub 2018 Apr 17. PubMed PMID: 29666238; PubMed Central PMCID: PMC5948957.

A Cell-Free Biosensor for Detecting Quorum Sensing Molecules in P. aeruginosa-Infected Respiratory Samples.

Wen KY, Cameron L, Chappell J, Jensen K, Bell DJ, Kelwick R, Kopniczky M, Davies JC, Filloux A, Freemont PS. CS Synth Biol. 2017 Dec 15;6(12):2293-2301. doi: 10.1021/acssynbio.7b00219. Epub 2017 Oct 5.
PubMed PMID: 28981256.

Biosynthesis of the antibiotic nonribosomal peptide penicillin in baker's yeast.

 Awan AR, Blount BA, Bell DJ, Shaw WM, Ho JCH, McKiernan RM, Ellis T. Nat Commun. 2017 May 4;8:15202. doi: 10.1038/ncomms15202. PubMed PMID: 28469278;
PubMed Central PMCID: PMC5418595.

With all due respect to Maholo, lab automation isn't anthropomorphic.

McClymont DW, Freemont PS. Nat Biotechnol. 2017 Apr 11;35(4):312-314. doi:
10.1038/nbt.3795. PubMed PMID: 28398331.

Streptomyces venezuelae TX-TL - a next generation cell-free synthetic biology tool.

Moore SJ, Lai HE, Needham H, Polizzi KM, Freemont PS. Biotechnol J. 2017 Apr;12(4). doi: 10.1002/biot.201600678. Epub 2017 Feb 24. PubMed PMID: 28139884.

Development of a Bacillus subtilis cell-free transcription-translation system for prototyping regulatory elements.

Kelwick R, Webb AJ, MacDonald JT, Freemont PS. Metab Eng. 2016 Nov;38:370-381. doi: 10.1016/j.ymben.2016.09.008. Epub 2016 Sep 30. PubMed PMID: 27697563.

EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.

Moore SJ, Lai HE, Kelwick RJ, Chee SM, Bell DJ, Polizzi KM, Freemont PS. ACS Synth Biol. 2016 Oct 21;5(10):1059-1069. Epub 2016 May 2. PubMed PMID: 27096716.