bibtex.bib

@article{reeve2014synthetic,
  title={How synthetic biology will reconsider natural bioluminescence and its applications},
  author={Reeve, Benjamin and Sanderson, Theo and Ellis, Tom and Freemont, Paul},
  journal={Bioluminescence: Fundamentals and Applications in Biotechnology-Volume 2},
  pages={3--30},
  year={2014},
  publisher={Springer, Berlin, Heidelberg}
}

@article{pinheiro2015plasmodium,
  title={Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism},
  author={Pinheiro, Miguel M and Ahmed, Md Atique and Millar, Scott B and Sanderson, Theo and Otto, Thomas D and Lu, Woon Chan and Krishna, Sanjeev and Rayner, Julian C and Cox-Singh, Janet},
  journal={Plos one},
  volume={10},
  number={4},
  pages={e0121303},
  year={2015},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{sanderson2017phenoplasm,
  title={PhenoPlasm: a database of disruption phenotypes for malaria parasite genes},
  author={Sanderson, Theo and Rayner, Julian C},
  journal={Wellcome open research},
  volume={2},
  year={2017},
  publisher={The Wellcome Trust}
}

@article{bushell2017functional,
  title={Functional profiling of a Plasmodium genome reveals an abundance of essential genes},
  author={Bushell*, Ellen and Gomes*, Ana Rita and Sanderson*, Theo and Anar, Burcu and Girling, Gareth and Herd, Colin and Metcalf, Tom and Modrzynska, Katarzyna and Schwach, Frank and Martin, Rowena E and others},
  journal={Cell},
  volume={170},
  number={2},
  pages={260--272},
  year={2017},
  publisher={Cell Press}
}

@phdthesis{sanderson2015investigating,
  title={Investigating the Plasmodium invadome with high-throughput reverse genetics},
  author={Sanderson, Theo},
  year={2015},
  school={University of Cambridge}
}

@article{bustamante2017synergistic,
  title={Synergistic malaria vaccine combinations identified by systematic antigen screening},
  author={Bustamante, Leyla Y and Powell, Gareth T and Lin, Yen-Chun and Macklin, Michael D and Cross, Nadia and Kemp, Alison and Cawkill, Paula and Sanderson, Theo and Crosnier, Cecile and Muller-Sienerth, Nicole and others},
  journal={Proceedings of the National Academy of Sciences},
  volume={114},
  number={45},
  pages={12045--12050},
  year={2017},
  publisher={National Academy of Sciences}
}

@article{sanderson2018plasmotron,
  title={PlasmoTron: an open-source platform for automated culture of malaria parasites},
  author={Sanderson, Theo and Rayner, Julian C},
  journal={BioRxiv},
  pages={241596},
  year={2018},
  publisher={Cold Spring Harbor Laboratory}
}

@article{bileschi2022using,
  title={Using deep learning to annotate the protein universe},
  author={Bileschi, Maxwell L and Belanger, David and Bryant, Drew H and Sanderson, Theo and Carter, Brandon and Sculley, D and Bateman, Alex and DePristo, Mark A and Colwell, Lucy J},
  journal={Nature Biotechnology},
  pages={1--6},
  year={2022},
  publisher={Nature Publishing Group}
}

@article{verzier2019plasmodium,
  title={Plasmodium knowlesi as a model system for characterising Plasmodium vivax drug resistance candidate genes},
  author={Verzier, Lisa H and Coyle, Rachael and Singh, Shivani and Sanderson*, Theo and Rayner*, Julian C},
  journal={PLoS neglected tropical diseases},
  volume={13},
  number={6},
  pages={e0007470},
  year={2019},
  publisher={Public Library of Science}
}

@article{carter2020critiquing,
  title={Critiquing protein family classification models using sufficient input subsets},
  author={Carter, Brandon and Bileschi, Maxwell and Smith, Jamie and Sanderson, Theo and Bryant, Drew and Belanger, David and Colwell, Lucy J},
  journal={Journal of Computational Biology},
  volume={27},
  number={8},
  pages={1219--1231},
  year={2020},
  publisher={Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~…}
}

@article{carrasquilla2019quantitation,
  title={Quantitation of vector uptake reveals non-Poissonian transfection dynamics in Plasmodium falciparum},
  author={Carrasquilla, Manuela and Sanderson, Theo and Montandon, Ruddy and Rayner, Julian and Pance, Alena and Lee, Marcus},
  journal={bioRxiv},
  pages={681981},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

@article{hillier2019landscape,
  title={Landscape of the Plasmodium interactome reveals both conserved and species-specific functionality},
  author={Hillier, Charles and Pardo, Mercedes and Yu, Lu and Bushell, Ellen and Sanderson, Theo and Metcalf, Tom and Herd, Colin and Anar, Burcu and Rayner, Julian C and Billker, Oliver and others},
  journal={Cell reports},
  volume={28},
  number={6},
  pages={1635--1647},
  year={2019},
  publisher={Cell Press}
}

@article{stanway2019genome,
  title={Genome-scale identification of essential metabolic processes for targeting the Plasmodium liver stage},
  author={Stanway*, Rebecca R and Bushell*, Ellen and Chiappino-Pepe*, Anush and Roques*, Magali and Sanderson, Theo and Franke-Fayard, Blandine and Caldelari, Reto and Golomingi, Murielle and Nyonda, Mary and Pandey, Vikash and others},
  journal={Cell},
  volume={179},
  number={5},
  pages={1112--1128},
  year={2019},
  publisher={Cell Press}
}

@article{aunin2020genomic,
  title={Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys},
  author={Aunin, Eerik and B{\"o}hme, Ulrike and Sanderson, Theo and Simons, Noah D and Goldberg, Tony L and Ting, Nelson and Chapman, Colin A and Newbold, Chris I and Berriman, Matthew and Reid, Adam J},
  journal={PLoS pathogens},
  volume={16},
  number={8},
  pages={e1008717},
  year={2020},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{carrasquilla2020defining,
  title={Defining multiplicity of vector uptake in transfected Plasmodium parasites},
  author={Carrasquilla, Manuela and Adjalley, Sophie and Sanderson, Theo and Marin-Menendez, Alejandro and Coyle, Rachael and Montandon, Ruddy and Rayner, Julian C and Pance, Alena and Lee, Marcus},
  journal={Scientific reports},
  volume={10},
  number={1},
  pages={1--11},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{hillier2019landscape,
  title={Landscape of the Plasmodium Interactome},
  author={Hillier, Charles and Pardo Calvo, Mercedes and Yu, Lu and Bushell, Ellen and Sanderson, Theo and Metcalf, Tom and Herd, Colin and Anar, Burcu and Rayner, Julian C and Billker, Oliver and others},
  year={2019},
  publisher={SSRN}
}

@article{houlihan2020pandemic,
  title={Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers},
  author={Houlihan, Catherine F and Vora, Nina and Byrne, Thomas and Lewer, Dan and Kelly, Gavin and Heaney, Judith and Gandhi, Sonia and Spyer, Moira J and Beale, Rupert and Cherepanov, Peter and others},
  journal={The Lancet},
  volume={396},
  number={10246},
  pages={e6--e7},
  year={2020},
  publisher={Elsevier}
}

@article{consortium2020scalable,
  title={Scalable and Robust SARS-CoV-2 Testing in an Academic Center},
  author={Consortium, Crick Covid},
  journal={Nature biotechnology},
  year={2020}
}

@article{ndegwa2021using,
  title={Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates},
  author={Ndegwa, Duncan N and Kundu, Prasun and Hostetler, Jessica B and Marin-Menendez, Alejandro and Sanderson, Theo and Mwikali, Kioko and Verzier, Lisa H and Coyle, Rachael and Adjalley, Sophie and Rayner, Julian C},
  journal={PLoS Pathogens},
  volume={17},
  number={7},
  pages={e1008864},
  year={2021},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{korbmacher2021apicoplast,
  title={An apicoplast-resident folate transporter is essential for sporogony of malaria parasites},
  author={Korbmacher, Francois and Drepper, Benjamin and Sanderson, Theo and Martin, Peer and Stach, Thomas and Maier, Alexander G and Matuschewski, Kai and Matz, Joachim M},
  journal={Cellular Microbiology},
  volume={23},
  number={1},
  pages={e13266},
  year={2021},
  publisher={John Wiley \& Sons, Inc. Chichester, UK}
}

@article{sanderson2017open,
  title={Open hardware for random access plate storage},
  author={Sanderson, Theo},
  journal={Authorea Preprints},
  year={2017},
  publisher={Authorea}
}

@article{buck2020standard,
  title={Standard operating procedures for SARS-CoV-2 detection by a clinical diagnostic RT-LAMP assay},
  author={Buck, Michael D and Poirier, Enzo Z and Cardoso, Ana and Frederico, Bruno and Canton, Johnathan and Barrell, Sam and Beale, Rupert and Byrne, Richard and Caidan, Simon and Crawford, Margaret and others},
  journal={medRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{balestrini2021clinical,
  title={Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy},
  author={Balestrini, Simona and Koepp, Matthias J and Gandhi, Sonia and Rickman, Hannah M and Shin, Gee Yen and Houlihan, Catherine F and Anders-Cannon, Jonny and Silvennoinen, Katri and Xiao, Fenglai and Zagaglia, Sara and others},
  journal={Epilepsy \& Behavior},
  volume={115},
  pages={107602},
  year={2021},
  publisher={Academic Press}
}

@article{hellewell2021estimating,
  title={Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections},
  author={Hellewell, Joel and Russell, Timothy W and Beale, Rupert and Kelly, Gavin and Houlihan, Catherine and Nastouli, Eleni and Consortium), [..] (as part of Crick Covid},
  journal={BMC medicine},
  volume={19},
  number={1},
  pages={1--10},
  year={2021},
  publisher={BioMed Central}
}

@article{russell2021regulators,
  title={Regulators of male and female sexual development critical for transmission of a malaria parasite},
  author={Russell*, Andrew JC and Sanderson*, Theo and Bushell*, Ellen and Talman*, Arthur M and Anar, Burcu and Girling, Gareth and Hunziker, Mirjam and Kent, Robyn S and Metcalf, Tom and Montandon, Ruddy and others},
  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

@article{sanderson2021proteinfer,
  title={ProteInfer: deep networks for protein functional inference},
  author={Sanderson, Theo and Bileschi, Maxwell L and Belanger, David and Colwell, Lucy},
  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

@article{sanderson2021variation,
  title={Variation at Spike position 142 in SARS-CoV-2 Delta genomes is a technical artifact caused by dropout of a sequencing amplicon},
  author={Sanderson, Theo and Barrett, Jeffrey C},
  journal={medRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{sanderson2021chronumental,
  title={Chronumental: time tree estimation from very large phylogenies},
  author={Sanderson, Theo},
  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

@article{vohringer2021genomic,
  title={Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021},
  author={V{\"o}hringer, Harald S and Sanderson, Theo and Sinnott, Matthew and De Maio, Nicola and Nguyen, Thuy and Goater, Richard and Schwach, Frank and Harrison, Ian and Hellewell, Joel and Ariani, Cristina and others},
  journal={medRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{vohringer2021genomic,
  title={Genomic reconstruction of the SARS-CoV-2 epidemic in England},
  author={V{\"o}hringer, Harald S and Sanderson, Theo and Sinnott, Matthew and De Maio, Nicola and Nguyen, Thuy and Goater, Richard and Schwach, Frank and Harrison, Ian and Hellewell, Joel and Ariani, Cristina V and others},
  journal={Nature},
  volume={600},
  number={7889},
  pages={506--511},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{sanderson2021mixology,
  title={Mixology: a tool for calculating required masses and volume s for laboratory solutions},
  author={Sanderson, Theo},
  year={2021}
}

@article{de2021impact,
  title={The impact of viral mutations on recognition by SARS-CoV-2 specific T cells},
  author={de Silva, Thushan I and Liu, Guihai and Lindsey, Benjamin B and Dong, Danning and Moore, Shona C and Hsu, Nienyun Sharon and Shah, Dhruv and Wellington, Dannielle and Mentzer, Alexander J and Angyal, Adrienn and others},
  journal={Iscience},
  volume={24},
  number={11},
  pages={103353},
  year={2021},
  publisher={Elsevier}
}

@article{hill2022origins,
  title={The origins and molecular evolution of SARS-CoV-2 lineage B. 1.1. 7 in the UK},
  author={Hill, Verity and Du Plessis, Louis and Peacock, Thomas P and Aggarwal, Dinesh and Colquhoun, Rachel and Carabelli, Alesandro M and Ellaby, Nicholas and Gallagher, Eileen and Groves, Natalie and Jackson, Ben and others},
  journal={Virus Evolution},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{robsongenomics,
  title={Genomics-informed outbreak investigations of SARS-CoV-2 using civet},
  author={Robson, SC and Connor, TR and Loman, NJ and Golubchik, T and Nunez, RTM and Bonsall, D and Rambaut, A and Snell, LB and Livett, R and Ludden, C and others}
}

@article{carrasquilla2022barcoding,
  title={Barcoding genetically distinct Plasmodium falciparum strains for comparative assessment of fitness and antimalarial drug resistance},
  author={Carrasquilla, Manuela and Drammeh, Ndey Fatou and Rawat, Mukul and Sanderson, Theo and Zenonos, Zenon and Rayner, Julian C and Lee, Marcus},
  journal={mBio},
  year={2022}
}

@article{hill2022origins,
  title={The origins and molecular evolution of SARS-CoV-2 lineage B. 1.1. 7 in the UK},
  journal={Virus Evolution},
  author={Hill, Verity and Du Plessis, Louis and Peacock, Thomas and Aggarwal, Dinesh and Colquhoun, Rachel and Carabelli, Alesandro and Ellaby, Nicholas and Gallagher, Eileen and Groves, Natalie and Jackson, Ben and others},
  year={2022}
}

@article{mears2022emergence,
  title={Emergence of new subgenomic mRNAs in SARS-CoV-2},
  author={Mears, Harriet V and Young, George R and Sanderson, Theo and Harvey, Ruth and Crawford, Margaret and Snell, Daniel M and Fowler, Ashley S and Hussain, Saira and Nicod, Jerome and Peacock, Thomas P and others},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{sanderson2021systematic,
  title={Systematic Errors Associated with Some Implementations of ARTIC V4 and a Fast Workflow to Prescreen Samples for New Problematic Sites},
  author={Sanderson, Theo and De Maio, Nicola and Hinrichs, Angie S. and Bernardi Schneider, Adriano de and Walker, Conor and Goldman, Nick and Turakhia, Yatish and Lanfear, Robert and Corbett-Detig, Russell},
  journal={Virological.org},
  year={2021},
  publisher={https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473/16}
}

@article{ishizaki2022crispr,
  title={CRISPR/Cas9 and genetic screens in malaria parasites: small genomes, big impact},
  author={Ishizaki, Takahiro and Hernandez, Sophia and Paoletta, Martina S and Sanderson, Theo and Bushell, Ellen SC},
  journal={Biochemical Society Transactions},
  year={2022}
}

@article{sanderson2022taxonium,
  title={Taxonium: a web-based tool for exploring large phylogenetic trees},
  author={Sanderson, Theo},
  journal={eLife},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}

@article{vohringer2022publisher,
  title={Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England},
  author={V{\"o}hringer, Harald S and Sanderson, Theo and Sinnott, Matthew and De Maio, Nicola and Nguyen, Thuy and Goater, Richard and Schwach, Frank and Harrison, Ian and Hellewell, Joel and Ariani, Cristina V and others},
  journal={Nature},
  pages={1--1},
  year={2022},
  publisher={Nature Publishing Group}
}

@article{mears2022emergence,
  title={Emergence of new subgenomic mRNAs in SARS-CoV-2 (preprint)},
  author={Mears, Harriet and Young, George and Sanderson, Theo and Harvey, Ruth and Crawford, Margaret and Snell, Daniel and Fowler, Ashley and Hussain, Saira and Nicod, J{\'e}r{\^o}me and Peacock, Thomas and others},
  year={2022}
}

@article{pastorio2022determinants,
  title={Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA. 1 and BA. 2},
  author={Pastorio, Chiara and Zech, Fabian and Noettger, Sabrina and Jung, Christoph and Jacob, Timo and Sanderson, Theo and Sparrer, Konstantin MJ and Kirchhoff, Frank},
  journal={Cell Host \& Microbe},
  volume={30},
  number={9},
  pages={1255--1268},
  year={2022},
  publisher={Cell Press}
}

@article{collins2010bbf,
  title={BBF RFC 57: Assembly of bioBricks by the gibson method},
  author={Collins, Bill and Copley, Hannah and Emmrich, Peter and Handley, Will and Hohmann, Anja and Knott, Emily and Masset, Paul and Reeve, Ben and Sanderson, Theo},
  journal={Retrieved from<. synbio. org. u gibson do nloads files RFC57. pdf},
  year={2010}
}

@article{kramer2022treenome,
  title={Treenome Browser: co-visualization of enormous phylogenies and millions of genomes},
  author={Kramer, Alexander M and Sanderson, Theo and Corbett-Detig, Russell},
  journal={bioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}