Responsible AI in biotechnology: balancing discovery, innovation and biosecurity risks

Authors: Nicole E. Wheeler

Source: Frontiers in Bioengineering and Biotechnology, Vol 13 (2025)

Subject Terms: artificial intellegence, biotechnology, AI safety, protein design and engineering, synthetic biology, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fbioe.2025.1537471/full; https://doaj.org/toc/2296-4185

Access URL: https://doaj.org/article/7f076c243d694cec81060efc3cb600ee

Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data

Authors: Siu Fung Stanley Ho, Nicole E. Wheeler, Andrew D. Millard, Willem van Schaik

Source: Microbiome, Vol 11, Iss 1, Pp 1-15 (2023)

Subject Terms: Bacteriophage, Metagenome, Microbiome, Machine learning, Phage, Benchmarking, Microbial ecology, QR100-130

File Description: electronic resource

Relation: https://doaj.org/toc/2049-2618

Access URL: https://doaj.org/article/527933f1b8424fd4b8cb3f74cc98fd0f

Increased power from conditional bacterial genome-wide association identifies macrolide resistance mutations in Neisseria gonorrhoeae

Authors: Kevin C. Ma, Tatum D. Mortimer, Marissa A. Duckett, Allison L. Hicks, Nicole E. Wheeler, Leonor Sánchez-Busó, Yonatan H. Grad

Source: Nature Communications, Vol 11, Iss 1, Pp 1-8 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/f01d8464f9184f78b8e150f301aabff4

Adaptation to the cervical environment is associated with increased antibiotic susceptibility in Neisseria gonorrhoeae

Authors: Kevin C. Ma, Tatum D. Mortimer, Allison L. Hicks, Nicole E. Wheeler, Leonor Sánchez-Busó, Daniel Golparian, George Taiaroa, Daniel H. F. Rubin, Yi Wang, Deborah A. Williamson, Magnus Unemo, Simon R. Harris, Yonatan H. Grad

Source: Nature Communications, Vol 11, Iss 1, Pp 1-11 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b6241a00f0f44ca29603bf59bca55610

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation

Authors: Sandra Van Puyvelde, Derek Pickard, Koen Vandelannoote, Eva Heinz, Barbara Barbé, Tessa de Block, Simon Clare, Eve L. Coomber, Katherine Harcourt, Sushmita Sridhar, Emily A. Lees, Nicole E. Wheeler, Elizabeth J. Klemm, Laura Kuijpers, Lisette Mbuyi Kalonji, Marie-France Phoba, Dadi Falay, Dauly Ngbonda, Octavie Lunguya, Jan Jacobs, Gordon Dougan, Stijn Deborggraeve

Source: Nature Communications, Vol 10, Iss 1, Pp 1-12 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d03041f0c2d4477dbba22683cea763a0

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

Authors: John A. Lees, Bart Ferwerda, Philip H. C. Kremer, Nicole E. Wheeler, Mercedes Valls Serón, Nicholas J. Croucher, Rebecca A. Gladstone, Hester J. Bootsma, Nynke Y. Rots, Alienke J. Wijmega-Monsuur, Elisabeth A. M. Sanders, Krzysztof Trzciński, Anne L. Wyllie, Aeilko H. Zwinderman, Leonard H. van den Berg, Wouter van Rheenen, Jan H. Veldink, Zitta B. Harboe, Lene F. Lundbo, Lisette C. P. G. M. de Groot, Natasja M. van Schoor, Nathalie van der Velde, Lars H. Ängquist, Thorkild I. A. Sørensen, Ellen A. Nohr, Alexander J. Mentzer, Tara C. Mills, Julian C. Knight, Mignon du Plessis, Susan Nzenze, Jeffrey N. Weiser, Julian Parkhill, Shabir Madhi, Thomas Benfield, Anne von Gottberg, Arie van der Ende, Matthijs C. Brouwer, Jeffrey C. Barrett, Stephen D. Bentley, Diederik van de Beek

Source: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/676c4fca20864aaa9d086a45a85f61c3

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

Authors: John A. Lees, T. Tien Mai, Marco Galardini, Nicole E. Wheeler, Samuel T. Horsfield, Julian Parkhill, Jukka Corander

Source: mBio, Vol 11, Iss 4 (2020)

Subject Terms: elastic net, pangenome, phenotype prediction, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/39a9c15c29234af282ab753ee02f2acb

Genomic, Transcriptomic, and Phenotypic Analyses of Neisseria meningitidis Isolates from Disease Patients and Their Household Contacts

Authors: Xiaoyun Ren, David A. Eccles, Gabrielle A. Greig, Jane Clapham, Nicole E. Wheeler, Stinus Lindgreen, Paul P. Gardner, Joanna K. MacKichan

Source: mSystems, Vol 2, Iss 6 (2017)

Subject Terms: Neisseria meningitidis, type IV pili, carriage, household contact, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/8bb1289837d14ce8a488114c57fb30b3

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.

Authors: Matt Bawn, Nabil-Fareed Alikhan, Gaëtan Thilliez, Mark Kirkwood, Nicole E Wheeler, Liljana Petrovska, Timothy J Dallman, Evelien M Adriaenssens, Neil Hall, Robert A Kingsley

Source: PLoS Genetics, Vol 16, Iss 6, p e1008850 (2020)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/7e6251bb2e0b44058beda314f4f6e81c

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica.

Authors: Nicole E Wheeler, Paul P Gardner, Lars Barquist

Source: PLoS Genetics, Vol 14, Iss 5, p e1007333 (2018)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC5940178?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/937587dae0294a458478b00511b00221

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling.

Authors: Stinus Lindgreen, Sinan Uğur Umu, Alicia Sook-Wei Lai, Hisham Eldai, Wenting Liu, Stephanie McGimpsey, Nicole E Wheeler, Patrick J Biggs, Nick R Thomson, Lars Barquist, Anthony M Poole, Paul P Gardner

Source: PLoS Computational Biology, Vol 10, Iss 10, p e1003907 (2014)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/02bde787cb66465185af2fb45564a032