Zachary Ardern, PhD

Zachary is an evolutionary biologist investigating the evolution and functions of young genes in pathogenic bacteria and viruses, working as a SEED fellow (Sanger Epidemiological and Evolutionary Dynamics)

Biography

My timeline

2022: Postdoctoral researcher, SEED fellow - Wellcome Sanger Institute
2021: Postdoctoral researcher - Karlsruhe Institute of Technology, Germany
2016: Postdoctoral research and junior group leader - Technical University of Munich, Germany
PhD in Biological Sciences - University of Auckland, New Zealand
2012: Graduated with BA|BSc degrees - University of Auckland, New Zealand

Publications

Key publications:

Alternative reading frames are an underappreciated source of protein sequence novelty Z Ardern Journal of Molecular Evolution, 1-11		2023
Between noise and function: Toward a taxonomy of the non-canonical translatome Z Ardern Cell Systems 14 (5), 343-345		2023
Highly similar average collateral effect of synonymous mutations across alternative reading frames: a potential role in evolvability S Wichmann, Z Ardern BioCosmos 3 (1), 1-11		2023
Elucidating the functional roles of prokaryotic proteins using big data and artificial intelligence Z Ardern, S Chakraborty, F Lenk, AK Kaster FEMS Microbiology Reviews 47 (1), fuad003		2023
THE CONTENTIOUS COMPATIBILITY OF EVOLUTION AND DESIGN: INTRODUCTION TO THE BOOK SYMPOSIUM: with Zachary Ardern,“The Contentious Compatibility of Evolution and Design … Z Ardern Zygon® 57 (4), 1019-1023		2022
Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection M Kreitmeier, Z Ardern, M Abele, C Ludwig, S Scherer, K Neuhaus Iscience 25 (2)		2022
Small proteins: overcoming size restrictions Z Ardern Nature Reviews Microbiology 20 (2), 65-65		2022
Biological factors in the synthetic construction of overlapping genes S Wichmann, S Scherer, Z Ardern BMC genomics 22, 1-17		2021
Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution I Jungreis, CW Nelson, Z Ardern, Y Finkel, NJ Krogan, K Sato, J Ziebuhr, ... Virology 558, 145-151		2021
SARS-CoV-2: don't ignore non-canonical genes Z Ardern, X Wei, WC Nelson		2021
Evidence for Numerous Embedded Antisense Overlapping Genes in Diverse E. coli Strains B Zehentner, Z Ardern, M Kreitmeier, S Scherer, K Neuhaus bioRxiv, 2020.11. 18.388249		2020
Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic CW Nelson, Z Ardern, TL Goldberg, C Meng, CH Kuo, C Ludwig, ... Elife 9, e59633		2020
Are antisense proteins in prokaryotes functional? Z Ardern, K Neuhaus, S Scherer Frontiers in molecular biosciences 7, 187		2020
OLGenie: estimating natural selection to predict functional overlapping genes CW Nelson, Z Ardern, X Wei Molecular Biology and Evolution 37 (8), 2440-2449		2020
Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data A Glaub, C Huptas, K Neuhaus, Z Ardern Journal of Biological Chemistry 295 (27), 8999-9011		2020
A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC) B Zehentner, Z Ardern, M Kreitmeier, S Scherer, K Neuhaus Frontiers in microbiology 11, 377		2020
Optimality in the standard genetic code is robust with respect to comparison code sets S Wichmann, Z Ardern Biosystems 185, 104023		2019
The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase S Vanderhaeghen, B Zehentner, S Scherer, K Neuhaus, Z Ardern Scientific reports 8 (1), 17875		2018
Dysfunction, disease, and the limits of selection Z Ardern Biological Theory 13 (1), 4-9		2018
Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome SM Hücker, Z Ardern, T Goldberg, A Schafferhans, M Bernhofer, ... PloS one 12 (9), e0184119		2017

Teaching and Supervisions

Teaching:

2024/2025:

Foundations of phylogenetic inference - Trainer

2023/2024:

Working with Bacterial Genomes - Training Lead, Trainer

Biography

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Publications

Teaching and Supervisions

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Contact: bioinfotraining@bio.cam.ac.uk

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