Publications

Some outputs from Australian BioCommons projects, events and presentations, including organisational documentation, project reports and research infrastructure roadmaps are self published and can be found in the Australian BioCommons document repository.

For metadata and training materials associated with our training events, please visit Australian BioCommons - Training Materials.

Peer reviewed publications from BioCommons team members:

  1. Al Bkhetan Z, Wang S. mgikit: demultiplexing toolkit for MGI fastq files. Bioinformatics. 2024 Sep;40(9):btae554. https://doi.org/10.1093/bioinformatics/btae554

  2. Goonasekera, N, Mahmoud, A, Suderman, K, Afgan, E. Galaxy Helm chart: a standardized method for deploying production Galaxy servers, Bioinformatics, 2024. btae486, https://doi.org/10.1093/bioinformatics/btae486

  3. Gareth Price (corresponding author) and the Galaxy community (including Australian contributors Olivier Allart, Madeline Bassetti, Catherine J Bromhead, Melissa L Burke, Patrick K Capon, Nuwan A Goonasekera, Ove Johan Ragnar Gustafsson, Christina Hall, Thomas W Harrop, Cameron J Hyde, Ross Lazarus, Justin Lee, Igor Makunin, Winnie Mok, Tiffanie M Nelson, Anna E Syme, Wai Cheng (Mike) Thang and Uwe Winter. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update, Nucleic Acids Research, 2024 52(W1):W83-94 https://doi.org/10.1093/nar/gkae410

  4. Brennan IG, Singhal S, Al Bkhetan Z. pipesnake: Generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci. Bioinformatics, 2024 40(5):btae195, https://doi.org/10.1093/bioinformatics/btae195

  5. Williams JJ, Tractenberg RE, Batut B, Becker EA, Brown AM, Burke ML, Busby B, Cooch NK, Dillman AA, Donovan SS, Doyle MA, van Gelder CWG, Hall CR, Hertweck KL, Jordan KL, Jungck JR, Latour AR, Lindvall JM, Lloret-Llinares M, McDowell GS, Morris R, Mourad T, Nisselle A, Ordóñez P, Paladin L, Palagi PM, Sukhai MA, Teal TK, Woodley L. An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond. PloS one. 2023 18(11):e0293879. https://doi.org/10.1371/journal.pone.0293879

  6. Mehta S, Bernt M, Chambers M, Fahrner M, Föll MC, Gruening B, Horro C, Johnson JE, Loux V, Rajczewski AT, Schilling O, Vandenbrouck Y, Gustafsson OJR, Thang WCM, Hyde C, Price G, Jagtap PD, Griffin TJ. A Galaxy of informatics resources for MS-based proteomics. Expert Rev Proteomics 2023 20(11): 251-266. https://doi.org/10.1080/14789450.2023.2265062

  7. Hiltemann S, Rasche H, Gladman S, Hotz HR, Larivière D, Blankenberg D, Jagtap PD, Wollmann T, Bretaudeau A, Goué N, Griffin TJ. Galaxy Training: A powerful framework for teaching! PLoS Comput Biol. 2023 19(1): e1010752.

  8. Hall CR, Griffin PC, Lonie AJ, Christiansen JH. Application of a bioinformatics training delivery method for reaching dispersed and distant trainees. PLoS Comput Biol. 2021 17(3): e1008715. https://doi.org/10.1371/journal.pcbi.1008715

  9. Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier W, Nekrutenko A, Taylor J, Weaver S. No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS Pathog 2020 16(8): e1008643. https://doi.org/10.1371/journal.ppat.1008643

Pre-prints from BioCommons team members:

  1. da Silva RF, Bard D, Chard K, de Witt S, Foster IT, Gibbs T, Goble C, Godoy W, Gustafsson J, Haus UU, Hudson S et al. Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows. arXiv preprint arXiv:2410.14943. 2024 Oct 19. https://doi.org/10.48550/arXiv.2410.03490

  2. Gilligan J, Inwood SN, Harrop TW, Keddell P, McPhail K, Sproston CJ, Williams DW, Petersen G, Hovius A, Kaspar J, Guhlin JG. Rapid and cost-effective production of high-quality insect genome sequences. bioRxiv. 2024:2024-10. https://doi.org/10.1101/2024.10.06.616902

  3. Gustafsson, O J R, Wilkinson, S R, Bacall, F, Pireddu, L, Soiland-Reyes, S, Leo, S, Owen, S, Juty, N, Fernández, J M, Grüning, B, Brown, T, Ménager, H, Capella-Gutierrez, S, Coppens, F, Goble, C. WorkflowHub: a registry for computational workflows. arXiv. October 99, 2024. https://doi.org/10.48550/arXiv.2410.06941

  4. Wilkinson, S R, Aloqalaa, M, Belhajjame, K, Crusoe, M R, de Paula Kinoshita, B, Gadelha, L, Garijo, D, Gustafsson, O J R, Juty, N, Kanwal, S, Khan, F Z, Köster, J, Peters-von Gehlen, K, Pouchard, L, Rannow, R K, Soiland-Reyes, S, Soranzo, N, Sufi, S, Sun, Z, Vilne, B, Wouters, M A, Yuen, D, Goble, C. Applying the FAIR Principles to Computational Workflows. arXiv. October 4, 2024. https://doi.org/10.48550/arXiv.2410.03490

  5. Simpson, L, Cantrill, D, Byrne, M, Allnutt, T, King, G, Lum, M, Al Bkhetan, Z, Andrew, R, Baker, W, Barrett, M, Batley, J, Berry, O, Binks, R, Bragg, J G, Broadhurst, L, Brown, G, Bruhl, J, Edwards, R, Ferguson, S, Forest, F, Gustafsson, J, Hammer, T A, Holmes, G, Jackson, C, James, E, Jones, A, Kersey, P, Leitch, I, Maurin, O, McLay, T G B, Murphy, D, Nargar, K, Nauheimer, L, Sauquet, H, Schmidt-Lebuhn, A N, Shepherd, K, Syme, A, Waycott, M, Wilson, T, Crayn, D M. The Genomics for Australian Plants (GAP) framework initiative–developing genomic resources for understanding the evolution and conservation of the Australian flora. July 8, 2024. https://doi.org/10.32942/X2RP70

  6. Batut B, Bernt M, Ansari MH, Kalaš M, Klemm P, Libouban R, Nasr E, Rioualen C, Thang WC, Zoabi R, Zierep P. How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources. BioHackrXiv. February 29, 2024 https://doi.org/10.37044/osf.io/s7tru

  7. Zierep P, Batut B, Kalaš M, Kayikcioglu T, Nasr E, Soranzo N, Thang WC, Wang J, Gustafsson OJR. How to increase the findability, visibility, and impact of Galaxy tools for your scientific community. BioHackrXiv. April 2, 2024. https://doi.org/10.37044/osf.io/qjbxc

  8. Lamothe L, Jensen JRB, Ienasescu H, Gustafsson OJR, Gaignard A, Repchevsky D, Svobodová R, et al. 2023. “An Evaluation of EDAM Coverage in the Tools Ecosystem and Prototype Integration of Galaxy and Workflowhub Systems.” BioHackrXiv. February 15, 2023. https://doi.org/10.37044/osf.io/79kje

Research publications citing the use of Australian BioCommons Services

A wide variety of research is enabled by Australian BioCommons services, and other project outputs.

2024

  1. Aguayo-Reyes A, Morales-León F, Quezada-Aguiluz M, Quezada M, Mella S, Riedel G, Herrera-Chávez N, Espine Y, González-Rocha G, Opazo-Capurro A. Community-acquired methicillin-resistant Staphylococcus aureus invasive infections: a case series from Central-South Chile. Frontiers in Medicine. 2024 May 15;11:1365756.

  2. Alexander AJ, Parry RH, Ratinier M, Arnaud F, Kohl A. The RNA interference response to alphanodavirus replication in Phlebotomus papatasi sand fly cells. Insect Molecular Biology. 2024 Jun 7.

  3. AlSharabati MR. Association of GLP-1R Gene Polymorphisms with the risk of Dyslipidemia in Palestinian Patients with Type 2 Diabetes Mellitus (Doctoral dissertation, Al-Quds University).

  4. Ang DA, Carter JM, Deka K, Tan JH, Zhou J, Chen Q, Chng WJ, Harmston N, Li Y. Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma. Nature Communications. 2024 Mar 21;15(1):2513.

  5. Arthur E, Jo YK. Draft genome sequence of Neofusicoccum caryigenum associated with pecan leaf dieback. Microbiology Resource Announcements. 2024 Mar 14:e00944-23.

  6. Bassicheto MC, Barbosa RS, Neves KD, dos Santos Monteiro C, Uemi M, Pascon RC, da Silva GF, Koolen HH, de Medeiros LS. Integrated workflows using metabolomics, genome mining, and biological evaluation reveal oxepine‑sulfur-containing anti-cryptococcal diketopiperazine produced by the endophyte Penicillium setosum. Fitoterapia. 2024 Nov 17:106301.

  7. Boren LS, Grosso RA, Hugenberg-Cox AN, Hill JT, Albert CM, Tuohy JM. Complete genome sequence of Deinococcus sonorensis type strain KR-87: a rare biofilm-producing representative of the genus Deinococcus. Microbiology Resource Announcements. 2024 Sep 16:e00732-24.

  8. Bell MG, Parry RH, Lee TS, Habarugira G, McMahon IE, Thompson MA, Modhiran N, Watterson D, Batovska J, Lynch SE, Hall RA. Synthetic recovery of Yada Yada virus expands insect-specific alphavirus knowledge and facilitates production of chimeric viruses. npj Viruses. 2024 Sep 30;2(1):45.

  9. Brandon A. A TRANSCRIPTOMIC ATLAS OF HUMAN CHOROIDAL STROMAL CELLS. Investigative Ophthalmology & Visual Science. 2024 Jun 17;65(7):4954

  10. Carey-Fung O, Beasley JT, Broad RC, Hellens RP, Johnson AA. Discovery of a conserved translationally repressive upstream open reading frame within the iron-deficiency response regulator IDEF2. BMC Plant Biology. 2024 Sep 30;24(1):891.

  11. Carney M, Pelaia TM, Chew T, Teoh S, Phu A, Kim K, Wang Y, Iredell J, Zerbib Y, McLean A, Schughart K. Host transcriptomics and machine learning for secondary bacterial infections in patients with COVID-19: a prospective, observational cohort study. The Lancet Microbe. 2024 Mar 1;5(3):e272-81.

  12. Carpenter L, Hubbard S, Basinski NS, Rowland S. Science students develop multiple employability literacies from large, early-year courses without employability modules. Journal of Teaching and Learning for Graduate Employability. 2024 Jan 22;15(1):66-90.

  13. Carrión Delgado LS. Determinación del oncobioma pulmonar a partir de datos producidos por NGS. https://repositorio.uisek.edu.ec/handle/123456789/5256 (Doctoral disseration, Universidad Internacional SEK).

  14. Chau D, Blackall PJ, Turni C, Omaleki L. Complete genome sequence of a Pasteurella multocida isolate from a pig in Australia. Microbiology Resource Announcements. 2024 Jul 30:e00241-24.

  15. Chen Y, Dougan KE, Nguyen Q, Bhattacharya D, Chan CX. Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates. NAR Genomics and Bioinformatics. 2024 Mar 1;6(1):lqae016.

  16. Chidambara Thanu V, Jabeen A, Ranganathan S. iBio-GATS—A Semi-Automated Workflow for Structural Modelling of Insect Odorant Receptors. International Journal of Molecular Sciences. 2024 Mar 6;25(5):3055.

  17. Chidambara Thanu V. A semi-automated workflow for structural modelling of insect odorant receptors (Doctoral dissertation, Macquarie University).

  18. Colgan DJ. The Families of Non-LTR Transposable Elements within Neritimorpha and Other Gastropoda. Genes. 2024 Jun 14;15(6):783.

  19. Conradie T, Caparros-Martin JA, Egan S, Kicic A, Koks S, Stick SM, Agudelo-Romero P. Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories. Viruses. 2024 Jun 13;16(6):953.

  20. Costa LV, Ramos JN, Albuquerque LD, Miranda RV, Valadão TB, Veras JF, Vieira EM, Forsythe S, Brandão ML, Vieira VV. Bacillus lumedeiriae sp. nov., a Gram-Positive, Spore-Forming Rod Isolated from a Pharmaceutical Facility Production Environment and Added to the MALDI Biotyper® Database. Microorganisms. 2024 Dec 5;12(12):2507.

  21. Crates R, von Takach B, Young CM, Stojanovic D, Neaves LE, Murphy L, Gautschi D, Hogg CJ, Heinsohn R, Bell P, Farquharson KA. Genomic insights into the critically endangered King Island scrubtit. Journal of Heredity. 2024 Sep;115(5):552-64.

  22. Dasi EA, Ergas SJ, Talla E, Cunningham JA. Biological Nutrient Removal in Sphalerite-and-Oyster-Shell-Packed Sequencing Batch Biofilm Reactors Operated with Varying Wastewater Conditions. SSRN, 2024. https://dx.doi.org/10.2139/ssrn.5030948

  23. Degradi L, Tava V, Esposto MC, Prigitano A, Bulgari D, Kunova A, Saracchi M, Cortesi P, Pasquali M. Genomic Insights into Fusarium verticillioides Diversity: The Genome of Two Clinical Isolates and Their Demethylase Inhibitor Fungicides Susceptibility. Pathogens. 2024 Dec 3;13(12):1062.

  24. Diepstraten ST, Yuan Y, La Marca JE, Young S, Chang C, Whelan L, Ross AM, Fischer KC, Pomilio G, Morris R, Georgiou A. Putting the STING back into BH3-mimetic drugs for TP53-mutant blood cancers. Cancer Cell. 2024 Apr 23.

  25. dos Santos Castro G, Fernandes Sousa T, Jarline Santos da Silva I, Sena Raposo D, Carlos Ipuchima da Silva J, Peñaloza E, Garrett R, Eduardo Beleza Yamagishi M, Ferreira da Silva G, Henrique Ferreira Koolen H. Amazonins: New Peptaibol Sequences from an Endophytic Strain of Trichoderma amazonicum. Chemistry & Biodiversity. 2024:e202400611.

  26. Dyall-Smith M, Pfeiffer F. Global distribution and diversity of haloarchaeal pL6-family plasmids. Genes. 2024 Aug 26;15(9):1123.

  27. Enriquez MM, Untiveros DP, Tengco MT, Sanchez LR, Cao EP. De Novo Genome Assembly and Sequence Analysis of Chlorogloeopsis sp. ULAP01 Isolated from a Copper Mine Tailing Environment. Philippine Journal of Science. 2024 Oct;153(5):1911-21.

  28. Evans S, Lu Z, McDonnell L, Anderson W, Peralta F, Watkins T, Ahmed H, Luna-Flores CH, Loan TD, Navone L, Trau M. The integration of tandem gene repeats via a bacterial type-II toxin-antitoxin-mediated gene amplification (ToxAmp) system and stability visualisation in Saccharomyces cerevisiae. bioRxiv. 2024:2024-01.

  29. Ewart KM, Ho S YW, Chowdhury A-A, Jaya FR, Kinjo Y, Bennett J, Bourguignon T, Rose HA, Lo N. Pervasive relaxed selection in termite genomes. Proc. R. Soc. B. 2024:291;20232439

  30. Fadhullah H, Purwoko D, Zulaeha S, Hanifah NF, Hartuti ED, Rahmadara G, Safarrida A, Reninta R, Evawati E, Roza I, Tajuddin T. Identification of Gene Candidates in Diterpenoid Biosynthesis of Curcuma longa: An mRNA Sequencing Approach: Identification of Gene Candidates in Diterpenoid. Journal of Tropical Life Science. 2024 Sep 19;14(3):509-36.

  31. Ferreira LY, Santos JP, do Nascimento Souza DG, Orellana LC, de Santana SF, Sousa AG, Fonseca PL, Silva AG, Santos VC, de Faria IJ, Olmo RP. Spiroplasma shows a Wolbachia-like effect in hampering virus replication in spider mite. Research Square. https://doi.org/10.21203/rs.3.rs-4868315/v1

  32. Ferreira LY, de Sousa AG, Silva JL, Santos JP, do Nascimento Souza DG, Orellana LC, de Santana SF, de Vasconcelos LB, Oliveira AR, Aguiar ER. Characterization of the Virome Associated with the Ubiquitous Two-Spotted Spider Mite, Tetranychus urticae. Viruses. 2024 Sep 27;16(10):1532.

  33. Filardo F, Nurulita S, Jones L, Gambley C, Bond S, Sharman M, Campbell P. Genomic variation in pepper vein yellows viruses in Australia, including a new putative variant, PeVYV-10. Archives of Virology. 2024 Jan;169(1):18.

  34. Francis EK. Innovative approaches for gastrointestinal nematode identification and resistance surveillance: Transitioning molecular diagnostics from the confines of research to the expanse of the field (Doctoral dissertation, The University of Sydney).

  35. Gardiner DM, Smith LJ, Rusu A, Aitken EA. The genomes of two Australian isolates of Verticillium dahliae recovered from cotton fields. Australasian Plant Pathology. 2024 Aug 29:1-7.

  36. Gilding EK, Jackson MA, Nguyen LT, Hamilton BR, Farquharson KA, Ho WL, Yap K, Hogg CJ, Belov K, Craik DJ. Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides. Nature Communications. 2024 Aug 3;15(1):6565.

  37. Green R, Qu X, Liu J, Yu T. BTR: a bioinformatics tool recommendation system. Bioinformatics. 2024 Apr 25:btae275.

  38. Gretgrix L. The Hidden Population Structure of Australian Terrestrial Invertebrates in a Fire Prone Landscape (Doctoral dissertation, La Trobe).

  39. Gu K, Mok L, Wakefield MJ, Chong MM. Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops. Scientific Reports. 2024 Mar 20;14(1):6713.

  40. Guevara Bahamonde MT. Caracterización genómica de resistencia antimicrobiana mediante secuenciación del genoma completo de Enterobacterias procedentes del biobanco del año 2023 del Hospital General Docente de Calderón, Quito-Ecuador. https://repositorio.uisek.edu.ec/handle/123456789/5382 (Doctoral dissertation, Universidad Internacional SEK)

  41. Guimarães KH. Análise de bioinformática do gênero varibaculum análise genômica, filogenética e de genes de resistência, patogenicidade e ocorrência concomitante a carcinogênese. http://bdta.ufra.edu.br/jspui/handle/123456789/3561 (Universidade Federal Rural da Amazônia).

  42. Hall MB, Coin LJ. Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data. GigaScience. 2024;13:giae010.

  43. Hall K, Reid CE, Tan QZ, Taylor RS, Bissett A, Ruff N, Nowak BF, Bowman JP. Active colonisers of the gastrointestinal tract of Atlantic salmon farmed in a warm water region. Research Square. https://doi.org/10.21203/rs.3.rs-4361310/v1

  44. Hall K, Reid CE, Hamlett J, Kaur D, Tan QZ, Taylor RS, Bissett A, Nowak B, Bowman JP. Characterization of bacteria colonizing the mucosal layer of the gastrointestinal tract of Atlantic salmon farmed in a warm water region. bioRxiv. 2024:2024-11.

  45. Hancock DG, Agudelo-Romero P, Kicic-Starcevich E, Lim J, Iosifidis T, Karpievitch YV, Zhang G, Martino DJ, Kicic A, Stick SM. Conservation of gene expression patterns between the amniotic epithelium at birth and a newborn's nasal epithelium. bioRxiv. 2024:2024-08. https://doi.org/10.1101/2024.08.22.609087

  46. Harding E. Expanding the global virome: utilising bioinformatics to discover new exogenous and endogenous viruses in vertebrates (Doctoral dissertation, UNSW Sydney).

  47. Harding EF, Mercer LK, Yan GJ, Waters PD, White PA. Invasion and amplification of endogenous retroviruses in Dasyuridae marsupial genomes. Molecular Biology and Evolution. 2024 Aug;41(8):msae160.

  48. Hendrickson EN. Disease-Vector Genomics: Developing Blackfly Genomic Resources for Informing Vector Biology and Transmission Dynamics (Doctoral dissertation, La Trobe).

  49. Hogg CJ, Farquharson KA, Brandies P, Silver LW, Ottewell K, McLennan EA, Richmond S, Belov K. The future is here: an easy‐to‐use toolkit for integrating genetics into conservation management. Animal Conservation. 2024 Jul.

  50. Huang W, Yang S, Wätjen AP, Gumulya Y, Fernández-Pacheco P, Marcellin E, Prakash S, Bang-Berthelsen CH, Turner MS. Isolation of an exopolysaccharide-producing Weissella confusa strain from lettuce and exploring its application as a texture modifying adjunct culture in a soy milk alternative. International Journal of Food Microbiology. 2024 Nov 22:110992.

  51. Huang Y, Dziegielewska KM, Habgood MD, Qiu F, Leandro AC, Callaghan PD, Curran JE, VandeBerg JL, Saunders NR. ABC Efflux Transporters and Solute Carriers in the Early Developing Brain of a Marsupial Monodelphis domestica (South American Gray Short‐Tailed Opossum). Journal of Comparative Neurology. 2024 Jul;532(7):e25655.

  52. Islam MS. Catechol-Escherichia coli UM146 interaction revealed through multi-omics. PhD Thesis. https://doi.org/10.7939/r3-shxs-h385

  53. Jansen van Vuren P, Parry RH, Pawęska JT. Detection of Dengue Virus 1 and Mammalian Orthoreovirus 3, with Novel Reassortments, in a South African Family Returning from Thailand, 2017. Viruses. 2024 Aug 9;16(8):1274.

  54. Junprung W, Nanakorn Z, Norouzitallab P, Supungul P, Vanrompay D, Bossier P, Tassanakajon A. Transcriptomic analysis of thermotolerant Artemia franciscana populations shows that thermal adaptation affects expression and regulation of metabolism-, stress-, and immune-related genes. Research Square. https://www.researchsquare.com/article/rs-4284321/v1

  55. Junprung W, Nanakorn Z, Norouzitallab P, Supungul P, Vanrompay D, Bossier P, Tassanakajon A. Thermal adaptation affects expression and regulation of metabolism-, stress-, and immune-related genes in Artemia franciscana populations. Aquaculture Reports. 2024 Dec 1;39:102511.

  56. Karanu SW, Ajene IJ, Lelmen EK, Ong’onge MA, Akutse KS, Khamis FM. Biochemistry and transcriptomic analyses of Phthorimaea absoluta (Lepidoptera: Gelechiidae) response to insecticides. Scientific Reports. 2024 Apr 4;14(1):7931.

  57. Karim T, Almatarneh MH, Rahman S, Alodhayb AN, Albrithen H, Hossain MM, Kawsar SM, Poirier RA, Uddin KM. In Silico Prediction of Antibacterial Activity of Quinolone Derivatives. ChemistrySelect. 2024 Sep;9(36):e202402780.

  58. Khosrotehrani K, Hashemi G, Li H, Tan SX, Zhou C, Dight J, Li KC, Nguyen Q, Roy E. SOX9 reactivation in cancer vessels shapes the tumor micro-environment through hypoxia and immune depletion promoting tumor growth and metastasis. Research Square. https://doi.org/10.21203/rs.3.rs-5457583/v1

  59. Kifle BA, Sime AM, Gemeda MT, Woldesemayat AA. Shotgun metagenomic insights into secondary metabolite biosynthetic gene clusters reveal taxonomic and functional profiles of microbiomes in natural farmland soil. Scientific Reports. 2024 Jul 2;14(1):15096.

  60. Labiba A, Al Abbad SS, Rahman S, Alodhayb A, Poirier RA, Uddin KM. Investigating Baxdrostat and Its Derivatives as Aldosterone Synthase Inhibitors for Resistant Hypertension: An In Silico Approach. ChemistrySelect. 2024 Feb 19;9(7):e202304929.

  61. Leech SM, Borg DJ, Rae KM, Kumar S, Clifton VL, Dekker Nitert M. Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics. Microbial Genomics. 2024 Jul 12;10(7):001269.

  62. Liao H, Lu D, Reisinger SN, Kleeman EA, van de Garde N, Gubert C, Hannan AJ. Mimicking bacterial infection in male mice changes sperm small RNA profiles and multigenerationally alters offspring behavior and physiology. Brain, Behavior, and Immunity. 2024 Apr 16.

  63. Li D, Donnelley M, Parsons D, Habgood MD, Schneider‐Futschik EK. Extent of foetal exposure to maternal elexacaftor/tezacaftor/ivacaftor during pregnancy. British Journal of Pharmacology. 2024 May 21.

  64. Lima AV. Novas variantes de KPC em isolados do Complexo Klebsiella pneumoniae resistentes à ceftazidima-avibactam. https://doi.org/10.11606/T.9.2024.tde-11032024-153612 (Doctoral dissertation, Universidade de São Paulo).

  65. Maclachlan KH, Gitareja K, Kang J, Cuddihy A, Cao Y, Hein N, Cullinane C, Ang CS, Brajanovski N, Pearson RB, Khot A. Targeting the ribosome to treat multiple myeloma. Molecular Therapy Oncology. 2024 Feb 7.

  66. Magnan C, Morsli M, Salipante F, Thiry B, Attar JE, Maio MD, Safaria M, Tran TA, Dunyach-Remy C, Ory J, Richaud-Morel B. Emergence of multidrug-resistant Staphylococcus haemolyticus in Neonatal Intensive Care Unit in Southern France, a Genomic Study. Emerging Microbes & Infections. 2024 May 8(just-accepted):2353291.

  67. Mansueto L, Kretzschmar T, Mauleon R, King GJ. Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research. bioRxiv. 2024:2024-10.

  68. Mansueto L, McNally KL, Kretzschmar T, Mauleon R. CannSeek? Yes we Can! An open-source single nucleotide polymorphism database and analysis portal for Cannabis sativa. GigaByte. 2024 Oct 8;2024:gigabyte135.

  69. Mansueto L, Tandayu E, Mieog J, Garcia-de Heer L, Das R, Burn A, Mauleon R, Kretzschmar T. HASCH-A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications. BMC genomics. 2024 Aug 29;25(1):818.

  70. Mansueto L, Kretzschmar T, Mauleon R, King GJ. Building a community-driven bioinformatics platform to facilitate Cannabis sativa multi-omics research. GigaByte. 2024 Oct 18;2024:gigabyte137.

  71. McDonald JB, Wade B, Andrews DM, Van TT, Moore RJ. Development of tools for the genetic manipulation of Campylobacter and their application to the N-glycosylation system of Campylobacter hepaticus, an emerging pathogen of poultry. mBio. 2024 Jul 29:e01101-24.

  72. Merizalde Reisancho AC. Predicción in silico de las variantes genéticas y su influencia sobre la patogénesis de la enfermedad de alzheimer (EA) https://repositorio.uta.edu.ec/jspui/handle/123456789/42321 (Bachelor's thesis, Universidad Técnica de Ambato. Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología. Carrera de Biotecnología).

  73. Mitic I, Michie KA, Jacques DA. Assessing the Validity of Leucine Zipper Constructs Predicted in AlphaFold2. bioRxiv. 2024:2024-10.

  74. Mohit E. Investigating streptomyces clavuligerus linear replicons for improved clavulanic acid production. (Doctoral thesis, University of Strathclyde, Glasgow). https://pureportal.strath.ac.uk/en/studentTheses/investigating-streptomyces-clavuligerus-linear-replicons-for-impr

  75. Molina Valencia ES. Anotación genómica de genes expresados en la biosíntesis de compuestos fenólicos en pitahaya (Hylocereus spp.) expuesta a condiciones de estrés (Bachelor's thesis, Universidad Técnica de Ambato). https://repositorio.uta.edu.ec/jspui/handle/123456789/42325

  76. Morin M, Jönsson M, Wang CK, Craik DJ, Degnan SM, Degnan BM. Seasonal tissue-specific gene expression in wild crown-of-thorns starfish reveals reproductive and stress-related transcriptional systems. Plos Biology. 2024 May 14;22(5):e3002620.

  77. Mu B. Bioprospecting, and Characterisation of plastic and plasticiser degrading enzymes from Great Australian Artesian Basin thermophiles for biorecycling and bioremediation (Doctoral dissertation, Queensland University of Technology). https://doi.org/10.5204/thesis.eprints.252544

  78. Nasr E, Henger A, Gruning B, Zierep P, Batut B. PathoGFAIR: a collection of FAIR and adaptable (meta) genomics workflows for (foodborne) pathogens detection and tracking. bioRxiv. 2024:2024-06. https://doi.org/10.1101/2024.06.26.600753

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  80. Nguyen DH, Tran QH, Le LT, Nguyen HH, Tran HT, Do TP, Ho AN, Tran QH, Thu HT, Bui VN, Chu HH. Genomic characterization and identification of candidate genes for putative podophyllotoxin biosynthesis pathway in Penicillium herquei HGN12. 1C. Microbial Biotechnology. 2024 Sep;17(9):e70007.

  81. Oberin R, Petautschnig S, Jarred EG, Qu Z, Tsai T, Youngson NA, Pulsoni G, Truong TT, Fernando D, Bildsoe H, Blücher RO. Fetal growth delay caused by loss of non-canonical imprinting is resolved late in pregnancy and culminates in offspring overgrowth. Elife. 2024 May 30;13:e81875.

  82. Olasz B, Smithers L, Evans GL, Anandan A, Murcha MW, Vrielink A. Structural analysis of the SAM domain of the Arabidopsis mitochondrial tRNA import receptor. Journal of Biological Chemistry. 2024 May 1;300(5).

  83. Opazo-Capurro A, Aguilar-Vera OA, González-Muñoz P, Amsteins-Romero L, Quiroga M, Encina A, Herrera-Chávez N, Quezada-Aguiluz M, Aguayo-Reyes A, Morales-León F, Illesca V. Genomic and phylogenomic characterization of carbapenem-resistant Pseudomonas aeruginosa ‘high-risk’clone O4/ExoS+/ST654 circulating in Chilean hospitals. Journal of Global Antimicrobial Resistance. 2024 Jun 5.

  84. Panichnantakul P, Aguilar LC, Daynard E, Guest M, Peters C, Vogel J, Oeffinger M. Protein UFMylation regulates early events during ribosomal DNA-damage response. Cell Reports. 2024 Sep 24;43(9).

  85. Paranthaman C, Blessy JJ, Asiffa JN, Jaswanthi D. Identification of Differentially Expressed Genes and Drug Targets in Prostate Cancer Using Next-Generation Sequencing. Research Square, 2024. https://doi.org/10.21203/rs.3.rs-4988338/v1

  86. Petrovskiy DV, Nikolsky KS, Kulikova LI, Rudnev VR, Butkova TV, Malsagova KA, Kopylov AT, Kaysheva AL. PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models. Scientific Reports. 2024 Jul 1;14(1):15000.

  87. Phu DH, Wongtawan T, Wintachai P, Nhung NT, Yen NT, Carrique-Mas J, Turni C, Omaleki L, Blackall PJ, Thomrongsuwannakij T. Molecular characterization of Campylobacter spp. isolates obtained from commercial broilers and native chickens in Southern Thailand using whole genome sequencing. Poultry Science. 2024 Jan 20:103485.

  88. Pires GP, Fioresi VS, Canal D, Canal DC, Fernandes M, Brustolini OJ, de Avelar Carpinetti P, Ferreira A, da Silva Ferreira MF. Effects of trimer repeats on Psidium guajava L. gene expression and prospection of functional microsatellite markers. Scientific Reports. 2024 Apr 29;14(1):9811.

  89. Powell D, Jackson N, Kaur P, Dudchenko O, Aiden EL, Georges A, Frère CH. The genome of the Australian water dragon (Intellagama lesueurii), an agamid model for urban adaptation. Journal of Heredity. 2024 Oct 4:esae054.

  90. Puente-Lelievre C, Ridone P, Douglas J, Amritkar K, Kacar B, Baker MA, Matzke NJ. Molecular and structural innovations of the stator motor complex at the dawn of flagellar motility. bioRxiv. 2024:2024-07. https://doi.org/10.1101/2024.07.22.604496

  91. Reddy TS, Sidharthan VK. Three-fold expansion of the genetic diversity of blunerviruses through plant (meta) transcriptome data-mining. Virology. 2024 Nov 1;599:110210.

  92. Ridone P, Baker MA. Hybrid Exb/Mot stators require substitutions distant from the chimeric pore to power flagellar rotation. Journal of Bacteriology. 2024 Sep 16:e00140-24.

  93. Saleh LK. The Role of Angiotensin-Converting Enzyme 1 and Angiotensin-Converting Enzyme 2 Genetic Polymorphism in Severe Acute Respiratory Syndrome Coronavirus-2 in Palestinian Population (Doctoral dissertation, Al-Quds University).

  94. Samaraweera AV. Determining the real function of a putative cyanobacterial amino acid binding protein (Doctoral dissertation, Macquarie University).

  95. Sayers C, Pandey V, Balakrishnan A, Michie K, Svedberg D, Hunziker M, Pardo M, Choudhary J, Berntsson R, Billker O. Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote. Cell Systems. 2024 Nov 13.

  96. Sergienko NM, Trewin AJ, Kiriazis H, Raaijmakers AJ, Donner DG, Garside VC, Smith KA, Bell JR, Mellor KM, Delbridge LM, McMullen JR. Sex-specific regulation of the cardiac transcriptome by the protein phosphatase 2A regulatory subunit B55α. npj Metabolic Health and Disease. 2024 Nov 6;2(1):32.

  97. Sermkaew N, Atipairin A, Wanganuttara T, Krobthong S, Aonbangkhen C, Yingchutrakul Y, Uchiyama J, Songnaka N. A Novel Bacitracin-like Peptide from Mangrove-Isolated Bacillus paralicheniformis NNS4-3 against MRSA and Its Genomic Insights. Antibiotics. 2024 Jul 30;13(8):716.

  98. Sharma P, Masouleh AK, Constantin L, Topp B, Furtado A, Henry RJ. Genome sequences to support conservation and breeding of Macadamia. Tropical Plants. 2024 Jan 1(tp-0024-0029):1-1.

  99. Sidharthan VK, Reddy V, Kiran G, Rajeswari V, Baranwal VK, Kumar MK, Kumar KS. Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae. Archives of Virology. 2024 Jul;169(7):150.

  100. Silver LW, Crates R, Stojanovic D, Young CM, Belov K, Farquharson KA, Heinsohn R, Hogg CJ. Genomic and transcriptomic resources for the brown thornbill (Acanthiza pusilla) to support the conservation of a critically endangered subspecies. F1000Research. 2024 Apr 23;13:337.

  101. Silver LW, Stojanovic D, Farquharson KA, Alexander L, Peel E, Belov K, Hogg CJ. A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot (Lathamus discolor). F1000Research. 2024 Apr 4;13:251.

  102. Silver LW, Farquharson KA, Peel E, Gilbert MT, Belov K, Morales HE, Hogg CJ. Temporal loss of genome-wide and immunogenetic diversity in a near-extinct parrot. bioRxiv. 2024:2024-11.

  103. Simão FA, Almeida MM, Rosa HS, Marques EA, Leão RS. Genetic determinants of antimicrobial resistance in polymyxin B resistant Pseudomonas aeruginosa isolated from airways of patients with cystic fibrosis. Brazilian Journal of Microbiology. 2024 Apr 15:1-1.

  104. Simpson L, Cantrill D, Byrne M, Allnutt T, King G, Lum M, Al Bkhetan Z, Andrew R, Baker W, Barrett M, Batley J. The Genomics for Australian Plants (GAP) framework initiative–developing genomic resources for understanding the evolution and conservation of the Australian flora.

  105. Soto KD, Alcalde-Rico M, Ugalde JA, Olivares-Pacheco J, Quiroz V, Brito B, Rivas LM, Munita JM, García PC, Wozniak A. Ceftazidime/avibactam resistance is associated with PER-3-producing ST309 lineage in Chilean clinical isolates of non-carbapenemase producing Pseudomonas aeruginosa. Frontiers in Cellular and Infection Microbiology. 2024 Jun 5;14:1410834.

  106. Sravani B, Sidharthan VK, Reddy V. Identification of nine putative novel members of plant-infecting alphaflexiviruses in public domain plant transcriptomes. VirusDisease. 2024 Oct 19:1-7.

  107. Staunton J, Ajuyah P, Harris A, Mayoh C, Wong M, Rumford M, Sullivan PJ, Ekert PG, Fuentes-Bolanos N, Cowley MJ, Lau LM. Novel paediatric case of a spinal high-grade astrocytoma with piloid features in a patient with Noonan Syndrome. npj Precision Oncology. 2024 Oct 19;8(1):236.

  108. Stupar M, Tan L, Kerr ED, De Voss CJ, Forde BM, Schulz BL, West NP. TcrXY is an acid-sensing two-component transcriptional regulator of Mycobacterium tuberculosis required for persistent infection. Nature Communications. 2024 Feb 22;15(1):1615.

  109. Tang S, Peel E, Belov K, Hogg CJ, Farquharson KA. Multi-omics resources for the Australian southern stuttering frog (Mixophyes australis) reveal assorted antimicrobial peptides. Scientific Reports. 2024 Feb 18;14(1):3991.

  110. Tea YK, Zhou Y, Ewart KM, Cheng G, Kawasaki K, DiBattista JD, Ho SYW, Lo N, Fan, S. The spotted parrotfish genome provides insights into the evolution of a coral reef dietary specialist (Teleostei: Labridae: Scarini: Cetoscarus ocellatus). Ecology and Evolution, 2024:14;e11148

  111. Tello Gallegos RP. Caracterización de la microbiota vaginal en pacientes VPH positivo mediante el análisis bioinformático de secuencias 16s ARN y su influencia en el riesgo, protección y persistencia del contagio por VPH. http://repositorio.uisek.edu.ec/handle/123456789/5259 (Doctoral dissertation, Universidad Internacional SEK)

  112. Tettamanti V, Marshall J, Cheney K, Cortesi F. Damsels in a hidden colour: development of ultraviolet sensitivity and colour patterns in damselfishes (Pomacentridae). bioRxiv. 2024:2024-08.

  113. Thai M, Bell TL, Kertesz MA. Mycovorax composti gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from button mushroom compost. International Journal of Systematic and Evolutionary Microbiology. 2024 Aug 27;74(8):006496.

  114. Tomasiak A, Piński A, Milewska-Hendel A, Andreu Godall I, Borowska-Żuchowska N, Morończyk J, Moreno-Romero J, Betekhtin A. H3K4me3 changes occur in cell wall genes during the development of Fagopyrum tataricum morphogenic and non-morphogenic calli. Frontiers in Plant Science. 2024 Sep 25;15:1465514.

  115. Tsai WA, Brosnan CA, Mitter N, Dietzgen RG. Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures. Pathogens. 2024 Aug 31;13(9):745.

  116. Umar M, Merlin TS, Puthiyedathu ST. Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov. FEMS Microbiology Letters. 2024 Sep 20:fnae074.

  117. van Vuren PJ, Parry RH, Paweska JT. Detection of Dengue Virus 1 and Mammalian Orthoreovirus 3, with Novel Reassortments, in a South African Family Returning from Thailand, 2017. Viruses 2024, 16(8), 1274

  118. Vargas-Maya NI, Maunakea AK, Ramírez-Montiel FB, Sultana R, Peres R, Cervantes QX, Nieto AL, Rangel-Serrano Á, Martínez-Álvarez JA, Páramo-Pérez I, Anaya-Velázquez F. Avirulent UG10 Entamoeba histolytica mutant derived from HM-1: IMSS strain shows limited genome variability and aberrant 5-methyl cytosine genomic distribution. Molecular and Biochemical Parasitology. 2024 Jul 11:111647.

  119. Villafuerte Guastay MC. Análisis de variantes genéticas en la Esclerosis Lateral Amiotrófica (ELA) y diseño de ARN guías (sgARN) (Bachelor's thesis, Universidad Técnica de Ambato). https://repositorio.uta.edu.ec/jspui/handle/123456789/42496

  120. Vincent D, Appels R. Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations. International Journal of Molecular Sciences. 2024 Aug 7;25(16):8614.

  121. Vincent D, Reddy P, Isenegger D. Integrated Proteomics and Metabolomics of Safflower Petal Wilting and Seed Development. Biomolecules. 2024 Mar 28;14(4):414.

  122. Von Wowern F, Makenga G, Thomsen SW, Thomsen LW, Hocke EF, Baraka V, Opot BH, Minja DT, Lusingu JP, Van-Geertruyden JP, Hansson H. Lack of selection of antimalarial drug resistance markers after intermittent preventive treatment of schoolchildren (IPTsc) against malaria in northeastern Tanzania. International Journal of Infectious Diseases. 2024 Sep 1;146:107102.

  123. Wang H, Wang X, Huang S, Yang S, Liao H, Wang X, Jin H, Wang J, Li X, Yan J, Yang Y. Complete genome sequence of “Candidatus Dehalogenimonas loeffleri” strain W, a highly salt-tolerant chlorinated alkane-dechlorinating bacterium isolated from estuarine sediments. Microbiology Resource Announcements. 2024 Nov 27:e00319-24.

  124. Wang LL, Cheng Q, Newton ND, Wolfinger MT, Morgan MS, Slonchak A, Khromykh AA, Cheng TY, Parry RH. Xinyang flavivirus, from Haemaphysalis flava ticks in Henan Province, China, defines a basal, likely tick-only Orthoflavivirus clade. Journal of General Virology. 2024 May 29;105(5):001991.

  125. Weber FAC. Transcriptómica comparativa durante el desarrollo de frutos de Opuntia albicarpa Scheinvar y Opuntia joconostle (Doctoral dissertation, Universidad Autónoma Chapingo).

  126. Wicaksono A, Buaboocha T. Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean. BMC genomics. 2024 Oct 23;25(1):992.

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2023

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  2. Alaux M, Dyer S, Sen TZ. Wheat Data Integration and FAIRification: IWGSC, GrainGenes, Ensembl and Other Data Repositories. InThe Wheat Genome 2023 Nov 14 (pp. 13-25). Cham: Springer International Publishing.

  3. Alam K, Roy B, Serebrenik A. Reusability Challenges of Scientific Workflows: A Case Study for Galaxy. arXiv preprint arXiv:2309.07291. 2023 Sep 13.

  4. Albert C, Hill J, Boren L, Scholz-Ng S, Fatema N, Grosso R, Soboslay E, Tuohy J. Complete Genome Sequence of Deinococcus aquaticus Type Strain PB314, a Non-Extremophile Representative of the Genus Deinococcus. Microbiology Resource Announcements. 2023 Jun 8:e00026-23.

  5. Al-Dossary O, Furtado A, KharabianMasouleh A, Alsubaie B, Al-Mssallem I, Henry RJ. Differentially Expressed Genes in Jojoba (Simmondsia chinensis) when Subjected to Water-Stress. Current Plant Biology. 2023 Dec 19:100311.

  6. Aleksandrova NA, Roche SG, Low YS, Landsberg MJ. Recent insights into mechanisms of cellular toxicity and cell recognition associated with the ABC family of pore-forming toxins. Biochemical Society Transactions. 2023 May 18:BST20221409.

  7. Alencar RM, Sepulveda CC, Martinez-Villegas L, Bahia AC, Santana RA, de Souza IB, D’Elia GM, Duarte AP, de Lacerda MV, Monteiro WM, Secundino NF. Unravelling the genome of the brackish water malaria vector Anopheles aquasalis. Scientific Reports. 2023 Nov 22;13(1):20472.

  8. Anusha BS, Bagchi P. Establishing Phylogeny, Functional Profile and Novel Drug for Nipah Virus Encephalitis. In Joint 3rd International Conference on Bioinformatics and Data Science (ICBDS 2022) 2023 Jun 5 (pp. 239-253). Atlantis Press.

  9. Bell PT, Baird T, Goddard J, Olagoke OS, Burke A, Subedi S, Davey TR, Anderson J, Sarovich DS, Price EP. Performance of next-generation molecular methods in the diagnosis of pleural space infections and their aetiology. medRxiv. 2023:2023-10.

  10. Bhardwaj M, Ram NR, Nikhil GN. Systematic metabolic pathway analysis of selective hydrolytic strains for anaerobic fermentation of food waste and identification of molecular markers during stress response. Materials Today: Proceedings. 2023 Jun 2.

  11. Black JG, van Rooyen AR, Heinze D, Gaffney R, Hoffmann AA, Schmidt TL, Weeks AR. Black JG, van Rooyen AR, Heinze D, Gaffney R, Hoffmann AA, Schmidt TL, Weeks AR. Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii). Molecular Ecology. 2023 Nov 28.

  12. Bosnar LM, Shindler AE, Wood J, Patch C, Franks AE. Attempts to limit sporulation in the probiotic strain Bacillus subtilis BG01-4TM through mutation accumulation and selection. Access Microbiology. 2023;5(5).

  13. Boutet-Dubois A, Magnan C, Lienard A, Pouget C, Bouchet F, Marchandin H, Larcher R, Lavigne JP, Pantel A. In Vivo-Acquired Resistance to Daptomycin during Methicillin-Resistant Staphylococcus aureus Bacteremia. Antibiotics. 2023 Nov 22;12(12):1647.

  14. Bowman JP. Genome-wide and constrained ordination-based analyses of EC code data support reclassification of the species of Massilia La Scola et al. 2000 into Telluria Bowman et al. 1993, Mokoshia gen. nov. and Zemynaea gen. nov. International Journal of Systematic and Evolutionary Microbiology. 2023 Aug 17;73(8):005991.

  15. Cafiero JH, Salvetti Casasco M, Lozano MJ, Lopez Garcia SL, Vacca C, Draghi WO, Lagares A, Del Papa MF. Genomic analysis of Sinorhizobium meliloti LPU63, an acid-tolerant and symbiotically efficient alfalfa-nodulating rhizobia. Frontiers in Agrononomy, 2023 July 27. Sec. Plant-Soil Interactions

  16. Caldas-Garcia GB, Santos VC, Fonseca PL, de Almeida JP, Costa MA, Aguiar ER. The Viromes of Six Ecosystem Service Provider Parasitoid Wasps. Viruses. 2023 Dec 16;15(12):2448.

  17. Castro GS, Sousa TF, da Silva GF, Pedroso RC, Menezes KS, Soares MA, Dias GM, Santos AO, Yamagishi ME, Faria JV, Januário AH. Characterization of Peptaibols Produced by a Marine Strain of the Fungus Trichoderma endophyticum via Mass Spectrometry, Genome Mining and Phylogeny-Based Prediction. Metabolites. 2023 Feb 3;13(2):221.

  18. Channale S, Thompson JP, Varshney RK, Thudi M, Zwart RS. Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance. Frontiers in plant science. 2023;14.

  19. Chen GY, Thorup NR, Miller AJ, Li YC, Ayres JS. Cooperation between physiological defenses and immune resistance produces asymptomatic carriage of a lethal bacterial pathogen. bioRxiv. 2023:2023-01.

  20. Chen SH, Bose U, Broadbent JA, Fegan N, Wilson R, Kocharunchitt C, Colgrave ML, Duffy LL, Bowman JP. Proteome analysis of Campylobacter jejuni poultry strain 2704 survival during 45 min exposure to peracetic acid. International Journal of Food Microbiology. 2023 Jan 16;385:110000.

  21. Chiang IK, Graus MS, Kirschnick N, Davidson T, Luu W, Harwood R, Jiang K, Li B, Wong YY, Moustaqil M, Lesieur E. The blood vasculature instructs lymphatic patterning in a SOX7‐dependent manner. The EMBO Journal. 2023 Mar 1;42(5):e109032.

  22. Choudhari S, Patil SK, Rathod S. Identification of hits as anti-obesity agents against human pancreatic lipase via docking, drug-likeness, in-silico ADME (T), pharmacophore, DFT, molecular dynamics, and MM/PB (GB) SA analysis. Journal of Biomolecular Structure and Dynamics. 2023 Sep 12:1-23.

  23. Clark K. Antibiotic resistance associated with captive kiwi (Apteryx spp.) microbiomes. University of Canterbury.

  24. Collet JM, Nidelet S, Fellous S. Genetic independence between traits separated by metamorphosis is widespread but varies with biological function. Proceedings of the Royal Society B. 2023 Nov 8;290(2010):20231784.

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  26. de Medeiros Paulino R. Granular and Biological Activated Carbon for the Management of Biogenic Taste and Odour Compounds in Drinking Water Treatment. UNSW Thesis. https://doi.org/10.26190/unsworks/25207

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  33. Farquharson KA, McLennan EA, Belov K, Hogg CJ. The genome sequence of the critically endangered Kroombit tinkerfrog (Taudactylus pleione). F1000Research. 2023 Jul 18;12:845.

  34. Filardo F, Waterhouse B, Jones L, Campbell P. Yambean mosaic virus and lettuce chlorosis virus in Australia. Australasian Plant Disease Notes. 2023 Dec;18(1):1-4.

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  39. Green R. Applying Deep Learning Techniques to Assist Bioinformatics Researchers in Analysis Pipeline Composition (Doctoral dissertation, University of Cincinnati).

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  41. Gunn BF, Murphy DJ, Walsh NG, Conran JG, Pires JC, Macfarlane TD, Crisp MD, Cook LG, Birch JL. Genomic data resolve phylogenetic relationships of Australian mat-rushes, Lomandra (Asparagaceae: Lomandroideae). Botanical Journal of the Linnean Society. 2023 Sep 23:boad034.

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  43. Hastings JF, Latham SL, Kamili A, Wheatley MS, Han JZ, Wong-Erasmus M, Phimmachanh M, Nobis M, Pantarelli C, Cadell AL, O’Donnell YE. Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma. Science Advances. 2023 Mar 3;9(9):eabp8314.

  44. Hazi A, Ebrahimie E, Levay EA, Mohammadi-Dehcheshmeh M, Zelko M, Govic A, Nasser H. Crosstalk between short-and long-term calorie restriction transcriptomic signatures with anxiety-like behavior, aging, and neurodegeneration: implications for drug repurposing. Frontiers in Behavioral Neuroscience. 2023;17.

  45. Hellens A, Kreisz P, Humphreys JL, Feil R, Lunn JE, Droge-Laser W, Beveridge CA, Fichtner F, Weiste C, Barbier FF. The transcription factor bZIP11 acts antagonistically with trehalose 6-phosphate to inhibit shoot branching. bioRxiv. 2023:2023-05.

  46. Hernández-Alomía F, Bastidas-Caldes C, Ballesteros I, Tenea GN, Molina CA, Castillejo P. Beta-Lactam Antibiotic Resistance Genes in the Microbiome of the Public Transport System of Quito, Ecuador. International Journal of Environmental Research and Public Health. 2023 Jan;20(3):1900.

  47. Hoffmann LB, McVicar EA, Harris RV, Collar-Fernández C, Clark MB, Hannan AJ, Pang TY. Increased paternal corticosterone exposure influences offspring behaviour and expression of urinary pheromones. BMC biology. 2023 Sep 5;21(1):186.

  48. Huang W, Dong A, Pham HT, Zhou C, Huo Z, Wätjen AP, Prakash S, Bang-Berthelsen CH, Turner MS. Evaluation of the fermentation potential of lactic acid bacteria isolated from herbs, fruits and vegetables as starter cultures in nut-based milk alternatives. Food Microbiology. 2023 Jun 1;112:104243.

  49. Huynh TB, Mai-Hoang TD, Bui-Nguyen TA, Ha TT, Phan MD, Tran-Van H. Characteristics and diversity of Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease in Vietnam. Aquaculture and Fisheries. 2023 Nov 25.

  50. Jabeen I, Mahamud SI, Islam S, Lamisa AB, Anjum A, Oishy SH, Shuvo SR. Genomic identification and characterization of prophages associated with Citrobacter freundii strains. Journal of Advanced BioTechnology and Experimental Therapeutics. 2023 Sep 6(3):648-658.

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  50. Stojilkovic B, Xiang H, Chen Y, Bauters L, Van de Put H, Steppe K, Liao J, de Almeida Engler J, Gheysen G. The nematode effector Mj-NEROSs interacts with ISP influencing plastid ROS production to suppress plant immunity. bioRxiv. 2022 Jan 1.

  51. Valadez-Moctezuma E, Samah S, Mascorro-Gallardo JO, Marbán-Mendoza N, Aranda-Osorio G, Flores-Girón E, Brito-Nájera G, Rodríguez de la O JL. The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia. Genetic Resources and Crop Evolution. 2022 Oct 11:1-20.

  52. Williams LJ, Tristram SG, Zosky GR. Geogenic Particles Induce Bronchial Susceptibility to NTHi.

  53. Yang Z, Feng Z, Li Z, Teasdale RD. Multifaceted Roles of Retromer in EGFR Trafficking and Signaling Activation. Cells. 2022 Oct 25;11(21):3358.

  54. Ying H, Hayward DC, Klimovich A, Bosch TC, Baldassarre L, Neeman T, Forêt S, Huttley G, Reitzel AM, Fraune S, Ball EE. The role of DNA methylation in genome defense in Cnidaria and other invertebrates. Molecular Biology and Evolution. 2022 Feb;39(2):msac018.

  55. Zavada NS. Genomic instability at a polypurine/polypyrimidine repeat sequence (Doctoral dissertation, Wright State University).

  56. Zhang S, Rautela J, Bediaga NG, Kolesnik TB, You Y, Nie J, Dagley LF, Bedo J, Wang H, Sun L, Sutherland R. CIS controls the functional polarization of GM-CSF-derived macrophages. Cellular & Molecular Immunology. 2022 Dec 5:1-5.

2021

  1. Backhaus A, Cytowski M, Elahi P, Beecroft S, De La Pierre M, Gayosso AE, Campbell L, Edwards L, Sivarajah Y. Pawsey Training Goes Remote: Experiences and Best Practices. Journal of Computational Science. 2021;12(2).

  2. Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host–Pathogen Interaction. Biology. 2021 Sep;10(9):840.

  3. Beier RC, Andrews K, Hume ME, Sohail MU, Harvey RB, Poole TL, Crippen TL, Anderson RC. Disinfectant and Antimicrobial Susceptibility Studies of Staphylococcus aureus Strains and ST398-MRSA and ST5-MRSA Strains from Swine Mandibular Lymph Node Tissue, Commercial Pork Sausage Meat and Swine Feces. Microorganisms. 2021 Nov;9(11):2401.

  4. Bisht K, McGirr C, Lee SY, Tseng HW, Fleming W, Alexander KA, Matsumoto T, Barbier V, Sims NA, Müller-Newen G, Winkler IG. Oncostatin M regulates hematopoietic stem cell (HSC) niches in the bone marrow to restrict HSC mobilization. Leukemia. 2021 Sep 13:1-5.

  5. Brandies PA, Hogg CJ. Ten simple rules for getting started with command-line bioinformatics. (2021) PLoS Comput Biol 17(2): e1008645. https://doi.org/10.1371/journal.pcbi.1008646

  6. Bryan ER, Barrero RA, Cheung E, Tickner JA, Trim LK, Richard D, McLaughlin EA, Beagley KW, Carey AJ. DNA damage contributes to transcriptional and immunological dysregulation of testicular cells during Chlamydia infection. American Journal of Reproductive Immunology. 2021 Feb 9:e13400.

  7. Cafiero JH, Martini MC, Lozano MJ, Vacca C, Lagares A, Tomatis PE, Del Papa MF. BioF is a novel B2 metallo‐β‐lactamase from Pseudomonas sp. isolated from an on‐farm biopurification system. Environmental Microbiology. 2021 Nov 1.

  8. Cherak Z, Loucif L, Ben Khedher M, Moussi A, Benbouza A, Baron SA, Rolain JM. Msphere. MCR-5-Producing Colistin-Resistant Cupriavidus gilardii Strain from Well Water in Batna, Algeria. 2021 Sep 1;6(5):e00575-21.

  9. Chiang IK, Luu W, Jiang K, Kirschnick N, Moustaqil M, Davidson T, Lesieur E, Skoczylas R, Kouskoff V, Kazenwadel J, Arriola-Martinez L. The blood vasculature instructs lymphatics patterning in a SOX7 dependent manner. bioRxiv. 2021 Jan 1.

  10. Chua TP, Bodiyabadu K, Machalek DA, Garland SM, Bradshaw CS, Plummer EL, Danielewski J, Vodstrcil LA, Doyle ML, Murray GL. Prevalence of Mycoplasma genitalium fluoroquinolone-resistance markers, and dual-class-resistance markers, in asymptomatic men who have sex with men. Journal of Medical Microbiology. 2021 Sep 30;70(9):001429.

  11. Colgan DJ. The potential for using shell proteins in gastropod systematics, assessed in patellogastropod limpets. Zoological Journal of the Linnean Society. 2021 Sep 24.

  12. Conrin M. Characterization of Caudovirales Isolated from Freshwater Samples against Pseudomonas fluorescens and Host Range Testing against Pseudomonas aeruginosa. Doctoral dissertation, University of Nebraska at Omaha.

  13. Dennis LP, Anderson K, Wylie M, Van In V, Nocillado J, Elizur A. NextGen molecular barcoding of larval grouper diet in an extensive green-water pond system. Aquaculture. 2021 Jan 30;531:735971.

  14. François CJ, Batinovic S, Petrovski S, Gendall AR. Draft Genome Sequence of Enterobacter asburiae NCR1, a Plant Growth-Promoting Rhizobacterium Isolated from a Cadmium-Contaminated Environment. Microbiology Resource Announcements. 2021 Sep 2;10(35):e00478-21.

  15. François CJ, Batinovic S, Petrovski S, Gendall AR. Draft Genome Sequence of Enterobacter mori Strain NSE2, Isolated from the Rhizosphere of a Sedum sp. Microbiology Resource Announcements. 2021 Aug 26;10(34):e00487-21.

  16. Gray JA, Chandry PS, Kaur M, Kocharunchitt C, Bowman JP, Fox EM. Characterisation of Listeria monocytogenes food-associated isolates to assess environmental fitness and virulence potential. International Journal of Food Microbiology. 2021 May 17:109247.

  17. Gutiérrez AV, Baron SA, Sardi FS, Saad J, Coltey B, Reynaud-Gaubert M, Drancourt M. Beyond phenotype: The genomic heterogeneity of co-infecting Mycobacterium abscessus smooth and rough colony variants in cystic fibrosis patients. Journal of Cystic Fibrosis. 2021 Feb 18.

  18. Harding EF, Russo AG, Yan GJ, Waters PD, White PA. Ancient viral integrations in marsupials: a potential antiviral defence. Virus Evolution. 2021;7(2):veab076.

  19. Huth L, Ash GJ, Idnurm A, Kiss L, Vaghefi N. The “bipartite” structure of the first genome of Ampelomyces quisqualis, a common hyperparasite and biocontrol agent of powdery mildews, may point to its evolutionary origin from plant pathogenic fungi. Genome Biology and Evolution. 2021 Aug;13(8):evab182.

  20. Kangale LJ, Zgheib R, Ghigo E, Raoult D, Fournier PE. Draft Genome Sequence of Herminiimonas contaminans Strain CCM 7991T, a Biopharmaceutical Contaminant. Microbiology Resource Announcements. 2021 Feb 18;10(7):e01432-20.

  21. Koehn LM, Huang Y, Habgood MD, Nie S, Chiou SY, Banati RB, Dziegielewska KM, Saunders NR. Efflux transporters in rat placenta and developing brain: transcriptomic and functional response to paracetamol. Scientific reports. 2021 Oct 6;11(1):1-6.

  22. Ku H, Kabwe M, Chan HT, Stanton C, Petrovski S, Batinovic S, Tucci J. Novel Drexlerviridae bacteriophage KMI8 with specific lytic activity against Klebsiella michiganensis and its biofilms. Plos One. 2021 Sep 7;16(9):e0257102.

  23. Laidoudi Y, Otranto D, Stolowy N, Amrane S, Santhakumari Manoj RR, Polette L, Watier-Grillot S, Mediannikov O, Davoust B, l'Ollivier C. Human and animal dirofilariasis in Southeast of France. Microorganisms. 2021 Jul;9(7):1544.

  24. Lau DC, McLeod S, Collaery S, Peou S, Tran AT, Liang M, Šlapeta J. Whole-genome reference of Dirofilaria immitis from Australia to determine single nucleotide polymorphisms associated with macrocyclic lactone resistance in the USA. Current Research in Parasitology and Vector-Borne Diseases. 2021 Jan 1;1:100007.

  25. Li A, Thwaite R, Kellie S, Barnes AC. Serum IgM heavy chain sub-isotypes and light chain variants revealed in giant grouper (Epinephelus lanceolatus) via protein A affinity purification, mass spectrometry and genome sequencing. Fish & Shellfish Immunology. 2021 Jun 1;113:42-50.

  26. Livingstone M, Caspe SG, Longbottom D. Complete Genome Sequence of Chlamydia abortus MRI-10/19, Isolated from a Sheep Vaccinated with the Commercial Live C. abortus 1B Vaccine Strain. Microbiology Resource Announcements. 2021 May 6;10(18):e00203-21.

  27. Maier, W., Bray, S., van den Beek, M. et al. Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nat Biotechnol 39, 1178–1179 (2021). https://doi.org/10.1038/s41587-021-01069-1

  28. McDougall F, Power M. Occurrence of Salmonella enterica in grey‐headed flying foxes from New South Wales. Australian Veterinary Journal. 2021 Sep 6.

  29. McDougall FK, Boardman WS, Power ML. Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins. Microbial Genomics. 2021 May 5;7(5):000571.

  30. Munro M. Increasing anthocyanin accumulation in plant stress. Doctoral dissertation, Queensland University of Technology.

  31. Naguleswaran A, Fernandes P, Bevkal S, Rehmann R, Nicholson P, Roditi I. Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host. bioRxiv. 2021 Jan 1.

  32. Niknafs S, Fortes MR, Cho S, Black JL, Roura E. Alanine-specific Appetite in Slow Growing Chickens is Associated with Impaired Glucose Transport and TCA Cycle. BMC Genomics Preprint: https://doi.org/10.21203/rs.3.rs-940072/v1

  33. Parry R, James ME, Asgari S. Uncovering the Worldwide Diversity and Evolution of the Virome of the Mosquitoes Aedes aegypti and Aedes albopictus. Microorganisms. 2021 Aug;9(8):1653.

  34. Parry R. Endosymbionts and viromes: interplays between Wolbachia pipientis and the virome of Aedes mosquitoes. PhD Thesis, School of Biological Sciences, The University of Queensland. https://doi.org/10.14264/abcdf38

  35. Peel E, Silver L, Brandies P, Hogg CJ, Belov K, A reference genome for the critically endangered woylie, Bettongia penicillata ogilbyi, Gigabyte, 2021 https://doi.org/10.46471/gigabyte.35

  36. Poli D. Diurnal and seasonal host-symbiont interactions in the coral reef demosponge Amphimedon queenslandica. PhD Thesis, Biological Sciences, The University of Queensland. https://doi.org/10.14264/717a53e

  37. Satgunaseelan L, Porazinski S, Strbenac D, Istadi A, Willet C, Chew T, Sadsad R, Palme CE, Lee JH, Boyer M, Yang JYH, Clark JR, Pajic M and Gupta R (2021) Oral Squamous Cell Carcinoma in Young Patients Show Higher Rates of EGFR Amplification: Implications for Novel Personalized Therapy. Front. Oncol. 11:750852. doi: 10.3389/fonc.2021.750852

  38. Smith CS, Lenz MF, Caldwell K, Oakey J. Identification of a canine coronavirus in Australian racing Greyhounds. Journal of Veterinary Diagnostic Investigation. 2021 Oct 26:10406387211054819.

  39. Tesan FC, Lorenzo R, Alleva K, Fox AR. AQPX-cluster aquaporins and aquaglyceroporins are asymmetrically distributed in trypanosomes. Communications biology. 2021 Aug 10;4(1):1-4.

  40. Voelker, J, Shepherd, M, Mauleon, R. A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species. Gigabyte, 1, 2021 https://doi.org/10.46471/gigabyte.28

  41. Vuong P, Lim DJ, Murphy DV, Wise MJ, Whiteley AS, Kaur P. Developing Bioprospecting Strategies for Bioplastics Through the Large-Scale Mining of Microbial Genomes. Frontiers in microbiology. 2021;12:1950.

  42. Wan C, Mahara S, Sun C, Doan A, Chua HK, Xu D, Bian J, Li Y, Zhu D, Sooraj D, Cierpicki T. Genome-scale CRISPR-Cas9 screen of Wnt/β-catenin signaling identifies therapeutic targets for colorectal cancer. Science Advances. 2021 May 1;7(21):eabf2567.

  43. Wickramasinghe NN, Ravensdale J, Coorey R, Dykes GA, Chandry PS. Transcriptional profiling of biofilms formed on chilled beef by psychrotrophic meat spoilage bacterium, Pseudomonas fragi 1793. Biofilm. 2021 Dec 1;3:100045.

  44. Yang Y, Huo L, Li X, Yan J, Löffler FE. Complete Genome Sequence of Sulfurospirillum sp. Strain ACSDCE, an Anaerobic Bacterium That Respires Tetrachloroethene under Acidic pH Conditions. Microbiology Resource Announcements. 2021 Jan 14;10(2):e01360-20.

2020

  1. Bishop C, Parry R, Asgari S. Effect of Wolbachia wAlbB on a positive-sense RNA negev-like virus: A novel virus persistently infecting Aedes albopictus mosquitoes and cells. Journal of General Virology. 2020 Feb 1;101(2):216-25.

  2. Black A, MacCannell DR, Sibley TR et al. Ten recommendations for supporting open pathogen genomic analysis in public health. Nat Med 26, 832–841 (2020). https://doi.org/10.1038/s41591-020-0935-z

  3. Boonchuen P, Maralit BA, Jaree P, Tassanakajon A, Somboonwiwat K. MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus. Scientific reports. 2020 Jan 21;10(1):1-5.

  4. Brandies PA, Tang S, Johnson RSP, Hogg CJ, Belov K. The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies, Gigabyte, 1, 2020 https://doi.org/10.46471/gigabyte.7

  5. Conrin M. Characterization of Caudovirales Isolated from Freshwater Samples against Pseudomonas fluorescens and Host Range Testing against Pseudomonas aeruginosa (Doctoral dissertation, University of Nebraska at Omaha).

  6. de Busserolles F, Cortesi F, Fogg L, Stieb SM, Luehrmann M, Marshall NJ. The visual ecology of Holocentridae, a nocturnal coral reef fish family with a deep-sea-like multibank retina. Journal of Experimental Biology 2020 : jeb.233098 doi: 10.1242/jeb.233098 Published 24 November 2020

  7. Elbialy A. The role of antioxidants in restoring MAPK 14 and a DNA damage marker level following autophagy suppression. Open Biol. 10: 200253. https://doi.org/10.1098/rsob.200253

  8. Fan X, Waardenberg AJ, Demuth M, Osteil P, Sun JQ, Loebel DA, Graham M, Tam PP, Fossat N. TWIST1 homodimers and heterodimers orchestrate lineage-specific differentiation. Molecular and cellular biology. 2020 Mar 16;40(11):e00663-19.

  9. Gunn BF, Murphy DJ, Walsh NG, Conran JG, Pires JC, Macfarlane TD, Birch JL. Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia. Molecular Phylogenetics and Evolution, Volume 149, 2020, 106836, ISSN 1055-7903, https://doi.org/10.1016/j.ympev.2020.106836.

  10. Hanrahan J. A genomic analysis of the emergence and spread of ciprofloxacin-resistant Neisseria gonorrhoeae in New South Wales, Australia to inform future strategies for disease control (Doctoral dissertation, University of New South Wales).

  11. Hernández I, Sant C, Martínez R, Fernández C. Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains. Frontiers in microbiology. 2020 Mar 10;11:208.

  12. Jeffress S, Arun-Chinnappa K, Stodart B, Vaghefi N, Tan YP, Ash G. Genome mining of the citrus pathogen Elsinoë fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters. PloS one. 2020 May 29;15(5):e0227396.

  13. Kidsley AK, O’Dea M, Ebrahimie E, Mohammadi-Dehcheshmeh M, Saputra S, Jordan D, Johnson JR, GordonD, Turni C, Djordjevic SP, Abraham S, Trott DJ. Genomic analysis of fluoroquinolone-susceptible phylogenetic group B2 extraintestinal pathogenic Escherichia coli causing infections in cats, Veterinary Microbiology, Volume 245, 2020, 108685, ISSN 0378-1135, https://doi.org/10.1016/j.vetmic.2020.108685.

  14. Kidsley AK, O’Dea M, Saputra S, Jordan D, Johnson JR, Gordon DM, Turni C, Djordjevic SP, Abraham S, Trott DJ. Genomic analysis of phylogenetic group B2 extraintestinal pathogenic E. coli causing infections in dogs in Australia, Veterinary Microbiology, Volume 248, 2020, 108783, ISSN 0378-1135, https://doi.org/10.1016/j.vetmic.2020.108783.

  15. Koehn LM, Huang Y, Habgood MD et al. Effects of paracetamol (acetaminophen) on gene expression and permeability properties of the rat placenta and fetal brain [version 2; peer review: 2 approved]. F1000Research 2020, 9:573 (https://doi.org/10.12688/f1000research.24119.2)

  16. Laidoudi Y. Helminthoses vectorielles: caractérisation, diagnostic et moyens de contrôle (Doctoral dissertation, Aix-Marseille).

  17. Laidoudi Y, Levasseur A, Medkour H, Maaloum M, Ben Khedher M, Sambou M, Bassene H, Davoust B, Fenollar F, Raoult D, Mediannikov O. An Earliest Endosymbiont, Wolbachia massiliensis sp. nov., Strain PL13 from the Bed Bug (Cimex hemipterus), Type Strain of a New Supergroup T. Int. J. Mol. Sci. 2020, 21, 8064.

  18. Lima JS. (2020). Investigating RNF43 Mutations as Biomarkers for ctDNA Surveillance of Colorectal Cancer (Thesis, Bachelor of Biomedical Sciences with Honours). University of Otago. Retrieved from http://hdl.handle.net/10523/10560

  19. Lin YS, Kweh KH, Koh TH, Lau QC, Rahman NBA. Genomic analysis of Lactococcus garvieae isolates, Pathology, Volume 52, Issue 6, 2020, Pages 700-707, ISSN 0031-3025, https://doi.org/10.1016/j.pathol.2020.06.009.

  20. Livingstone M, Aitchison K, Dagleish M, Longbottom D. De Novo Whole-Genome Sequencing and Annotation of Pathogenic Bovine Pasteurella multocida Type A:3 Strains. Resource Announcements Dec 2020, 9 (49) e01078-20; DOI: 10.1128/MRA.01078-20

  21. Madhav M, Parry R, Morgan JA, James P, Asgari S. Wolbachia endosymbiont of the horn fly (Haematobia irritans irritans): a Supergroup A strain with multiple horizontally acquired cytoplasmic incompatibility genes. Applied and environmental microbiology. 2020 Mar 2;86(6):e02589-19.

  22. Mamen O. (2020). Detection of antibiotic resistant bacteria in cow’s milk through cultivation based and molecular biological methods. (Thesis, Masters of Biotechnology). Norwegian University of Life Sciences, Ås. Retrieved from https://hdl.handle.net/11250/2678490

  23. Minhas V. (2020). Pathogenesis of Streptococcus pneumoniae - a molecular characterisation (Thesis, Doctor of Philosophy). University of Adelaide. Retrieved from http://hdl.handle.net/2440/128366

  24. Miyake H., Mitobe M, Kubota H, Takano H, Yokoyama K, Sadamasu K. Complete Genome Sequence of Ceftriaxone-Resistant Neisseria gonorrhoeae SS3160, Isolated in Tokyo, Japan. Microbiology Resource Announcements Sep 2020, 9 (39) e00886-20; DOI: 10.1128/MRA.00886-20

  25. Morison SA, Cramp RL, Alton LA, Franklin CE. Cooler temperatures slow the repair of DNA damage in tadpoles exposed to ultraviolet radiation: implications for amphibian declines at high altitude. Global change biology. 2020 Mar;26(3):1225-34.

  26. Parry R, Wille M, Turnbull OMH, Geoghegan JL, Holmes EC. Divergent Influenza-Like Viruses of Amphibians and Fish Support an Ancient Evolutionary Association. Viruses 2020, 12, 1042.

  27. Purushotham N, Jones A, Poudel B, Nasim J, Adorada D, Sparks A, Schwessinger B, Vaghefi N. Draft genome resource for Macrophomina phaseolina associated with charcoal rot in sorghum. Molecular Plant-Microbe Interactions. 2020 May 22;33(5):724-6.

  28. Quaife-Ryan GA, Mills RJ, Lavers G, Voges HK, Vivien CJ, Elliott DA, Ramialison M, Hudson JE, Porrello ER. β-Catenin drives distinct transcriptional networks in proliferative and nonproliferative cardiomyocytes. Development 2020 147: dev193417 doi: 10.1242/dev.193417 Published 30 November 2020

  29. Thomrongsuwannakij T, Blackall PJ, Djordjevic SP, Cummins ML & Chansiripornchai N (2020) A comparison of virulence genes, antimicrobial resistance profiles and genetic diversity of avian pathogenic Escherichia coli (APEC) isolates from broilers and broiler breeders in Thailand and Australia, Avian Pathology, 49:5, 457-466, DOI: 10.1080/03079457.2020.1764493

  30. Wunderlich G. Spatiotemporal Characterization of the Sydney Beach Sand Mycobiome using Traditional and Molecular Techniques - A Clinical Connection? Bachelor of Medical Science (Honours) thesis – University of Sydney

2019

  1. Banerjee B, Koner D, Hasan R, Bhattacharya S, Saha N. Transcriptome analysis reveals novel insights in air-breathing magur catfish (Clarias magur) in response to high environmental ammonia. Gene. 2019 Jun 30;703:35-49.

  2. Bye CR, Penna V, de Luzy IR, Gantner CW, Hunt CP, Thompson LH, Parish CL. Transcriptional profiling of xenogeneic transplants: examining human pluripotent stem cell-derived grafts in the rodent brain. Stem cell reports. 2019 Nov 12;13(5):877-90.

  3. Lin M, Xiang D, Chen X, Huo H. Role of characteristic components of Humulus lupulus in promoting human health. Journal of agricultural and food chemistry. 2019 Jul 9;67(30):8291-302.

  4. Ng HI, Tuong ZK, Fernando GJ, Depelsenaire AC, Meliga SC, Frazer IH, Kendall MA. Microprojection arrays applied to skin generate mechanical stress, induce an inflammatory transcriptome and cell death, and improve vaccine-induced immune responses. npj Vaccines. 2019 Oct 11;4(1):1-2.

  5. Olguín-Calderón D, González-Escobar JL, Ríos-Villa R, Dibildox-Alvarado E, Leon-Rodriguez D, de la Rosa AP. Modulation of caecal microbiome in obese mice associated with administration of amaranth or soybean protein isolates. Polish Journal of Food and Nutrition Sciences. 2019;69(1).

  6. Parry R, Asgari S. Discovery of novel crustacean and cephalopod flaviviruses: insights into the evolution and circulation of flaviviruses between marine invertebrate and vertebrate hosts. Journal of virology. 2019 May 8;93(14):e00432-19.

  7. Saad J, Phelippeau M, Khoder M, Lévy M, Musso D, Drancourt M. “Mycobacterium mephinesia”, a Mycobacterium terrae complex species of clinical interest isolated in French Polynesia. Scientific reports. 2019 Aug 1;9(1):1-1.

  8. Salavaty A, Rezvani Z, Najafi A. Survival analysis and functional annotation of long non‐coding RNAs in lung adenocarcinoma. Journal of cellular and molecular medicine. 2019 Aug;23(8):5600-17.

  9. Suen WW, Imoda M, Thomas AW, Nasir NN, Tearnsing N, Wang W, Bielefeldt-Ohmann H. An acute stress model in New Zealand white rabbits exhibits altered immune response to infection with West Nile Virus. Pathogens. 2019 Dec;8(4):195.

  10. Tam NT, Dwiyanti MS, Koide Y, Nagano AJ, Ky H, Tin HQ, Hien NL, Dung LV, Kishima Y. Profiling SNP and nucleotide diversity to characterize mekong delta rice landraces in southeast asian populations. The Plant Genome. 2019 Nov;12(3):190042.

  11. Tam NT. The genome constitution of rice resources in the Mekong Delta and their association with salinity stress (Doctoral dissertation, 北海道大学).

  12. Tettamanti V, de Busserolles F, Lecchini D, Marshall NJ, Cortesi F. Visual system development of the spotted unicornfish, Naso brevirostris (Acanthuridae). Journal of Experimental Biology. 2019 Dec 15;222(24):jeb209916.

  13. Van Holle A, Muylle H, Ruttink T, Van Landschoot A, Haesaert G, Naudts D, De Keukeleire D, Roldán-Ruiz I. Single nucleotide polymorphisms and biochemical markers as complementary tools to characterize hops (Humulus lupulus L.) in brewing practice. Journal of agricultural and food chemistry. 2019 Mar 21;67(13):3761-71.

  14. Yimagou EK, Anani H, Yacouba A, Hasni I, Baudoin JP, Raoult D, Khalil JB. Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care. New microbes and new infections. 2019 Nov 1;32:100615.

  15. Zoccola-McFarlane E. A transcriptomic and functional approach to investigation of antigen processing and adaptive immunity in Barramundi (Lates calcarifer). PhD Thesis - University of Queensland.