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

  2. 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

  3. 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

  4. 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.

  5. 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

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

  2. 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 Feb 1.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

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

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

  10. 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.

  11. 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.

  12. Mohit E. Investigating streptomyces clavuligerus linear replicons for improved clavulanic acid production. (Doctoral thesis, University of Strathclyde, Glasgow)

  13. Panichnantakul P, Aguilar LC, Daynard E, Guest M, Peters C, Vogel J, Oeffinger M. Protein UFMylation regulates early events of ribosomal DNA double-stranded break response. bioRxiv. 2024:2024-02.

  14. 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.

  15. Ridone P, Baker MA. Allosteric adaptation in the stator complex rescues bacterial motility in Exb/Mot chimeras. bioRxiv. 2024:2024-03.

  16. 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.

  17. 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.

2023

  1. Ajuyah P, Mayoh C, Lau LM, Barahona P, Wong M, Chambers H, Valdes-Mora F, Senapati A, Gifford AJ, D’Arcy C, Hansford JR. Histone H3-wild type diffuse midline gliomas with H3K27me3 loss are a distinct entity with exclusive EGFR or ACVR1 mutation and differential methylation of homeobox genes. Scientific reports. 2023 Mar 7;13(1):3775.

  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.

  25. Crates R, von Takach B, Young CM, Stojanovic D, Neaves L, Murphy L, Gautschi D, Hogg CJ, Heinsohn R, Bell P, Farquharson KA. Genomic insights into a critically endangered island endemic songbird provide a roadmap for preventing extinction. Authorea. September 14, 2023. Preprint: https://doi.org/10.22541/au.169471129.99174363/v1

  26. Damir HA, Ahmad W, Panicker NG, Mohamed LI, Omer EA, Kinne J, Wernery U, Adem A, Ali MA, Mustafa F. Investigation of a herpesvirus outbreak in mixed breeds of adult domestic ducks using next generation sequencing. Plos one. 2023 Jan 27;18(1):e0280923.

  27. 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

  28. Diouf FS, Beye M, Gaye M, Mbaye B, Alibar S, Sarr M, Dubourg G, Lagier JC, Sokhna C, Fenollar F, Fournier PE. Description of Streptococcus thalassemiae sp. nov., a Bacterium Isolated from Human Blood. International Journal of Microbiology. 2023 Aug 1;2023.

  29. Dodge TO, Farquharson KA, Ford C, Cavanagh L, Schubert K, Schumer M, Belov K, Hogg CJ. Genomes of two Extinct‐in‐the‐Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights. Molecular Ecology Resources. 2023 Mar 5.

  30. Edwards CL, Ng SS, de Labastida Rivera F, Corvino D, Engel JA, De Oca MM, Bukali L, Frame TC, Bunn PT, Chauhan SB, Singh SS. Human IL-10–producing Th1 cells exhibit a molecular signature distinct from Tr1 cells in malaria. The Journal of Clinical Investigation. 2023 Jan 3;133(1).

  31. Edwards CL, Engel JA, de Labastida Rivera F, Ng SS, Corvino D, de Oca MM, Frame TC, Chauhan SB, Singh SS, Kumar A, Wang Y. A molecular signature for IL-10–producing Th1 cells in protozoan parasitic diseases. JCI insight. 2023 Dec 12;8(24).

  32. Espinal RB, de Santana SF, Santos VC, Lizardo GN, Silva RJ, Corrêa RX, Loguercio LL, Neto AG, Pirovani CP, Fonseca PL, Aguiar ER. Uncovering a Complex Virome Associated with the Cacao Pathogens Ceratocystis cacaofunesta and Ceratocystis fimbriata. Pathogens. 2023 Feb;12(2):287.

  33. Faria N, Ghadi SC. Draft genome sequence of lysogenic Pseudomonas sp. strain VB3 isolated from Vashisht hot spring, India. Biologia. 2023 Jun 30:1-8.

  34. 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.

  35. 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.

  36. Foo CX, Bartlett S, Chew KY, Ngo MD, Bielefeldt-Ohmann H, Arachchige BJ, Matthews B, Reed S, Wang R, Smith C, Sweet MJ. GPR183 antagonism reduces macrophage infiltration in influenza and SARS-CoV-2 infection. European Respiratory Journal. 2023 Mar 1;61(3).

  37. Francis EK, Antonopoulos A, Westman ME, McKay-Demeler J, Laing R, Šlapeta J. A mixed amplicon metabarcoding and sequencing approach for surveillance of drug resistance to levamisole and benzimidazole in Haemonchus spp. International Journal for Parasitology. 2023 Aug 1.

  38. Gomila Pelegri N, Stanczak AM, Bottomley AL, Milthorpe BK, Gorrie CA, Padula MP, Santos J. Adipose-Derived Stem Cells Spontaneously Express Neural Markers When Grown in a PEG-Based 3D Matrix. International Journal of Molecular Sciences. 2023 Jul 28;24(15):12139.

  39. Gomila Pelegri N, Stanczak AM, Bottomley AL, Cummins ML, Milthorpe BK, Gorrie CA, Padula MP, Santos J. Neural Marker Expression in Adipose-Derived Stem Cells Grown in PEG-Based 3D Matrix Is Enhanced in the Presence of B27 and CultureOne Supplements. International Journal of Molecular Sciences. 2023 Nov 13;24(22):16269.

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

  41. Gu K, Mok L, Wakefield M, Chong M. Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops. bioRxiv. 2023:2023-03.

  42. 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.

  43. Gupta R, Strbenac D, Satgunaseelan L, Cheung VK, Narayanappa H, Ashford B, Mitchell J, Thind A, Palme CE, Ch’ng S, Low TH. Comparing Genomic Landscapes of Oral and Cutaneous Squamous Cell Carcinoma of the Head and Neck: Quest for Novel Diagnostic Markers. Modern Pathology. 2023 Apr 18:100190.

  44. 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.

  45. 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.

  46. 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.

  47. 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.

  48. 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.

  49. 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.

  50. 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.

  51. 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.

  52. Jackson, C., McLay, T., and Schmidt-Lebuhn, A. N.. 2023. hybpiper-nf and paragone-nf: containerization and additional options for target capture assembly and paralog resolution. Applications in Plant Sciences 11(4):e11532.

  53. James-Pearson L. Characterisation of the Australian Great Artesian Basin's Caldaquabacillus species and potential role in thermophilic plastic biodegradation (Doctoral dissertation, Queensland University of Technology).

  54. Jesudoss Chelladurai JR, Abraham A, Quintana TA, Ritchie D, Smith V. Comparative Genomic Analysis and Species Delimitation: A Case for Two Species in the Zoonotic Cestode Dipylidium caninum. Pathogens. 2023 May 3;12(5):675.

  55. Jin J, Mangal U, Seo JY, Kim JY, Ryu JH, Lee YH, Lugtu C, Hwang G, Cha JY, Lee KJ, Yu HS. Cerium oxide nanozymes confer a cytoprotective and bio-friendly surface micro-environment to methacrylate based oro-facial prostheses. Biomaterials. 2023 May 1;296:122063.

  56. Kavi Sidharthan V, Diksha D, Singh R, Choudhary S, Naika MB, Baranwal VK. Identification of two putative novel deltapartitiviruses and an enamovirus in coriander transcriptomes. Archives of Microbiology. 2023 Oct;205(10):1-6.

  57. Kleeman EA, Reisinger SN, Adithya P, Houston B, Stathatos G, Garnham AL, McLaughlin S, O'Bryan MK, Gubert C, Hannan AJ. Paternal immune activation by Poly I: C modulates sperm noncoding RNA profiles and causes transgenerational changes in offspring behavior. Brain, Behavior, and Immunity. 2023 Oct 10.

  58. Lilly JV, Rokita JL, Mason JL, Patton T, Stefankiewiz S, Higgins D, Trooskin G, Larouci CA, Arya K, Appert E, Heath AP. The children's brain tumor network (CBTN)-Accelerating research in pediatric central nervous system tumors through collaboration and open science. Neoplasia. 2023 Jan 1;35:100846.

  59. Lott MJ, Frankham GJ, Eldridge MD, Alquezar-Planas DE, Donnelly L, Zenger KR, Leigh KA, Kjeldsen SR, Field MA, Lemon J, Lunney D. Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to define meaningful conservation goals. bioRxiv. 2023:2023-12.

  60. Luciani CE, Carivali MB, Solis VE, Flores CR, Conci VC, Perotto MC, Celli MG. Viruses affecting chia crops and occurrence of cowpea mild mottle virus in chia-producing regions. Tropical Plant Pathology. 2023 Dec 13:1-1.

  61. Madhuvanthi CK, Muthulakshmi E, Ghosh Dasgupta M. Integrated mRNA and small RNA sequencing reveals post-transcriptional regulation of the sesquiterpene pathway in Santalum album L.(Indian sandalwood). 3 Biotech. 2023 Dec;13(12):387.

  62. Mahony TJ, Omaleki L, Briody T, Hayes B, Turni C. Improving bovine respiratory disease control through the characterisation of pathogen-host interactions.

  63. Marangon E. Coral reef symbioses under a changing climate: an integrative approach (Doctoral dissertation, James Cook University).

  64. Mathura SR, Sutton F, Bowrin V. Genome-wide identification, characterization, and expression analysis of the sweet potato (Ipomoea batatas [L.] Lam.) ARF, Aux/IAA, GH3, and SAUR gene families. BMC Plant Biology. 2023 Dec 7;23(1):622.

  65. McDougall F, Gordon D, Robins-Browne R, Bennett-Wood V, Boardman WS, Graham PL, Power M. Characterisation of typical enteropathogenic Escherichia coli (tEPEC) lineages and novel bfpA variants detected in Australian fruit bats (Pteropus poliocephalus). Science of The Total Environment. 2023 Dec 1;902:166336.

  66. Mevada V, Patel R, Dudhagara P, Chaudhari R, Vohra M, Khan V, JH Shyu D, Chen YY, Zala D. Whole Genome Sequencing and Pan-Genomic Analysis of Multidrug-Resistant Vibrio cholerae VC01 Isolated from a Clinical Sample. Microorganisms. 2023 Aug 7;11(8):2030.

  67. Morin M, Jönsson M, Wang CK, Craik DJ, Degnan SM, Degnan BM. Captivity induces a sweeping and sustained genomic response in a starfish. Molecular Ecology. 2023 Apr 3.

  68. Morin M, Jonsson M, Wang C, Craik DJ, Degnan SM, Degnan B. Seasonal tissue-specific gene expression reveals reproductive and stress-related transcriptional systems in wild crown-of-thorns starfish. bioRxiv. 2023:2023-12.

  69. Nibert ML, Xie Y, Xiao J, Gao Y, Liu D, Yang G, Tao J. Transcriptome mining of RNA viruses (family Totiviridae) in Eimeria necatrix and Eimeria stiedai. bioRxiv. 2023:2023-05.

  70. Olasz B, Smithers L, Evans GL, Anandan A, Murcha MW, Vrielink A. Structural analysis of the Sterile alpha motif (SAM) domain of the Arabidopsis mitochondrial tRNA import receptor. bioRxiv. 2023:2023-11.

  71. Oumarou Hama H, Boualam MA, Levasseur A, Ardagna Y, Adalian P, Chaix AC, Drancourt M. Old World medieval Treponema pallidum complex treponematosis: a case report. The Journal of Infectious Diseases. 2023 Jul 13:jiad248.

  72. Padovan A, Kennedy K, Gibb K. A Microcystin Synthesis mcyE/ndaF Gene Assay Enables Early Detection of Microcystin Production in a Tropical Wastewater Pond. Harmful Algae. 2023 Jul 5:102476.

  73. Paltiel M, Taylor M, Newson A. Protection of genomic data and the Australian Privacy Act: when are genomic data ‘personal information’?. International Data Privacy Law. 2023 Feb 1:ipad002.

  74. Parry RH, Slonchak A, Campbell LJ, Newton ND, Debat HJ, Gifford RJ, Khromykh AA. A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) from the UK. Journal of General Virology. 2023 Dec 7;104(12):001927.

  75. Peng B, Weintraub SJ, Lu Z, Evans S, Shen Q, McDonnell L, Plan M, Collier T, Cheah LC, Ji L, Howard CB. Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered Saccharomyces cerevisiae. ACS Synthetic Biology. 2023 Dec 12.

  76. Plumet L, Morsli M, Ahmad-Mansour N, Clavijo-Coppens F, Berry L, Sotto A, Lavigne JP, Costechareyre D, Molle V. Isolation and Characterization of New Bacteriophages against Staphylococcal Clinical Isolates from Diabetic Foot Ulcers. Viruses. 2023 Nov 22;15(12):2287.

  77. Prabhakar L. Meta-analysis of lean and obese RNA-seq datasets to identify genes targeting obesity. Bioinformation. 2023;19(3):331-5.

  78. Ranawaka B, An J, Lorenc MT, Jung H, Sulli M, Aprea G, Roden S, Llaca V, Hayashi S, Asadyar L, LeBlanc Z. A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology. Nature Plants. 2023 Aug 10:1-4

  79. Rathod S, Chavan P, Mahuli D, Rochlani S, Shinde S, Pawar S, Choudhari P, Dhavale R, Mudalkar P, Tamboli F. Exploring biogenic chalcones as DprE1 inhibitors for antitubercular activity via in silico approach. Journal of Molecular Modeling. 2023 Apr;29(4):113.

  80. Rivory P, Pillay K, Lee R, Taylor D, Ward MP, Šlapeta J. Fatal neural angiostrongyliasis in the Bolivian squirrel monkey (Saimiri boliviensis boliviensis) leading to defining Angiostongylus cantonensis risk map at a zoo in Australia. One Health. 2023 Sep 15:100628.

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  87. Sidharthan VK, Vanamala G, Rajeswari V, Baranwal VK. Identification of a putative novel cholivirus in the transcriptome of Gymnema sylvestre R. Br. Archives of Microbiology. 2023 May;205(5):186.

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2022

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  2. Ahmed FZ. Unravelling genes responsible for successful anthocyanin production in Nicotiana benthamiana (Doctoral dissertation, Queensland University of Technology)

  3. Balotf S, Wilson R, Nichols DS, Tegg RS, Wilson CR. Multi-omics reveals mechanisms of resistance to potato root infection by Spongospora subterranea. Scientific Reports. 2022 Jun 25;12(1):1-3.

  4. Bandara CJ. Development of a whole genome sequencing method for Tick-borne encephalitis virus in low viraemic samples (Master's thesis, Inland Norway University).

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  6. Cheney KL, Hudson J, de Busserolles F, Luehrmann M, Shaughnessy A, van den Berg C, Green NF, Marshall NJ, Cortesi F. Seeing Picasso: an investigation into the visual system of the triggerfish, Rhinecanthus aculeatus. Journal of Experimental Biology. 2022 Mar 4.

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  8. Decourtye L, McCallum-Loudeac JA, Zellhuber-McMillan S, Young E, Sircombe KJ, Wilson MJ. Characterization of a novel Lbx1 mouse loss of function strain. Differentiation. 2022 Jan 1;123:30-41.

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  11. Gong T, Jaratlerdsiri W, Jiang J, Willet C, Chew T, Patrick SM, Lyons RJ, Haynes AM, Pasqualim G, Brum IS, Stricker PD. Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers. Genome medicine. 2022 Dec;14(1):1-4.

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  18. Jaree P, Boonchuen P, Thawonsuwan J, Kondo H, Hirono I, Somboonwiwat K. Transcriptome profiling reveals the novel immunometabolism-related genes against WSSV infection from Fenneropenaeus merguiensis. Fish & Shellfish Immunology. 2022 Jan 1;120:31-44.

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  22. Lilly JV, Rokita JL, Mason JL, Patton T, Stefankiewiz S, Higgins D, Trooskin G, Larouci CA, Arya K, Appert E, Heath AP. The Children's Brain Tumor Network (CBTN)-Accelerating Research in Pediatric Central Nervous System Tumors through Collaboration and Open Science. bioRxiv. 2022 Jan 1.

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

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  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).

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  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.

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  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

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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.