Monash Bioinformatics Platform

Research Output 2014 2019

2019

A plasmid-encoded peptide from Staphylococcus aureus induces anti-myeloperoxidase nephritogenic autoimmunity

Ooi, J. D., Jiang, J-H., Eggenhuizen, P. J., Chua, L. L., van Timmeren, M., Loh, K. L., O’Sullivan, K. M., Gan, P. Y., Zhong, Y., Tsyganov, K., Shochet, L. R., Ryan, J., Stegeman, C. A., Fugger, L., Reid, H. H., Rossjohn, J., Heeringa, P., Holdsworth, S. R., Peleg, A. Y. & Kitching, A. R., 29 Jul 2019, In : Nature Communications. 10, 1, 14 p., 3392.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Characterization of Hypermutator Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis in Australia

Rees, V. E., Deveson Lucas, D. S., López-Causapé, C., Huang, Y., Kotsimbos, T., Bulitta, J. B., Rees, M. C., Barugahare, A., Peleg, A. Y., Nation, R. L., Oliver, A., Boyce, J. D. & Landersdorfer, C. B., 1 Apr 2019, In : Antimicrobial Agents and Chemotherapy. 63, 4, 11 p., e02538-18.

Research output: Contribution to journalArticleResearchpeer-review

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia

Schneider, M. V., Griffin, P. C., Tyagi, S., Flannery, M., Dayalan, S., Gladman, S., Watson-Haigh, N., Bayer, P. E., Charleston, M., Cooke, I., Cook, R., Edwards, R. J., Edwards, D., Gorse, D., McConville, M., Powell, D., Wilkins, M. R. & Lonie, A., 22 Mar 2019, In : Briefings in Bioinformatics. 20, 2, p. 384-389 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Gene expression signatures of circulating human type 1, 2, and 3 innate lymphoid cells

Li, S., Morita, H., Sokolowska, M., Tan, G., Boonpiyathad, T., Opitz, L., Orimo, K., Archer, S. K., Jansen, K., Tang, M. L. K., Purcell, D., Plebanski, M. & Akdis, C. A., Jun 2019, In : Journal of Allergy and Clinical Immunology. 143, 6, p. 2321-2325 5 p.

Research output: Contribution to journalLetterResearchpeer-review

iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

Chen, Z., Zhao, P., Li, F., Marquez-Lago, T. T., Leier, A., Revote, J., Zhu, Y., Powell, D. R., Akutsu, T., Webb, G. I., Chou, K-C., Smith, A. I., Daly, R. J., Li, J. & Song, J., 24 Apr 2019, (Accepted/In press) In : Briefings in Bioinformatics. 11 p., bbz041.

Research output: Contribution to journalArticleResearchpeer-review

Interplay between Follistatin, Activin A, and BMP4 Signaling Regulates Postnatal Thymic Epithelial Progenitor Cell Differentiation during Aging

Lepletier, A., Hun, M. L., Hammett, M. V., Wong, K., Naeem, H., Hedger, M., Loveland, K. & Chidgey, A. P., 25 Jun 2019, In : Cell Reports. 27, 13, p. 3887–3901–e4 19 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Metformin intervention prevents cardiac dysfunction in a murine model of adult congenital heart disease

Wilmanns, J. C., Pandey, R., Hon, O., Chandran, A., Schilling, J. M., Forte, E., Wu, Q., Cagnone, G., Bais, P., Philip, V., Coleman, D., Kocalis, H., Archer, S. K., Pearson, J. T., Ramialison, M., Heineke, J., Patel, H. H., Rosenthal, N. A., Furtado, M. B. & Costa, M. W., Feb 2019, In : Molecular Metabolism. 20, p. 102-114 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Topconfects: A package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list

Harrison, P. F., Pattison, A. D., Powell, D. R. & Beilharz, T. H., 28 Mar 2019, In : Genome Biology. 20, 1, 12 p., 67.

Research output: Contribution to journalArticleOtherpeer-review

Open Access
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2018

Age-Related Decline in Primary CD8+ T Cell Responses Is Associated with the Development of Senescence in Virtual Memory CD8+ T Cells

Quinn, K. M., Fox, A., Harland, K. L., Russ, B. E., Li, J., Nguyen, T. H. O., Loh, L., Olshanksy, M., Naeem, H., Tsyganov, K., Wiede, F., Webster, R., Blyth, C., Sng, X. Y. X., Tiganis, T., Powell, D., Doherty, P. C., Turner, S. J., Kedzierska, K. & La Gruta, N. L., 19 Jun 2018, In : Cell Reports. 23, 12, p. 3512-3524 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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A Metabolic Checkpoint for the Yeast-to-Hyphae Developmental Switch Regulated by Endogenous Nitric Oxide Signaling

Koch, B., Barugahare, A. A., Lo, T. L., Huang, C., Schittenhelm, R. B., Powell, D. R., Beilharz, T. H. & Traven, A., 20 Nov 2018, In : Cell Reports. 25, 8, p. 2244-2258 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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A novel role for Lyl1 in primitive erythropoiesis

Chiu, S. K., Saw, J. M. Y., Huang, Y., Sonderegger, S. E., Wong, N. C. L., Powell, D. R., Beck, D., Pimanda, J., Tremblay, C. & Curtis, D. J., 11 Oct 2018, In : Development. 145, 19, 9 p., dev162990.

Research output: Contribution to journalArticleResearchpeer-review

Best practice data life cycle approaches for the life sciences

Griffin, P. C., Khadake, J., LeMay, K. S., Lewis, S. E., Orchard, S., Pask, A., Pope, B., Roessner, U., Russell, K., Seemann, T., Treloar, A., Tyagi, S., Christiansen, J. H., Dayalan, S., Gladman, S., Hangartner, S. B., Hayden, H. L., Ho, W. W. H., Keeble-Gagnère, G., Korhonen, P. K. & 7 othersNeish, P., Prestes, P. R., Richardson, M. F., Watson-Haigh, N. S., Wyres, K. L., Young, N. D. & Schneider, M. V., 4 Jun 2018, In : F1000Research. 6, 22 p., 1618.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Concurrent host-pathogen transcriptional responses in a clostridium perfringens murine myonecrosis infection

Low, L-Y., Harrison, P. F., Gould, J., Powell, D. R., Choo, J. M., Forster, S. C., Chapman, R., Gearing, L. J., Cheung, J. K., Hertzog, P. & Rood, J. I., 1 Mar 2018, In : mBio. 9, 2, 15 p., e00473-18.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Early-Life Formation of the Microbial and Immunological Environment of the Human Airways

Pattaroni, C., Watzenboeck, M. L., Schneidegger, S., Kieser, S., Wong, N. C., Bernasconi, E., Pernot, J., Mercier, L., Knapp, S., Nicod, L. P., Marsland, C. P., Roth-Kleiner, M. & Marsland, B. J., 12 Dec 2018, In : Cell Host and Microbe. 24, 6, p. 857-865.e4 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Emergence of high-level colistin resistance in an acinetobacter baumannii clinical isolate mediated by inactivation of the global regulator H-NS

Lucas, D. D., Crane, B., Wright, A., Han, M-L., Moffatt, J., Bulach, D., Gladman, S. L., Powell, D., Aranda, J., Seemann, T., Machado, D., Pacheco, T., Marques, T., Viveiros, M., Nation, R., Li, J., Harper, M. & Boyce, J. D., 1 Jul 2018, In : Antimicrobial Agents and Chemotherapy. 62, 7, 17 p., e02442-17.

Research output: Contribution to journalArticleResearchpeer-review

Functional and genomic characterisation of a xenograft model system for the study of metastasis in triple-negative breast cancer

Johnstone, C. N., Pattison, A. D., Gorringe, K. L., Harrison, P. F., Powell, D. R., Lock, P., Baloyan, D., Ernst, M., Stewart, A. G., Beilharz, T. H. & Anderson, R. L., 29 May 2018, In : Disease Models and Mechanisms. 11, 5, 14 p., 032250.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Insights into the neurochemical signature of the Innervation of Beige Fat

Stefanidis, A., Wiedmann, N. M., Tyagi, S., Allen, A. M., Watt, M. J. & Oldfield, B. J., 1 May 2018, In : Molecular Metabolism. 11, p. 47-58 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Obesity Drives STAT-1-Dependent NASH and STAT-3-Dependent HCC

Grohmann, M., Wiede, F., Dodd, G. T., Gurzov, E. N., Ooi, G. J., Butt, T., Rasmiena, A. A., Kaur, S., Gulati, T., Goh, P. K., Treloar, A. E., Archer, S., Brown, W. A., Muller, M., Watt, M. J., Ohara, O., McLean, C. A. & Tiganis, T., 15 Nov 2018, In : Cell. 175, 5, p. 1289-1306 18 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Restricted cell cycle is essential for clonal evolution and therapeutic resistance of pre-leukemic stem cells

Tremblay, C., Saw, J., Chiu, S. K., Wong, N. C., Tsyganov, K., Ghotb, S., Graham, A. N., Yan, F., Guirguis, A., Sonderegger, S., Lee, N., Kalitsis, P., Reynolds, J., Ting, S., Powell, D., Jane, S. & Curtis, D., 1 Dec 2018, In : Nature Communications. 9, 1, 13 p., 3535.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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The evolutionary pattern of mutations in glioblastoma reveals therapy-mediated selection

Muscat, A. M., Wong, N. C., Drummond, K. J., Algar, E. M., Khasraw, M., Verhaak, R., Field, K., Rosenthal, M. A. & Ashley, D. M., 1 Jan 2018, In : Oncotarget. 9, 8, p. 7844-7858 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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The molecular characterisation of mitochondrial DNA deficient oocytes using a pig model

Tsai, T. S., Tyagi, S. & St John, J. C., 1 May 2018, In : Human Reproduction. 33, 5, p. 942-953 12 p.

Research output: Contribution to journalArticleResearchpeer-review

The transcriptome of human endometrial mesenchymal stem cells under TGFβR inhibition reveals improved potential for cell-based therapies

Gurung, S., Williams, S., Deane, J. A., Werkmeister, J. A. & Gargett, C. E., 4 Dec 2018, In : Frontiers in Cell and Developmental Biology. 6, DEC, 15 p., 164.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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The use of targeted next generation sequencing to explore candidate regulators of TGF-β1's impact on kidney cells

Wang, B., Ji, G., Naeem, H., Wang, J., Kantharidis, P., Powell, D. & Ricardo, S. D., Dec 2018, In : Frontiers in Physiology. 9, 14 p., 1755.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Wolbachia enhances insect-specific flavivirus infection in Aedes aegypti mosquitoes

Amuzu, H. E., Tsyganov, K., Koh, C., Herbert, R. I., Powell, D. R. & McGraw, E. A., 1 Jun 2018, In : Ecology and Evolution. 8, 11, p. 5441-5454 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2017

Cell Type of Origin Dictates the Route to Pluripotency

Nefzger, C. M., Rossello, F. J., Chen, J., Liu, X., Knaupp, A. S., Firas, J., Paynter, J. M., Pflueger, J., Buckberry, S., Lim, S. M., Williams, B., Alaei, S., Faye-Chauhan, K., Petretto, E., Nilsson, S. K., Lister, R., Ramialison, M., Powell, D. R., Rackham, O. J. L. & Polo, J. M., 5 Dec 2017, In : Cell Reports. 21, 10, p. 2649-2660 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Computing Minimum Reaction Modifications in a Boolean Metabolic Network

Tamura, T., Lu, W., Song, J. & Akutsu, T., 24 Nov 2017, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 6, p. 1853-1862 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Ticks from diverse genera encode chemokine-inhibitory evasin proteins

Hayward, J., Sanchez, J., Perry, A., Huang, C., Rodriguez Valle, M., Canals, M., Payne, R. J. & Stone, M. J., 22 Sep 2017, In : Journal of Biological Chemistry. 292, 38, p. 15670-15680 11 p.

Research output: Contribution to journalArticleResearchpeer-review

2014

The comparative genomics of monotremes, marsupials, and pinnippeds: Models to examine function of milk proteins

Sharp, J. A., Watt, A., Bisana, S., Modepalli, V., Wanyoni, S., Kumar, A., Kwek, J., Collins, R., Lefevre, C. & Nicholas, K. R., 2014, Milk Proteins: From Expression to Food. Singh, H., Boland, M. & Thompson, A. (eds.). 2nd ed. United Kingdom: Academic Press, p. 75-112 38 p.

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Otherpeer-review