2019 Publications crediting Galaxy Project
Schneider, Maria Victoria; Griffin, Philippa C; Tyagi, Sonika; Flannery, Madison; Dayalan, Saravanan; Gladman, Simon; Watson-Haigh, Nathan; Bayer, Philipp E; Charleston, Michael; Cooke, Ira;, Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia, Briefings in bioinformatics, 20, 2, 384-389, 2019, Oxford University Press, ,
Batut, Bérénice; Hiltemann, Saskia; Bagnacani, Andrea; Baker, Dannon; Bhardwaj, Vivek; Blank, Clemens; Bretaudeau, Anthony; Brillet-Guéguen, Loraine; Čech, Martin; Chilton, John;, Community-driven data analysis training for biology, Cell systems, 6, 6, 752-758. e1, 2018, Cell Press, ,
Lucas, Deanna Deveson; Crane, Bethany; Wright, Amy; Han, Mei-Ling; Moffatt, Jennifer; Bulach, Dieter; Gladman, Simon L; Powell, David; Aranda, Jesus; Seemann, Torsten;, Emergence of high-level colistin resistance in an Acinetobacter baumannii clinical isolate mediated by inactivation of the global regulator H-NS, Antimicrobial agents and chemotherapy, 62, 7, e02442-17, 2018, American Society for Microbiology Journals, ,
Gladman, Simon; Rasche, Eric; Grüning, Björn; Coraor, Nate; Benson, Derek; Lonie, Andrew; Taylor, James;, The usegalaxy.* servers: democratizing computational resources for life sciences at a new level, , , , , 2019, , ,
Dashper, SG; Mitchell, HL; Lê Cao, K-A; Carpenter, L; Gussy, MG; Calache, H; Gladman, SL; Bulach, DM; Hoffmann, B; Catmull, DV;, Temporal development of the oral microbiome and prediction of early childhood caries, Scientific Reports, 9, 1, 1-12, 2019, Nature Publishing Group, ,
Hiltemann, Saskia; Bagnacani, Andrea; Baker, Dannon; Bhardwaj, Vivek; Blank, Clemens; Bretaudeau, Anthony; Gu, Loraine; Chilton, John; Clements, Dave; Doppelt-Azeroual, Olivia;, Community-driven data analysis training for biology, BioRxiv, , , , 2018, Cold Spring Harbor Laboratory Press, ,
Baker, Dannon; Van Den Beek, Marius; Blankenberg, Daniel; Bouvier, Dave; Chilton, John; Coraor, Nate; Coppens, Frederik; Eguinoa, Ignacio; Gladman, Simon; Grüning, Björn;, No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics, , , , , 2020, ,
Published journal articles submitted in 2019
Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening (2019). Fleur Hammet, Khalid Mahmood, Thomas R Green, Tu Nguyen-Dumont, Melissa C Southey, Daniel D Buchanan, Andrew Lonie, Katherine L Nathanson, Fergus J Couch, Bernard J Pope & Daniel J Park. BioTechniquesVol. 67, No. 3. Published Online:3 Jul 2019https://doi.org/10.2144/btn-2019-0026
Mismatch repair gene pathogenic germline variants in a population-based cohort of breast cancer (2020). Tu Nguyen-Dumont, Jason A. Steen, Ingrid Winship, Daniel J. Park, Bernard J. Pope, Fleur Hammet, Maryam Mahmoodi, Helen Tsimiklis, Derrick Theys, Mark Clendenning, Graham G. Giles, John L. Hopper & Melissa C. Southey. Familial Cancer (2020) https://doi.org/10.1007/s10689-020-00164-7. Published 14 February 2020
Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software. Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope. GigaScience, Volume 8, Issue 9, September 2019, giz109, https://doi.org/10.1093/gigascience/giz109.
Journal articles submitted and in review in 2019
Molecular Drivers of Localized Prostate Cancer. Takafumi N. Yamaguchi1,#, Natalie Kurganovs1,2,3,4,#, Helen Zhu1,5,#, Katayoon Kasaian1,#, Chol-Hee Jung6,#, Julie Livingstone1,#, Natalie S. Fox1,5,#, Jocelyn Sietsma Penington7,#, Peter Georgeson6, Robert Lesurf1, Stefano Mangiola2,3,7, Michael Fraser1,4, Ken Chow2,3, Yu-Jia Shiah1, Michael J. Clarkson2,3, Lawrence E. Heisler1, Anne Nguyen2,3, Shadrielle Melijah G. Espiritu1, Ryan Stuchbery2,3, Vincent Huang1, Patrick J. McCoy2,3, Christopher M. Lalansingh1, Marek Cmero2,3,7, Richard Joveline1, Weerachai Jaratlerdsiri8, Adriana Salcedo1,5, Evie K. Chan8,9, Kathleen E. Houlahan1,5, Phillip D. Stricker10, Vinayak Bhandari1,5, M.S. Riana Bornman11, Dorota H.W. Sendorek1, Andrew Lonie6, Stephenie D. Prokopec1, Justin S. Peters2,3, Adrien Foucal1, Lachlan Mcintosh7, Michèle Orain12, Matthew Wakefield7, Valérie Picard13, Daniel J. Park6, Hélène Hovington13, Michael Kerger2, Alain Bergeron13, Veronica Sabelnykova1, Louis Lacombe13, Yves Fradet13, Andrew Ryan14, Bernard Têtu12, Vanessa M. Hayes8,9,11,15,16, John D. McPherson1,5, Anthony J. Costello2,3,17, Theodorus van der Kwast4, Bernard J. Pope6, Anthony T. Papenfuss7,18,19,20,21%, Robert G. Bristow4,5,22,%, Niall M. Corcoran2,3,17,%, Jüri Reimand1,5,%, Christopher M. Hovens2,3,%,*, Paul C. Boutros1,5,23,24,25,26,%,*
Rare germline genetic variants and risk of aggressive prostate cancer. Tú Nguyen-Dumont1,2, Robert J. MacInnis3,4, Jason A. Steen1, Derrick Theys,1 Helen Tsimiklis2,3, Fleur Hammet2,5, Maryam Mahmoodi2,5, Bernard J. Pope 5,6,7, Daniel J. Park2,7, Khalid Mahmood6,7, Gianluca Severi8,9, John Pedersen10, Damien Bolton11, Roger L. Milne1,3,4, Graham G. Giles3,4, Melissa C. Southey1,2,3,5
Genetic testing in Poland and Ukraine: should comprehensive germline testing of BRCA1 and BRCA2 be recommended for women with breast and ovarian cancer? Aleksander Myszka1#, Tu Nguyen-Dumont2,3#, Pawel Karpinski4, Maria M. Sasiadek5, Hayane Akopyan1,5, Jason A. Steen2, Derrick Theys2, Fleur Hammet2,3, Helen Tsimiklis2,3, Daniel J. Park3,6, Bernard J. Pope2,6,7, Ryszard Slezak4, Nataliya Kitsera5, Aleksandra Siekierzynska8, Melissa C. Southey2,3*
Conference presentations in 2019
Janis: A Python framework for Portable Pipelines (2019) Michael Franklin, Richard Lupat, Jiaan Yu, Evan Thomas, Daniel Park, Bernard Pope, Tony Papenfuss and Jason Li. Australian Bioinformatics and Computational Biology Society annual conference, Sydney, Australia
Janis: An open source tool to machine generate type-safe CWL and WDL workflows (2019). Richard Lupat, Michael Franklin, Bernard Pope, Daniel Park, Evan Thomas, Mohammad Bhuyan, Tony Papenfuss and Jason Li. BOSC COSI: Bioinformatics Open Source Conference, Basel, Switzerland
Revisiting the frequency of sex-chromosome abnormality using DNA methylation profiles from public datasets (2019) Chol-Hee JUNG1, Khalid Mahmood1, Bernard J. Pope1,2,3, Daniel J. Park1. Australasian Genomic Technologies Association Conference, Sunshine Coast, Australia
Portable variant-calling pipelines for cancer (2019) Michael Franklin, Richard Lupat, Jiaan Yu, Evan Thomas, Daniel Park, Bernie Pope, Jason Li. Victorian Cancer Bioinformatics Symposium, Victorian Comprehensive Cancer Centre, Melbourne, Australia.
2018 Publications
Afgan, E., Lonie, A., Taylor, J., Goonasekera, N., 2018. CloudLaunch: Discover and deploy cloud applications. Future Generation Computer Systems. https://doi.org/10.1016/j.future.2018.04.037
Amy, J., Bulach, D., Knight, D., Riley, T., Johanesen, P., Lyras, D., 2018a. Identification of large cryptic plasmids in Clostridioides (Clostridium) difficile. Plasmid 96–97, 25–38. https://doi.org/10.1016/j.plasmid.2018.04.001
Amy, J., Bulach, D., Knight, D., Riley, T., Johanesen, P., Lyras, D., 2018b. Identification of large cryptic plasmids in Clostridioides (Clostridium) difficile. Plasmid 96–97, 25–38. https://doi.org/10.1016/j.plasmid.2018.04.001
Bassett, J.K., English, D.R., Giles, G.G., Milne, R.L., Dugué, P.-A., Southey, M.C., Baglietto, L., Severi, G., Schmidt, D., Makalic, E., Hopper, J.L., Li, S., Moreno-Betancur, M., Buchanan, D.D., Wong, E.M., Joo, J.E., Jung, C.-H., Fiorito, G., Vineis, P., 2017. Association of DNA Methylation-Based Biological Age With Health Risk Factors and Overall and Cause-Specific Mortality. American Journal of Epidemiology 187, 529–538. https://doi.org/10.1093/aje/kwx291
Batut, B., Hiltemann, S., Bagnacani, A., Baker, D., Bhardwaj, V., Blank, C., Bretaudeau, A., Brillet-Guéguen, L., Čech, M., Chilton, J., Clements, D., Doppelt-Azeroual, O., Erxleben, A., Freeberg, M.A., Gladman, S., Hoogstrate, Y., Hotz, H.-R., Houwaart, T., Jagtap, P., Larivière, D., Le Corguillé, G., Manke, T., Mareuil, F., Ramírez, F., Ryan, D., Sigloch, F.C., Soranzo, N., Wolff, J., Videm, P., Wolfien, M., Wubuli, A., Yusuf, D., Taylor, J., Backofen, R., Nekrutenko, A., Grüning, B., 2018. Community-Driven Data Analysis Training for Biology. Cell Systems 6, 752-758.e1. https://doi.org/10.1016/j.cels.2018.05.012
Bulach, D.M., Carter, G.P., Stinear, T.P., Gonçalves da Silva, A., Howden, B.P., Williamson, D.A., Kwong, J.C., Lee, R.S., Seemann, T., Heffernan, H., Dyet, K.H., Woodhouse, R., 2017a. Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand. Journal of Antimicrobial Chemotherapy 73, 353–364. https://doi.org/10.1093/jac/dkx405
Bulach, D.M., Carter, G.P., Stinear, T.P., Gonçalves da Silva, A., Howden, B.P., Williamson, D.A., Kwong, J.C., Lee, R.S., Seemann, T., Heffernan, H., Dyet, K.H., Woodhouse, R., 2017b. Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand. Journal of Antimicrobial Chemotherapy 73, 353–364. https://doi.org/10.1093/jac/dkx405
Buultjens, A.H., Vandelannoote, K., Meehan, C.J., Eddyani, M., de Jong, B.C., Fyfe, J.A.M., Globan, M., Tobias, N.J., Porter, J.L., Tomita, T., Tay, E.L., Seemann, T., Howden, B.P., Johnson, P.D.R., Stinear, T.P., 2018. Comparative Genomics Shows That Mycobacterium ulcerans Migration and Expansion Preceded the Rise of Buruli Ulcer in Southeastern Australia. Appl. Environ. Microbiol. 84, e02612-17. https://doi.org/10.1128/AEM.02612-17
Chamberlain, J.A., Bassett, J.K., Brinkman, M.T., Hodge, A.M., English, D.R., Giles, G.G., Hopper, J.L., Dugué, P.-A., Milne, R.L., Southey, M.C., Schmidt, D.F., Makalic, E., Buchanan, D.D., Joo, J.E., Jung, C.-H., 2018. Dietary intake of one-carbon metabolism nutrients and DNA methylation in peripheral blood. The American Journal of Clinical Nutrition 108, 611–621. https://doi.org/10.1093/ajcn/nqy119
Deveson Lucas, 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., 2018. Emergence of High-Level Colistin Resistance in an Acinetobacter baumannii Clinical Isolate Mediated by Inactivation of the Global Regulator H-NS. Antimicrob. Agents Chemother. 62, e02442-17. https://doi.org/10.1128/AAC.02442-17
Dugué, P.-A., Bassett, J.K., Joo, J.E., Jung, C.-H., Ming Wong, E., Moreno-Betancur, M., Schmidt, D., Makalic, E., Li, S., Severi, G., Hodge, A.M., Buchanan, D.D., English, D.R., Hopper, J.L., Southey, M.C., Giles, G.G., Milne, R.L., 2018. DNA methylation-based biological aging and cancer risk and survival: Pooled analysis of seven prospective studies. International Journal of Cancer 142, 1611–1619. https://doi.org/10.1002/ijc.31189
Dugué, P.-A., Wilson, R., Lehne, B., Jayasekara, H., Wang, X., Jung, C.-H., Joo, J.E., Makalic, E., Schmidt, D.F., Baglietto, L., Severi, G., Gieger, C., Ladwig, K.-H., Peters, A., Kooner, Jaspal S., Southey, M., English, D., Waldenberger, M., Chambers, J.C., Giles, G., Milne, R., 2018. Alcohol consumption is associated with widespread changes in blood DNA methylation: analysis of cross-sectional and longitudinal data. bioRxiv 452953. https://doi.org/10.1101/452953
Afgan, V.Jalili, N. Goonasekera, J. Taylor, J. Goecks, 2018. Federated Galaxy: Biomedical Computing at the Frontier, in: 2018 IEEE 11th International Conference on Cloud Computing (CLOUD). Presented at the 2018 IEEE 11th International Conference on Cloud Computing (CLOUD), pp. 871–874. https://doi.org/10.1109/CLOUD.2018.00124
Emery-Corbin, S.J., Ansell, B.R.E., Jex, A.R., Georgeson, P., Pope, B.J., 2018. Annotation of the Giardia proteome through structure-based homology and machine learning. GigaScience 8. https://doi.org/10.1093/gigascience/giy150
FitzGerald, L.M., Jung, C., Wong, E.M., Joo, J.E., Gould, J.A., Vasic, V., Bassett, J.K., O’Callaghan, N., Nottle, T., Pedersen, J., Giles, G.G., Southey, M.C., 2018. Obtaining high quality transcriptome data from formalin-fixed, paraffin-embedded diagnostic prostate tumor specimens. Laboratory Investigation 98, 537–550. https://doi.org/10.1038/s41374-017-0001-8
Ford, L., Carter, G.P., Wang, Q., Seemann, T., Sintchenko, V., Glass, K., Williamson, D.A., Howard, P., Valcanis, M., Castillo, C.F.S., Sait, M., Howden, B.P., Kirk, M.D., 2018a. Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia. Foodborne Pathogens and Disease 15, 161–167. https://doi.org/10.1089/fpd.2017.2352
Ford, L., Wang, Q., Stafford, R., Ressler, K.-A., Norton, S., Shadbolt, C., Hope, K., Franklin, N., Krsteski, R., Carswell, A., Carter, G.P., Seemann, T., Howard, P., Valcanis, M., Castillo, C.F.S., Bates, J., Glass, K., Williamson, D.A., Sintchenko, V., Howden, B.P., Kirk, M.D., 2018b. Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing. Foodborne Pathogens and Disease 15, 285–292. https://doi.org/10.1089/fpd.2017.2353
Geurts, Y.M., Dugué, P.-A., Joo, J.E., Makalic, E., Jung, C.-H., Guan, W., Nguyen, S., Grove, M.L., Wong, E.M., Hodge, A.M., Bassett, J.K., FitzGerald, L.M., Tsimiklis, H., Baglietto, L., Severi, G., Schmidt, D.F., Buchanan, D.D., MacInnis, R.J., Hopper, J.L., Pankow, J.S., Demerath, E.W., Southey, M.C., Giles, G.G., English, D.R., Milne, R.L., 2017. Novel associations between blood DNA methylation and body mass index in middle-aged and older adults. International Journal Of Obesity 42, 887.
Gherardin, N.A., Souter, M.N., Koay, H.-F., Mangas, K.M., Seemann, T., Stinear, T.P., Eckle, S.B., Berzins, S.P., d’Udekem, Y., Konstantinov, I.E., Fairlie, D.P., Ritchie, D.S., Neeson, P.J., Pellicci, D.G., Uldrich, A.P., McCluskey, J., Godfrey, D.I., 2018. Human blood MAIT cell subsets defined using MR1 tetramers. Immunology & Cell Biology 96, 507–525. https://doi.org/10.1111/imcb.12021
Giulieri, S.G., Baines, S.L., Guerillot, R., Seemann, T., Gonçalves da Silva, A., Schultz, M., Massey, R.C., Holmes, N.E., Stinear, T.P., Howden, B.P., 2018. Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia. Genome Medicine 10, 65. https://doi.org/10.1186/s13073-018-0574-x
Gonçalves da Silva, A., Bulach, D.M., Carter, G.P., Strachan, J., Schultz, M.B., Ballard, S., Lee, R.S., Howden, B.P., Kwong, J.C., Baines, S.L., Stinear, T.P., Seemann, T., 2018a. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. Journal of Antimicrobial Chemotherapy 73, 3268–3278. https://doi.org/10.1093/jac/dky331
Gonçalves da Silva, A., Bulach, D.M., Carter, G.P., Strachan, J., Schultz, M.B., Ballard, S., Lee, R.S., Howden, B.P., Kwong, J.C., Baines, S.L., Stinear, T.P., Seemann, T., 2018b. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. Journal of Antimicrobial Chemotherapy 73, 3268–3278. https://doi.org/10.1093/jac/dky331
Griffin, P., Khadake, J., LeMay, K., Lewis, S., Orchard, S., Pask, A., Pope, B., Roessner, U., Russell, K., Seemann, T., Treloar, A., Tyagi, S., Christiansen, J., Dayalan, S., Gladman, S., Hangartner, S., Hayden, H., Ho, W., Keeble-Gagnere, G., Korhonen, P., Neish, P., Prestes, P., Richardson, M., Watson-Haigh, N., Wyres, K., Young, N., Schneider, M., 2018. Best practice data life cycle approaches for the life sciences [version 2; referees: 2 approved]. F1000Research 6. https://doi.org/10.12688/f1000research.12344.2
Guérillot, R., Li, L., Baines, S., Howden, B., Schultz, M.B., Seemann, T., Monk, I., Pidot, S.J., Gao, W., Giulieri, S., Gonçalves da Silva, A., D’Agata, A., Tomita, T., Peleg, A.Y., Stinear, T.P., Howden, B.P., 2018. Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq). Genome Medicine 10, 63. https://doi.org/10.1186/s13073-018-0572-z
Gulliver, E.L., Wright, A., Lucas, D.D., Mégroz, M., Kleifeld, O., Schittenhelm, R.B., Powell, D.R., Seemann, T., Bulitta, J.B., Harper, M., Boyce, J.D., 2018. Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of the GcvB seed binding region. RNA 24, 704–720. https://doi.org/10.1261/rna.063248.117
Herisse, M., Porter, J.L., Guerillot, R., Tomita, T., Goncalves Da Silva, A., Seemann, T., Howden, B.P., Stinear, T.P., Pidot, S.J., 2018. The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia. PeerJ 6, e4784. https://doi.org/10.7717/peerj.4784
Janic, A., Valente, L.J., Wakefield, M.J., Di Stefano, L., Milla, L., Wilcox, S., Yang, H., Tai, L., Vandenberg, C.J., Kueh, A.J., Mizutani, S., Brennan, M.S., Schenk, R.L., Lindqvist, L.M., Papenfuss, A.T., O’Connor, L., Strasser, A., Herold, M.J., 2018. DNA repair processes are critical mediators of p53-dependent tumor suppression. Nature Medicine 24, 947–953. https://doi.org/10.1038/s41591-018-0043-5
Jung, C.-H., Park, J.D., Georgeson, P., Mahmood, K., Milne, L.R., Southey, C.M., Pope, J.B., 2018. sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data. International Journal of Molecular Sciences 19. https://doi.org/10.3390/ijms19103172
Karthikaichamy, A., Deore, P., Srivastava, S., Coppel, R., Bulach, D., Beardall, J., Noronha, S., 2018. Temporal acclimation of Microchloropsis gaditana CCMP526 in response to hypersalinity. Bioresource Technology 254, 23–30. https://doi.org/10.1016/j.biortech.2018.01.062
Kondrashova, O., Topp, M., Nesic, K., Lieschke, E., Ho, G.-Y., Harrell, M.I., Zapparoli, G.V., Hadley, A., Holian, R., Boehm, E., Heong, V., Sanij, E., Pearson, R.B., Krais, J.J., Johnson, N., McNally, O., Ananda, S., Alsop, K., Hutt, K.J., Kaufmann, S.H., Lin, K.K., Harding, T.C., Traficante, N., Chenevix-Trench, G., Green, A., Webb, P., Gertig, D., Fereday, S., Moore, S., Hung, J., Harrap, K., Sadkowsky, T., Pandeya, N., Malt, M., Mellon, A., Robertson, R., Vanden Bergh, T., Jones, M., Mackenzie, P., Maidens, J., Nattress, K., Chiew, Y.E., Stenlake, A., Sullivan, H., Alexander, B., Ashover, P., Brown, S., Corrish, T., Green, L., Jackman, L., Ferguson, K., Martin, K., Martyn, A., Ranieri, B., White, J., Jayde, V., Mamers, P., Bowes, L., Galletta, L., Giles, D., Hendley, J., Schmidt, T., Shirley, H., Ball, C., Young, C., Viduka, S., Tran, H., Bilic, S., Glavinas, L., Brooks, J., Stuart-Harris, R., Kirsten, F., Rutovitz, J., Clingan, P., Glasgow, A., Proietto, A., Braye, S., Otton, G., Shannon, J., Bonaventura, T., Stewart, J., Begbie, S., Friedlander, M., Bell, D., Baron-Hay, S., Ferrier, A., Gard, G., Nevell, D., Pavlakis, N., Valmadre, S., Young, B., Camaris, C., Crouch, R., Edwards, L., Hacker, N., Marsden, D., Robertson, G., Beale, P., Beith, J., Carter, J., Dalrymple, C., Houghton, R., Russell, P., Links, M., Grygiel, J., Hill, J., Brand, A., Byth, K., Jaworski, R., Harnett, P., Sharma, R., Wain, G., Ward, B., Papadimos, D., Crandon, A., Cummings, M., Horwood, K., Obermair, A., Perrin, L., Wyld, D., Nicklin, J., Davy, M., Oehler, M.K., Hall, C., Dodd, T., Healy, T., Pittman, K., Henderson, D., Miller, J., Pierdes, J., Blomfield, P., Challis, D., McIntosh, R., Parker, A., Brown, B., Rome, R., Allen, D., Grant, P., Hyde, S., Laurie, R., Robbie, M., Healy, D., Jobling, T., Manolitsas, T., McNealage, J., Rogers, P., Susil, B., Sumithran, E., Simpson, I., Phillips, K., Rischin, D., Fox, S., Johnson, D., Lade, S., Loughrey, M., O’Callaghan, N., Murray, W., Waring, P., Billson, V., Pyman, J., Neesham, D., Quinn, M., Underhill, C., Bell, R., Ng, L.F., Blum, R., Ganju, V., Hammond, I., Leung, Y., McCartney, A., Buck, M., Haviv, I., Purdie, D., Whiteman, D., Zeps, N., deFazio, A., McNeish, I.A., Bowtell, D.D., Swisher, E.M., Dobrovic, A., Wakefield, M.J., Scott, C.L., Australian Ovarian Cancer Study (AOCS), 2018. Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nature Communications 9, 3970. https://doi.org/10.1038/s41467-018-05564-z
Kwong, Jason C, Chow, E.P.F., Stevens, K., Stinear, T.P., Seemann, T., Fairley, C.K., Chen, M.Y., Howden, B.P., 2018. Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study. Sex Transm Infect 94, 151. https://doi.org/10.1136/sextrans-2017-053287
Kwong, Jason C., Lane, C.R., Romanes, F., Gonçalves da Silva, A., Easton, M., Cronin, K., Waters, M.J., Tomita, T., Stevens, K., Schultz, M.B., Baines, S.L., Sherry, N.L., Carter, G.P., Mu, A., Sait, M., Ballard, S.A., Seemann, T., Stinear, T.P., Howden, B.P., 2018. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ 6, e4210. https://doi.org/10.7717/peerj.4210
Lacey, J.A., Allnutt, T.R., Vezina, B., Van, T.T.H., Stent, T., Han, X., Rood, J.I., Wade, B., Keyburn, A.L., Seemann, T., Chen, H., Haring, V., Johanesen, P.A., Lyras, D., Moore, R.J., 2018. Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens. BMC Genomics 19, 379. https://doi.org/10.1186/s12864-018-4771-1
Lee, J.Y.H., Monk, I.R., Gonçalves da Silva, A., Seemann, T., Chua, K.Y.L., Kearns, A., Hill, R., Woodford, N., Bartels, M.D., Strommenger, B., Laurent, F., Dodémont, M., Deplano, A., Patel, R., Larsen, A.R., Korman, T.M., Stinear, T.P., Howden, B.P., 2018. Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis. Nature Microbiology 3, 1175–1185. https://doi.org/10.1038/s41564-018-0230-7
Mahony, A.A., Buultjens, A.H., Ballard, S.A., Grabsch, E.A., Xie, S., Seemann, T., Stuart, R.L., Kotsanas, D., Cheng, A., Heffernan, H., Roberts, S.A., Coombs, G.W., Bak, N., Ferguson, J.K., Carter, G.C., Howden, B.P., Stinear, T.P., Johnson, P.D.R., 2018. Vancomycin-resistant Enterococcus faecium sequence type 796 – rapid international dissemination of a new epidemic clone. Antimicrobial Resistance & Infection Control 7, 44. https://doi.org/10.1186/s13756-018-0335-z
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