Publications

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2015

  1. Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC. POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA Devel Cell doi:10.1016/j.devcel.2015.05.024 [online]
  2. Moustafa AM, Seemann T, Gladman S, Adler B, Harper M, Boyce JD, Bennett MD. Comparative genomic analysis of Asian haemorrhagic septicaemia-associated strains of Pasteurella multocida identifies more than 100 haemorrhagic septicaemia-specific genes. PLOS ONE (accepted 17 Jun 2015)
  3. Gao W, Monk IR, Tobias NJ, Gladman S, Seemann T, Stinear TP, Howden BP. Large tandem chromosome expansions facilitate niche adaptation during persistent infection with drug-resistant Staphylococcus aureus. MGen (accepted 17 Jun 2015)
  4. Harrison PF, Powell DR, Clancy J, Preiss T, Boag P, Seemann T, Beilharz TH. PAT-seq: A method to study the integration of 3' UTR dynamics with gene-expression in the eukaryotic transcriptome. RNA 2015 Aug 1;21(8) [online]
  5. Ablordey AS, Vandelannoote K, Frimpong IA, Amissah NA, Eddyani M, Durnez L, Portaels F, de Jong BC, Leirs H, Porter JL, Mangas KM, Lam MMC, Buultjens B, Seemann T, Tobias NJ, Stinear TP. Whole genome comparisons suggest random distribution of Mycobacterium ulcerans genotypes in a Buruli ulcer endemic region of Ghana PLOS Negl Trop Dis. 2015 Mar 31;9(5):e0003798 [online]
  6. Zhu W, Ausin I, Seleznev A, Méndez-Vigo B, Picó F, Sureshkumar S, Sundaramoorthi V, Bulach D, Powell DR, Seemann T, Alonso-Blanco C, Balasubramanian S. Natural variation identifies ICARUS1, a universal gene required for cell proliferation and growth at high temperatures in Arabidopsis thaliana PLOS Genetics 2015 May 7;DOI:10.1371/journal.pgen.1005085 [online]
  7. Baines SL, Holt KE, Schultz MB, Seemann T, Howden BO, Jensen, SO, van Hal SJ, Coombs GW, Firth N, Powell DR, Stinear TP, Howden BP. Convergent Adaptation in the Dominant Global Hospital Clone ST239 of Methicillin-Resistant Staphylococcus aureus mBio 2015 Mar 3;6(2):e00080. [online]

2014

  1. Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalas M, Kajan L, Kibukawa E, Powell DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA. Community-driven development for computational biology at Sprints, Hackathons and Codefests BMC Bioinformatics. 2014 Nov 27;15 Suppl 14:S7. [online]
  2. Boritsch EC, Supply P, Honore N, Seemann T, Stinear TP, Brosch R. A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent. Mol Microbiol. 2014 Sep;93(5):835-52. [online]
  3. Kennan RM, Gilhuus M, Frosth S, Seemann T, Dhungyel OP, Whittington RJ, Boyce JD, Powell DR, Aspan A, Jorgensen HJ, Bulach DM, Rood JI. Genomic evidence for a globally distributed, bimodal population in the ovine footrot pathogen Dichelobacter nodosus MBio. 2014 Sep 30;5(5):e01821-14. [online]
  4. Albert M, Al-Obaid K, Al Fouzan W, Sheikh A, Udo E, Izumiya J, Bulach D, Seemann T. Isolation of Salmonella enterica serovar Kentucky ST 198 strain and its H2S-negative variant from a patient: implications for diagnosis J. Clin. Microbiol. 2014 Nov;52(11):4090-3 [online]
  5. Bager RJ, Kurdirkiene E, da Piedade I, Seemann T, Nielsen TK, Pors SE, Mattsson AH, Boyce JD, Adler B, Bojesen AM. In silico prediction of Gallibacterium anatis pan-immunogens Vet Res. 2014 Aug 8;45(1):80 [online]
  6. van der Zwan YG, Rijlaarsdam MA, Rossello FJ, Notini AJ, de Boer S, Watkins DN, Gillis AJ, Dorssers LC, White SJ, Looijenga LH. Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines. PLoS One 2014 Jun 2;9(6):e98330. [online]
  7. Seemann T. Prokka: rapid prokaryotic genome annotation Bioinformatics 2014 Jul 15;30(14):2068-9. [online] Access the recommendation on F1000Prime
  8. Lim SK, Stuart R, Mackin K, Carter G, Kotsanas D, Francis M, Easton M, Dimovski K, Elliot B, Riley T, Hogg G, Paul E, Korman T, Seemann T, Stinear TP, Lyras D, Jenkin GA. Emergence of a ribotype 244 strain of Clostridium difficile associated with severe disease and related to the epidemic ribotype 027 strain Clin Infect Dis. 2014 Jun;58(12):1723-30. [online]
  9. Chua KYL, Monk IR, Seemann T, Tuck KL, Porter JL, Stepnell J, Coombs GW, Davies JK, Stinear TP, Howden BP. Hyperexpression of alpha-Hemolysin Explains Enhanced Virulence of Sequence Type 93 Community-Associated Methicillin-Resistant Staphylococcus aureus BMC Microbiology 2014 Feb 10;14:31. [online]
  10. Stinear TP, Holt KE, Chua K, Stepnell J, Tuck KL, Coombs G, Harrison PF, Seemann T, Howden BJ. Adaptive Change Inferred from Genomic Population Analysis of the ST93 Epidemic Clone of Community-Associated Methicillin Resistant Staphylococcus aureus Genome Biol Evol. 2014 Jan;6(2):366-78. [online]
  11. Davies JK, Harrison PF, Lin Y-H, Bartley S, Khoo CA, Seemann T, Ryan CS, Kahler CM, Hill SA. The use of high-throughput DNA sequencing in the investigation of antigenic variation: application to Neisseria species PLOS ONE 2014 Jan 22;9(1):e86704. [online]

2013

  1. Panepinto JC, Heinz E, Traven A. The cellular roles of Ccr4-NOT in model and pathogenic fungi - implications for fungal virulence Front. Genet. 20 December 2013. [online]
  2. Seemann T Ten recommendations for creating usable bioinformatics command line software GigaScience 13 Nov 2013; 2:15 [online]
  3. Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Genome Biol Evol. 2013;5(12):2285-303. [online]
  4. Möller S, Afgan E, Banck M, Cock PJA, Kalas M, Kajan Laszlo, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Tille A, Guimera RV, Katayama T, Chapman B. Sprints, Hackathons and Codefests as community gluons in computational biology. EMBnet.journal North America, 19 Oct 2013. [online]
  5. Rossello FJ, Tothill RW, Britt K, Marini KD, Falzon J, Thomas DM, Peacock CD, Marchionni L, Li J, Bennett S, Tantoso E, Brown T, Chan P, Martelotto LG, Watkins DN. Next-Generation Sequence Analysis of Cancer Xenograft Models PLoS ONE Sep 26;8(9):e74432. [online]
  6. Marcsisin RA, Bartpho T, Bulach DM, Srikram A, Sermswan RW, Adler B, Murray GL. Use of a high-throughput screen to identify Leptospira mutants unable to colonise the carrier host or cause disease in the acute model of infection. J Med Microbiol. 2013 Oct;62(Pt 10):1601-8. [online]
  7. Zhang K, Murray G, Seemann T, Srikram A, Bartpho T, Sermswan R, Adler B, Hoke D. Leptospiral LruA is required for virulence and modulates an interaction with mammalian Apolipoprotein A-1 Infect Immun. 2013 Oct;81(10):3872-9 [online]
  8. Lam MMC, Seemann T, Tobias NJ, Chen H, Haring V, Moore RJ, Ballard S, Grayson LM, Johnson PDR, Howden BP, Stinear TP. Comparative Analysis of the Complete Genome of an Epidemic Hospital Sequence Type 203 Clone of Vancomycin-Resistant Enterococcus faecium BMC Genomics 2013 Sep 1;14(1):595. [online]
  9. Henry R, Lo M, Khoo C, Zhang H, Boysen RI, Picardeau M, Murray GL, Bulach DM, Adler B. Precipitation of Iron on the Surface of Leptospira interrogans Is Associated with Mutation of the Stress Response Metalloprotease HtpX. Appl Environ Microbiol. 2013 Aug;79(15):4653-60. [online]
  10. Howden BP, Holt KE, Lam MMC, Seemann T, Ballard S, Coombs G, Tong S, Grayson LM, Johnson PDR, Stinear TP. Genomic Insights to Control the Emergence of Vancomycin-Resistant Enterococci mBio 2013 Aug 13;4(4):e00412-13. [online]
  11. Howden BP, Beaume M, Harrison PF, Hernandez D, Schrenzel J, Seemann T, Francois P, Stinear TP. Analysis of the small RNA transcriptional response in multidrug resistant Staphylococcus aureus after antimicrobial exposure Antimicrob Agents Chemother. 2013 Aug;57(8):3864-74 [online]
  12. King AM, Bartpho T, Sermswan RW, Bulach DM, Eshghi A, Picardeau M, Adler B, Murray GL. Leptospiral outer membrane protein LipL41 is not essential for acute leptospirosis, but requires a small chaperone, Lep, for stable expression. Infect Immun. 2013 Aug;81(8):2768-76. [online]
  13. McEvoy C, Tsuji B, Gao W, Seemann T, Porter J, Doig K, Ngo D, Howden BJ, Stinear TP. Decreased Vancomycin Susceptibility in Staphylococcus aureus caused by IS256 Tempering of WalKR Expression Antimicrob Agents Chemother. 2013 Apr 29;57(7):3240-3249. [online]
  14. Dunstan RA, Heinz E, Wijeyewickrema LC, Pike RN, Purcell AW, Evans TJ, Praszkier J, Robins-Browne RM, Strugnell RA, Korotkov KV, Lithgow T. Assembly of the type II secretion system such as found in Vibrio cholerae depends on the novel Pilotin AspS PLoS Pathog 2013 Jan;9(1):e1003117 [online]
  15. Mangiamele P, Nicholson B, Wannemuehler Y, Seemann T, Logue C, Li G, Tivendale K, Nolan LK. Complete Genome Sequence of the Avian Pathogenic Escherichia coli Strain APEC O78 Genome Announc. 2013 May 2;1(2):e0002613. [online]
  16. Sherry N, Porter J, Seemann T, Watkins A, Stinear TP, Howden BP. Outbreak investigation using high-throughput genome sequencing within a diagnostic microbiology laboratory J Clin Microbiol. 2013 May;51(5):1396-401. [online]
  17. Bartley SN, Tzeng YL, Heel K, Lee CW, Mowlaboccus S, Seemann T, Lu W, Lin YH, Ryan CS, Peacock C, Stephens DS, Davies JK, Kahler CM. Attachment and Invasion of Neisseria meningitidis to Host Cells Is Related to Surface Hydrophobicity, Bacterial Cell Size and Capsule. PLoS One. 2013;8(2):e55798. [online]
  18. Gohil S, Kats LM, Seemann T, Fernandez KM, Siddiqui G, Cooke BM. Bioinformatic prediction of the exportome of Babesia bovis and identification of novel proteins in parasite-infected red blood cells Int J Parasitol. 2013 Feb 7. pii: S0020-7519(13)00036-2. [online]
  19. Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Medigue C, Parkhill J, Cruveiller S, Brosch R. Genome analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis Nat Genet. 2013 Feb;45(2):172-9. [online]
  20. Heinz E, Lithgow T. Back to basics: A revealing secondary reduction of the mitochondrial protein import pathway in diverse intracellular parasites Biochim Biophys Acta. 2013 Feb;1833(2):295-303. [online]
  21. Tobias N, Doig K, Medema M, Chen HL, Haring V, Moore R, Seemann T, Stinear TP. Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans ecovar Liflandii J Bacteriol. 2013 Feb;195(3):556-64. [online]
  22. Johnson TJ, Danzeisen JL, Trampel D, Nolan LK, Seemann T, Bager R, Bojesen AM. Genome analysis and phylogenetic relatedness of Gallibacterium anatis strains from poultry PLOS ONE 2013 Jan 24;8(1):e54844 [online]
  23. Vinh NX, Chetty M, Coppel R, Gaudana S, Wangikar PP. A model of the circadian clock in the cyanobacterium Cyanothece sp. ATCC 51142. BMC Bioinformatics 2013 Jan 21;14 Suppl 2:S14. [online]
  24. Powell DR, Seemann T. VAGUE: a graphical front-end for the Velvet assembler Bioinformatics 2013 Jan 15;29(2):264-5. [online]
  25. Murray GL, Lo M, Bulach DM, Srikram A, Seemann T, Quinsey NS, Sermswan RW, Allen A, Adler B. Evaluation of 238 antigens of Leptospira borgpetersenii serovar Hardjo for protection against kidney colonisation Vaccine 2013 Jan 7;31(3):495-499. [online]

2012

  1. Ma C, Gunther S, Cooke B, Coppel RL. Geneious plugins for the access of PlasmoDB and PiroplasmaDB databases. Parasitol Int. 2012 Nov 24;62(2):134-136. [online]
  2. Hewitt VL, Heinz E, Shingu-Vazquez M, Qu Y, Jelicic B, Lo TL, Beilharz TH, Dumsday G, Gabriel K, Traven A, Lithgow T. A model system for mitochondrial biogenesis reveals evolutionary rewiring of protein import and membrane assembly pathways Proc Natl Acad Sci USA. 2012 Dec 4;109(49):E3358-66. [online]
  3. Rainczuk AK, Yamaryo-Botte Y, Brammananth R, Stinear TP, Seemann T, Coppel RL, McConville MJ, Crellin PK. The lipoprotein LpqW is essential for the mannosylation of periplasmic glycolipids in Corynebacteria J Biol Chem. 2012 Dec 14;287(51):42726-38. [online]
  4. Vinh NX, Chetty M, Coppel R, Wangikar PP. Issues impacting genetic network reverse engineering algorithm validation usingsmall networks. Biochim Biophys Acta. 2012 Dec;1824(12):1434-41. [online]
  5. Blasdell KR, Voysey R, Bulach DM, Trinidad L, Tesh RB, Boyle DB, Walker PJ. Malakal virus from Africa and Kimberley virus from Australia are geographic variants of a widely distributed ephemerovirus. Virology. 2012 Nov 10;433(1):236-44. [online]
  6. Traven A, Jänicke A, Harrison P, Swaminathan A, Seemann T, Beilharz TH. Transcriptional Profiling of a Yeast Colony Provides New Insight into the Heterogeneity of Multicellular Fungal Communities PLoS ONE 2012;7(9):e46243 [online]
  7. Webb CT, Heinz E, Lithgow T. Evolution of the β-barrel assembly machinery Trends Microbiol. 2012 Dec;20(12):612-20. [online]
  8. Sunarto A, Liongue C, McColl KA, Adams MM, Bulach D, Crane MS, Schat KA, Slobedman B, Barnes AC, Ward AC, Walker PJ. Koi herpesvirus encodes and expresses a functional interleukin-10. J Virol. 2012 Nov;86(21):11512-20. [online]
  9. Chandry PS, Gladman S, Moore SC, Seemann T, Crandall KA, Fegan N. A Genomic Island in Salmonella enterica ssp. salamae Provides New Insights on the Genealogy of the Locus of Enterocyte Effacement. PLoS ONE 2012;7(7):e41615. [online]
  10. Doig KD, Holt KE, Fyfe JAM, Lavender CJ, Eddyani M, Portaels F, Yeboah-Manu D, Pluschke G, Seemann T, Stinear TP. On the origin of Mycobacterium ulcerans, the causative agent of buruli ulcer BMC Genomics 2012 Jun 19;13:258. [online]
  11. Boyle DB, Bulach DM, Amos-Ritchie R, Adams MM, Walker PJ, Weir R. Genomic sequences of Australian bluetongue virus prototype serotypes reveal global relationships and possible routes of entry into Australia. J Virol. 2012 Jun;86(12):6724-31. [online]
  12. Blasdell KR, Voysey R, Bulach D, Joubert DA, Tesh RB, Boyle DB, Walker PJ. Kotonkan and Obodhiang viruses: African ephemeroviruses with large and complex genomes. Virology. 2012 Apr 10;425(2):143-53. [online]
  13. Dawes FE, Bulach DM, Kuzevski A, Bettelheim KA, Venturini C, Djordjevic SP, Walker MJ. Molecular characterization of a 21.4 kilobase antibiotic resistance plasmid from an α-hemolytic Escherichia coli O108:H- human clinical isolate. PLoS One. 2012;7(4):e34718 [online]
  14. Boyce JD, Seemann T, Adler B, Harper M. Pathogenomics of Pasteurella multocida. Curr Top Microbiol Immunol. 2012;361:23-38. [online]
  15. Lam MMC, Seemann T, Bulach DM, Gladman SL, Chen H, Haring V, Moore RJ, Ballard S, Grayson ML, Johnson PDR, Howden BP, Stinear TP. Comparative Analysis of the First Complete Enterococcus faecium Genome J Bacteriol. 2012 May;194(9):2334-41. [online]
  16. Castro-Nallar E, Chen H, Gladman S, Moore SC, Seemann T, Powell IB, Hillier A, Crandall KA, Chandry PS. Population Genomics and Phylogeography of an Australian Dairy Factory Derived Lytic Bacteriophage Genome Biol Evol. 2012;4(3):382-93. [online]
  17. Shepard S, Danzeisen J, Isaacson R, Seemann T, Achtman M, Johnson T. Genome Sequences and Phylogenetic Analysis of K88- and F18-Positive Porcine Enterotoxigenic Escherichia coli J. Bacteriol. 2012 Jan;194(2):395-405. [online]
  18. Henry R, Vithanage N, Harrison PF, Seemann T, Coutts S, Moffatt JH, Nation RL, Li J, Harper M, Adler B. Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids and poly-beta-1,6-N-acetylglucosamine Antimicrob Agents Chemother. 2012 Jan;56(1):59-69. [online]

2011

  1. Howden BP, McEvoy CRE, Allen DL, Harrison PF, Jensen SO, Firth N, Bell J, Coombs G, Bennett-Wood V, Robins-Browne R, Davies JK, Seemann T, Stinear TP. Evolution of multidrug resistance during Staphylococcus aureus infection involves the essential cell wall biosynthesis regulator WalKR PLoS Pathog. 2011 Nov;7(11):e1002359. [online]
  2. Chua KYL, Seemann T, Harrison PF, Monagle S, Korman TM, Johnson PDR, Coombs GW, Howden BO, Davies JK, Howden BP, Stinear TP. The Dominant Australian Community-Acquired Methicillin-Resistant Staphylococcus aureus Clone ST93-IV [2B] is Highly Virulent and Genetically Distinct PLoS ONE 2011;6(10):e25887. [online]
  3. Vinh NX, Chetty M, Coppel R, Wangikar PP. GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion. Bioinformatics. 2011 Oct 1;27(19):2765-6. [online]
  4. Bannam T, Yan X, Harrison PF, Seemann T, Keyburn A, Stubenrauch C, Weeramantri L, Cheung J, McClane B, Boyce JD, Moore R, Rood JI. Necrotic enteritis-derived Clostridium perfringens with three closely related independently conjugative toxin and antibiotic resistance plasmids mBio 2011 Sep 27;2(5):e00190-11. [online]
  5. Naughton S, Parker D, Seemann T, Thomas T, Turnbull L, Rose B, Bye P, Cordwell S, Whitchurch C, Manos J. Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung PLoS ONE 2011 Sep;6(9):e24526 [online]
  6. Wynne JW, Bull TJ, Seemann T, Bulach DM, Wagner J, Kirkwood CD, Michalski WP. Exploring the zoonotic potential of Mycobacterium avium subspecies paratuberculosis through comparative genomics. PLoS ONE 2011:6(7):e22171. [online]
  7. Johnson TJ, Fernandez-Alarcon C, Bojesen AM, Nolan LK, Trampel DW, Seemann T. Complete Genome Sequence of Gallibacterium anatis strain UMN179, isolated from a laying hen with peritonitis. J Bacteriol. 2011 Jul;193(14):3676-7 [online]
  8. Adler B, Lo M, Seemann T, Murray GL. Pathogenesis of leptospirosis: The influence of genomics. Vet Microbiol. 2011 Nov 21;153(1-2):73-81. [online]
  9. Carter GP, Awad MM, Hao Y, Thelen T, Bergin IL, Howarth PM, Seemann T, Rood JI, Aronoff DM, Lyras D. TcsL is an essential virulence factor in Clostridium sordellii ATCC9714. Infect Immun. 2011 Mar;79(3):1025-32. [online]

2010

  1. Ma C, Harrison PF, Wang L, Coppel RL. Automated estimation of parasitaemia of Plasmodium yoelii-infected mice by digital image analysis of Giemsa-stained thin blood smears Malaria Journal 2010 Dec 1; 9:348. [online]
  2. Pidot S, Porter J, Tobias N, Catmull D, Seemann T, Kidd S, Davies J, Dashper S, Stinear T. Regulation of the 18 kDa heat shock protein in Mycobacterium ulcerans: an alpha-crystallin ortholog that promotes biofilm formation Molecular Microbiology 2010 Dec;78(5):1216-31. [online]
  3. Pidot SJ, Porter JL, Marsollier L, Chauty A, Migot-Nabias F, Badaut C, Benard A, Ruf MT, Seemann T, Johnson PD, Davies JK, Jenkin GA, Pluschke G, Stinear TP. Serological Evaluation of Mycobacterium ulcerans Antigens Identified by Comparative Genomics. PLoS Negl Trop Dis. 2010 Nov 2;4(11):e872. [online]
  4. Wynne JW, Seemann T, Bulach D, Coutts SA, Talaat AM, Michalski WP. Re-sequencing the Mycobacterium avium subsp. paratuberculosis K10 genome: improved annotation and revised genome sequence. J Bacteriol. 2010 Dec;192(23):6319-20. [online]
  5. Moffatt JH, Harper M, Harrison P, Hale JD, Vinogradov E, Seemann T, Henry R, Crane B, St Michael F, Cox AD, Adler B, Nation RL, Li J, Boyce JD. Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide. Antimicrob Agents Chemother. 2010 Dec;54(12):4971-7. [online]
  6. Johnson PD, Ballard SA, Grabsch EA, Stinear TP, Seemann T, Young HL, Grayson ML, Howden BP. A Sustained Hospital Outbreak of Vancomycin-Resistant Enterococcus faecium Bacteremia due to Emergence of vanB E. faecium Sequence Type 203. J Infect Dis. 2010;202(8):1278-86. [online]
  7. Howden BP, Seemann T, Harrison PF, McEvoy CR, Stanton JA, Rand CJ, Mason CW, Jensen SO, Firth N, Davies JK, Johnson PD, Stinear TP. Complete Genome Sequence of Staphylococcus aureus strain JKD6008, a ST239 clone of Methicillin-Resistant Staphylococcus aureus with intermediate level vancomycin resistance. J Bacteriol. 2010 Nov;192(21):5848-9. [online]
  8. Chua K, Seemann T, Harrison PF, Davies JK, Coutts SJ, Chen H, Haring V, Moore R, Howden BP, Stinear TP. Complete Genome Sequence of Staphylococcus aureus strain JKD6159, a Unique Australian clone of ST93-IV Community Methicillin-Resistant Staphylococcus aureus. J Bacteriol. 2010 Oct;192(20):5556-7. [online]
  9. Fyfe JAM, Lavender CJ, Handasyde KA, Legione AR, O'Brien CR, Stinear TP, Pidot SJ, Seemann T, Benbow EM, Wallace JR, McCowan C, Johnson PDR. A Major Role for Mammals in the Ecology of Mycobacterium ulcerans. PLoS Negl Trop Dis. 2010 4(8):e791. [online]
  10. Robinson N, Piedrafita D, Snibson K, Harrison P, Meeusen EN. Immune cell kinetics in the ovine abomasal mucosa following hyperimmunization and challenge with Haemonchus contortus. Vet Res. 2010 Jul-Aug;41(4):37. [online]
  11. Röltgen K, Qi W, Ruf MT, Mensah-Quainoo E, Pidot SJ, Seemann T, Stinear TP, Käser M, Yeboah-Manu D, Pluschke G. Single Nucleotide Polymorphism Typing of Mycobacterium ulcerans Reveals Focal Transmission of Buruli Ulcer in a Highly Endemic Region of Ghana PLoS Negl Trop Dis. 2010 Jul 20;4(7):e751. [online]
  12. Gao W, Chua K, Davies JK, Newton HJ, Seemann T, Harrison PF, Holmes NE, Rhee HW, Hong JI, Hartland EL, Stinear TP, Howden BP. Two Novel Point Mutations in Clinical Staphylococcus aureus Reduce Linezolid Susceptibility and Switch on the Stringent Response to Promote Persistent Infection PLoS Pathog. 2010 Jun 10;6(6):e1000944 [online]
  13. Steen JA, Steen JA, Harrison P, Seemann T, Wilkie I, Harper M, Adler B, Boyce JD. Fis is essential for capsule production in Pasteurella multocida and regulates expression of other important virulence factors PLoS Pathog. 2010 Feb 5;6(2):e1000750 [online]

2009

  1. Stepto N, Coffey V, Carey A, Ponnampalam A, Canny B, Powell D, Hawley J. Global gene expression in skeletal muscle from well-trained strength and endurance athletes Med Sci Sports Exerc. 2009 Mar;41(3):546-565. [online]
  2. Sehgal MS, Gondal I, Dooley LS, Coppel R. How to improve postgenomic knowledge discovery using imputation. EURASIP J Bioinform Syst Biol. 2009:717136. [online]
  3. Tobias NJ, Seemann T, Pidot SJ, Porter JL, Marsollier L, Marion E, Letournel F, Zakir T, Azuolas J, Wallace JR, Hong H, Davies JK, Howden BP, Johnson PD, Jenkin GA, Stinear TP. Mycolactone Gene Expression Is Controlled by Strong SigA-Like Promoters with Utility in Studies of Mycobacterium ulcerans and Buruli Ulcer PLoS Negl Trop Dis 2009 3(11):e553. [online]
  4. K. Chua, G. Coombs, T. Seemann, J.K. Davies, R. Moore, V. Haring, T.P. Stinear, B.P. Howden Whole Genome Sequence of ST93-MRSA-IV, a Unique Australian Clone of Community-Associated, Methicillin-Resistant Staphylococcus aureus 49th ICAAC, Interscience Conference on Antimicrobial Agents and Chemotherapy San Francisco, California 12-15 Sep 2009. [online]
  5. Newton HJ, Sloan J, Bulach DM, Seemann T, Allison CC, Tauschek M, Robins-Browne RM, Paton JC, Whittam TS, Paton AW, Hartland EL. Shiga Toxin producing Escherichia coli Strains Negative for Locus of Enterocyte Effacement Emerg Infect Dis. 2009 Mar;15(3):372-80. [online]

2008

  1. Pidot SJ, Hong H, Seemann T, Porter JL, Yip MJ, Men A, Johnson M, Wilson P, Davies JK, Leadlay PF, Stinear TP. Deciphering the Genetic Basis for Polyketide Variation Among Mycobacteria Producing Mycolactones BMC Genomics 2008 Oct 7;9:462 [online]
  2. Nicholas KR, Kumar A, Strahm Y, Powell DR, Seemann T, Daly KA, Brennan A, Menzies K, Sharp J, Digby M, Lefevre C. MammoSapiens: eResearch of the lactation program.Building online facilities for collaborative molecular and evolutionary analysis of lactation and other biological systems from gene sequences and gene expression data. eResearch Australasia 2008 29 Sep - 1 Oct, Melbourne, Australia. [online]
  3. Stinear TP, Seemann T, Harrison PF, Jenkin GA, Davies JK, Johnson PD, Abdellah Z, Arrowsmith C, Chillingworth T, Churcher C, Clarke K, Cronin A, Davis P, Goodhead I, Holroyd N, Jagels K, Lord A, Moule S, Mungall K, Norbertczak H, Quail MA, Rabbinowitsch E, Walker D, White B, Whitehead S, Small PL, Brosch R, Ramakrishnan L, Fischbach MA, Parkhill J, Cole ST. Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res. 2008 May;18(5):729-41. [online]
  4. Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, Creno S, Kuczek ES, Bommezzadri S, Davis JC, McGrath A, Johnson MJ, Boursaux-Eude C, Seemann T, Rouy Z, Coppel RL, Rood JI, Lajus A, Davies JK, Medigue C, Adler B. Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis. PLoS ONE. 2008 Feb 13;3(2):e1607. [online]

2007

  1. Myers GS, Parker D, Al-Hasani K, Kennan RM, Seemann T, Ren Q, Badger JH, Selengut JD, Deboy RT, Tettelin H, Boyce JD, McCarl VP, Han X, Nelson WC, Madupu R, Mohamoud Y, Holley T, Fedorova N, Khouri H, Bottomley SP, Whittington RJ, Adler B, Songer JG, Rood JI, Paulsen IT. Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus Nat Biotechnol. 2007 May;25(5):569-75. [online]
  2. Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, Garnier T, Meurice G, Simon D, Bouchier C, Ma L, Tichit M, Porter JL, Ryan J, Johnson PD, Davies JK, Jenkin GA, Small PL, Jones LM, Tekaia F, Laval F, Daffé M, Parkhill J, Cole ST. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer Genome Res. 2007 Feb;17(2):192-200. [online]
  3. Dix TI, Powell DR, Allison L, Bernal J, Jaeger S, Stern L. Comparative analysis of long DNA sequences by per element information content using different contexts. BMC Bioinformatics. 2007 May 3;8 Suppl 2:S10. [online]

2006

  1. Torsten Seemann, Victorian Bioinformatics Consortium, Asia Pacific Biotech News, Vol 10, No 24, 30 December 2006 [online]
  2. Strahm Y, Powell D, Lefevre C. EST-PAC a web package for EST annotation and protein sequence prediction. Source Code Biol Med. 2006 Oct 12;1:2. [online]
  3. Bulach DM, Zuerner RL, Wilson P, Seemann T, McGrath A, Cullen PA, Davis J, Johnson M, Kuczek E, Alt DP, Peterson-Burch B, Coppel RL, Rood JI, Davies JK, Adler B. Genomic Reduction in Leptospira borgpetersenii reflects Limited Transmission Potential., Proc Natl Acad Sci USA 2006 Sep 26;103(39):14560-5. [online]
  4. Zuerner R, Bulach D, Seemann T et al, Chapter Comparative Analysis of Pathogenic Leptospira Genomes Molecular Biology of Spirochetes, Volume 373 NATO Science Series: Life and Behavioural Sciences, Edited by: F.C. Cabello, D. Hulinska and H.P. Godfrey October 2006, IOS Press. The Netherlands. ISBN: 1-58603-665-2 [online]
  5. Bannam TL, Teng WL, Bulach D, Lyras D, Rood JI. Functional identification of conjugation and replication regions of the tetracycline resistance plasmid pCW3 from Clostridium perfringens. J Bacteriol. 2006 Jul;188(13):4942-51. [online]
  6. Bulach DM, Seemann T, Zuerner RL, Adler B. The organization of Leptospira at a genomic level. In, Bacterial Genomes and Infectious Diseases (Chan VL, Sherman PM, Bourke B, Eds). pp 109-123. Humana Press, Totowa, USA. 2006. ISBN 1-58829-496-X [online]
  7. Lo M, Bulach DM, Powell DR, Haake DA, Matsunaga J, Paustian ML, Zuerner RL, Adler B. Effects of temperature on gene expression patterns in Leptospira interrogans serovar Lai as assessed by whole-genome microarrays. Infect Immun. 2006 Oct;74(10):5848-59.
  8. O'Connor JR, Lyras D, Farrow KA, Adams V, Powell DR, Hinds J, Cheung JK, Rood JI. Construction and analysis of chromosomal Clostridium difficile mutants. Mol Microbiol. 2006 Sep;61(5):1335-51. [online]
  9. Gunesekere IC, Kahler CM, Powell DR, Snyder LA, Saunders NJ, Rood JI, Davies JK. Comparison of the RpoH-dependent regulon and general stress response in Neisseria gonorrhoeae. J Bacteriol. 2006 Jul;188(13):4769-76. [online]
  • 2005

    1. B Adler, D Bulach, P Cullen, J Davies, J Rood, R Coppel, T Seemann, R Zuerner, D Alt, A McGrath, P Wilson and E Kuczek: What Can We Learn From Comparative Genomics of Leptospira?, (abstract), 4th International Leptospirosis Society Meeting Abstracts and Proceedings, November 2005, pp 130.
    2. D M Bulach, T Seemann, A McGrath, E Kuczek, R L Coppel, J K Davies, J I Rood, D P Alt, R L Zuerner and B Adler: The Genome of Leptospira Biflexa, (abstract), 4th International Leptospirosis Society Meeting Abstracts and proceedings, November 2005, pp 136. [online]
    3. Matsoso LG, Kana BD, Crellin PK, Lea-Smith D, Peolis A, Powell DR, Dawes SS, Rubin H, Coppel RL, Mizrahi V. Function of the cytochrome bc1-aa3 branch of the respiratory network in mycobacteria and network adaptation occurring in response to its disruption. J Bacteriol. 2005 Sep;187(18):6300-6308. [online]

    2004

    1. Adler B, Bulach D, Cullen P, Davies J, Rood J, Coppel R, Seemann T, Zuerner R, Alt D, McGrath A, Wilson P, Kuczek E. What can we learn from comparative genomics of Leptospira?, Aust. Soc. Microbiol. SY 11.1 Sydney, Australia. (2004).

    2003

    1. A McGrath, J Davis, P J Wilson, D Bulach, T Seemann, J Davies, R Coppel, B Adler, E S Kuczek. Assembly and Annotation of the Leptospira Borgpetersenii Serovar Hardjobovis Genome Sequence, Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology (ISMB 2003) , Brisbane,QLD, Australia, 29 June - 3 July 2003, 1pp. [online]