Publications

Separovich RJ, Wilkins MR. Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast. J Biol Chem. 2021 Aug;297(2):100939. doi: 10.1016/j.jbc.2021.100939.

Kim KW, Deveson IW, Pang CNI, Yeang M, Naing Z, Adikari T, Hammond JM, Stevanovski I, Beukers AG, Verich A, Yin S, McFarlane D, Wilkins MR, Stelzer-Braid S, Bull RA, Craig ME, van Hal SJ, Rawlinson WD. Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing. Sci Rep. 2021 Feb 16;11(1):3934. doi: 10.1038/s41598-021-83642-x.

B?hm JW, Sia KCS, Jones C, Evans K, Mariana A, Pang I, Failes T, Zhong L, Mayoh C, Landman R, Collins R, Erickson SW, Arndt G, Raftery MJ, Wilkins MR, Norris MD, Haber M, Marshall GM, Lock RB. Combination efficacy of ruxolitinib with standard-of-care drugs in CRLF2-rearranged Ph-like acute lymphoblastic leukemia. Leukemia. 2021 Nov;35(11):3101-3112. doi: 10.1038/s41375-021-01248-8.

Vázquez-Campos X, Kinsela AS, Bligh MW, Payne TE, Wilkins MR, Waite TD. Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. Front Microbiol. 2021 Oct 18;12:732575. doi: 10.3389/fmicb.2021.732575.

Hamey JJ, Nguyen A, Wilkins MR. Discovery of Arginine Methylation, Phosphorylation, and Their Co-occurrence in Condensate-Associated Proteins in Saccharomyces cerevisiae. J Proteome Res. 2021 May 7;20(5):2420-2434. doi: 10.1021/acs.jproteome.0c00927.

Deshpande NP, Riordan SM, Gorman CJ, Nielsen S, Russell TL, Correa-Ospina C, Fernando BSM, Waters SA, Castaño-Rodríguez N, Man SM, Tedla N, Wilkins MR, Kaakoush NO. Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus. Genome Med. 2021 Aug 19;13(1):133. doi: 10.1186/s13073-021-00951-6.

Separovich RJ, Wong MWM, Chapman TR, Slavich E, Hamey JJ, Wilkins MR. Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential. J Biol Chem. 2021 Jan-Jun;296:100192. doi: 10.1074/jbc.RA120.015995.

Lorenzi L, Chiu HS, Avila Cobos F, Gross S, Volders PJ, Cannoodt R, Nuytens J, Vanderheyden K, Anckaert J, Lefever S, Tay AP, de Bony EJ, Trypsteen W, Gysens F, Vromman M, Goovaerts T, Hansen TB, Kuersten S, Nijs N, Taghon T, Vermaelen K, Bracke KR, Saeys Y, De Meyer T, Deshpande NP, Anande G, Chen TW, Wilkins MR, Unnikrishnan A, De Preter K, Kjems J, Koster J, Schroth GP, Vandesompele J, Sumazin P, Mestdagh P. Publisher Correction: The RNA Atlas expands the catalog of human non-coding RNAs. Nat Biotechnol. 2021 Nov;39(11):1467. doi: 10.1038/s41587-021-00996-3.

Kinsela AS, Bligh MW, Vázquez-Campos X, Sun Y, Wilkins MR, Comarmond MJ, Rowling B, Payne TE, Waite TD. Biogeochemical Mobility of Contaminants from a Replica Radioactive Waste Trench in Response to Rainfall-Induced Redox Oscillations. Environ Sci Technol. 2021 Jul 6;55(13):8793-8805. doi: 10.1021/acs.est.1c01604.

Pang TCY, Xu Z, Mekapogu AR, Pothula S, Becker T, Corley S, Wilkins MR, Goldstein D, Pirola R, Wilson J, Apte M. HGF/c-Met Inhibition as Adjuvant Therapy Improves Outcomes in an Orthotopic Mouse Model of Pancreatic Cancer. Cancers (Basel). 2021 Jun 2;13(11):2763. doi: 10.3390/cancers13112763.

Zaman MS, Barman SK, Corley SM, Wilkins MR, Malladi CS, Wu MJ. Transcriptomic insights into the zinc homeostasis of MCF-7 breast cancer cells via next-generation RNA sequencing. Metallomics. 2021 Jun 8;13(6):mfab026. doi: 10.1093/mtomcs/mfab026.

Khan MAM, Deshpande NP, Shuttleworth LA, Osborne T, Collins D, Wilkins MR, Gurr GM, Reynolds OL. Raspberry ketone diet supplement reduces attraction of sterile male Queensland fruit fly to cuelure by altering expression of chemoreceptor genes. Sci Rep. 2021 Sep 3;11(1):17632. doi: 10.1038/s41598-021-96778-7.

Hamey JJ, Rakow S, Bouchard C, Senst JM, Kolb P, Bauer UM, Wilkins MR, Hart- Smith G. Systematic investigation of PRMT6 substrate recognition reveals broad specificity with a preference for an RG motif or basic and bulky residues. FEBS J. 2021 Oct;288(19):5668-5691. doi: 10.1111/febs.15837.

Bayat A, Deshpande NP, Wilkins MR, Parameswaran S. Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach. IEEE/ACM Trans Comput Biol Bioinform. 2020 Jan-Feb;17(1):334-338. doi: 10.1109/TCBB.2018.2875479.

Smith DL, Erce MA, Lai YW, Tomasetig F, Hart-Smith G, Hamey JJ, Wilkins MR. Crosstalk of Phosphorylation and Arginine Methylation in Disordered SRGG Repeats of Saccharomycescerevisiae Fibrillarin and Its Association with Nucleolar Localization. J Mol Biol. 2020 Jan 17;432(2):448-466. doi: 10.1016/j.jmb.2019.11.006.

Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun. 2020 Oct 16;11(1):5301. doi: 10.1038/s41467-020-19045-9.

Separovich RJ, Pang CNI, Wilkins MR. Controlling the Controllers: Regulation of Histone Methylation by Phosphosignalling. Trends Biochem Sci. 2020 Dec;45(12):1035-1048. doi: 10.1016/j.tibs.2020.08.004.

Leitner A, Bonvin AMJJ, Borchers CH, Chalkley RJ, Chamot-Rooke J, Combe CW, Cox J, Dong MQ, Fischer L, Götze M, Gozzo FC, Heck AJR, Hoopmann MR, Huang L, Ishihama Y, Jones AR, Kalisman N, Kohlbacher O, Mechtler K, Moritz RL, Netz E, Novak P, Petrotchenko E, Sali A, Scheltema RA, Schmidt C, Schriemer D, Sinz A, Sobott F, Stengel F, Thalassinos K, Urlaub H, Viner R, Vizcaíno JA, Wilkins MR, Rappsilber J. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure. 2020 Nov 3;28(11):1259-1268. doi: 10.1016/j.str.2020.09.011.

Yang L, Chen Z, Stout ES, Delerue F, Ittner LM, Wilkins MR, Quinlan KGR, Crossley M. Methylation of a CGATA element inhibits binding and regulation by GATA-1. Nat Commun. 2020 May 22;11(1):2560. doi: 10.1038/s41467-020-16388-1.

Separovich RJ, Wong MWM, Chapman TR, Slavich E, Hamey JJ, Wilkins MR. Post- translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential. J Biol Chem. 2021 Jan-Jun;296:100192. doi: 10.1074/jbc.RA120.015995.

Emery-Corbin SJ, Hamey JJ, Ansell BRE, Balan B, Tichkule S, Stroehlein AJ, Cooper C, McInerney BV, Hediyeh-Zadeh S, Vuong D, Crombie A, Lacey E, Davis MJ, Wilkins MR, Bahlo M, Svärd SG, Gasser RB, Jex AR. Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia. Mol Biol Evol. 2020 Dec 16;37(12):3525-3549. doi: 10.1093/molbev/msaa186.

Kim KW, Allen DW, Briese T, Couper JJ, Barry SC, Colman PG, Cotterill AM, Davis EA, Giles LC, Harrison LC, Harris M, Haynes A, Horton JL, Isaacs SR, Jain K, Lipkin WI, McGorm K, Morahan G, Morbey C, Pang ICN, Papenfuss AT, Penno MAS, Sinnott RO, Soldatos G, Thomson RL, Vuillermin P, Wentworth JM, Wilkins MR, Rawlinson WD, Craig ME; ENDIA STUDY GROUP. Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes. Pediatr Diabetes. 2020 Mar;21(2):271-279. doi: 10.1111/pedi.12952.

Anande G, Deshpande NP, Mareschal S, Batcha AMN, Hampton HR, Herold T, Lehmann S, Wilkins MR, Wong JWH, Unnikrishnan A, Pimanda JE. RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia. Clin Cancer Res. 2020 Jul 15;26(14):3597-3607. doi: 10.1158/1078-0432.CCR-20-0184.

Pang CNI, Ballouz S, Weissberger D, Thibaut LM, Hamey JJ, Gillis J, Wilkins MR, Hart-Smith G. Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. Mol Cell Proteomics. 2020 Nov;19(11):1876-1895. doi: 10.1074/mcp.RA120.002154.

Nadkarni MA, Deshpande NP, Wilkins MR, Hunter N. Intra-species variation within Lactobacillus rhamnosus correlates to beneficial or harmful outcomes: lessons from the oral cavity. BMC Genomics. 2020 Sep 24;21(1):661. doi: 10.1186/s12864-020-07062-3.

Bartolec TK, Smith DL, Pang CNI, Xu YD, Hamey JJ, Wilkins MR. Cross-linking Mass Spectrometry Analysis of the Yeast Nucleus Reveals Extensive Protein- Protein Interactions Not Detected by Systematic Two-Hybrid or Affinity Purification-Mass Spectrometry. Anal Chem. 2020 Jan 21;92(2):1874-1882. doi: 10.1021/acs.analchem.9b03975.

Paramsothy S, Nielsen S, Kamm MA, Deshpande NP, Faith JJ, Clemente JC, Paramsothy R, Walsh AJ, van den Bogaerde J, Samuel D, Leong RWL, Connor S, Ng W, Lin E, Borody TJ, Wilkins MR, Colombel JF, Mitchell HM, Kaakoush NO. Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis. Gastroenterology. 2019 Apr;156(5):1440-1454.e2. doi: 10.1053/j.gastro.2018.12.001.

Winter DL, Wilkins MR, Donald WA. Differential Ion Mobility-Mass Spectrometry for Detailed Analysis of the Proteome. Trends Biotechnol. 2019 Feb;37(2):198-213. doi: 10.1016/j.tibtech.2018.07.018.

Lowe BR, Maxham LA, Hamey JJ, Wilkins MR, Partridge JF. Histone H3 Mutations: An Updated View of Their Role in Chromatin Deregulation and Cancer. Cancers (Basel). 2019 May 13;11(5):660. doi: 10.3390/cancers11050660.

Tay AP, Liang A, Wilkins MR, Pang CNI. Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle. Curr Protoc Bioinformatics. 2019 Jun;66(1):e71. doi: 10.1002/cpbi.71.

Lai YW, Pang CNI, Campbell LT, Chen SCA, Wilkins MR, Carter DA. Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces. Front Microbiol. 2019 Oct 1;10:2195. doi: 10.3389/fmicb.2019.02195.

Schneider MV, Griffin PC, Tyagi S, Flannery M, Dayalan S, Gladman S, Watson-Haigh N, Bayer PE, Charleston M, Cooke I, Cook R, Edwards RJ, Edwards D, Gorse D, McConville M, Powell D, Wilkins MR, Lonie A. Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Brief Bioinform. 2019 Mar 22;20(2):384-389. doi: 10.1093/bib/bbx071.

Kim KW, Horton JL, Pang CNI, Jain K, Leung P, Isaacs SR, Bull RA, Luciani F, Wilkins MR, Catteau J, Lipkin WI, Rawlinson WD, Briese T, Craig ME. Higher abundance of enterovirus A species in the gut of children with islet autoimmunity. Sci Rep. 2019 Feb 11;9(1):1749. doi: 10.1038/s41598-018-38368-8.

Winter DL, Mastellone J, Kabir KMM, Wilkins MR, Donald WA. Separation of Isobaric Mono- and Dimethylated RGG-Repeat Peptides by Differential Ion Mobility-Mass Spectrometry. Anal Chem. 2019 Sep 17;91(18):11827-11833. doi: 10.1021/acs.analchem.9b02504.

Tay AP, Liang A, Hamey JJ, Hart-Smith G, Wilkins MR. MS2-Deisotoper: A Tool for Deisotoping High-Resolution MS/MS Spectra in Normal and Heavy Isotope-Labelled Samples. Proteomics. 2019 Sep;19(17):e1800444. doi: 10.1002/pmic.201800444.

Wook Kim K, Allen DW, Briese T, Couper JJ, Barry SC, Colman PG, Cotterill AM, Davis EA, Giles LC, Harrison LC, Harris M, Haynes A, Horton JL, Isaacs SR, Jain K, Lipkin WI, Morahan G, Morbey C, Pang ICN, Papenfuss AT, Penno MAS, Sinnott RO, Soldatos G, Thomson RL, Vuillermin PJ, Wentworth JM, Wilkins MR, Rawlinson WD, Craig ME; ENDIA Study Group. Distinct Gut Virome Profile of Pregnant Women With Type 1 Diabetes in the ENDIA Study. Open Forum Infect Dis. 2019 Jan 16;6(2):ofz025. doi: 10.1093/ofid/ofz025.

Corley SM, Troy NM, Bosco A, Wilkins MR. QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis. Sci Rep. 2019 Dec 11;9(1):18895. doi: 10.1038/s41598-019-55434-x.

Uthicke S, Deshpande NP, Liddy M, Patel F, Lamare M, Wilkins MR. Little evidence of adaptation potential to ocean acidification in sea urchins living in “Future Ocean” conditions at a CO2 vent. Ecol Evol. 2019 Aug 18;9(17):10004-10016. doi: 10.1002/ece3.5563.

Hamey JJ, Wilkins MR. Methylation of Elongation Factor 1A: Where, Who, and Why? Trends Biochem Sci. 2018 Mar;43(3):211-223. doi: 10.1016/j.tibs.2018.01.004.

Johnson RN, O’Meally D, Chen Z, Etherington GJ, Ho SYW, Nash WJ, Grueber CE, Cheng Y, Whittington CM, Dennison S, Peel E, Haerty W, O’Neill RJ, Colgan D, Russell TL, Alquezar-Planas DE, Attenbrow V, Bragg JG, Brandies PA, Chong AY, Deakin JE, Di Palma F, Duda Z, Eldridge MDB, Ewart KM, Hogg CJ, Frankham GJ, Georges A, Gillett AK, Govendir M, Greenwood AD, Hayakawa T, Helgen KM, Hobbs M, Holleley CE, Heider TN, Jones EA, King A, Madden D, Graves JAM, Morris KM, Neaves LE, Patel HR, Polkinghorne A, Renfree MB, Robin C, Salinas R, Tsangaras K, Waters PD, Waters SA, Wright B, Wilkins MR, Timms P, Belov K. Adaptation and conservation insights from the koala genome. Nat Genet. 2018 Aug;50(8):1102-1111. doi: 10.1038/s41588-018-0153-5.

Hamey JJ, Separovich RJ, Wilkins MR. MT-MAMS: Protein Methyltransferase Motif Analysis by Mass Spectrometry. J Proteome Res. 2018 Oct 5;17(10):3485-3491. doi: 10.1021/acs.jproteome.8b00396.

Corley SM, Mendoza-Reinoso V, Giles N, Singer ES, Common JE, Wilkins MR, Beverdam A. Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation. Cell Death Dis. 2018 Oct 31;9(11):1106. doi: 10.1038/s41419-018-1141-5.

Edwards RJ, Tuipulotu DE, Amos TG, O’Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA. Draft genome assembly of the invasive cane toad, Rhinella marina. Gigascience. 2018 Sep 1;7(9):giy095. doi: 10.1093/gigascience/giy095.

Alshekaili J, Chand R, Lee CE, Corley S, Kwong K, Papa I, Fulcher DA, Randall KL, Leiding JW, Ma CS, Wilkins MR, Uzel G, Goodnow CC, Vinuesa CG, Tangye SG, Cook MC. STAT3 regulates cytotoxicity of human CD57+ CD4+ T cells in blood and lymphoid follicles. Sci Rep. 2018 Feb 23;8(1):3529. doi: 10.1038/s41598-018-21389-8.

Deshpande NP, Riordan SM, Castaño-Rodríguez N, Wilkins MR, Kaakoush NO. Signatures within the esophageal microbiome are associated with host genetics, age, and disease. Microbiome. 2018 Dec 17;6(1):227. doi: 10.1186/s40168-018-0611-4.

You J, Corley SM, Wen L, Hodge C, Höllhumer R, Madigan MC, Wilkins MR, Sutton G. RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients. Sci Rep. 2018 Jan 10;8(1):389. doi: 10.1038/s41598-017-18480-x.

Tay AP, Geoghegan V, Yagoub D, Wilkins MR, Hart-Smith G. MethylQuant: A Tool for Sensitive Validation of Enzyme-Mediated Protein Methylation Sites from Heavy-Methyl SILAC Data. J Proteome Res. 2018 Jan 5;17(1):359-373. doi: 10.1021/acs.jproteome.7b00601.

Winter DL, Hart-Smith G, Wilkins MR. Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification. J Mol Biol. 2018 Jan 5;430(1):102-118. doi: 10.1016/j.jmb.2017.11.009.

Varela C, Schmidt SA, Borneman AR, Pang CNI, Krömerx JO, Khan A, Song X, Hodson MP, Solomon M, Mayr CM, Hines W, Pretorius IS, Baker MS, Roessner U, Mercurio M, Henschke PA, Wilkins MR, Chambers PJ. Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains. Metab Eng. 2018 Sep;49:178-191. doi: 10.1016/j.ymben.2018.08.006.

Chia SZ, Lai YW, Yagoub D, Lev S, Hamey JJ, Pang CNI, Desmarini D, Chen Z, Djordjevic JT, Erce MA, Hart-Smith G, Wilkins MR. Knockout of the Hmt1p Arginine Methyltransferase in <i>Saccharomyces cerevisiae</i> Leads to the Dysregulation of Phosphate-associated Genes and Processes. Mol Cell Proteomics. 2018 Dec;17(12):2462-2479. doi: 10.1074/mcp.RA117.000214.

Ignatius Pang CN, Goel A, Wilkins MR. Investigating the Network Basis of Negative Genetic Interactions in Saccharomyces cerevisiae with Integrated Biological Networks and Triplet Motif Analysis. J Proteome Res. 2018 Mar 2;17(3):1014-1030. doi: 10.1021/acs.jproteome.7b00649.
Smith DL, Götze M, Bartolec TK, Hart-Smith G, Wilkins MR. Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms. Anal Chem. 2018 Aug 7;90(15):9101-9108. doi: 10.1021/acs.analchem.8b01525.

Twine NA, Harkness L, Adjaye J, Aldahmash A, Wilkins MR, Kassem M. Molecular Phenotyping of Telomerized Human Bone Marrow Skeletal Stem Cells Reveals a Genetic Program of Enhanced Proliferation and Maintenance of Differentiation Responses. JBMR Plus. 2018 May 24;2(5):257-267. doi: 10.1002/jbm4.10050.

Transcriptional response of Nautella italica R11 towards its macroalgal host uncovers new mechanisms of host-pathogen interaction.
Hudson J, Gardiner M, Deshpande N, Egan S.
Mol Ecol. 2017 Dec 7. doi: 10.1111/mec.14448.

Pyomelanin produced by Vibrio cholerae confers resistance to predation by Acanthamoeba castellanii.
Noorian P, Hu J, Chen Z, Kjelleberg S, Wilkins MR, Sun S, McDougald D.
FEMS Microbiol Ecol. 2017 Dec 1;93(12).

Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline.
Hobbs M, King A, Salinas R, Chen Z, Tsangaras K, Greenwood AD, Johnson RN, Belov K, Wilkins M R, Timms P.
Sci Rep. 2017 Nov 20;7(1):15838.

Improved Quantitative Plant Proteomics via the Combination of Targeted and Untargeted Data Acquisition.
Hart-Smith G, Reis RS, Waterhouse PM, Wilkins MR.
Front Plant Sci. 2017 Sep 27;8:1669. doi: 10.3389/fpls.2017.01669.

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment.
Vázquez-Campos X, Kinsela AS, Bligh MW, Harrison JJ, Payne TE, Waite TD.
Appl Environ Microbiol. 2017 Aug 17;83(17). pii: e00729-17.

Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes.
Unnikrishnan A, Papaemmanuil E, Beck D, Deshpande NP, Verma A, Kumari A, Woll PS, Richards LA, Knezevic K, Chandrakanthan V, Thoms JAI, Tursky ML, Huang Y, Ali Z, Olivier J, Galbraith S, Kulasekararaj AG, Tobiasson M, Karimi M, Pellagatti A, Wilson SR, Lindeman R, Young B, Ramakrishna R, Arthur C, Stark R, Crispin P, Curnow J, Warburton P, Roncolato F, Boultwood J, Lynch K, Jacobsen SEW, Mufti GJ, Hellstrom-Lindberg E, Wilkins MR, MacKenzie KL, Wong JWH, Campbell PJ, Pimanda JE.
Cell Rep. 2017 Jul 18;20(3):572-585. doi: 10.1016/j.celrep.2017.06.067.
PMID: 28723562

Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia
Maria Victoria Schneider, Philippa C. Griffin, Sonika Tyagi, Madison Flannery Saravanan Dayalan, Simon Gladman, Nathan Watson-Haigh, Philipp E. Bayer Michael Charleston, Ira Cooke, Rob Cook, Richard J. Edwards, David Edwards Dominique Gorse, Malcolm McConville, David Powell, Marc R. Wilkins, Andrew Lonie.
Briefings in Bioinformatics. 2017 Jun 30. bbx071, https://doi.org/10.1093/bib/bbx071

METTL21B is a novel human lysine methyltransferase of translation elongation factor 1A: discovery by CRISPR/Cas9 knock out.
Hamey JJ, Wienert B, Quinlan KGR, Wilkins MR.
Mol Cell Proteomics. 2017 Jun 29. pii: mcp.M116.066308. doi: 10.1074/mcp.M116.066308. [Epub ahead of print]
PMID: 28663172 Free Article

Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols.
Corley SM, MacKenzie KL, Beverdam A, Roddam LF, Wilkins MR.
BMC Genomics. 2017 May 23;18(1):399. doi: 10.1186/s12864-017-3797-0.

PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks.
Tay AP, Pang CNI, Winter DL, Wilkins MR.
J Proteome Res. 2017 May 5;16(5):1988-2003. doi: 10.1021/acs.jproteome.6b01052. Epub 2017 Apr 6.
PMID:28349685

A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B.
Soboleva TA, Parker BJ, Nekrasov M, Hart-Smith G, Tay YJ, Tng WQ, Wilkins M, Ryan D, Tremethick DJ.
PLoS Genet. 2017 Feb 24;13(2):e1006633. doi: 10.1371/journal.pgen.1006633. eCollection 2017 Feb.

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E.
Waters SA, McAteer SP, Kudla G, Pang I, Deshpande NP, Amos TG, Leong KW, Wilkins MR, Strugnell R, Gally DL, Tollervey D, Tree JJ.
EMBO J. 2017 Feb 1;36(3):374-387.

Transcriptome and network analyses in Saccharomyces cerevisiae reveal that amphotericin B and lactoferrin synergy disrupt metal homeostasis and stress response.
Pang CN, Lai YW, Campbell LT, Chen SC, Carter DA, Wilkins MR.
Sci Rep. 2017 Jan 12;7:40232. doi: 10.1038/srep40232.
PMID: 28079179 Free PMC Article

Transcriptomic Analysis Shows Decreased Cortical Expression of NR4A1, NR4A2 and RXRB in Schizophrenia and Provides Evidence for Nuclear Receptor Dysregulation.
Corley SM, Tsai SY, Wilkins MR, Shannon Weickert C.
PLoS One. 2016 Dec 16;11(12):e0166944. doi: 10.1371/journal.pone.0166944.
PMID: 27992436 Free PMC Article

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E.
Waters SA, McAteer SP, Kudla G, Pang I, Deshpande NP, Amos TG, Leong KW, Wilkins MR, Strugnell R, Gally DL, Tollervey D, Tree JJ.
EMBO J. 2016 Nov 11. pii: e201694639. [Epub ahead of print]
PMID: 27836995 Free Article

The activity of a yeast Family 16 methyltransferase, Efm2, is affected by a conserved tryptophan and its N?terminal region
JJ Hamey, G Hart?Smith, MA Erce, MR Wilkins
FEBS Open Bio 6 (12), 1320-1330

Characterization of SNP and Structural Variations in the Mitochondrial Genomes of Tilletia indica and Its Closely Related Species Formed Basis for a Simple Diagnostic Assay
MK Tan, H Raman, G Chambers, I Sharma, Z Chen, N Deshpande, MR WIlkins
PloS one 11 (11), e0166086

Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity.
Kasumovic MM, Chen Z, Wilkins MR.
BMC Genomics. 2016 Oct 24;17(1):827.
PMID: 27776492

Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells.
Deshpande NP, Wilkins MR, Castaño-Rodríguez N, Bainbridge E, Sodhi N, Riordan SM, Mitchell HM, Kaakoush NO.
Sci Rep. 2016 Sep 28;6:34288.

Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii.
Taha, Siddiqui KS, Campanaro S, Najnin T, Deshpande N, Williams TJ, Aldrich-Wright J, Wilkins M, Curmi PM, Cavicchioli R.
Environ Microbiol. 2016 Sep;18(9):2810-24.

Lai YW, Campbell LT, Wilkins MR, Pang CN, Chen S, Carter DA. Synergy and antagonism between iron chelators and antifungal drugs in Cryptococcus. Int J Antimicrob Agents. 2016 Jul 20.

Corley SM, Canales CP, Carmona-Mora P, Mendoza-Reinosa V, Beverdam A, Hardeman EC, Wilkins MR, Palmer SJ. RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome. BMC Genomics. 2016 Jun 13;17(1):450.

Watson-Haigh NS, Revote J, Suchecki R, Tyagi S, Corley SM, Shang CA, McGrath A, Towards an open, collaborative, reusable framework for sharing hands-on bioinformatics training workshops. Brief Bioinform. 2016 Mar 16.

Hart-Smith, G., D. Yagoub, A.P. Tay, R. Pickford, and M.R. Wilkins, Large-scale mass spectrometry-based identifications of enzyme-mediated protein methylation are subject to high false discovery rates. Mol Cell Proteomics, 2016 Mar;15(3):989-1006.

Low JK, Im H, Erce MA, Hart-Smith G, Snyder MP, Wilkins MR, Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays. Proteomics. 2016 Feb;16(3):465-76.

Hamey JJ, Winter DL, Yagoub D, Overall CM, Hart-Smith G, Wilkins MR, Novel N-terminal and Lysine Methyltransferases That Target Translation Elongation Factor 1A in Yeast and Human. Mol Cell Proteomics. 2016 Jan;15(1):164-76.

Reis RS, Hart-Smith G, Eamens AL, Wilkins MR, Waterhouse PM, MicroRNA Regulatory Mechanisms Play Different Roles in Arabidopsis. J Proteome Res. 2015 Nov 6;14(11):4743-51.

Yagoub D, Hart-Smith G, Moecking J, Erce MA, Wilkins MR, Yeast proteins Gar1p, Nop1p, Npl3p, Nsr1p, and Rps2p are natively methylated and are substrates of the arginine methyltransferase Hmt1p. Proteomics. 2015 Sep;15(18):3209-18.

Yap JY, Rohner T, Greenfield A, Van Der Merwe M, McPherson H, Glenn W, Kornfeld G, Marendy E, Pan AY, Wilton A, Wilkins MR, Rossetto M, Delaney SK. Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution. PLoS One. 2015 Jun 10;10(6):e0128126.

Reis RS, Hart-Smith G, Eamens AL, Wilkins MR, Waterhouse PM. Gene regulation by translational inhibition is determined by Dicer partnering proteins. Nat Plants. 2015 Feb 9;1:14027.

Deshpande, N.P., M.R. Wilkins, H.M. Mitchell, and N.O. Kaakoush, Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group. FEMS Microbiol Lett, 2015. 362(22).

Jugder, B.E., Z. Chen, D.T. Ping, H. Lebhar, J. Welch, and C.P. Marquis, An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture. Microb Cell Fact, 2015. 14: p. 42.

Kaakoush, N.O., N.P. Deshpande, S.M. Man, J.A. Burgos-Portugal, F.A. Khattak, M.J. Raftery, M.R. Wilkins, H.M. Mitchell, Transcriptomic and proteomic analyses reveal key innate immune signatures in the host response to the gastrointestinal pathogen Campylobacter concisus. Infect Immun, 2015. 83(2): p. 832-45.

Nahidi, L., S.M. Corley, M.R. Wilkins, J. Wei, M. Alhagamhmad, A.S. Day, . . . S.T. Leach, The major pathway by which polymeric formula reduces inflammation in intestinal epithelial cells: a microarray-based analysis. Genes Nutr, 2015. 10(5): p. 479.

Shum, A.M., D.C. Fung, S.M. Corley, M.C. McGill, N.L. Bentley, T.C. Tan, . . . P. Polly, Cardiac and skeletal muscles show molecularly distinct responses to cancer cachexia. Physiol Genomics, 2015. 47(12): p. 588-99.

Tay, A.P., C.N. Pang, N.A. Twine, G. Hart-Smith, L. Harkness, M. Kassem, and M.R. Wilkins, Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J Proteome Res, 2015. 14(9): p. 3541-54.

Yagoub, D., A.P. Tay, Z. Chen, J.J. Hamey, C. Cai, S.Z. Chia, . . . M.R. Wilkins, Proteogenomic Discovery of a Small, Novel Protein in Yeast Reveals a Strategy for the Detection of Unannotated Short Open Reading Frames. J Proteome Res, 2015. 14(12): p. 5038-47.

Harkness L, Twine NA, Abu Dawud R, Jafaria A, Aldahmasha A, Wilkins MR, Adjayec J, Kassem M, Molecular characterisation of stromal populations derived from human embryonic stem cells: Similarities to immortalised bone marrow derived stromal stem cells. Bone Reports, 2015. 3: 32–39.

Winter DL, Abeygunawardena D, Hart-Smith D, Erce MA, Wilkins MR,  Lysine methylation modulates the protein-protein interactions of yeast cytochrome C Cyc1p. Proteomics, 2015 Jul;15(13): 2166-76.

Gilchrist AS, Shearman DC, Frommer M, Raphael KA, Deshpande NP, Wilkins MR, Sherwin WB, Sved JA, The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species. BMC Genomics, 2015, 15:1153.

Williams, K.L., A.A. Gooley, M.R. Wilkins, and N.H. Packer, A Sydney proteome story. J Proteomics, 2014. 107: p. 13-23.

Gilchrist, A.S., D.C. Shearman, M. Frommer, K.A. Raphael, N.P. Deshpande, M.R. Wilkins, . . . J.A. Sved, The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species. BMC Genomics, 2014. 15: p. 1153.

Hobbs, M., A. Pavasovic, A.G. King, P.J. Prentis, M.D. Eldridge, Z. Chen, . . . P. Timms, A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity. BMC Genomics, 2014. 15: p. 786.

Wang, Y., K.J. Jackson, J. Davies, Z. Chen, B.A. Gaeta, J. Rimmer, . . . A.M. Collins, IgE-associated IGHV genes from venom and peanut allergic individuals lack mutational evidence of antigen selection. PLoS One, 2014. 9(2): p. e89730.

Zhang, L., J.J. Hamey, G. Hart-Smith, M.A. Erce, and M.R. Wilkins, Elongation factor methyltransferase 3–a novel eukaryotic lysine methyltransferase. Biochem Biophys Res Commun, 2014. 451(2): p. 229-34.

Yagoub, D., M.R. Wilkins, A.J. Lay, D.C. Kaczorowski, D. Hatoum, S. Bajan, . . . E.M. McGowan, Sphingosine kinase 1 isoform-specific interactions in breast cancer. Mol Endocrinol, 2014. 28(11): p. 1899-915.

Winter, D.L., M.A. Erce, and M.R. Wilkins, A web of possibilities: network-based discovery of protein interaction codes. J Proteome Res, 2014. 13(12): p. 5333-8.

Twine, N.A., L. Chen, C.N. Pang, M.R. Wilkins, and M. Kassem, Identification of differentiation-stage specific markers that define the ex vivo osteoblastic phenotype. Bone, 2014. 67: p. 23-32.

Tan, M.K., D. Collins, Z. Chen, A. Englezou, and M.R. Wilkins, A brief overview of the size and composition of the myrtle rust genome and its taxonomic status. Mycology, 2014. 5(2): p. 52-63.

Pang, C.N., A.P. Tay, C. Aya, N.A. Twine, L. Harkness, G. Hart-Smith, . . . M.R. Wilkins, Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: validation of genes and alternative mRNA splicing. J Proteome Res, 2014. 13(1): p. 84-98.

Nadkarni, M.A., Z. Chen, M.R. Wilkins, and N. Hunter, Comparative genome analysis of Lactobacillus rhamnosus clinical isolates from initial stages of dental pulp infection: identification of a new exopolysaccharide cluster. PLoS One, 2014. 9(3): p. e90643.

Low, J.K., G. Hart-Smith, M.A. Erce, and M.R. Wilkins, The Saccharomyces cerevisiae poly(A)-binding protein is subject to multiple post-translational modifications, including the methylation of glutamic acid. Biochem Biophys Res Commun, 2014. 443(2): p. 543-8.

Kaakoush, N.O., N.P. Deshpande, S.M. Man, J.A. Burgos-Portugal, F.A. Khattak, M.J. Raftery, . . . H.M. Mitchell, Transcriptomic and proteomic analyses reveal key innate immune signatures in the host response to the gastrointestinal pathogen Campylobacter concisus. Infect Immun, 2014.

Hook, S.E., N.A. Twine, S.L. Simpson, D.A. Spadaro, P. Moncuquet, and M.R. Wilkins, 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes. Aquat Toxicol, 2014. 153: p. 73-88.

Hook, S.E., H.L. Osborn, F. Gissi, P. Moncuquet, N.A. Twine, M.R. Wilkins, and M.S. Adams, RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium. Mar Genomics, 2014. 16: p. 45-53.

Hart-Smith, G., S.Z. Chia, J.K. Low, M.J. McKay, M.P. Molloy, and M.R. Wilkins, Stoichiometry of Saccharomyces cerevisiae lysine methylation: insights into non-histone protein lysine methyltransferase activity. J Proteome Res, 2014. 13(3): p. 1744-56.

Twine, N.A., C. Janitz, M.R. Wilkins, and M. Janitz, Sequencing of hippocampal and cerebellar transcriptomes provides new insights into the complexity of gene regulation in the human brain. Neurosci Lett, 2013. 541: p. 263-8.

Tay, A.P., N.O. Kaakoush, N.P. Deshpande, Z. Chen, H. Mitchell, and M.R. Wilkins, Genome Sequence of Campylobacter showae UNSWCD, Isolated from a Patient with Crohn’s Disease. Genome Announc, 2013. 1(1).

Schramm, S.J., S.S. Li, V. Jayaswal, D.C. Fung, A.E. Campain, C.N. Pang, . . . M.R. Wilkins, Disturbed protein-protein interaction networks in metastatic melanoma are associated with worse prognosis and increased functional mutation burden. Pigment Cell Melanoma Res, 2013. 26(5): p. 708-22.

Schramm, S.J., V. Jayaswal, A. Goel, S.S. Li, Y.H. Yang, G.J. Mann, and M.R. Wilkins, Molecular interaction networks for the analysis of human disease: utility, limitations, and considerations. Proteomics, 2013. 13(23-24): p. 3393-405.

Low, J.K., G. Hart-Smith, M.A. Erce, and M.R. Wilkins, Analysis of the proteome of Saccharomyces cerevisiae for methylarginine. J Proteome Res, 2013. 12(9): p. 3884-99.

Jayaswal, V., S.J. Schramm, G.J. Mann, M.R. Wilkins, and Y.H. Yang, VAN: an R package for identifying biologically perturbed networks via differential variability analysis. BMC Res Notes, 2013. 6: p. 430.

Hook, S.E., N.A. Twine, S.L. Simpson, D.A. Spadaro, P. Moncuquet, and M.R. Wilkins, 454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: Transcriptome assembly and toxicant induced changes. Aquat Toxicol, 2013.

Funnell, A.P., K.S. Mak, N.A. Twine, G.J. Pelka, L.J. Norton, T. Radziewic, . . . M. Crossley, Generation of mice deficient in both KLF3/BKLF and KLF8 reveals a genetic interaction and a role for these factors in embryonic globin gene silencing. Mol Cell Biol, 2013. 33(15): p. 2976-87.

Erce, M.A., J.K. Low, G. Hart-Smith, and M.R. Wilkins, A conditional two-hybrid (C2H) system for the detection of protein-protein interactions that are mediated by post-translational modification. Proteomics, 2013. 13(7): p. 1059-64.

Erce, M.A., D. Abeygunawardena, J.K. Low, G. Hart-Smith, and M.R. Wilkins, Interactions affected by arginine methylation in the yeast protein-protein interaction network. Mol Cell Proteomics, 2013. 12(11): p. 3184-98.

Deshpande, N.P., Y.K. Wong, M. Manefield, M.R. Wilkins, and M. Lee, Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium. Genome Announc, 2013. 1(5).

Deshpande, N.P., N.O. Kaakoush, M.R. Wilkins, and H.M. Mitchell, Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association. BMC Genomics, 2013. 14: p. 585.

Chen, Z., M.R. Wilkins, N. Hunter, and M.A. Nadkarni, Draft Genome Sequences of Two Clinical Isolates of Lactobacillus rhamnosus from Initial Stages of Dental Pulp Infection. Genome Announc, 2013. 1(1).

Yeung, W.C., A. Al-Shabeeb, C.N. Pang, M.R. Wilkins, J. Catteau, N.J. Howard, . . . M.E. Craig, Children with islet autoimmunity and enterovirus infection demonstrate a distinct cytokine profile. Diabetes, 2012. 61(6): p. 1500-8.

Webster, R.A., S.P. Blaber, B.R. Herbert, M.R. Wilkins, and G. Vesey, The role of mesenchymal stem cells in veterinary therapeutics – a review. N Z Vet J, 2012. 60(5): p. 265-72.

Scott, G.M., S.S. Chow, M.E. Craig, C.N. Pang, B. Hall, M.R. Wilkins, . . . W.D. Rawlinson, Cytomegalovirus infection during pregnancy with maternofetal transmission induces a proinflammatory cytokine bias in placenta and amniotic fluid. J Infect Dis, 2012. 205(8): p. 1305-10.

Pang, C.N., A. Goel, S.S. Li, and M.R. Wilkins, A multidimensional matrix for systems biology research and its application to interaction networks. J Proteome Res, 2012. 11(11): p. 5204-20.

Low, J.K. and M.R. Wilkins, Protein arginine methylation in Saccharomyces cerevisiae. FEBS J, 2012. 279(24): p. 4423-43.

Hart-Smith, G., J.K. Low, M.A. Erce, and M.R. Wilkins, Enhanced methylarginine characterization by post-translational modification-specific targeted data acquisition and electron-transfer dissociation mass spectrometry. J Am Soc Mass Spectrom, 2012. 23(8): p. 1376-89.

Goel, A. and M.R. Wilkins, Dynamic hubs show competitive and static hubs non-competitive regulation of their interaction partners. PLoS One, 2012. 7(10): p. e48209.

Funnell, A.P., L.J. Norton, K.S. Mak, J. Burdach, C.M. Artuz, N.A. Twine, . . . M. Crossley, The CACCC-binding protein KLF3/BKLF represses a subset of KLF1/EKLF target genes and is required for proper erythroid maturation in vivo. Mol Cell Biol, 2012. 32(16): p. 3281-92.

Fung, D.C., S.S. Li, A. Goel, S.H. Hong, and M.R. Wilkins, Visualization of the interactome: what are we looking at? Proteomics, 2012. 12(10): p. 1669-86.

Erce, M.A., C.N. Pang, G. Hart-Smith, and M.R. Wilkins, The methylproteome and the intracellular methylation network. Proteomics, 2012. 12(4-5): p. 564-86.

Couttas, T.A., M.J. Raftery, M.P. Padula, B.R. Herbert, and M.R. Wilkins, Methylation of translation-associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases. Proteomics, 2012. 12(7): p. 960-72.

Chong, H.S., L. Campbell, M.P. Padula, C. Hill, E. Harry, S.S. Li, . . . D. Carter, Time-course proteome analysis reveals the dynamic response of Cryptococcus gattii cells to fluconazole. PLoS One, 2012. 7(8): p. e42835.

Ayer, A., S. Fellermeier, C. Fife, S.S. Li, G. Smits, A.J. Meyer, . . . G.G. Perrone, A genome-wide screen in yeast identifies specific oxidative stress genes required for the maintenance of sub-cellular redox homeostasis. PLoS One, 2012. 7(9): p. e44278.

Twine, N.A., K. Janitz, M.R. Wilkins, and M. Janitz, Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer’s disease. PLoS One, 2011. 6(1): p. e16266.

Li, S.S., K. Xu, and M.R. Wilkins, Visualization and analysis of the complexome network of Saccharomyces cerevisiae. J Proteome Res, 2011. 10(10): p. 4744-56.

Kaakoush, N.O., N.P. Deshpande, M.R. Wilkins, C.G. Tan, J.A. Burgos-Portugal, M.J. Raftery, . . . H. Mitchell, The pathogenic potential of Campylobacter concisus strains associated with chronic intestinal diseases. PLoS One, 2011. 6(12): p. e29045.

Kaakoush, N.O., N.P. Deshpande, M.R. Wilkins, M.J. Raftery, K. Janitz, and H. Mitchell, Comparative analyses of Campylobacter concisusstrains reveal the genome of the reference strain BAA-1457 is not representative of the species. Gut Pathog, 2011. 3: p. 15.

Goel, A., S.S. Li, and M.R. Wilkins, Four-dimensional visualisation and analysis of protein-protein interaction networks. Proteomics, 2011. 11(13): p. 2672-82.

Fung, D.C., A. Lo, L. Jankova, S.J. Clarke, M. Molloy, G.R. Robertson, and M.R. Wilkins, Classification of cancer patients using pathway analysis and network clustering. Methods Mol Biol, 2011. 781: p. 311-36.

Deshpande, N.P., N.O. Kaakoush, H. Mitchell, K. Janitz, M.J. Raftery, S.S. Li, and M.R. Wilkins, Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity. PLoS One, 2011. 6(7): p. e22170.

Couttas, T.A., M.J. Raftery, M.A. Erce, and M.R. Wilkins, Monitoring cytoplasmic protein complexes with blue native gel electrophoresis and stable isotope labelling with amino acids in cell culture: analysis of changes in the 20S proteasome. Electrophoresis, 2011. 32(14): p. 1819-23.

Pang, C.N., E. Gasteiger, and M.R. Wilkins, Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications. BMC Genomics, 2010. 11: p. 92.

Okoli, A.S., M.R. Wilkins, M.J. Raftery, and G.L. Mendz, Response of Helicobacter hepaticus to bovine bile. J Proteome Res, 2010. 9(3): p. 1374-84.

Ma, L., C.N. Pang, S.S. Li, and M.R. Wilkins, Proteins deleterious on overexpression are associated with high intrinsic disorder, specific interaction domains, and low abundance. J Proteome Res, 2010. 9(3): p. 1218-25.

Kaakoush, N.O., S.M. Man, S. Lamb, M.J. Raftery, M.R. Wilkins, Z. Kovach, and H. Mitchell, The secretome of Campylobacter concisus. FEBS J, 2010. 277(7): p. 1606-17.

Joshi, H.J., C.W. von der Lieth, N.H. Packer, and M.R. Wilkins, GlycoViewer: a tool for visual summary and comparative analysis of the glycome. Nucleic Acids Res, 2010. 38(Web Server issue): p. W667-70.

Fung, D.C., M.R. Wilkins, D. Hart, and S.H. Hong, Using the clustered circular layout as an informative method for visualizing protein-protein interaction networks. Proteomics, 2010. 10(14): p. 2723-7.

Erce, M.A., J.K. Low, and M.R. Wilkins, Analysis of the RNA degradosome complex in Vibrio angustum S14. FEBS J, 2010. 277(24): p. 5161-73.

Erce, M.A., J.K. Low, P.E. March, M.R. Wilkins, and K.M. Takayama, Identification and functional analysis of RNase E of Vibrio angustum S14 and two-hybrid analysis of its interaction partners. Biochim Biophys Acta, 2009. 1794(8): p. 1107-14.

Huang, K.Y., M. Filarsky, M.P. Padula, M.J. Raftery, B.R. Herbert, and M.R. Wilkins, Micropreparative fractionation of the complexome by blue native continuous elution electrophoresis. Proteomics, 2009. 9(9): p. 2494-502.

Widjaja, Y.Y., C.N. Pang, S.S. Li, M.R. Wilkins, and T.D. Lambert, The Interactorium: visualising proteins, complexes and interaction networks in a virtual 3-D cell. Proteomics, 2009. 9(23): p. 5309-15.

Wilkins, M.R., Hares and tortoises: the high- versus low-throughput proteomic race. Electrophoresis, 2009. 30 Suppl 1: p. S150-5.

Couttas, T.A., M.J. Raftery, G. Bernardini, and M.R. Wilkins, Immonium ion scanning for the discovery of post-translational modifications and its application to histones. J Proteome Res, 2008. 7(7): p. 2632-41.

Deshpande, N., M.R. Wilkins, N. Packer, and H. Nevalainen, Protein glycosylation pathways in filamentous fungi. Glycobiology, 2008. 18(8): p. 626-37.

Ho, E., R. Webber, and M.R. Wilkins, Interactive three-dimensional visualization and contextual analysis of protein interaction networks. J Proteome Res, 2008. 7(1): p. 104-12.

Krycer, J.R., C.N. Pang, and M.R. Wilkins, High throughput protein-protein interaction data: clues for the architecture of protein complexes. Proteome Sci, 2008. 6: p. 32.

Pang, C.N., J.R. Krycer, A. Lek, and M.R. Wilkins, Are protein complexes made of cores, modules and attachments? Proteomics, 2008. 8(3): p. 425-34.

Pang, C.N. and M.R. Wilkins, Online resources for the molecular contextualization of disease. Methods Mol Med, 2008. 141: p. 287-308.