By Professor Marc Wilkins

Journal articles

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, 2021, 'Multi-omics of the esophageal microenvironment identifies signatures associated with progression of Barrett’s esophagus', Genome Medicine, 13, pp. 133, http://dx.doi.org/10.1186/s13073-021-00951-6

Khan MAM; Deshpande NP; Shuttleworth LA; Osborne T; Collins D; Wilkins MR; Gurr GM; Reynolds OL, 2021, 'Raspberry ketone diet supplement reduces attraction of sterile male Queensland fruit fly to cuelure by altering expression of chemoreceptor genes', Scientific Reports, 11, http://dx.doi.org/10.1038/s41598-021-96778-7

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, 2021, 'Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing', Scientific Reports, 11, pp. 3934, http://dx.doi.org/10.1038/s41598-021-83642-x

Bӧhm 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, 2021, 'Combination efficacy of ruxolitinib with standard-of-care drugs in CRLF2-rearranged Ph-like acute lymphoblastic leukemia', Leukemia, 35, pp. 3101 - 3112, http://dx.doi.org/10.1038/s41375-021-01248-8

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, 2021, 'Publisher Correction: The RNA Atlas expands the catalog of human non-coding RNAs (Nature Biotechnology, (2021), 39, 11, (1453-1465), 10.1038/s41587-021-00936-1)', Nature Biotechnology, 39, pp. 1467, http://dx.doi.org/10.1038/s41587-021-00996-3

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, 2021, 'The RNA Atlas expands the catalog of human non-coding RNAs', Nature Biotechnology, 39, pp. 1453 - 1465, http://dx.doi.org/10.1038/s41587-021-00936-1

Vazquez Campos X; Kinsela A; Bligh M; Payne TE; Wilkins M; Waite D, 2021, 'Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site', Frontiers in Microbiology, 12, pp. 732575 - 732575, http://dx.doi.org/10.3389/fmicb.2021.732575

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

Manandhar B; Pandzic E; Deshpande N; Chen S-Y; Wasinger VC; Kockx M; Glaros E; Ong KL; Thomas S; Wilkins M; Whan R; Cochran BJ; Rye KA, 2021, 'The Anti-Oxidant Function Of Apolipoprotein A-I Rescues Pancreatic beta-Cells From Cholesterol-Induced Mitochondrial Dysfunction', ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 41, http://dx.doi.org/10.1161/atvb.41.suppl_1.122

Separovich RJ; Wilkins MR, 2021, 'Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast', Journal of Biological Chemistry, 297, http://dx.doi.org/10.1016/j.jbc.2021.100939

Kinsela AS; Bligh MW; Vázquez-Campos X; Sun Y; Wilkins MR; Comarmond MJ; Rowling B; Payne TE; Waite TD, 2021, 'Biogeochemical Mobility of Contaminants from a Replica Radioactive Waste Trench in Response to Rainfall-Induced Redox Oscillations', Environmental Science and Technology, 55, pp. 8793 - 8805, http://dx.doi.org/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, 2021, 'Hgf/c-met inhibition as adjuvant therapy improves outcomes in an orthotopic mouse model of pancreatic cancer', Cancers, 13, pp. 2763, http://dx.doi.org/10.3390/cancers13112763

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

Hamey JJ; Nguyen A; Wilkins MR, 2021, 'Discovery of Arginine Methylation, Phosphorylation, and Their Co-occurrence in Condensate-Associated Proteins in Saccharomyces cerevisiae', Journal of Proteome Research, 20, pp. 2420 - 2434, http://dx.doi.org/10.1021/acs.jproteome.0c00927

Separovich RJ; Wong MWM; Chapman TR; Slavich E; Hamey JJ; Wilkins MR, 2021, 'Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential', Journal of Biological Chemistry, 296, http://dx.doi.org/10.1074/JBC.RA120.015995

Separovich RJ; Wong MWM; Chapman TR; Slavich E; Hamey JJ; Wilkins MR, 2020, 'Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential.', J Biol Chem, pp. 100192, http://dx.doi.org/10.1074/jbc.RA120.015995

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, 2020, 'A high-stringency blueprint of the human proteome', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-020-19045-9

Separovich RJ; Pang CNI; Wilkins MR, 2020, 'Controlling the Controllers: Regulation of Histone Methylation by Phosphosignalling', Trends in Biochemical Sciences, 45, pp. 1035 - 1048, http://dx.doi.org/10.1016/j.tibs.2020.08.004

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; Svard SG; Gasser RB; Jex AR, 2020, 'Eukaryote-conserved methylarginine is absent in diplomonads and functionally compensated in Giardia', Molecular Biology and Evolution, 37, pp. 3525 - 3549, http://dx.doi.org/10.1093/molbev/msaa186

Yang L; Chen Z; Stout ES; Delerue F; Ittner LM; Wilkins MR; Quinlan KGR; Crossley M, 2020, 'Methylation of a CGATA element inhibits binding and regulation by GATA-1', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-020-16388-1

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, 2020, 'Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry', Structure, 28, pp. 1259 - 1268, http://dx.doi.org/10.1016/j.str.2020.09.011

Pang CNI; Ballouz S; Weissberger D; Thibaut LM; Hamey JJ; Gillis J; Wilkins MR; Hart-Smith G, 2020, 'Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes', Molecular and Cellular Proteomics, 19, pp. 1876 - 1895, http://dx.doi.org/10.1074/mcp.RA120.002154

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

Anande G; Deshpande NP; Mareschal S; Batcha AMN; Hampton HR; Herold T; Lehmann S; Wilkins MR; Wong JWH; Unnikrishnan A; Pimanda JE, 2020, 'RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia', Clinical Cancer Research, 26, pp. 3597 - 3607, http://dx.doi.org/10.1158/1078-0432.CCR-20-0184

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, 2020, 'Higher frequency of vertebrate-infecting viruses in the gut of infants born to mothers with type 1 diabetes', Pediatric Diabetes, 21, pp. 271 - 279, http://dx.doi.org/10.1111/pedi.12952

Bartolec TK; Smith DL; Pang CNI; Xu YD; Hamey JJ; Wilkins MR, 2020, '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', Analytical Chemistry, 92, pp. 1874 - 1882, http://dx.doi.org/10.1021/acs.analchem.9b03975

Smith DL; Erce MA; Lai YW; Tomasetig F; Hart-Smith G; Hamey JJ; Wilkins MR, 2020, 'Crosstalk of Phosphorylation and Arginine Methylation in Disordered SRGG Repeats of Saccharomyces cerevisiae Fibrillarin and Its Association with Nucleolar Localization', Journal of Molecular Biology, 432, pp. 448 - 466, http://dx.doi.org/10.1016/j.jmb.2019.11.006

Bayat A; Deshpande NP; Wilkins MR; Parameswaran S, 2020, 'Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach', IEEE ACM Transactions on Computational Biology and Bioinformatics, 17, pp. 334 - 338, http://dx.doi.org/10.1109/TCBB.2018.2875479

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, 2019, 'Higher abundance of enterovirus A species in the gut of children with islet autoimmunity', Scientific Reports, 9, pp. 1749, http://dx.doi.org/10.1038/s41598-018-38368-8

Corley SM; Troy NM; Bosco A; Wilkins MR, 2019, 'QuantSeq. 3′ Sequencing combined with Salmon provides a fast, reliable approach for high throughput RNA expression analysis', Scientific Reports, 9, http://dx.doi.org/10.1038/s41598-019-55434-x

Lai YW; Pang CNI; Campbell LT; Chen SCA; Wilkins MR; Carter DA, 2019, 'Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces', Frontiers in Microbiology, 10, pp. 2195, http://dx.doi.org/10.3389/fmicb.2019.02195

Winter DL; Mastellone J; Kabir KMM; Wilkins MR; Donald WA, 2019, 'Separation of Isobaric Mono- And Dimethylated RGG-Repeat Peptides by Differential Ion Mobility-Mass Spectrometry', Analytical Chemistry, 91, pp. 11827 - 11833, http://dx.doi.org/10.1021/acs.analchem.9b02504

Uthicke S; Deshpande NP; Liddy M; Patel F; Lamare M; Wilkins MR, 2019, 'Little evidence of adaptation potential to ocean acidification in sea urchins living in “Future Ocean” conditions at a CO2 vent', Ecology and Evolution, 9, pp. 10004 - 10016, http://dx.doi.org/10.1002/ece3.5563

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

Bertoldo MJ; Cheung MY; Sia ZK; Agapiou D; Corley SM; Wilkins MR; Richani D; Harrison CA; Gilchrist RB, 2019, 'Non-canonical cyclic AMP SMAD1/5/8 signalling in human granulosa cells', Molecular and Cellular Endocrinology, 490, pp. 37 - 46, http://dx.doi.org/10.1016/j.mce.2019.04.003

Tay AP; Liang A; Wilkins MR; Pang CNI, 2019, 'Visualizing Post-Translational Modifications in Protein Interaction Networks Using PTMOracle', Current Protocols in Bioinformatics, 66, pp. e71, http://dx.doi.org/10.1002/cpbi.71

Lowe BR; Maxham LA; Hamey JJ; Wilkins MR; Partridge JF, 2019, 'Histone H3 mutations: An updated view of their role in chromatin deregulation and cancer', Cancers, 11, pp. 1 - 24, http://dx.doi.org/10.3390/cancers11050660

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, 2019, 'Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis', Gastroenterology, 156, pp. 1440 - 1454.e2, http://dx.doi.org/10.1053/j.gastro.2018.12.001

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, 2019, 'Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia', Briefings in Bioinformatics, 20, pp. 384 - 389, http://dx.doi.org/10.1093/bib/bbx071

Winter DL; Wilkins MR; Donald WA, 2019, 'Differential Ion Mobility–Mass Spectrometry for Detailed Analysis of the Proteome', Trends in Biotechnology, 37, pp. 198 - 213, http://dx.doi.org/10.1016/j.tibtech.2018.07.018

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; 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, 2019, 'Distinct gut virome profile of pregnant women with type 1 diabetes in the ENDIA study', Open Forum Infectious Diseases, 6, http://dx.doi.org/10.1093/ofid/ofz025

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

Chia SZ; Lai YW; Yagoub D; Lev S; Hamey JJ; Ignatius Pang CN; Desmarini D; Chen Z; Djordjevic JT; Erce MA; Hart-Smith G; Wilkins MR; Pang I, 2018, 'Knockout of the Hmt1p arginine methyltransferase in saccharomyces cerevisiae leads to the dysregulation of phosphate-associated genes and processes', Molecular and Cellular Proteomics, 17, pp. 2462 - 2479, http://dx.doi.org/10.1074/mcp.RA117.000214

You J; Corley SM; Wen L; Hodge C; Höllhumer R; Madigan MC; Wilkins MR; Sutton G, 2018, 'RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients', Scientific Reports, 8, pp. 389, http://dx.doi.org/10.1038/s41598-017-18480-x

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, 2018, 'STAT3 regulates cytotoxicity of human CD57+ CD4+ T cells in blood and lymphoid follicles', Scientific Reports, 8, pp. 3529, http://dx.doi.org/10.1038/s41598-018-21389-8

Corley S; Mendoza-Reinoso V; Giles N; Singer ES; Common JE; Wilkins M; Beverdam A, 2018, 'Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation', Cell Death and Disease, 9, pp. 1106, http://dx.doi.org/10.1038/s41419-018-1141-5

Hamey JJ; Separovich RJ; Wilkins MR, 2018, 'MT-MAMS: Protein Methyltransferase Motif Analysis by Mass Spectrometry', Journal of Proteome Research, 17, pp. 3485 - 3491, http://dx.doi.org/10.1021/acs.jproteome.8b00396

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, 2018, 'Draft genome assembly of the invasive cane toad, Rhinella marina', Gigascience, 7, http://dx.doi.org/10.1093/gigascience/giy095

Twine NA; Harkness L; Adjaye J; Aldahmash A; Wilkins MR; Kassem M, 2018, 'Molecular Phenotyping of Telomerized Human Bone Marrow Skeletal Stem Cells Reveals a Genetic Program of Enhanced Proliferation and Maintenance of Differentiation Responses', Jbmr Plus, 2, pp. 257 - 267, http://dx.doi.org/10.1002/jbm4.10050

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, 2018, 'Systems-based approaches enable identification of gene targets which improve the flavour profile of low-ethanol wine yeast strains', Metabolic Engineering, 49, pp. 178 - 191, http://dx.doi.org/10.1016/j.ymben.2018.08.006

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