By Professor Marc Wilkins

Books

, 2007, Proteome Research: Concepts, Technology and Application, Wilkins MR; Appel RD; Williams KK; Hochstrasser DF, (eds.), Springer Publishing Company, Heidelberg

Book Chapters

Pang I, 2019, 'Protein Post-Translational Modification Prediction', in Encyclopedia of Bioinformatics and Computational Biology, pp. 15 - 27, http://dx.doi.org/10.1016/B978-0-12-809633-8.20265-3

Wong J; Pang I; Wilkins M; Tree J, 2018, 'Systems-level analysis of bacterial regulatory small RNA networks', in Systems Biology, Springer, pp. 97 - 127

Wilkins MR, 2013, 'Protein–Protein Interactions – Interpreting Data from Large-Scale Screens', in Encyclopedia of Biophysics, Springer Berlin Heidelberg, pp. 2083 - 2086, http://dx.doi.org/10.1007/978-3-642-16712-6_190

Wilkins MR, 2012, 'Interpreting data from large-scale screens.', in Roberts G (ed.), Encyclopedia of Biophysics, Springer, 11, http://www.springerreference.com/docs/html/chapterdbid/305477.html

Wilkins MR, 2008, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics, pp. 113 - 120

Bek EJ; Wilkins MR, 2008, 'Using Yeast to Study Protein-Protein Interactions Relevant to Disease', in Witt S (ed.), Yeast as a model for Human Disease, Signpost Research Press, pp. 145 - 176

Wilkins MR, 2007, 'Biomarker Identification: The Role of Experimental Design, Statistics, and Data Sharing', in Clinical Proteomics, pp. 113 - 120

Packer N; Gooley AA; Wilkins MR, 2007, 'One gene, many proteins', in Wilkins M; Appel R; Williams K; Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, Springer Publishing Company, Netherlands, pp. 95 - 121

Pang CN; Wilkins MR, 2007, 'Online resources for the molecular contextualisation of disease', in Clinical Bioinformatics, Humana Press, USA

Hernandez P; Binz PA; Wilkins MR, 2007, 'Protein Identification in Proteomics', in Wilkins M; Appel R; Williams K; Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, Springer Publishing Company, Netherlands, pp. 41 - 67

Wilkins MR; Appel RD, 2007, 'Ten years of the proteome', in Wilkins M; Appel R; Williams K; Hochstrasser D (ed.), Proteome Research: concepts, technology and practice, Springer Publishing Company, Netherlands, pp. 1 - 13

Wilkins MR; Hunt S, 2006, 'Bioinformatics and Experimental Design for Biomarker Discovery', in Proteomics of Human Bodyfluids: Principles, Methods and Applications, Humana Press, USA, pp. 147

Binz PA; Muller M; Walther D; Bienvenut WV; Gras R; Hoogland C; Bouchet G; Gasteiger E; Fabbretti R; Gay S; Palagi P; Wilkins MR; Rouge V; Tonella L; Paesano S; Rossellat G; Karmime A; Bairoch A; Sanchez JC; Appel RD; Hochstrasser DF, 2005, 'Signal traitment and virtual images production (1/2): A molecular scanner to highly automate proteomic research and to display proteome images', in Acceleration and Improvement of Protein Identification by Mass Spectrometry, pp. 151 - 168, http://dx.doi.org/10.1007/1-4020-3319-2_4

Gasteiger E; Hoogland C; Gattiker A; Duvaud S; Wilkins MR; Appel R; Bairoch A, 2005, 'Protein Identification and Analysis Tools in the ExPASy Server', in Link AJ (ed.), 2-D Protein Gel Electrophoresis Protocols, Humana Press, Totowa, N.J., pp. 571 - 607

Cooper CA; Joshi HJ; Harrison M; Wilkins MR; Packer N, 2003, 'Querying GlycosuiteDB', in Conn PM (ed.), Handbook of Proteomic Methods, Humana Press, Totowa, NJ, pp. 233 - 240

Cooper CA; Joshi HJ; Harrison MJ; Wilkins MR; Packer NH, 2003, 'Querying GlycoSuiteDB', in Handbook of Proteomic Methods, Humana Press, pp. 233 - 239, http://dx.doi.org/10.1007/978-1-59259-414-6_15

Tyler MI; Wilkins MR, 2000, 'Identification of Proteins by Amino Acid Composition After Acid Hydrolysis', in Principles and Practice, Springer Berlin Heidelberg, pp. 143 - 161, http://dx.doi.org/10.1007/978-3-642-57105-3_7

Binz P; Wilkins MR; Gasteiger E; Bairoch A; Appel RD; Hochstrasser DF, 1999, 'Internet Resources for Protein Identification and Characterization', in , Wiley, pp. 277 - 299, http://dx.doi.org/10.1002/9783527613960.ch17

Wilkins MR; Gasteiger E; Bairoch A; Sanchez J-C; Williams KL; Appel RD; Hochstrasser DF, 1999, 'Protein Identification and Analysis Tools in the ExPASy Server', in 2-D Proteome Analysis Protocols, Springer Nature, pp. 531 - 552, http://dx.doi.org/10.1385/1-59259-584-7:531

Wilkins MR; Gooley AA, 1997, 'Protein Identification in Proteome Projects', in Principles and Practice, Springer Berlin Heidelberg, pp. 35 - 64, http://dx.doi.org/10.1007/978-3-662-03493-4_3

Journal articles

Cheng Y; Jones JP; Yu TT; Olzomer EM; Su J; Katen A; Black DSC; Hart-Smith G; Childress ES; Beretta M; Wilkins MR; Mateos IA; Santos WL; Hoehn KL; Byrne FL; Kumar N, 2024, 'Corrigendum to “Design, synthesis and biological evaluation of glucose metabolism inhibitors as anticancer agents” [Bioorg. Chem. 151 (2024) 107665] (Bioorganic Chemistry (2024) 151, (S0045206824005704), (10.1016/j.bioorg.2024.107665))', Bioorganic Chemistry, 151, http://dx.doi.org/10.1016/j.bioorg.2024.107725

Cheng Y; Jones JP; Yu TT; Olzomer EM; Su J; Katen A; Black DSC; Hart-Smith G; Childress ES; Wilkins MR; Mateos IA; Santos WL; Hoehn KL; Byrne FL; Kumar N, 2024, 'Design, synthesis and biological evaluation of glucose metabolism inhibitors as anticancer agents', Bioorganic Chemistry, 151, http://dx.doi.org/10.1016/j.bioorg.2024.107665

Hogg CJ; Edwards RJ; Farquharson KA; Silver LW; Brandies P; Peel E; Escalona M; Jaya FR; Thavornkanlapachai R; Batley K; Bradford TM; Chang JK; Chen Z; Deshpande N; Dziminski M; Ewart KM; Griffith OW; Marin Gual L; Moon KL; Travouillon KJ; Waters P; Whittington CM; Wilkins MR; Helgen KM; Lo N; Ho SYW; Ruiz Herrera A; Paltridge R; Marshall Graves JA; Renfree M; Shapiro B; Ottewell K; Belov K, 2024, 'Erratum: Author Correction: Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial (Nature ecology & evolution (2024) 8 7 DOI: 10.1038/s41559-024-02436-2)', Nature ecology & evolution, 8, pp. 1776, http://dx.doi.org/10.1038/s41559-024-02519-0

Hogg CJ; Edwards RJ; Farquharson KA; Silver LW; Brandies P; Peel E; Escalona M; Jaya FR; Thavornkanlapachai R; Batley K; Bradford TM; Chang JK; Chen Z; Deshpande N; Dziminski M; Ewart KM; Griffith OW; Marin Gual L; Moon KL; Travouillon KJ; Waters P; Whittington CM; Wilkins MR; Helgen KM; Lo N; Ho SYW; Ruiz Herrera A; Paltridge R; Marshall Graves JA; Renfree M; Shapiro B; Ottewell K; Belov K; Gibson C; Maxwell R; Spencer Z; Napangati Y; Butler M; West J; West J; James M; Napangati N; Gibson L; West P; Gibson A; West S; West K; Japaltjari W; Blackwood E, 2024, 'Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial', Nature Ecology and Evolution, 8, pp. 1311 - 1326, http://dx.doi.org/10.1038/s41559-024-02436-2

Separovich RJ; Karakatsanis NM; Gao K; Fuh D; Hamey JJ; Wilkins MR, 2024, 'Proline-directed yeast and human MAP kinases phosphorylate the Dot1p/DOT1L histone H3K79 methyltransferase', FEBS Journal, 291, pp. 2590 - 2614, http://dx.doi.org/10.1111/febs.17062

Hargett S; Lahiri S; Kowalski GM; Corley S; Nelson ME; Lackner C; Olzomer EM; Aleksovska I; Hearn BA; Shrestha R; Janitz M; Gorrell MD; Bruce CR; Wilkins M; Hoehn KL; Byrne FL, 2024, 'Bile acids mediate fructose-associated liver tumour growth in mice', Biochimica et Biophysica Acta - Molecular Basis of Disease, 1870, http://dx.doi.org/10.1016/j.bbadis.2024.167029

Karakatsanis NM; Hamey JJ; Wilkins MR, 2024, 'Taking Me away: the function of phosphorylation on histone lysine demethylases', Trends in Biochemical Sciences, 49, pp. 257 - 276, http://dx.doi.org/10.1016/j.tibs.2023.12.004

Manandhar B; Pandzic E; Deshpande N; Chen SY; Wasinger VC; Kockx M; Glaros EN; Ong KL; Thomas SR; Wilkins MR; Whan RM; Cochran BJ; Rye KA, 2024, 'ApoA-I Protects Pancreatic β-Cells from Cholesterol-Induced Mitochondrial Damage and Restores Their Ability to Secrete Insulin', Arteriosclerosis, Thrombosis, and Vascular Biology, 44, pp. E20 - E38, http://dx.doi.org/10.1161/ATVBAHA.123.319378

Kopecky C; Haug M; Reischl B; Deshpande N; Manandhar B; King TW; Lee V; Wilkins MR; Morris M; Polly P; Friedrich O; Rye KA; Cochran BJ, 2024, 'Effect of insulin insufficiency on ultrastructure and function in skeletal muscle', Journal of Cachexia, Sarcopenia and Muscle, 15, pp. 112 - 123, http://dx.doi.org/10.1002/jcsm.13380

Hamey JJ; Nguyen A; Haddad M; Vázquez-Campos X; Pfeiffer PG; Wilkins MR, 2024, 'Methylation of elongation factor 1A by yeast Efm4 or human eEF1A-KMT2 involves a beta-hairpin recognition motif and crosstalks with phosphorylation', Journal of Biological Chemistry, 300, http://dx.doi.org/10.1016/j.jbc.2024.105639

Li Y; Wu B; Hossain MJ; Quagliata L; O’Meara C; Wilkins MR; Corley S; Khachigian LM, 2023, 'Flubendazole inhibits PD-1 and suppresses melanoma growth in immunocompetent mice', Journal of Translational Medicine, 21, http://dx.doi.org/10.1186/s12967-023-04289-y

Mu A; Klare WP; Baines SL; Ignatius Pang CN; Guérillot R; Harbison-Price N; Keller N; Wilksch J; Nhu NTK; Phan MD; Keller B; Nijagal B; Tull D; Dayalan S; Chua HHC; Skoneczny D; Koval J; Hachani A; Shah AD; Neha N; Jadhav S; Partridge SR; Cork AJ; Peters K; Bertolla O; Brouwer S; Hancock SJ; Álvarez-Fraga L; De Oliveira DMP; Forde B; Dale A; Mujchariyakul W; Walsh CJ; Monk I; Fitzgerald A; Lum M; Correa-Ospina C; Roy Chowdhury P; Parton RG; De Voss J; Beckett J; Monty F; McKinnon J; Song X; Stephen JR; Everest M; Bellgard MI; Tinning M; Leeming M; Hocking D; Jebeli L; Wang N; Ben Zakour N; Yasar SA; Vecchiarelli S; Russell T; Zaw T; Chen T; Teng D; Kassir Z; Lithgow T; Jenney A; Cole JN; Nizet V; Sorrell TC; Peleg AY; Paterson DL; Beatson SA; Wu J; Molloy MP; Syme AE; Goode RJA; Hunter AA; Bowland G; West NP; Wilkins MR; Djordjevic SP; Davies MR; Seemann T; Howden BP; Pascovici D; Tyagi S; Schittenhelm RB; De Souza DP; McConville MJ; Iredell JR; Cordwell SJ; Strugnell RA; Stinear TP; Schembri MA; Walker MJ; Pang I, 2023, 'Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria', Nature Communications, 14, pp. 1530, http://dx.doi.org/10.1038/s41467-023-37200-w

Hamey JJ; Wilkins MR, 2023, 'The protein methylation network in yeast: A landmark in completeness for a eukaryotic post-translational modification', Proceedings of the National Academy of Sciences of the United States of America, 120, http://dx.doi.org/10.1073/pnas.2215431120

Bartolec TK; Vázquez-Campos X; Norman A; Luong C; Johnson M; Payne RJ; Wilkins MR; Mackay JP; Low JKK; Vazquez Campos X, 2023, 'Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein–protein interactions in the human cell', Proceedings of the National Academy of Sciences of the United States of America, 120, http://dx.doi.org/10.1073/pnas.2219418120

Kronen M; Vázquez-Campos X; Wilkins MR; Lee M; Manefield MJ; Vazquez Campos X, 2023, 'Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae', mSystems, 8, pp. e00119 - e00123, http://dx.doi.org/10.1128/msystems.00119-23

Kinsela AS; Payne TE; Bligh MW; Vázquez-Campos X; Wilkins MR; Comarmond MJ; Rowling B; Waite TD, 2022, 'Contaminant release, mixing and microbial fluctuations initiated by infiltrating water within a replica field-scale legacy radioactive waste trench', Science of the Total Environment, 851, http://dx.doi.org/10.1016/j.scitotenv.2022.158241

Bell KJ; Saad S; Tillett BJ; McGuire HM; Bordbar S; Yap YA; Nguyen LT; Wilkins MR; Corley S; Brodie S; Duong S; Wright CJ; Twigg S; de St Groth BF; Harrison LC; Mackay CR; Gurzov EN; Hamilton-Williams EE; Mariño E, 2022, 'Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation', Microbiome, 10, http://dx.doi.org/10.1186/s40168-021-01193-9

Mediati DG; Wong JL; Gao W; McKellar S; Pang CNI; Wu S; Wu W; Sy B; Monk IR; Biazik JM; Wilkins MR; Howden BP; Stinear TP; Granneman S; Tree JJ, 2022, 'Publisher Correction: RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance (Nature Communications, (2022), 13, 1, (3558), 10.1038/s41467-022-31177-8)', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-33167-2

Mediati DG; Wong JL; Gao W; McKellar S; Pang CNI; Wu S; Wu W; Sy B; Monk IR; Biazik JM; Wilkins MR; Howden BP; Stinear TP; Granneman S; Tree JJ, 2022, 'RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for intermediate vancomycin resistance', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-31177-8

Bartolec TK; Hamey JJ; Keller A; Chavez JD; Bruce JE; Wilkins MR, 2022, 'Differential Proteome and Interactome Analysis Reveal the Basis of Pleiotropy Associated With the Histidine Methyltransferase Hpm1p', Molecular and Cellular Proteomics, 21, http://dx.doi.org/10.1016/j.mcpro.2022.100249

Tay AP; Hamey JJ; Martyn GE; Wilson LOW; Wilkins MR, 2022, 'Identification of Protein Isoforms Using Reference Databases Built from Long and Short Read RNA-Sequencing', Journal of Proteome Research, 21, pp. 1628 - 1639, http://dx.doi.org/10.1021/acs.jproteome.1c00968

Separovich RJ; Wong MWM; Bartolec TK; Hamey JJ; Wilkins MR, 2022, 'Site-specific Phosphorylation of Histone H3K36 Methyltransferase Set2p and Demethylase Jhd1p is Required for Stress Responses in Saccharomyces cerevisiae', Journal of Molecular Biology, 434, pp. 167500, http://dx.doi.org/10.1016/j.jmb.2022.167500

Deshpande N; Wilkins MR; Khachigian LM, 2022, 'RNA sequencing identifies genes reliant upon Ser26 in the zinc finger transcription factor, early growth response-1', Vascular Pharmacology, 143, http://dx.doi.org/10.1016/j.vph.2022.106952

You J; Corley SM; Wen L; Hodge C; Höllhumer R; Madigan MC; Wilkins MR; Sutton G, 2021, 'Author Correction: RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients (Scientific Reports, (2018), 8, 1, (389), 10.1038/s41598-017-18480-x)', Scientific Reports, 11, http://dx.doi.org/10.1038/s41598-021-98363-4

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

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