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Items: 1 to 50 of 166

1.

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.

Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J.

Brief Bioinform. 2018 Aug 29. doi: 10.1093/bib/bby077. [Epub ahead of print]

PMID:
30184176
2.

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

Li F, Li C, Marquez-Lago TT, Leier A, Akutsu T, Purcell AW, Smith AI, Lithgow T, Daly RJ, Song J, Chou KC.

Bioinformatics. 2018 Jun 27. doi: 10.1093/bioinformatics/bty522. [Epub ahead of print]

PMID:
29947803
3.

MicroRNAs as potential therapeutics to enhance chemosensitivity in advanced prostate cancer.

Lin HM, Nikolic I, Yang J, Castillo L, Deng N, Chan CL, Yeung NK, Dodson E, Elsworth B, Spielman C, Lee BY, Boyer Z, Simpson KJ, Daly RJ, Horvath LG, Swarbrick A.

Sci Rep. 2018 May 18;8(1):7820. doi: 10.1038/s41598-018-26050-y.

4.

Enduring epigenetic landmarks define the cancer microenvironment.

Pidsley R, Lawrence MG, Zotenko E, Niranjan B, Statham A, Song J, Chabanon RM, Qu W, Wang H, Richards M, Nair SS, Armstrong NJ, Nim HT, Papargiris M, Balanathan P, French H, Peters T, Norden S, Ryan A, Pedersen J, Kench J, Daly RJ, Horvath LG, Stricker P, Frydenberg M, Taylor RA, Stirzaker C, Risbridger GP, Clark SJ.

Genome Res. 2018 May;28(5):625-638. doi: 10.1101/gr.229070.117. Epub 2018 Apr 12.

5.

Identification of Novel Response and Predictive Biomarkers to Hsp90 Inhibitors Through Proteomic Profiling of Patient-derived Prostate Tumor Explants.

Nguyen EV, Centenera MM, Moldovan M, Das R, Irani S, Vincent AD, Chan H, Horvath LG, Lynn DJ, Daly RJ, Butler LM.

Mol Cell Proteomics. 2018 Aug;17(8):1470-1486. doi: 10.1074/mcp.RA118.000633. Epub 2018 Apr 9.

PMID:
29632047
6.

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences.

Chen Z, Zhao P, Li F, Leier A, Marquez-Lago TT, Wang Y, Webb GI, Smith AI, Daly RJ, Chou KC, Song J.

Bioinformatics. 2018 Jul 15;34(14):2499-2502. doi: 10.1093/bioinformatics/bty140.

PMID:
29528364
7.

Helicobacter pylori Type IV Secretion System and Its Adhesin Subunit, CagL, Mediate Potent Inflammatory Responses in Primary Human Endothelial Cells.

Tafreshi M, Guan J, Gorrell RJ, Chew N, Xin Y, Deswaerte V, Rohde M, Daly RJ, Peek RM Jr, Jenkins BJ, Davies EM, Kwok T.

Front Cell Infect Microbiol. 2018 Feb 6;8:22. doi: 10.3389/fcimb.2018.00022. eCollection 2018.

8.

Impact of the Anticancer Drug NT157 on Tyrosine Kinase Signaling Networks.

Su SP, Flashner-Abramson E, Klein S, Gal M, Lee RS, Wu J, Levitzki A, Daly RJ.

Mol Cancer Ther. 2018 May;17(5):931-942. doi: 10.1158/1535-7163.MCT-17-0377. Epub 2018 Feb 12.

PMID:
29440449
9.

Ablation of Grb10 Specifically in Muscle Impacts Muscle Size and Glucose Metabolism in Mice.

Holt LJ, Brandon AE, Small L, Suryana E, Preston E, Wilks D, Mokbel N, Coles CA, White JD, Turner N, Daly RJ, Cooney GJ.

Endocrinology. 2018 Mar 1;159(3):1339-1351. doi: 10.1210/en.2017-00851.

PMID:
29370381
10.

Effect of FAK inhibitor VS-6063 (defactinib) on docetaxel efficacy in prostate cancer.

Lin HM, Lee BY, Castillo L, Spielman C, Grogan J, Yeung NK, Kench JG, Stricker PD, Haynes AM, Centenera MM, Butler LM, Shreeve SM, Horvath LG, Daly RJ.

Prostate. 2018 Mar;78(4):308-317. doi: 10.1002/pros.23476. Epub 2018 Jan 5.

PMID:
29314097
11.

Author Correction: Tyrosine dephosphorylated cortactin downregulates contractility at the epithelial zonula adherens through SRGAP1.

Liang X, Budnar S, Gupta S, Verma S, Han SP, Hill MM, Daly RJ, Parton RG, Hamilton NA, Gomez GA, Yap AS.

Nat Commun. 2017 Dec 5;8(1):2021. doi: 10.1038/s41467-017-02131-w.

12.

The pseudokinases SgK269 and SgK223: A novel oncogenic alliance in human cancer.

O'Rourke RL, Daly RJ.

Cell Adh Migr. 2017 Dec 21:1-5. doi: 10.1080/19336918.2017.1394570. [Epub ahead of print]

PMID:
29105536
13.

Structure of SgK223 pseudokinase reveals novel mechanisms of homotypic and heterotypic association.

Patel O, Griffin MDW, Panjikar S, Dai W, Ma X, Chan H, Zheng C, Kropp A, Murphy JM, Daly RJ, Lucet IS.

Nat Commun. 2017 Oct 27;8(1):1157. doi: 10.1038/s41467-017-01279-9.

14.

Aurora Kinase B, a novel regulator of TERF1 binding and telomeric integrity.

Chan FL, Vinod B, Novy K, Schittenhelm RB, Huang C, Udugama M, Nunez-Iglesias J, Lin JI, Hii L, Chan J, Pickett HA, Daly RJ, Wong LH.

Nucleic Acids Res. 2017 Dec 1;45(21):12340-12353. doi: 10.1093/nar/gkx904.

15.

Tyrosine dephosphorylated cortactin downregulates contractility at the epithelial zonula adherens through SRGAP1.

Liang X, Budnar S, Gupta S, Verma S, Han SP, Hill MM, Daly RJ, Parton RG, Hamilton NA, Gomez GA, Yap AS.

Nat Commun. 2017 Oct 5;8(1):790. doi: 10.1038/s41467-017-00797-w. Erratum in: Nat Commun. 2017 Dec 5;8(1):2021.

16.

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection.

Song J, Wang H, Wang J, Leier A, Marquez-Lago T, Yang B, Zhang Z, Akutsu T, Webb GI, Daly RJ.

Sci Rep. 2017 Jul 31;7(1):6862. doi: 10.1038/s41598-017-07199-4.

17.

A distinct plasma lipid signature associated with poor prognosis in castration-resistant prostate cancer.

Lin HM, Mahon KL, Weir JM, Mundra PA, Spielman C, Briscoe K, Gurney H, Mallesara G, Marx G, Stockler MR, PRIMe Consortium, Parton RG, Hoy AJ, Daly RJ, Meikle PJ, Horvath LG.

Int J Cancer. 2017 Nov 15;141(10):2112-2120. doi: 10.1002/ijc.30903. Epub 2017 Aug 8.

PMID:
28741687
18.

Phosphoproteomic Profiling Reveals ALK and MET as Novel Actionable Targets across Synovial Sarcoma Subtypes.

Fleuren EDG, Vlenterie M, van der Graaf WTA, Hillebrandt-Roeffen MHS, Blackburn J, Ma X, Chan H, Magias MC, van Erp A, van Houdt L, Cebeci SAS, van de Ven A, Flucke UE, Heyer EE, Thomas DM, Lord CJ, Marini KD, Vaghjiani V, Mercer TR, Cain JE, Wu J, Versleijen-Jonkers YMH, Daly RJ.

Cancer Res. 2017 Aug 15;77(16):4279-4292. doi: 10.1158/0008-5472.CAN-16-2550. Epub 2017 Jun 20.

19.

Signalome-wide assessment of host cell response to hepatitis C virus.

Haqshenas G, Wu J, Simpson KJ, Daly RJ, Netter HJ, Baumert TF, Doerig C.

Nat Commun. 2017 May 8;8:15158. doi: 10.1038/ncomms15158.

20.

Homo- and Heterotypic Association Regulates Signaling by the SgK269/PEAK1 and SgK223 Pseudokinases.

Liu L, Phua YW, Lee RS, Ma X, Jenkins Y, Novy K, Humphrey ES, Chan H, Shearer R, Ong PC, Dai W, Saunders DN, Lucet IS, Daly RJ.

J Biol Chem. 2016 Oct 7;291(41):21571-21583. Epub 2016 Aug 16.

21.

Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling.

Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ.

Mol Cell Proteomics. 2016 Aug;15(8):2671-85. doi: 10.1074/mcp.M116.058313. Epub 2016 Jun 3.

22.

Quantitative phosphotyrosine profiling of patient-derived xenografts identifies therapeutic targets in pediatric leukemia.

Dolai S, Sia KC, Robbins AK, Zhong L, Heatley SL, Vincent TL, Hochgräfe F, Sutton R, Kurmasheva RT, Revesz T, White DL, Houghton PJ, Smith MA, Teachey DT, Daly RJ, Raftery MJ, Lock RB.

Cancer Res. 2016 May;76(9):2766-2777. doi: 10.1158/0008-5472.CAN-15-2786. Epub 2016 Mar 9.

23.

PP1 initiates the dephosphorylation of MASTL, triggering mitotic exit and bistability in human cells.

Rogers S, Fey D, McCloy RA, Parker BL, Mitchell NJ, Payne RJ, Daly RJ, James DE, Caldon CE, Watkins DN, Croucher DR, Burgess A.

J Cell Sci. 2016 Apr 1;129(7):1340-54. doi: 10.1242/jcs.179754. Epub 2016 Feb 12.

24.

The kinome 'at large' in cancer.

Fleuren ED, Zhang L, Wu J, Daly RJ.

Nat Rev Cancer. 2016 Feb;16(2):83-98. doi: 10.1038/nrc.2015.18. Review.

PMID:
26822576
25.

Dataset from the global phosphoproteomic mapping of early mitotic exit in human cells.

Rogers S, McCloy RA, Parker BL, Chaudhuri R, Gayevskiy V, Hoffman NJ, Watkins DN, Daly RJ, James DE, Burgess A.

Data Brief. 2015 Aug 24;5:45-52. doi: 10.1016/j.dib.2015.08.010. eCollection 2015 Dec.

26.

The pseudokinase SgK223 promotes invasion of pancreatic ductal epithelial cells through JAK1/Stat3 signaling.

Tactacan CM, Phua YW, Liu L, Zhang L, Humphrey ES, Cowley M, Pinese M, Biankin AV, Daly RJ.

Mol Cancer. 2015 Jul 29;14:139. doi: 10.1186/s12943-015-0412-3.

27.

Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs.

McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A.

Mol Cell Proteomics. 2015 Aug;14(8):2194-212. doi: 10.1074/mcp.M114.046938. Epub 2015 Jun 8.

28.

Cytokine profiling of docetaxel-resistant castration-resistant prostate cancer.

Mahon KL, Lin HM, Castillo L, Lee BY, Lee-Ng M, Chatfield MD, Chiam K, Breit SN, Brown DA, Molloy MP, Marx GM, Pavlakis N, Boyer MJ, Stockler MR, Daly RJ, Henshall SM, Horvath LG.

Br J Cancer. 2015 Apr 14;112(8):1340-8. doi: 10.1038/bjc.2015.74. Epub 2015 Mar 31.

29.

The tyrosine phosphatase PTPN14 (Pez) inhibits metastasis by altering protein trafficking.

Belle L, Ali N, Lonic A, Li X, Paltridge JL, Roslan S, Herrmann D, Conway JR, Gehling FK, Bert AG, Crocker LA, Tsykin A, Farshid G, Goodall GJ, Timpson P, Daly RJ, Khew-Goodall Y.

Sci Signal. 2015 Feb 17;8(364):ra18. doi: 10.1126/scisignal.2005547.

PMID:
25690013
30.

Professor Robert Sutherland FAA, AO (1947-2012).

Watts CK, Daly RJ.

Horm Mol Biol Clin Investig. 2013 Dec;16(3):113-4. doi: 10.1515/hmbci-2013-0046. No abstract available.

PMID:
25436862
31.

FAK signaling in human cancer as a target for therapeutics.

Lee BY, Timpson P, Horvath LG, Daly RJ.

Pharmacol Ther. 2015 Feb;146:132-49. doi: 10.1016/j.pharmthera.2014.10.001. Epub 2014 Oct 12. Review.

PMID:
25316657
32.

Profiling the tyrosine phosphoproteome of different mouse mammary tumour models reveals distinct, model-specific signalling networks and conserved oncogenic pathways.

Ali NA, Wu J, Hochgräfe F, Chan H, Nair R, Ye S, Zhang L, Lyons RJ, Pinese M, Lee HC, Armstrong N, Ormandy CJ, Clark SJ, Swarbrick A, Daly RJ.

Breast Cancer Res. 2014 Sep 9;16(5):437. doi: 10.1186/s13058-014-0437-3.

33.

Circulating microRNAs are associated with docetaxel chemotherapy outcome in castration-resistant prostate cancer.

Lin HM, Castillo L, Mahon KL, Chiam K, Lee BY, Nguyen Q, Boyer MJ, Stockler MR, Pavlakis N, Marx G, Mallesara G, Gurney H, Clark SJ, Swarbrick A, Daly RJ, Horvath LG.

Br J Cancer. 2014 May 13;110(10):2462-71. doi: 10.1038/bjc.2014.181. Epub 2014 Apr 8.

34.

Grb10 deletion enhances muscle cell proliferation, differentiation and GLUT4 plasma membrane translocation.

Mokbel N, Hoffman NJ, Girgis CM, Small L, Turner N, Daly RJ, Cooney GJ, Holt LJ.

J Cell Physiol. 2014 Nov;229(11):1753-64. doi: 10.1002/jcp.24628.

PMID:
24664951
35.

Phosphoproteomic profiling identifies focal adhesion kinase as a mediator of docetaxel resistance in castrate-resistant prostate cancer.

Lee BY, Hochgräfe F, Lin HM, Castillo L, Wu J, Raftery MJ, Martin Shreeve S, Horvath LG, Daly RJ.

Mol Cancer Ther. 2014 Jan;13(1):190-201. doi: 10.1158/1535-7163.MCT-13-0225-T. Epub 2013 Nov 5.

36.

A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties.

Murphy JM, Zhang Q, Young SN, Reese ML, Bailey FP, Eyers PA, Ungureanu D, Hammaren H, Silvennoinen O, Varghese LN, Chen K, Tripaydonis A, Jura N, Fukuda K, Qin J, Nimchuk Z, Mudgett MB, Elowe S, Gee CL, Liu L, Daly RJ, Manning G, Babon JJ, Lucet IS.

Biochem J. 2014 Jan 15;457(2):323-34. doi: 10.1042/BJ20131174.

37.

Phosphoproteomic analysis of anaplastic lymphoma kinase (ALK) downstream signaling pathways identifies signal transducer and activator of transcription 3 as a functional target of activated ALK in neuroblastoma cells.

Sattu K, Hochgräfe F, Wu J, Umapathy G, Schönherr C, Ruuth K, Chand D, Witek B, Fuchs J, Li PK, Hugosson F, Daly RJ, Palmer RH, Hallberg B.

FEBS J. 2013 Nov;280(21):5269-82. doi: 10.1111/febs.12453. Epub 2013 Aug 22.

38.

Global characterization of signalling networks associated with tamoxifen resistance in breast cancer.

Browne BC, Hochgräfe F, Wu J, Millar EK, Barraclough J, Stone A, McCloy RA, Lee CS, Roberts C, Ali NA, Boulghourjian A, Schmich F, Linding R, Farrow L, Gee JM, Nicholson RI, O'Toole SA, Sutherland RL, Musgrove EA, Butt AJ, Daly RJ.

FEBS J. 2013 Nov;280(21):5237-57. doi: 10.1111/febs.12441. Epub 2013 Aug 19.

39.

Temporal regulation of EGF signalling networks by the scaffold protein Shc1.

Zheng Y, Zhang C, Croucher DR, Soliman MA, St-Denis N, Pasculescu A, Taylor L, Tate SA, Hardy WR, Colwill K, Dai AY, Bagshaw R, Dennis JW, Gingras AC, Daly RJ, Pawson T.

Nature. 2013 Jul 11;499(7457):166-71. doi: 10.1038/nature12308.

40.

Characterization of the novel broad-spectrum kinase inhibitor CTx-0294885 as an affinity reagent for mass spectrometry-based kinome profiling.

Zhang L, Holmes IP, Hochgräfe F, Walker SR, Ali NA, Humphrey ES, Wu J, de Silva M, Kersten WJ, Connor T, Falk H, Allan L, Street IP, Bentley JD, Pilling PA, Monahan BJ, Peat TS, Daly RJ.

J Proteome Res. 2013 Jul 5;12(7):3104-16. doi: 10.1021/pr3008495. Epub 2013 Jun 25.

PMID:
23692254
41.

Neuropilin-2 promotes extravasation and metastasis by interacting with endothelial α5 integrin.

Cao Y, Hoeppner LH, Bach S, E G, Guo Y, Wang E, Wu J, Cowley MJ, Chang DK, Waddell N, Grimmond SM, Biankin AV, Daly RJ, Zhang X, Mukhopadhyay D.

Cancer Res. 2013 Jul 15;73(14):4579-4590. doi: 10.1158/0008-5472.CAN-13-0529. Epub 2013 May 20.

42.

Involvement of Lyn and the atypical kinase SgK269/PEAK1 in a basal breast cancer signaling pathway.

Croucher DR, Hochgräfe F, Zhang L, Liu L, Lyons RJ, Rickwood D, Tactacan CM, Browne BC, Ali N, Chan H, Shearer R, Gallego-Ortega D, Saunders DN, Swarbrick A, Daly RJ.

Cancer Res. 2013 Mar 15;73(6):1969-80. doi: 10.1158/0008-5472.CAN-12-1472. Epub 2013 Feb 1.

43.

TCPTP regulates SFK and STAT3 signaling and is lost in triple-negative breast cancers.

Shields BJ, Wiede F, Gurzov EN, Wee K, Hauser C, Zhu HJ, Molloy TJ, O'Toole SA, Daly RJ, Sutherland RL, Mitchell CA, McLean CA, Tiganis T.

Mol Cell Biol. 2013 Feb;33(3):557-70. doi: 10.1128/MCB.01016-12. Epub 2012 Nov 19.

44.

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Kolle G, Newell F, Pinese M, Mead RS, Humphris JL, Kaplan W, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chou A, Chin VT, Chantrill LA, Mawson A, Samra JS, Kench JG, Lovell JA, Daly RJ, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N; Australian Pancreatic Cancer Genome Initiative, Kakkar N, Zhao F, Wu YQ, Wang M, Muzny DM, Fisher WE, Brunicardi FC, Hodges SE, Reid JG, Drummond J, Chang K, Han Y, Lewis LR, Dinh H, Buhay CJ, Beck T, Timms L, Sam M, Begley K, Brown A, Pai D, Panchal A, Buchner N, De Borja R, Denroche RE, Yung CK, Serra S, Onetto N, Mukhopadhyay D, Tsao MS, Shaw PA, Petersen GM, Gallinger S, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Lawlor RT, Capelli P, Corbo V, Scardoni M, Tortora G, Tempero MA, Mann KM, Jenkins NA, Perez-Mancera PA, Adams DJ, Largaespada DA, Wessels LF, Rust AG, Stein LD, Tuveson DA, Copeland NG, Musgrove EA, Scarpa A, Eshleman JR, Hudson TJ, Sutherland RL, Wheeler DA, Pearson JV, McPherson JD, Gibbs RA, Grimmond SM.

Nature. 2012 Nov 15;491(7424):399-405. doi: 10.1038/nature11547. Epub 2012 Oct 24.

45.

New insights into signalling networks regulating breast cancer stem cells.

Swarbrick A, Daly RJ.

Breast Cancer Res. 2012 Sep 21;14(5):321. doi: 10.1186/bcr3209.

46.

RON is not a prognostic marker for resectable pancreatic cancer.

Tactacan CM, Chang DK, Cowley MJ, Humphrey ES, Wu J, Gill AJ, Chou A, Nones K, Grimmond SM, Sutherland RL, Biankin AV, Daly RJ; Australian Pancreratic Genome Initiative.

BMC Cancer. 2012 Sep 7;12:395. doi: 10.1186/1471-2407-12-395.

47.

Gab2 signaling in chronic myeloid leukemia cells confers resistance to multiple Bcr-Abl inhibitors.

Wöhrle FU, Halbach S, Aumann K, Schwemmers S, Braun S, Auberger P, Schramek D, Penninger JM, Laßmann S, Werner M, Waller CF, Pahl HL, Zeiser R, Daly RJ, Brummer T.

Leukemia. 2013 Jan;27(1):118-29. doi: 10.1038/leu.2012.222. Epub 2012 Aug 3.

PMID:
22858987
48.

Annexin A6 is a scaffold for PKCα to promote EGFR inactivation.

Koese M, Rentero C, Kota BP, Hoque M, Cairns R, Wood P, Vilà de Muga S, Reverter M, Alvarez-Guaita A, Monastyrskaya K, Hughes WE, Swarbrick A, Tebar F, Daly RJ, Enrich C, Grewal T.

Oncogene. 2013 Jun 6;32(23):2858-72. doi: 10.1038/onc.2012.303. Epub 2012 Jul 16.

PMID:
22797061
49.

Functional characterization of cancer-associated Gab1 mutations.

Ortiz-Padilla C, Gallego-Ortega D, Browne BC, Hochgräfe F, Caldon CE, Lyons RJ, Croucher DR, Rickwood D, Ormandy CJ, Brummer T, Daly RJ.

Oncogene. 2013 May 23;32(21):2696-702. doi: 10.1038/onc.2012.271. Epub 2012 Jul 2.

PMID:
22751113
50.

Grb10 regulates the development of fiber number in skeletal muscle.

Holt LJ, Turner N, Mokbel N, Trefely S, Kanzleiter T, Kaplan W, Ormandy CJ, Daly RJ, Cooney GJ.

FASEB J. 2012 Sep;26(9):3658-69. doi: 10.1096/fj.11-199349. Epub 2012 May 23.

PMID:
22623587

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