The University of Southampton

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Phone:: (023) 8059 4401
Email:: rob.ewing@soton.ac.uk

Dr Rob M Ewing Bsc (Hons) Applied Biology, DPhil Molecular Genetics

Associate Professor in Proteomics and Systems Biology, Principal Investigator in molecular interaction networks in cancer and development,Director of the Graduate School of Biological Sciences

Related links: Personal homepage

Dr Rob M Ewing is Associate Professor in Proteomics and Systems Biology within Biological Sciences at the University of Southampton.

Career History

2013-present: Associate Professor in Proteomics and Systems Biology. University of Southampton, UK.
2007-2013: Assistant Professor. School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
2003-2007: Team Leader, Bioinformatics. MDS Proteomics, Toronto, Canada.
2001-2003: Senior Bioinformatics Scientist. Incyte Genomics, California, USA.
1999-2001: Postdoctoral Fellow. Carnegie Institute, Stanford University, California, USA.
1997-1999: Postdoctoral Fellow. Information Genetique et Structurale, CNRS, Marseille, France.

Academic Qualifications

1997: DPhil Molecular Genetics, Dept. Plant Sciences, University of Oxford, UK.
1989: BSc (Hons) Applied Biology. University of Bath, UK.

Research

Publications

Teaching

Contributions

Contact

Overview

Proteins are the 'molecular machines' of the cell, and perform many of the essential functions in biological systems. In many cases, however, proteins do not act alone but rather physically interact with other proteins and other types of biomolecules to carry out their functions. These sets of interacting proteins, termed 'protein complexes' are themselves organized into larger networks of proteins that function in a coordinated manner. Understanding which proteins interact with which, and where and when these interactions occur, is therefore essential to understanding protein function. The broad goal of our research is to understand these protein interaction networks, ultimately defining a 'systems-wide' protein interaction map that will both provide insights into the function of individual proteins as well as the organization of proteins within the cell.

Biological Questions

Our work focuses on understanding protein interactions in the context of human disease and development. Specifically, we are interested in protein interaction networks in cancer cells, and understanding how somatic mutations in important oncoproteins perturb protein interactions networks to promote tumourigenesis. Most recently we have focused on uncovering the network of protein-protein interactions that underlie Wnt signalling, a critically important signal transduction pathway during embryogenesis, and in many human cancers. In addition, we have used proteomic and computational techniques to begin to understand how embryonic stem cells maintain pluripotency, the capability to differentiate into many different tissues of the body.

Technologies

We are very much technology-focused, using and seeking to improve techniques for defining protein interaction networks. We use proteomic techniques (proteomics allows us to identify and quantify thousands of proteins at once) and also develop computational and statistical techniques for analysing the large amounts of data that proteomics experiments generate, and to organize those data into biological networks.

Research group

Biomedical Sciences

Affiliate research group

Molecular and Cellular Biosciences

Articles

Kontogeorgaki, S., Sanchez Garcia, R., Zygalakis, K., Ewing, R., & Macarthur, B. (2017). Noise-processing by signaling networks. Scientific Reports, 7, [532]. DOI: 10.1038/s41598-017-00659-x

Stumpf, P., Ewing, R., & Macarthur, B. D. (2016). Single-cell pluripotency regulatory networks. Proteomics, 16(17), 2303-2312. DOI: 10.1002/pmic.201500528

Song, J., Du, Z., Ravasz, M., Dong, B., Wang, Z., & Ewing, R. M. (2015). A protein interaction between beta-catenin and Dnmt1 regulates Wnt Signaling and DNA methylation in colorectal cancer cells. Molecular Cancer Research. DOI: 10.1158/1541-7786.MCR-13-0644

Rast-Somssich, M. I., Broholm, S., Jenkins, H., Canales, C., Vlad, D., Kwantes, M., ... Tsiantis, M. (2015). Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta. Genes & Development, 29(22), 2391-2404. DOI: 10.1101/gad.269050.115

Bowler, E., Wang, Z., & Ewing, R. (2015). How do oncoprotein mutations rewire protein–protein interaction networks? Expert Review of Proteomics, 12(5), 449-455. DOI: 10.1586/14789450.2015.1084875

Tomechko, S. E., Lundberg, K. C., Jarvela, J., Bebek, G., Chesnokov, N. G., Schlatzer, D., ... Silver, R. F. (2015). Proteomic and bioinformatics profile of paired human alveolar macrophages and peripheral blood monocytes. Proteomics, 15(22), 3797-3805. DOI: 10.1002/pmic.201400496

Scott, A., Song, J., Ewing, R., & Wang, Z. (2014). Regulation of protein stability of DNA methyltransferase 1 by post-translational modifications. Acta Biochimica et Biophysica Sinica, 46(3), 199-203. DOI: 10.1093/abbs/gmt146

Hao, Y., Wang, C., Cao, B., Hirsch, B. M., Song, J., Markowitz, S. D., ... Wang, Z. (2013). Gain of interaction with IRS1 by p110?-helical domain mutants is crucial for their oncogenic functions. Cancer Cell, 23(5), 583-593. DOI: 10.1016/j.ccr.2013.03.021

Song, J., Wang, Z., & Ewing, R. M. (2013). Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks. Molecular BioSystems. DOI: 10.1039/C3MB70417C

Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J-P., St-Denis, N. A., Li, T., ... Nesvizhskii, A. I. (2013). The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nature Methods, 10(8), 730-736. DOI: 10.1038/nmeth.2557

Jayapandian, C. P., Zhao, M., Ewing, R. M., Zhang, G-Q., & Sahoo, S. S. (2012). A semantic proteomics dashboard (SemPoD) for data management in translational research. BMC Systems Biology, 6, S20-[13pp]. DOI: 10.1186/1752-0509-6-S3-S20

Saha, S., Dazard, J-E., Xu, H., & Ewing, R. M. (2012). Computational framework for analysis of prey–prey associations in interaction proteomics identifies novel human protein–protein interactions and networks. Journal of Proteome Research, 11(9), 4476-4487. DOI: 10.1021/pr300227y

Song, J., Saha, S., Gokulrangan, G., Tesar, P. J., & Ewing, R. M. (2012). DNA and chromatin modification networks distinguish stem cell pluripotent ground states. Molecular & Cellular Proteomics, 11(10), 1036-1047. DOI: 10.1074/mcp.M111.011114

Yuan, Y., Kadiyala, C. S., Ching, T-T., Hakimi, P., Saha, S., Xu, H., ... Feng, Z. (2012). Enhanced energy metabolism contributes to the extended life span of calorie-restricted Caenorhabditis elegans. The Journal of Biological Chemistry, 287(37), 31414-31426. DOI: 10.1074/jbc.M112.377275

Schlatzer, D. M., Dazard, J-E., Ewing, R. M., Ilchenko, S., Tomcheko, S. E., Eid, S., ... Cooke, K. R. (2012). Human biomarker discovery and predictive models for disease progression for idiopathic pneumonia syndrome following allogeneic stem cell transplantation. Molecular & Cellular Proteomics, 11(6), M111.015479. DOI: 10.1074/mcp.M111.015479

Song, J., Hao, Y., Du, Z., Wang, Z., & Ewing, R. M. (2012). Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry. Journal of Proteome Research, 11(12), 5630-5641. DOI: 10.1021/pr300598t

Saha, S., Roman, T., Galnte, A., Koyuturk, M., & Ewing, R. M. (2012). Network-based approaches for extending the Wnt signaling pathway and identifying context-specific sub-networks. International Journal of Computational Biology and Drug Design.

Saha, S., Roman, T., Galante, A., Koyutürk, M., & Ewing, R. M. (2012). Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks. International Journal of Computational Biology and Drug Design, 5(3-4), 185-205. DOI: 10.1504/IJCBDD.2012.049203

Dazard, J-E. J., Saha, S., & Ewing, R. M. (2012). ROCS: a reproducibility index and confidence score for interaction proteomics. BMC Bioinformatics, 13(1), 128. DOI: 10.1186/1471-2105-13-128

Erten, S., Bebek, G., Ewing, R. M., & Koyutürk, M. (2011). DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. BioData Mining, 4, 19-[20pp]. DOI: 10.1186/1756-0381-4-19

Nibbe, R. K., Chowdhury, S. A., Koyutürk, M., Ewing, R., & Chance, M. R. (2011). Protein-protein interaction networks and subnetworks in the biology of disease. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 3(3), 357-367. DOI: 10.1002/wsbm.121

Du, Z., Song, J., Wang, Y., Zhao, Y., Guda, K., Yang, S., ... Wang, Z. (2010). DNMT1 stability is regulated by proteins coordinating deubiquitination and acetylation-driven ubiquitination. Science Signaling, 3(146), p.ra80. DOI: 10.1126/scisignal.2001462

Saha, S., Kaur, P., & Ewing, R. M. (2010). The bait compatibility index: computational bait selection for interaction proteomics experiments. Journal of Proteome Research, 9(10), 4972-4981. DOI: 10.1021/pr100267t

Nibbe, R. K., Markowitz, S., Myeroff, L., Ewing, R., & Chance, M. R. (2009). Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Molecular & Cellular Proteomics, 8(4), 827-845. DOI: 10.1074/mcp.M800428-MCP200

St-Germain, J. R., Taylor, P., Tong, J., Jin, L. L., Nikolic, A., Stewart, I. I., ... Moran, M. F. (2009). Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition. Proceedings of the National Academy of Sciences of the United States of America, 106(47), 20127-20132. DOI: 10.1073/pnas.0910957106

Schlatzer, D. M., Dazard, J-E., Dharsee, M., Ewing, R. M., Ilchenko, S., Stewart, I., ... Chance, M. R. (2009). Urinary protein profiles in a rat model for diabetic complications. Molecular & Cellular Proteomics, 8(9), 2145-2158. DOI: 10.1074/mcp.M800558-MCP200

Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., ... Pandey, A. (2008). Correspondence. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology, 26(2), 164-167. DOI: 10.1038/nbt0208-164

Bukhman, Y. V., Dharsee, M., Ewing, R., Chu, P., Topaloglou, T., Le Bihan, T., ... Ng, N. F. (2008). Design and analysis of quantitative differential proteomics investigations using LC-MS technology. Journal of Bioinformatics and Computational Biology, 6(1), 107-123. DOI: 10.1142/S0219720008003321

Ewing, R. M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., ... Figeys, D. (2007). Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular Systems Biology, 3(89), 89. DOI: 10.1038/msb4100134

Le Bihan, T., Goh, T., Stewart, I. I., Salter, A. M., Bukhman, Y. V., Dharsee, M., ... Wiśniewski, J. R. (2006). Differential analysis of membrane proteins in mouse fore- and hindbrain using a label-free approach. Journal of Proteome Research, 5(10), 2701-2710. DOI: 10.1021/pr060190y

Moran, M. F., Tong, J., Taylor, P., & Ewing, R. M. (2006). Emerging applications for phospho-proteomics in cancer molecular therapeutics. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, 1766(2), 230-241. DOI: 10.1016/j.bbcan.2006.06.002

Klok, E. J., Wilson, I. W., Wilson, D., Chapman, S. C., Ewing, R. M., Somerville, S. C., ... Dennis, E. S. (2002). Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. The Plant Cell, 14(10), 2481-2494. DOI: 10.1105/tpc.004747

Gutierrez, R. A., Ewing, R. M., Cherry, J. M., & Green, P. J. (2002). Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proceedings of the National Academy of Sciences, 99(17), 11513-11518. DOI: 10.1073/pnas.152204099

Ramonell, K. M., Zhang, B., Ewing, R. M., Chen, Y., Xu, D., Stacey, G., & Somerville, S. (2002). Microarray analysis of chitin elicitation in Arabidopsis thaliana. Molecular Plant Pathology, 3(5), 301-311. DOI: 10.1046/j.1364-3703.2002.00123.x

Finkelstein, D., Ewing, R., Gollub, J., Sterky, F., Cherry, J. M., & Somerville, S. (2002). Microarray data quality analysis: lessons from the Arabidopsis functional genomics consortium. Plant Molecular Biology, 48(1-2), 119-131. DOI: 10.1023/A:1013765922672

Ewing, R. M., & Cherry, J. M. (2001). Visualization of expression clusters using Sammon's non-linear mapping. Bioinformatics, 17(7), 658-659. DOI: 10.1093/bioinformatics/17.7.658

Ewing, R. M., & Claverie, J. M. (2000). EST databases as multi-conditional gene expression datasets. Pacific Symposium on Biocomputing, 5, 427-439.

Ewing, R. M., Poirot, O., & Claverie, J. M. (1999). Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets. In Silicio Biology, 1(4), 197-213.

Ewing, R. M., Ben Kahla, A., Poirot, O., Lopez, F., Audic, S., & Claverie, J. M. (1999). Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Research, 9(10), 950-959. DOI: 10.1101/gr.9.10.950

Coleman, M. P., Conforti, L., Buckmaster, E. A., Tarlton, A., Ewing, R. M., Brown, M. C., ... Perry, V. H. (1998). An 85-kb tandem triplication in the slow Wallerian degeneration (Wlds) mouse. Proceedings of the National Academy of Sciences, 95(17), 9985-9990. DOI: 10.1073/pnas.95.17.9985

Ewing, R. M., Jenkins, G. I., & Langdale, J. A. (1998). Transcripts of maize RbcS genes accumulate differentially in C3 and C4 tissues. Plant Molecular Biology, 36(4), 593-599. DOI: 10.1023/A:1005947306667

Book Chapter

Apfel, J., Parikh, J., Reischmann, P., Ewing, R., Müller, O., Dominguez, I., & Xia, Y. (2015). The Wnt signaling network in cancer. In S. Thiagalingam (Ed.), Systems Biology of Cancer. Cambridge, GB: Cambridge University Press.

Conference

Squires, S. E., Ewing, R., Prugel-Bennett, A., & Niranjan, M. (2017). A method of integrating spatial proteomics and protein-protein interaction network data. In Lecture Notes in Computer Science. (Lecture Notes in Computer Science). Springer.

BIOL2012 Exploring proteins: structure and function

External memberships/affiliations

International Society for Computational Biology
American Society for Mass Spectrometry
American Society for Biochemistry and Molecular Biology

Dr Rob M Ewing
Biological Sciences
Faculty of Natural & Environmental Sciences
Life Sciences Building 85
University of Southampton
Highfield Campus
Southampton
SO17 1BJ

Room Number:85/6053

Telephone:(023) 8059 4401
Email:rob.ewing@soton.ac.uk

Dr Rob M Ewing's personal home page

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