Bioinformatics

The Computational Biology and Bioinformatics team provides support to scientists at the Institute, covering a range of research projects that require large-scale exploratory data analysis, advanced statistics and mathematical modelling. We aim to provide insights that advance our understanding of cancer biology; specifically, we offer our expertise in:

  • Analysis of large datasets from high-throughput technologies (next generation sequencing, microarrays, metabolomics and RNAi screening).
  • Functional and pathway analyses using Ingenuity Pathway Analysis and GeneGo Metacore.
  • Data-mining with Oncomine Research Premium Edition and Oncomine Gene Browser.
  • Complex statistical analyses (mixed modelling, Bayesian and multivariate analyses), machine learning, and graph and network theory-based analyses.
  • Power and sample size estimation, experimental design, data presentation and visualisation.
  • Mathematical modelling and simulation of biological processes (such as cell migration, chemotaxis and cell-cell interactions).
  • Computer programming in R (including Bioconductor), Matlab, Fortran, Perl, Python, PHP and Bash.

Recent Publications

2016

Birch J, Clarke CJ, Campbell AD, Campbell K, Mitchell L, Liko D, Kalna G, Strathdee D, Sansom OJ, Neilson M, Blyth K, Norman JC. The initiator methionine tRNA drives cell migration and invasion leading to increased metastatic potential in melanoma. Biol Open. 2016 Aug 19. pii: bio.019075. doi: 10.1242/bio.019075. [Epub ahead of print]

2015

Cardaci S, Zheng L, MacKay G, van den Broek NJ, MacKenzie ED, Nixon C, Stevenson D, Tumanov S, Bulusu V, Kamphorst JJ, Vazquez A, Fleming S, Schiavi F, Kalna G, Blyth K, Strathdee D, Gottlieb E. Pyruvate carboxylation enables growth of SDH-deficient cells by supporting aspartate biosynthesis. Nat Cell Biol 17: 1317-26, 2015

Daskalaki E, Blackburn G, Kalna G, Zhang T, Anthony N, Watson DG. A study of the effects of exercise on the urinary metabolome using normalisation to individual metabolic output. Metabolites 5: 119-39, 2015

Huels DJ, Ridgway RA, Radulescu S, Leushacke M, Campbell AD, Biswas S, Leedham S, Serra S, Chetty R, Moreaux G, Parry L, Matthews J, Song F, Hedley A, Kalna G, Ceteci F, Reed KR, Meniel VS, Maguire A, Doyle B, Soderberg O, Barker N, Watson A, Larue L, Clarke AR, Sansom OJ. E-cadherin can limit the transforming properties of activating beta-catenin mutations. EMBO J 34: 2321-33, 2015

Mardilovich K, Baugh M, Crighton D, Kowalczyk D, Gabrielsen M, Munro J, Croft DR, Lourenco F, James D, Kalna G, McGarry L, Rath O, Shanks E, Garnett MJ, McDermott U, Brookfield J, Charles M, Hammonds T, Olson MF. LIM kinase inhibitors disrupt mitotic microtubule organization and impair tumor cell proliferation. Oncotarget 2015. doi: 10.18632/oncotarget.6288. Epub 2015 Nov 3

Munkley J, Lafferty NP, Kalna G, Robson CN, Leung HY, Rajan P, Elliott DJ. Androgen-regulation of the protein tyrosine phosphatase PTPRR activates ERK1/2 signalling in prostate cancer cells. BMC Cancer 15: 9, 2015

Roberts HM, Ling MR, Insall R, Kalna G, Spengler J, Grant MM, Chapple IL. Impaired neutrophil directional chemotactic accuracy in chronic periodontitis patients. J Clin Periodontol 42: 1-11, 2015

Schug ZT, Peck B, Jones DT, Zhang Q, Grosskurth S, Alam IS, Goodwin LM, Smethurst E, Mason S, Blyth K, McGarry L, James D, Shanks E, Kalna G, Saunders RE, Jiang M, Howell M, Lassailly F, Thin MZ, Spencer-Dene B, Stamp G, van den Broek NJ, Mackay G, Bulusu V, Kamphorst JJ, Tardito S, Strachan D, Harris AL, Aboagye EO, Critchlow SE, Wakelam MJ, Schulze A, Gottlieb E. Acetyl-CoA synthetase 2 promotes acetate utilization and maintains cancer cell growth under metabolic stress. Cancer Cell 27: 57-71, 2015

Zheng L, Cardaci S, Jerby L, MacKenzie ED, Sciacovelli M, Johnson TI, Gaude E, King A, Leach JD, Edrada-Ebel R, Hedley A, Morrice NA, Kalna G, Blyth K, Ruppin E, Frezza C, Gottlieb E. Fumarate induces redox-dependent senescence by modifying glutathione metabolism. Nat Commun 6: 6001, 2015

2014

Macpherson IR, Rainero E, Mitchell LE, van den Berghe PV, Speirs C, Dozynkiewicz MA, Chaudhary S, Kalna G, Edwards J, Timpson P, Norman JC. CLIC3 controls recycling of late endosomal MT1-MMP and dictates invasion and metastasis in breast cancer. J Cell Sci. 127(18):3893-901 (2014).

Morran DC, Wu J, Jamieson NB, Mrowinska A, Kalna G, Karim SA, Au AY, Scarlett CJ, Chang DK, Pajak MZ; Australian Pancreatic Cancer Genome Initiative (APGI), Oien KA, McKay CJ, Carter CR, Gillen G, Champion S, Pimlott SL, Anderson KI, Evans TR, Grimmond SM, Biankin AV, Sansom OJ, Morton JP. Targeting mTOR dependency in pancreatic cancer. Gut. 63(9). 1481-9 (2014)

Tyrrell BJ, Neilson M, Insall RH, Machesky LM. Predicting cell shapes in melanomas. Pigment Cell Melanoma Res 27: 5-6, 2014

2013

Ahmad I, Kalna G, Ismail M, Birrell F, Asterling S, McCartney E, Greene D, Davies J, Leung HY. Prostate gland lengths and iceball dimensions predict micturition functional outcome following salvage prostate cryotherapy in men with radiation recurrent prostate cancer. PLoS One 8(8), (2013).

Ahmad I, Singh LB, Yang ZH, Kalna G, Fleming J, Fisher G, Cooper C, Cuzick J, Berney DM, Moller H, Scardino P, Leung HY. Mir143 expression inversely correlates with nuclear ERK5 immunoreactivity in clinical prostate cancer. Br J Cancer 108(1), 149-154 (2013).

Costea DE, Hills A, Osman AH, Thurlow J, Kalna G, Huang X, Pena Murillo C, Parajuli H, Suliman S, Kulasekara KK, Johannessen AC, Partridge M. Identification of two distinct carcinoma-associated fibroblast subtypes with differential tumor-promoting abilities in oral squamous cell carcinoma. Cancer Res 73(13), 3888-3901 (2013).

Davidson AJ, Ura S, Thomason PA, Kalna G, Insall RH. Abi Is Required for Modulation and Stability but Not Localization or Activation of the SCAR/WAVE Complex. Eukaryot Cell 12(11), 1509-1516 (2013).

Galban-Horcajo F, Fitzpatrick AM, Hutton AJ, Dunn SM, Kalna G, Brennan KM, Rinaldi S, Yu RK, Goodyear CS, Willison HJ. Antibodies to heteromeric glycolipid complexes in multifocal motor neuropathy. Eur J Neurol 20(1), 62-70 (2013).

Muinonen-Martin AJ, Knecht DA, Veltman DM, Thomason PA, Kalna G, Insall RH. Measuring chemotaxis using direct visualization microscope chambers. Methods Mol Biol 1046, 307-321 (2013).

Myant KB, Cammareri P, McGhee EJ, Ridgway RA, Huels DJ, Cordero JB, Schwitalla S, Kalna G, Ogg EL, Athineos D, Timpson P, Vidal M, Murray GI, Greten FR, Anderson KI, Sansom OJ. ROS production and NF-kappaB activation triggered by RAC1 facilitate WNT-driven intestinal stem cell proliferation and colorectal cancer initiation. Cell Stem Cell 12(6), 761-773 (2013).

Rinaldi S, Brennan KM, Kalna G , Walgaard C, van Doorn P, Jacobs, BC, Yu RK, Mansson JE, Goodyear, CS, Willison HJ. Antibodies to heteromeric glycolipid complexes in guillain-barré syndrome. PLoS One, 8(12), e82337 (2013).

Zanivan S, Meves A, Behrendt K, Schoof EM, Neilson LJ, Cox J, Tang HR, Kalna G, van Ree JH, van Deursen JM, Trempus CS, Machesky LM, Linding R, Wickstrom SA, Fassler R, Mann M. In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis. Cell Rep 3(2), 552-566 (2013).

Zheng L, Mackenzie ED, Karim SA, Hedley A, Blyth K, Kalna G, Watson DG, Szlosarek P, Frezza C, Gottlieb E. Reversed argininosuccinate lyase activity in fumarate hydratase-deficient cancer cells. Cancer Metab 1(1), 1-12 (2013).

2012

Dawson JC, Timpson P, Kalna G, Machesky LM. Mtss1 regulates epidermal growth factor signaling in head and neck squamous carcinoma cells. Oncogene 31(14), 1781-1793 (2012).

von Thun A, Birtwistle M, Kalna G ,Grindlay J, Strachan D, Kolch W, von Kriegsheim A, Norman J. ERK2 drives tumour cell migration in 3D icroenvironments by suppressing expression of Rab17 and Liprin-β2. J Cell Sci 125(Pt6), 1465–1477 (2012).

Group Members

Gabriela Kalna
Ann Hedley
Matthew Neilson

Research

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Read more about the Research Groups working at the Beatson Institute.

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Seminars

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Find out more about our seminars including our Distinguished Seminar Programme.

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