Ashfaq Ali

Ashfaq Ali NBIS expert

Metabolomic, Transcriptomics, Proteomics, Systems Biology, Genomics, Genetics, Gene Environment Interactions

I obtained my PhD in biological sciences from Lund University focusing on plant pathogen interactions using global transcriptomics (gene expression and RNA-sequencing) and proteomics. The project included RNA-seq assisted proteomics for broader coverage of non-model organisms proteomes and analyses of transcriptomics and proetomics data simultaneously.

During my postdoc in statistical genetics at the Genetic and Moelcular Epidemiology Unit at the department of clinical science at Lund University, Sweden I worked with novel approaches in studying Gene Environment interactions in obesity and type 2 diabetes. Here my projects involved novel approaches in clinical validation of loci from GWAS (Genome wide association studies). Here I also worked with integrated analyses of transcriptomics and methylation data and functional annotation of GWAS loci.

I then moved to the Department of Systems Medicine at Steno Diabetes Centre Copenhagen where I studies various Type 1 and Type 2 diabetes related questions using targeted and un-targeted metabolomics and lipidomics data. These included patient stratification using clinical and metabolomics data for disease outcomes and treatment response. I also worked with Genome scale metabolic networks for integrated analyses of metabolomics and transcriptomics data from T2D target tissues.

I have been involved in large consortia projects involving industry-academia partnerships and have extensive knowledge and experience in analyses of multi-omics data in relation to clinical associations and vertical/multimodal integration using systems biology and statistical approaches.

Selected publications

Ahmad, S., Rukh, G., Varga, T. V., Ali, A., Kurbasic, A., Shungin, D., Ericson, U., Koivula, R. W., Chu, A. Y., Rose, L. M., and others (2013) Gene\times physical activity interactions in obesity: combined analysis of 111,421 individuals of European ancestry. PLoS genetics, 9, e1003607.

Resjö, S., Ali, A., Meijer, H. J. G., Seidl, M. F., Snel, B., Sandin, M., Levander, F., Govers, F., and Andreasson, E. (2014) Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family. Journal of proteome research, 13, 1848–1859.

Ali, A., Alexandersson, E., Sandin, M., Resjö, S., Lenman, M., Hedley, P., Levander, F., and Andreasson, E. (2014) Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions. BMC genomics, 15, 497.

Ali, A., Varga, T. V., Stojkovic, I. A., Schulz, C.-A., Hallmans, G., Barroso, I., Poveda, A., Renström, F., Orho-Melander, M., and Franks, P. W. (2016) Do genetic factors modify the relationship between obesity and hypertriglyceridemia? Findings from the GLACIER and the MDC studies. Circulation: Genomic and Precision Medicine, CIRCGENETICS–115.

Broholm, C., Olsson, A. H., Perfilyev, A., Gillberg, L., Hansen, N. S., Ali, A., Mortensen, B., Ling, C., and Vaag, A. (2016) Human adipogenesis is associated with genome-wide DNA methylation and gene-expression changes. Epigenomics, 8, 1601–1617.

Statistical power considerations in genotype-based recall randomized controlled trials (2016) Scientific Reports, 6.

Luukkonen, P. K., Zhou, Y., Haridas, P. A. N., Dwivedi, O. P., Hyötyläinen, T., Ali, A., Juuti, A., Leivonen, M., Tukiainen, T., Ahonen, L., and others (2017) Impaired hepatic lipid synthesis from polyunsaturated fatty acids in TM6SF2 E167K variant carriers with NAFLD. Journal of hepatology, 67, 128–136.

Resjö, S., Brus, M., Ali, A., Meijer, H. J. G., Sandin, M., Govers, F., Levander, F., Grenville-Briggs, L., and Andreasson, E. (2017) Proteomic analysis of Phytophthora infestans reveals the importance of cell wall proteins in pathogenicity. Molecular & Cellular Proteomics, mcp–M116.

Safai, N., Suvitaival, T., Ali, A., Spégel, P., Al-Majdoub, M., Carstensen, B., Vestergaard, H., and Ridderstråle, M. (2018) Effect of metformin on plasma metabolite profile in the Copenhagen Insulin and Metformin Therapy (CIMT) trial. Diabetic Medicine.

Luukkonen, P., Sadevirta, S., Zhou, Y., Ali, A., Ahonen, L., Lallukka, S., Gaggini, M., Jian, C., Hakkarainen, A., Lundbom, N., and others (2018) Saturated fat is more metabolically harmful for the human liver than polyunsaturated fat or simple sugars. Journal of Hepatology, 68, S836.

Safai, N., Ali, A., Rossing, P., and Ridderstråle, M. (2018) Stratification of type 2 diabetes based on routine clinical markers. Diabetes research and clinical practice, 141, 275–283.

Al-Majdoub, M., Geidenstam, N., Ali, A., Ridderstråle, M., Storm, P., Groop, L., Bennet, L., and Spégel, P. (2017) Branched-chain amino acids are associated with odd-chain fatty acids in normoglycaemic individuals. Diabetes & metabolism, 43, 475–479.