Resarch Projects

– The assessment of microRNA profile in diabetic nephropathy by microarray and bioinformatics analysis

In this study, using different computational and experimental approaches, we could detect differentially expressed miRNAs in a diabetic nephropathy mouse model. Then, the miRNA-target interaction networks were constructed to identify the central nodes and key functions. Furthermore, we developed a high performance machine learning methods to predict potential drug targets in diabetic nephropathy.

– The microRNA-protein interaction network analysis in diabetic nephropathy with a combination of experimental and computational approaches
– The evaluation of microRNA roles in controlling of TGFB signaling pathway and renal fibrosis
– The assessment of cross-talk between Hypoxia and TGFB signaling pathways in chronic kidney disease
– Mathematical modeling of  Hypoxia pathway in chronic kidney disease (In partnership with Isfahan University of Technology)
In this project, identifying and modeling of hypoxia pathway are done by use of stochastic Petri nets and with the comparison of modeling results and experimental data, it is observed that the model describes the biological process behavior truly.
– Mathematical modeling of  TGFB signaling pathways (In partnership with Isfahan University of Technology)
– Developing an efficient linkage analysis strategy for autosomal dominant polycystic kidney disease (ADPKD)

Autosomal dominant polycystic kidney disease (ADPKD) is the most commongenetic cause of end stage renal disease. Although imaging techniques are a means of accuratediagnosis when the cysts appear in the third or fourth decades of the patient's life, they are oflittle value for early diagnosis. Genetic tests are required for pre-implantation genetic diagnosis(PGD), genetic counseling or decision making for kidney donation to an affected relative. Mutation of the PKD1 gene is responsible for the most cases of ADPKD.However, directgenetic testing is limited by the large size of this gene and the presence of many mutationswithout hot spots. Therefore, indirect diagnosis with linkage analysis using informativemicrosatellite markers has been suggested.

– The evaluation of therapeutic effects of epigenetics alternations in acute kidney injury

In this study we aim to evaluate the effect of a FDA approved histone deacetylase inhibitor on regeneration of acute kidney injury and expression kinetic of a chemokine in the level of mRNA and protein in the mouse model of ischemia reperfusion.


– Analysis of Time-course Microarray Data: Comparison of Common Tools

The aim of this study was to compare common algorithms recently developed for the detection of differentially expressed genes in time-course microarray data. Limma, timecourse, EDGE, BETR, and gprege R packages were compared using both biological and synthetic one-sample microarray datasets in which only test group is followed over time. Also, limma, BETR, and TTCA were compared for the analysis of two-sample datasets with time-series data for all experimental groups

– Study of expression changes of novel microRNA and its targets in samples of male DBA mouse model of diabetic nephropathy and comparison with normal mice

The purpose of this study is evaluation of this miRNA expression separately in the cortex and modulus of kidneys of diabetic nephropathy mice compared to healthy mice. First, the validity of the previous results should be examined and then differentiating in the expression of a number of target genes confirmed or predicted in the kidney should be studied. These target genes are chosen based on an early bioinformatics studies. We hope that the results of this plan will be helpful in clarifying the role of this miRNA and its mechanism in pathogenesis of DN, and it will be a step towards better understanding of diabetic nephropathy.


– Gene expression re-analysis of human kidney’s diabetic nephropathy to identify potential drug targets by using systems biology approaches
Here we reanalyzed two microarray datasets originally deposited by Woroniecka KI et al, that they compared the expression profiles of diabetic nephropathy and normal individuals in glomerulus and tubules. We designed a new reanalyzed study for making a multilayer network. Therefore, we decided to observe DN in different sights of view among differential expression (DE) genes, transcription factor genes, kinase genes who controlled TF genes and related microRNAs to identify new important targets genes and pathways and microRNAs and their interaction together.

– Remote ischemic precondition, a novel way of renal protection?!

Ischemia is the main cause of Acute Kidney Injury (AKI) mostly leading to renal failure. A novel treatment strategy that has been claimed to prevent this condition is called remote ischemic preconditioning (rIPC). It is defined as transient brief episodes of ischemia at a remote site before a subsequent prolonged ischemic injury of kidney. The recent studies have suggested to apply this protective method before high risk procedures for AKI like cardiac catheterization and CABG. The method has been mostly done by inflating a cuff at the patient’s limb. Although it is cost-free and noninvasive, further studies should be done to find out whether it is really beneficial. In this study we try to investigate the truth of the statement in the first step and then find an optimal way for its clinical application.