Dr. Adil Mardinoglu is an expert in the field of Systems Biology and Bioinformatics. He received his Bachelor’s degree from Istanbul Technical University, Turkey in Electronic and Telecommunication Engineering and his Ph.D. from Waterford Institute of Technology, Ireland in drug targeting applications. He worked as a postdoctoral researcher at Trinity College Dublin, Ireland and Chalmers University of Technology, Gothenburg, Sweden. His recent research activities include the generation of the context specific genome-scale metabolic models for healthy human cell-types e.g. adipocytes, hepatocytes and myocytes as well as certain types of cancer e.g. liver cancer. He employed the reconstructed comprehensive models for revealing the molecular mechanisms of obesity associated diseases as well as for discovery of the novel biomarkers and drug targets. He also reconstructed personalized and population based models for liver cancer patients in order to identify anticancer drug targets that can inhibit the growth of, or kill tumors.
Sunjae Lee, PhD
Dr. Sunaje Lee received his Ph. D. degree in Bioinformatics at the Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), South Korea. During his PhD training course, he has participated in several research projects of bioinformatics and synthetic biology, including regulatory network reconstruction, metabolic regulome analysis, and synthetic ribosome binding site (RBS) design. His research interests covers developing network-based approaches to investigate dysregulated metabolism of human diseases. Here, in Mardinoglu lab at SciLifeLab, Sweden, he is working on developing integrative network approach, combining regulatory networks, signaling networks, and metabolic networks, to investigate driving factors of metabolic disorders, including obesity, insulin resistance, and hepatocellular carcinoma.
Cheng Zhang, PhD
Dr. Cheng Zhang received his B.Sc. degree in Bioengineering and Ph.D. degree in Fermentative Engineering at Department of Biotechnology, East China University of Science and Technology (ECUST). He also studied in Systems and Synthetic Biology group in Chalmers University as a visiting student for two years during his Ph.D. period. Dr. Cheng Zhang is an experienced bioinformatician. He participated in a number of projects in bioinformatics and systems biology, and published several research and review papers in reputed journals. His main research interests including developing and expanding genome-scale metabolic models to other omics level, and applying them into clinic such as investigating the driving factors, biomarkers or potential therapeutic strategies for obesity, non-alcoholic fatty liver disease and hepatocellular carcinoma.
POSTDOCTORAL FELLOWS AND PHD STUDENTS
Gholamreza Bidkhori, PhD
Dr. Gholamreza Bidkhori received his B.Sc. in Genetics from the University of Isfahan and his Ph.D. in Bioinformatics from the University of Tehran, Iran, where his research focused on Lung Cancer Systems Biology in 2013. He then worked as lecturer and researcher in the field of cancer modeling at the University of Tehran. After a post doc at VTT technical research center of Finland as a metabolic modeler, he joined sysmedicine lab in 2016. He is specialized in network reconstruction, Kinetic modeling and parameter estimation, constraint-based modeling, omics data analysis and integration of the data into the signaling, gene regulatory and metabolic networks.
Zhengtao Liu, PhD
Dr. Zhengtao Liu received his B.S.M. degree in Clinical Medicine and Ph.D. degree in Surgery and Oncology at Guangxi Meidcal University (GXMU). He worked as a post-doc fellow and research assistant in Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Zhejiang University (ZJU). He was participated a number of national major projects on prevention and treatment of hepatocellular carcinoma (HCC). On the period of his study and work, he published several original and review paper that related to non-alcoholic fatty liver disease (NAFLD), metabolic syndrome, and HCC. His main interests mainly locate on the impact of lipid related genetic variations on HCC development. He dedicates to construct cellular and animal models to demonstrate mechanism of these genetic impacts on progress from NAFLD to HCC, and investigates to validate them in human cohort.
Rui Benfeitas, PhD
Dr. Rui Benfeitas received his B. Sc. in Biology from the University of Coimbra (Portugal), and a M. Sc. in Biochemistry from the University of Lisbon (Portugal). His Ph. D. in Computational Biology was carried both at the University of Coimbra and at the University of Lleida (Spain). During his graduate studies, he studied multiple defense mechanisms against oxidative stress using mathematical modeling, bioinformatics and biostatistics. He has also collaborated in Synthetic Biology projects. His work as a redox biologist has already resulted in several publications, seminars and conference communications. His work integrates metabolic networks with other biological networks including protein-protein interaction networks and regulatory networks. He is interested in studying the redox response cells and tissues under different clinical conditions.
Battisti Umberto Maria, PhD
Dr. Battisti Umberto Maria received his B.M.Sc. in Chemistry and Pharmaceutical Sciences from the University of Modena and Reggio Emilia (Italy). His Ph. D. in Medicinal Chemistry was carried at the same university with several national and international PhD visiting fellowships. During his graduate studies, the main project was the development of new AMPA positive allosteric modulators. He worked as a postdoctoral researcher at University of Modena and Reggio Emilia (Italy), and Virginia Commonwealth University (USA). During the years he was involved in several areas, from CNS diseases to viral and parasitic infections. His work as a medicinal chemist has already resulted in several publications, seminars and conference communications. His main research interests including drugs design employing classical medicinal chemistry approaches, the design of multi-steps synthetic strategies and stereoselective synthesis.
Fady Akladios, PhD
Dr. Fady Akladios, an Australian registered pharmacist, received his PhD in Medicinal Chemistry and Chemical Biology from Charles Sturt University (CSU), Australia. His PhD focused on induction of oxidative stress in cancer cells via novel therapeutic approaches targeting redox and metal homeostases. His main research interests are drug design and chemical synthesis of probes for selective perturbation of biological processes. Fady will be a member of the research team working on the design and synthesis of small molecules inhibitors of target enzymes playing critical role in regulation of cell metabolism.
Chunxia Gao, PhD
Dr. Chunxia Gao, a Chinese registered Pharmacist, recently completed her PhD degree in Chemistry from University of Gothenburg, Sweden. During her PhD studies, she was involved in several different projects and collaborated with various groups to develop anti-cancer inhibitors and antibiotics, which she applied computer-aided drug design approaches. Her work has already resulted in some potential inhibitors and publications. Chunxia will be a member of the research team working on designing small inhibitors that target enzymes involving in cell metabolism.
Kemal Sanli, PhD
Dr. Kemal Sanli received his B.Sc. degree in Molecular Biology and Genetics from Istanbul Technical University, Turkey. He holds a M.Sc. degree in Bioinformatics and Systems Biology, which he studied at Chalmers University of Technology, Sweden. Dr. Sanli completed his Ph.D. studies at the Biological and Environmental Sciences Department of the University of Gothenburg, in Metagenomics, a young field combining paradigms from multiple disciplines including Microbiology, Microbial Ecology, Bioinformatics and Statistics and Systems Biology. He applied the metagenomic methodology on multi-species biofilms retrieved from the natural sea water. He is currently continuing the application of metagenomics on human-associated biofilms where he employs genome-scale metabolic modeling on pathogenic biofilm species. He has also partaken in several bioinformatics software development projects including FANTOM and PACFM.
Sumit Deshmukh, MSc
Sumit Deshmukh accomplished his B. Pharmacy from University of Pune, India. Currently, he is studying at Univeristy of skövde for master program in Molecular Biotechnology. He is pursuing his master thesis, working on Liver cancer and learning differential expression and gene ontology analysis in the supervision of Dr Adil Mardinoglu and Dr Sunjae lee.
Alen Lovric, MSc
Alen Lovric received his M.Sc. degree in Environmental Health from Faculty of Medicine, University of Rijeka, Croatia. Currently, he is a M.Sc. student in Molecular Biotechnology program at Skövde University, involving areas of Molecular Biology, Biotechnology and Systems Biology. As part of our research group he is pursuing his master’s thesis, working on T2D and integration of obtained metabolomics data with clinical and proteomics data under the supervision of Dr. Adil Mardinoglu and Dr. Cheng Zhang.
Muhammad Arif, MSc
Muhammad Arif received his B.Sc. degree from Bandung Institute of Technology, Indonesia in Electrical Engineering and recently completed his master degree at KTH Royal Institute of Technology in the same area, focusing on network analysis and classification algorithm. His research interests are network theory, machine learning and high performance computing. He is currently working on identification of gene expression patterns through the use of integrated networks.
Mohamed Al Shobky, MSc
Mohamed Al Shobky is an Egyptian-registered Clinical Pharmacist received his B.Sc. degree in Clinical Pharmaceutical Science, Zagazig University, Egypt. Currently, he is an M.Sc. student of tumour biology programme with a major in Systems Biology at Skövde University. Within our research group, he is pursuing his master thesis working on the identification of novel anticancer drug targets utilising various systems biology approaches, under the Supervision of Dr. Adil Mardinoglu and Dr. Sunjae Lee.
Ezgi Elmas, MSc
Ezgi Elmas received her B.Sc degree in Biological Science from Mugla Sitki Kocman University, Turkey. Currently, she is studying at Mugla Sitki Kocman University as a Master student. Her subject is effects of various plant growth regulators on physiological and biochemical parameters of wheat seedlings under drought stress. She is pursuing her master thesis, working on liver cancer and between redox response cells and tissues, under the Supervision of Dr. Adil Mardinoglu and Dr. Sunjae Lee.
Dorinês Rosário, MSc
Dorinês Rosário received her B.Sc. in Nuclear Medicine from Escola Superior de Tecnologia da Saúde de Lisboa, Portugal. Currently, she is a M. Sc. student in Molecular Techniques in Life Science, a collaboration between Karolinska Institutet, KTH and Stockholm University, mainly focused in molecular biology and bioinformatics. Integrating our research group, she is pursuing her master’s thesis preforming reconstruction of metabolic models to understand the contribution of gut microbiota in Type 2 Diabetes, under the supervision of Dr. Adil Mardinoglu and Dr. Cheng Zhang.
FORMER LAB MEMBERS
- Azadeh Mohammad Pour, King’s College London, United Kingdom
- Baris Sadik, Bogazici University, Turkey
- Christofer Boren, KTH – Royal Institute of Technology, Sweden
- Tim Kuijpers, Eindhoven University of Technology, Netherlands
- Pisanu Buphamalai, KTH – Royal Institute of Technology, Sweden
- Bunjamin Memishi, Universidad Politecnica de Madrid
- Christmas party@SciLifeLab, December 2016