Dr Zeyneb Kurt
BSc (Yildiz Technical, Turkey), MSc (Yildiz Technical, Turkey), PhD (Yildiz Technical, Turkey)
Information School
Lecturer in Data Science
Full contact details
Information School
The Wave
2 Whitham Road
Sheffield
S10 2AH
- Profile
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Between 2015 and 2018, I worked as a post-doctoral researcher at University of California, Los Angeles (UCLA), USA, with a focus in bioinformatics, biostatistics, and computational biology fields. During that period, I was awarded with two postdoctoral fellowships: i) American Heart Association for two years and ii) UCLA Iris Cantor/Women’s Health Center Postdoctoral Fellowship for one year.
Later on, I worked as an assistant professor in the Department of Computer Engineering at Yildiz Technical University between 2018 and 2020 and then joined the Department of Computer and Information Sciences at Northumbria University in 2020 August as an assistant professor.
I joined the Information School at University of Sheffield in November 2023.
- Research interests
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My current research interests include bioinformatics, computational biology, statistics, image processing, and machine learning. More specifically, for example, I employ machine learning and statistical methods to understand impacts of specific interventions (such as Qigong) on wellbeing of participants; to help with self-monitoring and tracking the changes in wellbeing of NHS staff members and understanding these changes using data from an online diary; to predict sub-types in a cancer cohort using functional genomics data and pathological tissue images. I am also interested in the use of explainable AI and deep learning models in my research.
I would be happy to supervise PhD students who are interested in pursuing their career in bioinformatics and health informatics. For example, developing/employing data science and machine learning models to understand the key mechanisms underlying diseases by integrating multi-omics data resources; to assess/monitor the change in wellbeing of the participants of a particular intervention study; employing explainable AI to predict the subtypes of different cancer types from the pathological images; predicting the associations between circular RNA, microRNA, and target genes which drive a particular type of cancer.
- Publications
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Journal articles
- Deep neural networks integrating genomics and histopathological images for predicting stages and survival time-to-event in colon cancer. PLOS ONE, 19(9). View this article in WRRO
- Integrative multiomics in the lung reveals a protective role of asporin in pulmonary arterial hypertension. Circulation. View this article in WRRO
- Bioinformatics analysis of the potentially functional circRNA-miRNA-mRNA network in breast cancer. PLOS ONE, 19(4). View this article in WRRO
- OpenSAFELY: The impact of COVID‐19 on azathioprine, leflunomide and methotrexate monitoring, and factors associated with change in monitoring rate. British Journal of Clinical Pharmacology. View this article in WRRO
- Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse. eLife, 12. View this article in WRRO
- NaProGraph: Network analyzer for interactions between nucleic acids and proteins. Current Bioinformatics. View this article in WRRO
- A self-monitoring wellbeing screening methodology for keyworkers, ‘My Personal Wellbeing’, using an integrative wellbeing model. BMC Health Services Research, 23(1). View this article in WRRO
- A pilot study on the impacts of lung-strengthening Qigong on wellbeing. Complementary Therapies in Medicine, 71. View this article in WRRO
- Correction: Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biology, 23(1), 156.
- Is the use of deep learning an appropriate means to locate debris in the ocean without harming aquatic wildlife?. Marine Pollution Bulletin, 181. View this article in WRRO
- Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biology, 23(1). View this article in WRRO
- Transcription factor MAFF (MAF basic leucine zipper transcription factor F) regulates an atherosclerosis relevant network connecting inflammation and cholesterol metabolism. Circulation, 143(18), 1809-1823. View this article in WRRO
- 1812-P: Multitissue Single-Cell Analysis Reveals Differential Tissue, Cellular, and Molecular Sensitivity between Fructose and High-Fat Diets. Diabetes, 68(Supplement_1).
- The genetic architecture of diet‐induced hepatic fibrosis in mice. Hepatology, 68(6), 2182-2196. View this article in WRRO
- Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease. Biology of Sex Differences, 9(1). View this article in WRRO
- The memory of environmental chemical exposure in C. elegans is dependent on the jumonji demethylases jmjd-2 and jmjd-3/utx-1. Cell Reports, 23(8), 2392-2404. View this article in WRRO
- Abstract 468: Cross-species Comparison of Genetic Networks of Coronary Artery Disease. Arteriosclerosis, Thrombosis, and Vascular Biology, 38(Suppl_1).
- Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-alcoholic Fatty Liver Disease. Cell Systems, 6(1), 103-115.e7.
- Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-Alcoholic Fatty Liver Disease.
- Estimation of the proteomic cancer co-expression sub networks by using association estimators. PLOS ONE, 12(11). View this article in WRRO
- Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States. PLOS Genetics, 13(9). View this article in WRRO
- Applications and Limitations of Mouse Models for Understanding Human Atherosclerosis. Cell Metabolism, 25(2), 248-261.
- Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC Genomics, 17(1). View this article in WRRO
- Comprehensive review of association estimators for the inference of gene networks. TURKISH JOURNAL OF ELECTRICAL ENGINEERING & COMPUTER SCIENCES, 24, 695-718.
- Structural analysis of treatment cycles representing transitions between nursing organizational units inferred from diabetes. PLoS ONE, 10(6).
- A comprehensive comparison of association estimators for gene network inference algorithms. Bioinformatics, 30(15), 2142-2149.
- Netmes: Assessing Gene Network Inference Algorithms by Network-Based Measures. Evolutionary Bioinformatics, 10, EBO.S13481-EBO.S13481.
- Optimal Multilayer Perceptron structure for classification of HIV sub-type viruses. World Academy of Science, Engineering and Technology, 58, 7-11.
Chapters
- Linear Discriminant Analysis in Ottoman Alphabet Character Recognition, Lecture Notes in Electrical Engineering (pp. 601-607). Springer US
Conference proceedings papers
- Integrative Multiomics in the Lung Reveals a Protective Role of Asporin in Pulmonary Arterial Hypertension. D95. SURVEYING THE ZOO: -OMICS FOR MECHANISTIC DISCOVERY IN PULMONARY VASCULAR DISEASE
- Investigation of association estimators in network inference algorithms on breast cancer proteomic data. 2017 25th Signal Processing and Communications Applications Conference (SIU), 15 May 2017 - 18 May 2017.
- Impacts of the different spline orders on the B-spline association estimator. 13th IEEE International Conference on BioInformatics and BioEngineering, 10 November 2013 - 13 November 2013.
- Comparison of several classification algorithms for gender recognition from face images. 2012 IEEE 16th International Conference on Intelligent Engineering Systems (INES), 13 June 2012 - 15 June 2012.
- Improvement of the measurement update step of EKF-SLAM. 2012 IEEE 16th International Conference on Intelligent Engineering Systems (INES), 13 June 2012 - 15 June 2012.
- A comparison of EKF, UKF, FastSLAM2.0, and UKF-based FastSLAM algorithms. 2012 IEEE 16th International Conference on Intelligent Engineering Systems (INES), 13 June 2012 - 15 June 2012.
- Comparison of feature extraction and feature selection approaches to decide whether a face image belongs to a male or a female. 2011 IEEE 19th Signal Processing and Communications Applications Conference (SIU), 20 April 2011 - 22 April 2011.
- Lossy compression of color images based on color spaces. 2010 IEEE 18th Signal Processing and Communications Applications Conference, 22 April 2010 - 24 April 2010.
- Searching optimal sigma parameter in Radial Basis Kernel Support Vector Machine for classification of HIV sub-type viruses. SIGMAP 2010 - Proceedings of the International Conference on Signal Processing and Multimedia Applications (pp 163-166)
- Simultaneous localization and mapping using Extended Kalman Filter. 2009 IEEE 17th Signal Processing and Communications Applications Conference, 9 April 2009 - 11 April 2009.
- Simultaneous Localization and Mapping Using Extended Kalman Filter. 2009 IEEE 17TH SIGNAL PROCESSING AND COMMUNICATIONS APPLICATIONS CONFERENCE, VOLS 1 AND 2 (pp 914-917)
- A simultaneous localization and map building algorithm based on sequential Monte Carlo method. 2008 IEEE 16th Signal Processing, Communication and Applications Conference, 20 April 2008 - 22 April 2008.
- A Simultaneous Localization and Map Building Algorithm Based on Sequential Monte Carlo Method. 2008 IEEE 16TH SIGNAL PROCESSING, COMMUNICATION AND APPLICATIONS CONFERENCE, VOLS 1 AND 2 (pp 709-712)
- A Database of Non-Manual Signs in Turkish Sign Language. 2007 IEEE 15th Signal Processing and Communications Applications, 11 June 2007 - 13 June 2007.
- Global feature based female facial beauty decision system. European Signal Processing Conference (pp 1945-1949)
- Ottoman Alphabet Character Recognition by LDA. 2007 IEEE 15th Signal Processing and Communications Applications, 11 June 2007 - 13 June 2007.
- A database of non-manual signs in Turkish sign language. 2007 IEEE 15TH SIGNAL PROCESSING AND COMMUNICATIONS APPLICATIONS, VOLS 1-3 (pp 929-+)
- Destek vektör maki̇nesi̇ yöntemi̇ i̇le yüz güzelli̇ǧi̇ karari. 2006 IEEE 14th Signal Processing and Communications Applications Conference, Vol. 2006
Preprints
- OpenSAFELY: The impact of COVID-19 on azathioprine, leflunomide, and methotrexate monitoring, and factors associated with change in monitoring rate, Cold Spring Harbor Laboratory.
- Integrative Multiomics to Dissect the Lung Transcriptional Landscape of Pulmonary Arterial Hypertension, Cold Spring Harbor Laboratory.
- Deep Neural Networks integrating genomics and histopathological images
for predicting stages and survival time-to-event in colon cancer.
- A Self-Monitoring Wellbeing Screening Methodology for Keyworkers, ‘My Personal Wellbeing’, using an Integrative Wellbeing Model, Research Square Platform LLC.
- DepEst: an R package of important dependency estimators for gene network inference algorithms, Cold Spring Harbor Laboratory.
- Deep neural networks integrating genomics and histopathological images for predicting stages and survival time-to-event in colon cancer. PLOS ONE, 19(9). View this article in WRRO
- Research group
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I am Head of the Health Informatics Research Group.
I am the second supervisor for PhD students:- Terence Egbelo, Thesis Title: Compound bioactivity prediction using KG metapath (First supervisor is: Prof Val Gillet)
- Hannah Okesade, Thesis Title: Interpretable Machine Learning Algorithms for Predictive (Eco-)Toxicology (First supervisor is: Prof Val Gillet)
I am an external supervisor for PhD students:- Zoe Moorton, Thesis Title: Identification of the type of the debris in marine ecosystem using explainable deep learning methods (Start Date: 01/10/2022; 1st supervisor is: Prof Wai Lok Woo)
- Olalekan Ogundipe, Thesis Title: Deep Neural Networks integrating functional genomics and histopathological images data for predicting sub-types in colon cancer (Start Date: 18/01/2021; 1st supervisor: Prof Wai Lok Woo)
- Sultan Sevgi Turgut, Thesis Title: Single-Cell Analysis of the Human Pancreas by Using Artificial Intelligence Techniques (1st supervisor: Prof Nizamettin Aydin)
Completed PhD supervisions (as an external supervisor):
- Sajjad Nematzadeh, Thesis Title: Use of AI for Predicting Secondary Structures of RNAs and Proteins (Completion Date: August 2023; 1st supervisor: Prof Nizamettin Aydin)
- Grants
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Fundings/Awards I earned as PI or Co-I in Bioinformatics, Computational Biology, and Health Informatics fields:
- An Integrative Wellbeing Framework and Open Online System for NHS and Integrated Care Staff in England and beyond - Funded by NHS England (£40,000 Co-I, 2022)
- Histological sub-classification of medulloblastoma tumours - Funded by Northumbria University Application Seed Funding (~£13,000 Co-I, 2022).
- Co-develop an integrative evaluation model and tools with NHS to support wellbeing and trauma informed care - Funded by Northumbria University Participatory Research Evaluation Fund (£6,000 Co-I, 2022).
- Impact of Qigong intervention on Wellbeing - Funded by UWTSD Confucius Institute (£4,000 PI, 2021)
- Online Wellbeing Diary - Funded by NHS England (£10,000 Co-I, 2021)
- Identifying subtypes in pancreatic cancer with a novel single-cell RNA sequencing-based ensemble classification model- Funded by CIS R&I ECR Support Fund (£3,500 PI, 2021)
- American Heart Association Postdoctoral Fellowship - for two years ($110,000 - awarded in 2017)
- UCLA Iris Cantor/Women’s Health Center Postdoctoral Fellowship - for one year ($20,000 - awarded in 2017)
- Teaching activities
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INF210 - Practical Programming for Data Science 2
INF212- AI and Machine Learning for Advanced Analytics
INF6050 - Database Design
INF6505 Database Design and Data Management
- Professional activities and memberships
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I am the Department Deputy Research Ethics Coordinator (PGR, PGT and UG students)
- Fellowship of the Higher Education Academy, since April 2022.
- American Heart Association Membership (2015-2018)
- IEEE Engineering in Medicine and Biology Society Membership
I regularly review manuscripts for the journals:
- IEEE Journal of Biomedical and Health Informatics
- BMC Bioinformatics
- BMC Cancer
- BMC Gastroenterology
- PLOS ONE
- Journal of Big Data
- The International Journal of Biological Markers
- Journal of Integrative and Complementary Medicine
- World Federation for Ultrasound in Medicine and Biology (WFUMB) Ultrasound Open
Other than that, I served as a technical committee member in 2021, 2022 and 2023 for the International Conference on Artificial Intelligence, Virtual Reality and Visualization（AIVRV). Also, I have co-led and delivered a 2-day workshop in 2023 April on ‘Story telling with Data’ organised by Innovate UK KTN (Knowledge Transfer Network) and Mondelez for Mondelez-funded PGRs and and give talks on data science project life cycle, data wrangling, principles of exploratory data analysis.