Kurt, Zeyneb, Dr

Dr Zeyneb Kurt

BSc (Yildiz Technical, Turkey), MSc (Yildiz Technical, Turkey), PhD (Yildiz Technical, Turkey)

Information School

Lecturer in Data Science

z.kurt@sheffield.ac.uk

The Wave

Full contact details

Dr Zeyneb Kurt
Information School
The Wave
2 Whitham Road
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S10 2AH

Profile

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 ��߲ݴ�ý in November 2023.

Research interests

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

Journal articles

Ogundipe O, Kurt Z & Woo WL (2024) . PLOS ONE, 19(9).
Hong J, Medzikovic L, Sun W, Wong B, Ruffenach G, Rhodes CJ, Brownstein A, Liang LL, Aryan L, Li M , Vadgama A et al (2024) . Circulation.
Erdogan C, Suer I, Kaya M, Ozturk S, Aydin N & Kurt Z (2024) . PLOS ONE, 19(4).
Brown AD, Fisher L, Curtis HJ, Wiedemann M, Hulme WJ, Speed V, Hopcroft LEM, Cunningham C, Costello RE, Galloway JB , Russell MD et al (2024) . British Journal of Clinical Pharmacology.
Kurt Z, Cheng J, Barrere-Cain R, McQuillen CN, Saleem Z, Hsu N, Jiang N, Pan C, Franzén O, Koplev S , Wang S et al (2023) . eLife, 12.
nematzadeh S, Aydin N, Kurt Z & Torkamanian-Afshar M (2023) . Current Bioinformatics.
Elvin G, Kurt Z, Kennedy A, Sice P, Walton L & Patel P (2023) . BMC Health Services Research, 23(1).
Kurt Z, Sice P, Krajewska K, Elvin G, Xie H, Ogwu S, Wang P & Turgut SS (2022) . Complementary Therapies in Medicine, 71.
Khaliq AM, Erdogan C, Kurt Z, Turgut SS, Grunvald MW, Rand T, Khare S, Borgia JA, Hayden DM, Pappas SG , Govekar HR et al (2022) . Genome Biology, 23(1), 156.
Moorton Z, Kurt Z & Woo WL (2022) . Marine Pollution Bulletin, 181.
Khaliq AM, Erdogan C, Kurt Z, Turgut SS, Grunvald MW, Rand T, Khare S, Borgia JA, Hayden DM, Pappas SG , Govekar HR et al (2022) . Genome Biology, 23(1).
von Scheidt M, Zhao Y, de Aguiar Vallim TQ, Che N, Wierer M, Seldin MM, Franzén O, Kurt Z, Pang S, Bongiovanni D , Yamamoto M et al (2021) . Circulation, 143(18), 1809-1823.
ARNESON D, MAJID S, AHN IS, KURT Z, DIAMANTE G, ZHANG G, GOMEZ-PINILLA F & YANG XIA (2019) . Diabetes, 68(Supplement_1).
Hui ST, Kurt Z, Tuominen I, Norheim F, C.Davis R, Pan C, Dirks DL, Magyar CE, French SW, Chella Krishnan K , Sabir S et al (2018) . Hepatology, 68(6), 2182-2196.
Kurt Z, Barrere-Cain R, LaGuardia J, Mehrabian M, Pan C, Hui ST, Norheim F, Zhou Z, Hasin Y, Lusis AJ & Yang X (2018) . Biology of Sex Differences, 9(1).
Camacho J, Truong L, Kurt Z, Chen Y-W, Morselli M, Gutierrez G, Pellegrini M, Yang X & Allard P (2018) . Cell Reports, 23(8), 2392-2404.
Kurt Z, Barrere-Cain RE, Sun C, Zhao Y, Pan C, Ruusalepp A, Franzén O, Koplev S, Bjorkegren JL, Lusis AJ & Yang X (2018) . Arteriosclerosis, Thrombosis, and Vascular Biology, 38(Suppl_1).
Chella Krishnan K, Kurt Z, Barrere-Cain R, Sabir S, Das A, Floyd R, Vergnes L, Zhao Y, Che N, Charugundla S , Qi H et al (2018) . Cell Systems, 6(1), 103-115.e7.
Krishnan KC, Kurt Z, Barrere-Cain R, Sabir S, Das A, Floyd R, Vergnes L, Zhao Y, Che N, Charugundla S , Qi H et al (2018) .
Erdoğan C, Kurt Z & Diri B (2017) . PLOS ONE, 12(11).
Shu L, Chan KHK, Zhang G, Huan T, Kurt Z, Zhao Y, Codoni V, Trégouët D-A, Yang J, Wilson JG , Luo X et al (2017) . PLOS Genetics, 13(9).
von Scheidt M, Zhao Y, Kurt Z, Pan C, Zeng L, Yang X, Schunkert H & Lusis AJ (2017) . Cell Metabolism, 25(2), 248-261.
Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S , Zhang B et al (2016) . BMC Genomics, 17(1).
KURT Z, AYDIN N & ALTAY G (2016) . TURKISH JOURNAL OF ELECTRICAL ENGINEERING & COMPUTER SCIENCES, 24, 695-718.
Dehmer M, Kurt Z, Emmert-Streib F, Them C, Schulc E & Hofer S (2015) . PLoS ONE, 10(6).
Kurt Z, Aydin N & Altay G (2014) . Bioinformatics, 30(15), 2142-2149.
Altay G, Kurt Z, Dehmer M & Emmert-Streib F (2014) . Evolutionary Bioinformatics, 10, EBO.S13481-EBO.S13481.
Kurt Z & Yavuz O (2009) Optimal Multilayer Perceptron structure for classification of HIV sub-type viruses. World Academy of Science, Engineering and Technology, 58, 7-11.

Chapters

Kurt Z, Turkmen HI & Karsligil ME (2009) , Lecture Notes in Electrical Engineering (pp. 601-607). Springer US

Conference proceedings papers

Hong J, Medzikovic L, Sun W, Ruffenach G, Wong B, Rhodes CJ, Brownstein AJ, Liang L, Aryan L, Li M , Vadgama A et al (2024) . D95. SURVEYING THE ZOO: -OMICS FOR MECHANISTIC DISCOVERY IN PULMONARY VASCULAR DISEASE
Erdogan C, Kurt Z & Diri B (2017) . 2017 25th Signal Processing and Communications Applications Conference (SIU), 15 May 2017 - 18 May 2017.
Kurt Z, Aydin N & Altay G (2013) . 13th IEEE International Conference on BioInformatics and BioEngineering, 10 November 2013 - 13 November 2013.
Sakarkaya M, Yanbol F & Kurt Z (2012) . 2012 IEEE 16th International Conference on Intelligent Engineering Systems (INES), 13 June 2012 - 15 June 2012.
Kurt Yavuz Z & Yavuz S (2012) . 2012 IEEE 16th International Conference on Intelligent Engineering Systems (INES), 13 June 2012 - 15 June 2012.
Kurt-Yavuz Z & Yavuz S (2012) . 2012 IEEE 16th International Conference on Intelligent Engineering Systems (INES), 13 June 2012 - 15 June 2012.
Basmaci ES, Kaymakcioglu U & Kurt Z (2011) . 2011 IEEE 19th Signal Processing and Communications Applications Conference (SIU), 20 April 2011 - 22 April 2011.
Boke SB, Diri B & Yavuz ZK (2010) . 2010 IEEE 18th Signal Processing and Communications Applications Conference, 22 April 2010 - 24 April 2010.
Kurt Z & Yavuz O (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)
Yavuz S, Kurt Z & Bicer MS (2009) . 2009 IEEE 17th Signal Processing and Communications Applications Conference, 9 April 2009 - 11 April 2009.
Yavuz S, Kurt Z & Bicer MS (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)
Kurt Z & Yavuz S (2008) . 2008 IEEE 16th Signal Processing, Communication and Applications Conference, 20 April 2008 - 22 April 2008.
Kurt Z & Yavuz S (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)
Aran O, Ari I, Guvensan A, Haberdar H, Kurt Z, Turkmen I, Uyar A & Akarun L (2007) . 2007 IEEE 15th Signal Processing and Communications Applications, 11 June 2007 - 13 June 2007.
Türkmen HI, Kurt Z & Karsligil ME (2007) Global feature based female facial beauty decision system. European Signal Processing Conference (pp 1945-1949)
Kurt Z, Turkmen HI & Karsligil ME (2007) . 2007 IEEE 15th Signal Processing and Communications Applications, 11 June 2007 - 13 June 2007.
Aran O, Ari I, Guevensan A, Haberdar H, Kurt Z, Tuerkmen I, Uyar A & Akarun L (2007) A database of non-manual signs in Turkish sign language. 2007 IEEE 15TH SIGNAL PROCESSING AND COMMUNICATIONS APPLICATIONS, VOLS 1-3 (pp 929-+)
Türkmen HI, Kurt Z & Karsligil ME (2006) . 2006 IEEE 14th Signal Processing and Communications Applications Conference, Vol. 2006

Preprints

Brown AD, Fisher L, Curtis HJ, Wiedemann M, Hulme WJ, Hopcroft LEM, Cunningham C, Speed V, Costello RE, Galloway JB , Russell MD et al (2023) , Cold Spring Harbor Laboratory.
Hong J, Wong B, Rhodes CJ, Kurt Z, Schwantes-An T-H, Mickler EA, Gräf S, Eyries M, Lutz KA, Pauciulo MW , Trembath RC et al (2023) , Cold Spring Harbor Laboratory.
Ogundipe O, Kurt Z & Woo WL (2022) Deep Neural Networks integrating genomics and histopathological images for predicting stages and survival time-to-event in colon cancer.
Elvin G, Kurt Z, Kennedy A, Sice P, Walton L & Patel P (2022) , Research Square Platform LLC.
Altay G, Kurt Z, Altay N & Aydin N (2017) , Cold Spring Harbor Laboratory.

Research group

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: )

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: )

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

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

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

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.

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Information School

Information School

Dr Zeyneb Kurt

Journal articles

Chapters

Conference proceedings papers

Preprints

Links

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