Photo of Reza Rafiee

Accepting PhD Students

PhD projects

GeneRank: A machine learning approach to detect and rank gene signatures from biological repositories with an application in lung cancer | Please see the details below (MSc/PhD Supervision)

20082019
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Personal profile

Achievements

Reza is an Artificial Intelligence (AI) expert and machine learning scientist. He is currently a lecturer (Education) in data analytics and machine learning at EEECS while working on developing bioinformatics tools for various cancer subtypes in collaboration with Stratified Medicine Group at CCRCB in QUB. He is a Fellow of the Higher Education Academy (FHEA) and has a PhD in Machine Learning from Newcastle University (UK), MSc degree in AI and Robotics from Iran University of Science and Technology (IUST) and BEng degree (Hons.) in Computer Engineering from Iran Azad University. Prior to the current position, he did several successful tours of duty at academia and software industry (Full Publications). He has significantly contributed to several biomarker & subgroup discovery projects and machine learning based projects including:

  1. Developed a web-based immune based classification software for solid tumours which can be accessed at http://smg.qub.ac.uk/
  2. Developed a novel assay and molecular classification method based on a minimal DNA methylation signature suitable for routine diagnostic purpose, his developed web-based classifiers can be accessed via http://www.newgene.org.uk/medulloblastoma.htm or http://medullo.ncl.ac.uk:3838/landing/
  3. Biostatistical analysis of an infant Medulloblastoma cohort with focus on high-risk factors (https://github.com/RRafiee)
  4. Developed a NanoString classifier based on RNA-Seq data, in collaboration with Institute Curie in Paris
  5. Developed an analysis pipeline for the WGES (Whole Genome/Exome Sequencing) data of diagnostics/relapsed Medulloblastoma using GATK (Genome Analysis Toolkit)
  6. Integrating high-dimensional biological cohorts using tensor decomposition techniques
  7. Developed a novel algorithm and software to rank popular videos accross Youtube repository. A Youtube channel with more than 100K subscribers and million views is the outcome of this algorithm.   

 

PREVIOUS POSITIONS/EDUCATION

May 2019 - Present   Academic Lecturer (Education) in Data Analytics and Machine Learning at EEECS, Queen's University Belfast, UK

Jun 2017 - Apr 2019   Postdoctoral Research Fellow at Stratified Medicine Group (SMG) in Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK

Jan 2014 - May 2017   Postdoctoral Research Associate at Northern Institute for Cancer Research, Newcastle University, UK

Aug 2013 - Dec 2013   Software Developer at Prophet Technology Ltd, Gateshead, UK

Apr 2009 - Jul 2013   PhD in Machine Learning (Image Processing/Computer Vision), Newcastle University, UK

Sep 2006 - Jan 2009   Founder/CEO and Software Team Leader, Modern Enterprise Technology Corporation (METech), IRAN

Sep 2001 - Apr 2009   Academic Lecturer at Iran Azad University, IRAN

Sep 1998 - Jan 2001   MSc in Artificial Intellignece and Robotics, Iran University of Science and Technology, IRAN 

 

 

Research Interests

  1. High-throughput genomic analysis, integrating complex and multi-scale biological datasets
  2. Developing AI-based methods and applying them to clinically annotated omics data accross multiple cancer subtypes
  3. Developing commercial and clinically applicable AI-based software 
  4. All statistical pattern recognition techniques, but not limited to, unsupervised, semi-supervised and supervised learning
  5. High-dimensional data processing and mining in Illumina 450K/EPIC DNA Methylation and RNA-Seq (NGS data)
  6. Mass-Spec DNA methylation and NanoString mRNA gene expression processing
  7. Developing bioinformatics tools, pipelines and software for the analysis of genetic and epigenetic features of cancer-associated diseases in large cohorts
  8. Developing video search engines using Youtube APIs 

Particulars

MSc/PhD Supervision

I am seeking new talented MSc/PhD students with strong background in mathematics, machine learning and software development to join an existing research/development project. Please send your CV and a statement of research interests to my email.  

 

Teaching

Data Analysis and Visualisation (CSC3062)

Databases (CSC1023)

Fingerprint Dive into the research topics where Reza Rafiee is active. These topic labels come from the works of this person. Together they form a unique fingerprint.

  • 15 Similar Profiles
DNA Methylation Medicine & Life Sciences
Medulloblastoma Medicine & Life Sciences
Software Medicine & Life Sciences
Brain Neoplasms Medicine & Life Sciences
Image retrieval Engineering & Materials Science
Neoplasms Medicine & Life Sciences
Methylation Medicine & Life Sciences
Cohort Studies Medicine & Life Sciences

Network Recent external collaboration on country level. Dive into details by clicking on the dots.

Research Output 2008 2019

IMMUNE BASED CLASSIFICATION OF SOLID TUMOURS (ICST): AN ONLINE SOFTWARE PACKAGE

Rafiee, G., McCabe, N., Knight, L., McCavigan, A., Savage, K. & Kennedy, R., 2019

Research output: Other contribution

Software
Neoplasms
Atlases
Paraffin
Formaldehyde

The Molecular Landscape and Clinical Experience in Infant Medulloblastoma

Hicks, D. & Rafiee, G., 20 Nov 2019, (Accepted).

Research output: Contribution to conferencePaper

In Vitro Modelling of Tumour Evolution and Radiotherapy Resistance in Medulloblastoma

Richardson, S., Hill, R., Selby, M., Lindsey, J., Rafiee, G., Bailey, S., Williamson, D. & Clifford, S., 22 Jun 2018, In : Journal of Neuro-Oncology. 20, Supplement 2, p. i136 1 p.

Research output: Contribution to journalArticle

Open Access
28 Citations (Scopus)

Subgroup-directed Clinical and Molecular Stratification of Disease Risk in Infant Medulloblastoma

Hicks, D., Rafiee, G., Schwalbe, E. C., Lindsey, J. C., Hill, R. M., Smith, A., Crosier, S., Joshi, A., Robson, K., Wharton, S., Jacques, T., Williamson, D., Bailey, S. & Clifford, S. C., 21 Jun 2018, In : Journal of Neuro-Oncology. 20, suppl_2, p. i123-i123

Research output: Contribution to journalArticle

Medu-06: Novel Molecular Subgroups Improve Clinical Classification And Outcome Prediction For Childhood Medulloblastoma

Schwalbe, E., Lindsey, J., Nakjang, S., Crosier, S., Smith, A., Hicks, D., Rafiee, G., Hill, R., Iliasova, A., Stone, T., Pizer, B., Michalski, A., Joshi, A., Robson, K., Wharton, S., Jacques, T., Bailey, S., Williamson, D. & Clifford, S., 31 May 2017, In : Journal of Neuro-Oncology. 19, Supplement 4, p. iv38 1 p.

Research output: Contribution to journalArticle

Open Access

Prizes

Fellow of The Higher Education Academy (FHEA)

Reza Rafiee (Recipient), 18 Jul 2019

Prize: Fellowship awarded competitively

File
academy
education

Activities 2019 2019

  • 1 Public lecture/debate/seminar

From Machine Learning to Accurate Cancer Diagnosis

Reza Rafiee (Advisor)
02 Oct 2019

Activity: Talk or presentation typesPublic lecture/debate/seminar