Researcher

Dr Hamid Alinejad-Rokny

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Biography

Dr Rokny is a UNSW Scientia Fellow and Head of Systems Biology and Health Data Analytics Lab at the UNSW Graduate School of Biomedical Engineering. He is also Heath Data Analytics Program Leader of AI-enabled Processes (AIP) Research Centre. Dr Rokny received his master degree in Artificial Intelligence/Machine Learning and his Ph.D in Systems Biology from UNSW Australia, Dec 2017. Before finishing his Ph.D, Hamid joined to Prof Alistair...view more

Dr Rokny is a UNSW Scientia Fellow and Head of Systems Biology and Health Data Analytics Lab at the UNSW Graduate School of Biomedical Engineering. He is also Heath Data Analytics Program Leader of AI-enabled Processes (AIP) Research Centre. Dr Rokny received his master degree in Artificial Intelligence/Machine Learning and his Ph.D in Systems Biology from UNSW Australia, Dec 2017. Before finishing his Ph.D, Hamid joined to Prof Alistair Forrest Lab at Harry Perkins Institute of Medical Research to study transcriptional regulation in mammals by cutting-edge machine learning techniques.

His research focuses on using cutting-edge Systems Biology and Advanced Health Data Analytics techniques in conjunction with genome-wide data to understand the impact of genomic variants on genetic diseases and disorders. Dr Rokny is currently leading multiple international projects (jointly with UWA, Uni Adelaide, SUT, and Texas Biomed) investigating the impacts of non-coding regulatory variants in genetic diseases (in particular neurodevelopmental disorders and breast cancer) through integration of Hi-C, ChIP-seq, RNA-seq, and genomic variants. He is keen to see accurate diagnostic genomic tools implemented into the clinic to improve the health care and genomic-based treatments in the Australian health system.

As a young and early career scientist, Dr Rokny has published 33 publications; he has been able to secure several national and international grants/fellowships. He has been also invited to serve as Keynote Speaker, organising committee member of national and international conferences.
He has recently received a UNSW Scientia Fellowship and joined the Graduate School of Biomedical Engineering in Oct 2019.


My Grants

  • NSW Cancer Council, "Single-cell analyses of interacting cells in circulating tumour cell clusters", 2020-2021.
  • UNSW Cellular Genomics Futures Institute grant, UNSW Sydney, "CRISPRi screening of regulatory regions using snRNA-seq readout and integration with Hi-C data", 2020-2021. 
  • UNSW Cellular Genomics Futures Institute grant, UNSW Sydney, "decoding 3D genome architecture in individual single-cells to establish molecular mechanisms of gene regulation in cancer", 2020-2021. 
  • Government of Western Australia department of health, clinical excellence, MERIT award for NHMRC Investigator ‘near-miss’ funding, 2020-2021.
  • Academic Start-up Funding (ASUF), Faculty of Engineering, UNSW Sydney, 2019-2023.
  • UNSW Scientia Development and Collaboration Support Fund, UNSW Sydney, 2019-2023.
  • Quebec Autism Research Training (QART) program, 2019-2021.
  • Fonds de recherche du Québec - Santé (FRQS) research grant, 2019-2021.
  • Government of Western Australia, Department of Health, clinical excellence, MERIT award for NHMRC ‘near-miss’ funding, 2018-2019.
  • Vice-Chancellor's Research Fellowship Fund, RMIT University, 2018, Offered.

My Qualifications

  • Bachelor: Software Engineering, 2004-2009
  • Master: Artificial Intelligence, 2009-2011.
  • Industry: Data Scientist, 2011-2014.
  • Ph.D: Machine Learning and Computational Biology, UNSW Australia, 2014-2018.
  • Post-Doctoral: Harry Perkins Institute of Medical Research, UWA Australia, 2017-2019.

My Awards

  • UNSW Scientia Fellowship, UNSW Sydney, 2019-2023.
  • MBSJ2019 (The 42nd Annual Meeting of the Molecular Biology Society of Japan) Foreign Travel Award, Fukuoka, Japan, 2019.
  • RIKEN-HUGO scholarship award for best presentation in the Human Genome Meeting 2019, Seoul, South Korea, 2019.
  • Travel grants from Institute for Research in Fundamental Sciences as invited speaker, 2016.
  • Travel grants from University of Tehran as invited speaker, 2015.
  • HDR conference support grant from the University of New South Wales, 2014.
  • UNSW scholarship from the University of New South Wales, Australia, 2013 - 2017.
  • Top-up scholarship from the faculty of medicine, UNSW Australia, 2013-2017.
  • Scholarship from the University of Newcastle, Australia, 2012-2013.
  • Travel grant from Faculty of Engineering, The University Newcastle, Australia, 2012.
  • Ranked first among all Master students, 2011.
  • Best student among university students, Master by Research (e.g. "MS.c Thesis" and "Seminar Course"), 2011.
  • Prize in a national mathematics Olympiad in IRAN, I was ranked the fourth top person among 10,000 people, 2000.

My Research Activities

Dr Rokny’s research focuses on using cutting-edge systems biology and advanced health data analytics techniques in conjunction with genome-wide data to understand the impact of genomic variants on genetic diseases and disorders. He is also interested to develop novel machine learning techniques, in particular, deep convolutional neural network, clustering, clustering, classification, feature selection, and evolutionary algorithms.
Dr Rokny has extensive experience in the analysis of next generation sequencing (NGS) data from different platforms (Roche, SOLiD, Illumina, and Helicos) and protocols (Hi-C, Structural variants, Single point mutations, GWAS, RNA-seq, CAGE, small RNA, ChIP-seq, and Single-cell). The move to UNSW Biomedical Engineering school has allowed him to translate his engineering and medical research on mammalian systems onto clinically relevant questions such as identification of novel biomarkers, drug targets.

Dr. Rokny is currently looking for Ph.D/Master/Honours students to join his Systems Biology and Health Data Analytics Lab. The research projects will mainly focus on using cutting-edge Systems Biology and Advanced Health Data Analytics techniques in conjunction with genome-wide data to understand biological and medical related problems.

There are several scholarships available for both international and domestic students. Please see the following links for more informations:

  • Key-dates: https://research.unsw.edu.au/key-dates
  • UNSW Post-Graduate Research Scholarship for international students,
  • UNSW Post-Graduate Research Scholarship for domestic students
  • Australia awards and endeavour scholarships and fellowships
  • Determine your eligibility for a scholarship: https://selfassessment.research.unsw.edu.au/
  • Meet english requirement: https://www.unsw.edu.au/english-requirements-policy 

My Research Supervision


Supervision keywords


Areas of supervision

  • Machine Learning
  • Bioinformatics
  • Systems Biology
  • Genomics
  • Health Data Analytics

There are multiple open Ph.D/Master/Honours positions in my Lab. Also Ph.D scholarships are available for outstanding applicants to study one of the following topics:

  • Enhancing chromosome conformation capture resolution with deep convolutional neural network.
  • A novel integrative approach to build up transcriptional regulatory networks in neurodevelopmental disorders.
  • Analysis of associations between genetic and transcriptomic variations in different populations.
  • Deep convolutional neural network in the classification of Single-cell data.
  • Using advanced data analytics techniques to get new insight into gene expression profiling in cancers.

Please send me the following documents when you are querying about the scholarships:

  • CV
  • Transcripts (undergraduate and postgraduate study)
  • English test result/plan for international applicants
  • Please note that UNSW offers scholarships for outstanding post-graduate students. However, if you have your own funding, it will simplify the process.

 


Currently supervising

  • Hanwen Liang, MS student, (administered by UNSW)
  • Zahra Rahaei, PhD student, (administered by SUT)
  • Mahshid Khatami, Master student (administered by SUT)
Previous students:
  • Masroor Bayati, Honours student,  2017-2018. Scholarship awarded for Ph.D Degree from University of Toronto.
  • Narges Rezaei, Honours student, 2018-2019. Scholarship awarded for Ph.D Degree from University of California, US.
  • Hamed Dashti, Honours student, 2016-2018. Scholarship awarded for Master Degree from University of Zurich,.
  • Rasaa Ghavami, Master student, 2017-2019. Scholarship awarded for PhD degree from Sharif University of Technology.
  • Fariba Raoufi, Master student, 2016-2017.
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Location

Graduate School of Biomedical Engineering, Level 1, Room 1002, Biological Sciences Building (E26)

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Contact

+61 2 9385 1725
+61 450 166 114