Researcher

Dr Hamid Alinejad-Rokny

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Biography

Dr Rokny joined UNSW on a highly prestigious and competitive UNSW Scientia Program (UNSW Scientia Program aims to attract the best and brightest scientists with outstanding research records in October 2019.  He is now Head of Translational Genomics Data Analytics Lab (TGDA), 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...view more

Dr Rokny joined UNSW on a highly prestigious and competitive UNSW Scientia Program (UNSW Scientia Program aims to attract the best and brightest scientists with outstanding research records in October 2019.  He is now Head of Translational Genomics Data Analytics Lab (TGDA), 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 (Ranked 1st) and his Ph.D in Systems Biology and Genomics from UNSW Australia, Dec 2017.
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 received 28 prizes, honours, awards and also was able to secure multiple national and international awards and grants (totally $1.27M) including highly competitive tenure-track UNSW Scientia Program, two NHMRC MERIT awards, two international awards for my work on Autism from the International Quebec Autism Research Training (QART) program and the International Fellowship Fonds de recherche du Québec - Santé (FRQS), two awards from UNSW Cellular Genomics Futures Institute, four external and one internal travel grants to present my research at national and international conferences and workshops. He has also received the best presentation prize in prestigious international conference Human Genome Meeting (HUGO) 2019. Dr Rokny also awarded highly competitive international PhD scholarship from UNSW. Additionally, He has been invited to serve as Keynote Speaker and program committee members of national and international conferences including prestigious International HUGO 2020 (HUGO ECR symposium organization team), Pasteur Institute (invited talk), Harry Perkins Institute of Medical Research.


My Grants

  • MERIT award for NHMRC Investigator funding (CI-A), offered, 2020-2021.
  • 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

•    Honorary Lecturer Fellow, University of Macquarie, Oct 2020-current
•    Awarded Travel grant from Institute for Research in Fundamental Sciences as invited speaker, Feb 2020
•    Health Data Analytics Program Leader, AI-enabled Processes (AIP) Research Centre, Dec 2019-curent
•    Awarded MBSJ2019 (42nd Annual Meeting of the Molecular Biology) Travel Award, Japan, Dec 2019
•    Prize RIKEN-HUGO award for best oral presentation in HUGO 2019, South Korea, Oct 2019
•    Awarded highly competitive tenure-track UNSW Scientia Fellowship Program in Aug 2019
•    Offered, Vice-chancellor fellowship grant from RMIT Australia, May 2019 (declined in favour of UNSW Scientia Program).
•    Awarded HDR conference support grant from UNSW Sydney, Jul 2015
•    Awarded Travel grant from University of Tehran as invited speaker, Tehran, Feb 2015
•    Prize, Ph.D scholarship from UNSW Sydney, Mar 2013
•    Prize, Top-up scholarship from the faculty of medicine, UNSW Sydney, Mar 2013
•    Prize, Ph.D Scholarship from the University of Newcastle, Australia, Jul 2012
•    Prize, Travel award from Faculty of Engineering, The University Newcastle, Australia, Jul 2012
•    Awarded Government scholarship for Bachelor and Master degrees, (tuition fee waived)
•    Dean’s award, for being Top Student during Master’s degree, Science and Research University of Tehran, 2010
•    Honour, Ranked 1 (of 700) with the overall GPA (19.31/20) in Master’s degree (Top Student), Science and Research University of Tehran, Sep 2010
•    Prize in a National Mathematics Olympiad, ranked the fourth top person among 10,000 people.


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 Translational Genomics Data Analytics Lab (TGDA). 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 information:

  • 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
  • Deep Learning
  • Data Mining
  • 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

  • Ali Afrasiabi, PhD student, 2020-2024, (administered by UNSW).
  • Sunday Offor, PhD student, 2019-2023, (administered by UNSW), co-supervision with Assoc Prof Irina Voineagu.
  • Ning Liu, PhD student, 2019-2023, (administered by University of Adelaide), co-supervision with Dr James Breen.
  • Ted Wong, PhD student, 2019-2023, (administered by University of Sydney), co-supervision with Dr. Boris Guennewig.
  • Callum Macphillamy, PhD student, 2020-2024, (administered by University of Adelaide), co-supervision with Dr Wai Yee Low.
  • Zahra Rahaei, PhD student, 2018-2022, (administered by SUT).
  • Mahshid Khatami, Master student, 2018-2020, (administered by SUT).

Previous supervision and mentoring:

  • Hanwen Liang, MS student, 2019-2020, (administered by UNSW).
  • Rasaa Ghavami, Master student, 2017-2019. Scholarship awarded for PhD degree from SUT.
  • Narges Rezaei, Honours student, 2018-2019. Scholarship awarded for Ph.D Degree from University of California, US.
  • Masroor Bayati, Honours student,  2017-2018. Scholarship awarded for Ph.D Degree from University of Toronto.
  • Hamed Dashti, Honours student, 2016-2018. Scholarship awarded for Master Degree from University of Zurich.
  • Fariba Raoufi, Master student, 2016-2017.

My Teaching

Biomedical Informatics (BIOM9540)

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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