Dr Hamid Alinejad-Rokny
Lecturer

Dr Hamid Alinejad-Rokny

  • 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.
Engineering
Grad Sch: Biomedical Eng

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. Dr Rokny is currently running UNSW BioMedical Machine Learning Laboratory (BML) at the UNSW Graduate School of Biomedical Engineering (GSBmE), where he is leading a team of 1 post-doc, 2 research assistants, 5 PhDs, 3 Masters, 2 Hons as well as 8 researchers in overseas universities as co-supervisor/mentor. 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 Machine Learning 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 65 publications, including 10 as first & 35 as senior author. He has also been able to secure several national and international grants/fellowships. Throughput his career, he has received 28 prizes, honours, awards and also was able to secure multiple national and international awards and grants (totally $13.2M as Chief Investigator (CI) including highly competitive tenure-track UNSW Scientia Program Fellowship, CSIRO Next-Generation Graduate Program (leading CI), Australian National Health and Medical Research Council (NHMRC) IDEAS grant, Australian Research Council Discovery Early Career Researcher Award (DECRA 2022), two NHMRC MERIT awards, two international awards for his 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.

Phone
+61 2 9385 1725
Location
BioMedical Machine Learning Lab (BML), Graduate School of Biomedical Engineering, Level 1, Room 1002, Biological Sciences Building (E26)
  • Journal articles | 2022
    Argha A; Celler BG; Alinejad-Rokny H; Lovell NH, 2022, 'Blood Pressure Estimation from Korotkoff Sound Signals Using an End-to-End Deep Learning-Based Algorithm', IEEE Transactions on Instrumentation and Measurement, vol. 71, pp. 1 - 10, http://dx.doi.org/10.1109/TIM.2022.3217865
    Journal articles | 2022
    Dashti H; Dehzangi I; Bayati M; Breen J; Beheshti A; Lovell N; Rabiee HR; Alinejad-Rokny H, 2022, 'Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer', BMC Bioinformatics, vol. 23, http://dx.doi.org/10.1186/s12859-022-04652-8
    Journal articles | 2022
    Ghareyazi A; Kazemi A; Hamidieh K; Dashti H; Tahaei MS; Rabiee HR; Alinejad-Rokny H; Dehzangi I, 2022, 'Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types', BMC Bioinformatics, vol. 23, pp. 298, http://dx.doi.org/10.1186/s12859-022-04840-6
    Journal articles | 2022
    Labani M; Afrasiabi A; Beheshti A; Lovell NH; Alinejad-Rokny H, 2022, 'PeakCNV: A multi-feature ranking algorithm-based tool for genome-wide copy number variation-association study', Computational and Structural Biotechnology Journal, vol. 20, pp. 4975 - 4983, http://dx.doi.org/10.1016/j.csbj.2022.09.001
    Journal articles | 2022
    Parhami P; Fateh M; Rezvani M; Alinejad-Rokny H, 2022, 'A comparison of deep neural network models for cluster cancer patients through somatic point mutations', Journal of Ambient Intelligence and Humanized Computing, http://dx.doi.org/10.1007/s12652-022-04351-5
    Journal articles | 2022
    Razzak I; Naz S; Alinejad-Rokny H; Nguyen TN; Khalifa F, 2022, 'A Cascaded Mutliresolution Ensemble Deep Learning Framework for Large Scale Alzheimer's Disease Detection using Brain MRIs', IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. PP, pp. 1 - 9, http://dx.doi.org/10.1109/TCBB.2022.3219032
    Journal articles | 2016
    Lloyd SB; Lichtfuss M; Amarasena TH; Alcantara S; De Rose R; Tachedjian G; Alinejad-Rokny H; Venturi V; Davenport MP; Winnall WR; Kent SJ, 2016, 'High fidelity simian immunodeficiency virus reverse transcriptase mutants have impaired replication in vitro and in vivo', Virology, vol. 492, pp. 1 - 10, http://dx.doi.org/10.1016/j.virol.2016.02.008
    Journal articles | 2015
    Martyushev AP; Petravic J; Grimm AJ; Alinejad-Rokny H; Gooneratne SL; Reece JC; Cromer D; Kent SJ; Davenport MP, 2015, 'Epitope-specific CD8+ T cell kinetics rather than viral variability determine the timing of immune escape in simian immunodeficiency virus infection', Journal of Immunology, vol. 194, pp. 4112 - 4121, http://dx.doi.org/10.4049/jimmunol.1400793
    Journal articles | 2014
    Ebrahimi D; Alinejad-Rokny H; Davenport MP, 2014, 'Insights into the motif preference of APOBEC3 enzymes', PLoS ONE, vol. 9, http://dx.doi.org/10.1371/journal.pone.0087679
    Journal articles | 2011
    Minaei-Bidgoli B; Parvin H; Alizadeh H; Alinejad-Rokny H; Punch WF, 2011, 'Effects of resampling method and adaptation on clustering ensemble efficacy', Artificial Intelligence Review, pp. 1 - 22, http://dx.doi.org/10.1007/s10462-011-9295-x

Dr Rokny received extensive research funding support relative to career stage (total of $2.6M as sole/leading Chief Investigator (CI) and $10.6M as co-CI), demonstrating an impressive upward research career trajectory. These include:

  • ·     CSIRO Next-Generation Graduate Program (leading CI), ($1.7M including $700K for my Lab, Nov 2022)
  • ·     Australian National Health and Medical Research Council (NHMRC) IDEAS grant (CIB), ($600K, Nov 2022)
  • ·     Industry research partnership funding (CID), Australian Digital Domains Group, Nov 2022, ($3.6M)
  • ·     GROW Funding (CIA), a competitive internal funding form USNW SYDNEY, Jun 2022, ($40K)
  • ·     Industry research partnership funding (CIE), from Australian digital companies Truuth/Locii, May 2022, ($3.2M)
  • ·     Tyree Foundation Institute of Health Engineering Catalyst Awards 2021 (sole CI), Nov 2021, ($30K)
  • ·     Australian Research Council Discovery Early Career Researcher Award (DECRA 2022 – sole CI), ($462K)
  • ·     The Minor Research Equipment Grant-in-Aid Program Fund (sole CI), UNSW SYDNEY, July 2021, ($61K)
  • ·     Industry research partnership funding (CIC), from PORSPA advance company, May 2021, ($2.1M)
  • ·     GROW Funding (sole CI), a highly competitive internal funding form USNW SYDNEY, Jun 2021, ($20K)
  • ·     MERIT award offered for NHMRC Investigator Grant (sole CI), WA Dept of Health, Jun 2020, ($95K), declined because of moving to UNSW
  • ·     NSW Cancer Council (CIB), in collab with Lowy Cancer Research Centre, Apr 2020, ($100K)
  • ·     UNSW Cellular Genomics Futures Institute grant (CIB), in collab with Garvan Institute, May 2020, ($50K)
  • ·     UNSW Cellular Genomics Futures Institute grant (CIC), in collab with UNSW BABS, May 2020, ($50K)
  • ·     Highly competitive tenure-track UNSW Scientia Fellowship Program (sole CI), UNSW, Oct 2019, ($680k)
  • ·     Academic Start-up Funding (sole CI), Faculty of Engineering, UNSW, Dec 2019, ($90K)
  • ·     Highly competitive International Quebec Autism Research Training Fellowship (sole CI), collab with U of Montreal, Nov 2019, ($120K)
  • ·     Highly prestigious Int. Fellowship Fonds de recherche du Québec Santé (FRQS) (sole CI), Oct 2019, ($90K)
  • ·     MERIT award for NHMRC Investigator Grant Application (sole CI), WA Dept of Health, Sep 2019, ($50K)

As a very young early career researcher, Dr Rokny has an exceptional track record in securing a range of national and international awards and prizes, despite my early career status. These include:

  • ·     Adjunct Research Scientist, CSIRO, Aug 2022-present
  • ·     Honorary Lecturer Fellow, University of Macquarie, Oct 2020-current
  • ·     Travel support award from Institute for Research in Fundamental Sciences, Iran, invited speaker, ($1.9K), Feb 2020
  • ·     Health Data Analytics Program Leader, AI-enabled Processes (AIP) Research Centre, Dec 2019-curent
  • ·     MBSJ2019 (42nd Annual Meeting of the Molecular Biology) Travel support award, Japan, ($1K), Dec 2019
  • ·     RIKEN-HUGO award for best oral presentation in Human Genome Meeting 2019, South Korea, ($0.2K), Oct 2019
  • ·     Highly competitive tenure-track UNSW Scientia Fellowship Program award in Aug 2019 ($680K)
  • ·     Vice-chancellor fellowship award from RMIT, ($350K), May 2019 (declined in favour of UNSW Scientia Program).
  • ·     HDR conference support award from UNSW Sydney, ($3K), Jul 2015
  • ·     Travel support award from University of Tehran as invited speaker, Tehran, ($2K), Feb 2015
  • ·     Ph.D scholarship from UNSW Sydney, ($87.5K for 3.5 years), Mar 2013
  • ·     Top-up scholarship from the faculty of medicine, UNSW Sydney, ($30K for 3 years), Mar 2013
  • ·     Ph.D Scholarship award from The University of Newcastle, Australia, Jul 2012
  • ·     Travel award from Faculty of Engineering, The University Newcastle, Australia, ($1K), Jul 2012
  • ·     Government scholarships for Bachelor and Master degrees, (tuition fee waived)
  • ·     Dean’s award as ranked 1 student (out of 700 Master students), Science and Research University of Tehran, Sep 2010

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 Research Associate/Assistant, Ph.D/Master/Honours students to join his BML Lab. The research projects will mainly focus on using cutting-edge Medical Artificial Intelligence, 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

Research Assistants:

Mona (Sedigheh) Abedini, Research Assistant, 2022-2023, (administered by UNSW).

PhD Students:

  • Ivan Bakhshayeshi, PhD student, 2023-2027, (administered by UNSW).
  • Reza Ghamsari, PhD student, 2022-2026, (administered by UNSW).
  • Mahdieh Labani, PhD student, 2021-2025, (administered by Macquarie University).
  • 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.
  • Ted Wong, PhD student, 2019-2025, (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.
  • Ning Liu, PhD student, 2019-2023, (administered by University of Adelaide), co-supervision with Dr James Breen.
  • Zahra Rahaei, PhD student, 2018-2023, (administered by SUT).

Master by Research Students:

  • Yuheng Liang, Master by student, 2023-2025, (administered by UNSW).

Master Students:

  • Gabrielle Younes, Master student, 2023-2024, (administered by UNSW).
  • Sally Chen, Master student, 2023-2024, (administered by UNSW).
  • Aravind Venkateswaran, Master student, 2022-2023, (administered by UNSW).
  • Sascha Graham, Master student, 2022-2023, (administered by UNSW).
  • Weilin Wu, Master student, 2021-2022, (administered by UNSW).
  • Anthony Xu, Master student, 2021-2022, (administered by UNSW).
  • Yuheng Liang, Master student, 2021-2022, (administered by UNSW).

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.
  • Mahshid Khatami, Master student, 2018-2020, (administered by SUT).
  • Fariba Raoufi, Master student, 2016-2017.

My Teaching

Biomedical Informatics (BIOM9540)

Biomedical Engineering (BIOM4951, BIOM4952, BIOM4953)