Lecturer

Dr Hamid Alinejad-Rokny

Bachelor: Software Engineering, 2004-2009
Master: Artificial Intelligence, 2009-2012.
Industry: Data Scientist, 2012-2014.
Ph.D: Machine Learning and Computational Biology, UNSW Sydney, 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

E-mail

h.alinejad@unsw.edu.au

Location

UNSW BioMedical Machine Learning Lab (BML), Graduate School of Biomedical Engineering, Level 1, Room 1002, Biological Sciences Building (E26)

Book Chapters | 2021

Wang S; Beheshti A; Wang Y; Lu J; Sheng QZ; Elbourn S; Alinejad-Rokny H; Galanis E, 2021, 'Assessment2Vec: Learning Distributed Representations of Assessments to Reduce Marking Workload', in Artificial Intelligence in Education, Springer International Publishing, pp. 384 - 389, http://dx.doi.org/10.1007/978-3-030-78270-2_68
Journal articles | 2023

Alizadehsani R; Roshanzamir M; Izadi NH; Gravina R; Kabir HMD; Nahavandi D; Alinejad-Rokny H; Khosravi A; Acharya UR; Nahavandi S; Fortino G, 2023, 'Swarm Intelligence in Internet of Medical Things: A Review', Sensors, 23, pp. 1466 - 1466, http://dx.doi.org/10.3390/s23031466

Journal articles | 2023

Ghamsari R; Rosenbluh J; Menon AV; Lovell NH; Alinejad-Rokny H, 2023, 'Technological Convergence: Highlighting the Power of CRISPR Single-Cell Perturbation Toolkit for Functional Interrogation of Enhancers', Cancers, 15, pp. 3566 - 3566, http://dx.doi.org/10.3390/cancers15143566

Journal articles | 2023

Hong L; Modirrousta MH; Hossein Nasirpour M; Mirshekari Chargari M; Mohammadi F; Moravvej SV; Rezvanishad L; Rezvanishad M; Bakhshayeshi I; Alizadehsani R; Razzak I; Alinejad-Rokny H; Nahavandi S, 2023, 'GAN-LSTM-3D: An efficient method for lung tumour 3D reconstruction enhanced by attention-based LSTM', CAAI Transactions on Intelligence Technology, http://dx.doi.org/10.1049/cit2.12223

Journal articles | 2023

Jafari M; Shoeibi A; Khodatars M; Ghassemi N; Moridian P; Alizadehsani R; Khosravi A; Ling SH; Delfan N; Zhang YD; Wang SH; Gorriz JM; Alinejad-Rokny H; Acharya UR, 2023, 'Automated diagnosis of cardiovascular diseases from cardiac magnetic resonance imaging using deep learning models: A review', Computers in Biology and Medicine, 160, http://dx.doi.org/10.1016/j.compbiomed.2023.106998

Journal articles | 2023

Khozeimeh F; Alizadehsani R; Shirani M; Tartibi M; Shoeibi A; Alinejad-Rokny H; Harlapur C; Sultanzadeh SJ; Khosravi A; Nahavandi S; Tan RS; Acharya UR, 2023, 'ALEC: Active learning with ensemble of classifiers for clinical diagnosis of coronary artery disease', Computers in Biology and Medicine, 158, http://dx.doi.org/10.1016/j.compbiomed.2023.106841

Journal articles | 2023

Labani M; Beheshti A; Argha A; Alinejad-Rokny H, 2023, 'A Comprehensive Investigation of Genomic Variants in Prostate Cancer Reveals 30 Putative Regulatory Variants', International Journal of Molecular Sciences, 24, pp. 2472 - 2472, http://dx.doi.org/10.3390/ijms24032472

Journal articles | 2023

Parhami P; Fateh M; Rezvani M; Alinejad-Rokny H, 2023, 'A comparison of deep neural network models for cluster cancer patients through somatic point mutations', Journal of Ambient Intelligence and Humanized Computing, 14, pp. 10883 - 10898, http://dx.doi.org/10.1007/s12652-022-04351-5

Journal articles | 2023

Rahaie Z; Rabiee HR; Alinejad-Rokny H, 2023, 'DeepGenePrior: A deep learning model for prioritizing genes affected by copy number variants', PLoS Computational Biology, 19, pp. e1011249, http://dx.doi.org/10.1371/journal.pcbi.1011249

Journal articles | 2023

Shabani N; Beheshti A; Farhood H; Bower M; Garrett M; Alinejad-Rokny H, 2023, 'A Rule-Based Approach for Mining Creative Thinking Patterns from Big Educational Data', AppliedMath, 3, pp. 243 - 267, http://dx.doi.org/10.3390/appliedmath3010014

Journal articles | 2023

Shamsi A; Asgharnezhad H; Bouchani Z; Jahanian K; Saberi M; Wang X; Razzak I; Alizadehsani R; Mohammadi A; Alinejad-Rokny H, 2023, 'A novel uncertainty-aware deep learning technique with an application on skin cancer diagnosis', Neural Computing and Applications, http://dx.doi.org/10.1007/s00521-023-08930-1

Journal articles | 2023

Shoeibi A; Khodatars M; Jafari M; Ghassemi N; Moridian P; Alizadehsani R; Ling SH; Khosravi A; Alinejad-Rokny H; Lam HK; Fuller-Tyszkiewicz M; Acharya UR; Anderson D; Zhang Y; Gorriz JM, 2023, 'Diagnosis of brain diseases in fusion of neuroimaging modalities using deep learning: A review', Information Fusion, 93, pp. 85 - 117, http://dx.doi.org/10.1016/j.inffus.2022.12.010

Journal articles | 2023

Wang S; Beheshti A; Wang Y; Lu J; Sheng QZ; Elbourn S; Alinejad-Rokny H, 2023, 'Learning Distributed Representations and Deep Embedded Clustering of Texts', Algorithms, 16, http://dx.doi.org/10.3390/a16030158

Journal articles | 2022

Afrasiabi A; Alinejad-Rokny H; Khosh A; Rahnama M; Lovell N; Xu Z; Ebrahimi D, 2022, 'The low abundance of CpG in the SARS-CoV-2 genome is not an evolutionarily signature of ZAP', Scientific Reports, 12, pp. 2420, http://dx.doi.org/10.1038/s41598-022-06046-5

Journal articles | 2022

Afrasiabi A; Keane JT; Ong LTC; Alinejad-Rokny H; Fewings NL; Booth DR; Parnell GP; Swaminathan S, 2022, 'Genetic and transcriptomic analyses support a switch to lytic phase in Epstein Barr virus infection as an important driver in developing Systemic Lupus Erythematosus', Journal of Autoimmunity, 127, pp. 102781, http://dx.doi.org/10.1016/j.jaut.2021.102781

Journal articles | 2022

Alinejad-Rokny H; Modegh RG; Rabiee HR; Sarbandi ER; Rezaie N; Tam KT; Forrest ARR, 2022, 'MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments', PLoS Computational Biology, 18, pp. e1010241, http://dx.doi.org/10.1371/journal.pcbi.1010241

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, 71, pp. 1 - 10, http://dx.doi.org/10.1109/TIM.2022.3217865

Journal articles | 2022

Band SS; Ardabili S; Yarahmadi A; Pahlevanzadeh B; Kiani AK; Beheshti A; Alinejad-Rokny H; Dehzangi I; Chang A; Mosavi A; Moslehpour M, 2022, 'A Survey on Machine Learning and Internet of Medical Things-Based Approaches for Handling COVID-19: Meta-Analysis', Frontiers in Public Health, 10, pp. 869238, http://dx.doi.org/10.3389/fpubh.2022.869238

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, 23, http://dx.doi.org/10.1186/s12859-022-04652-8

Journal articles | 2022

Debnath T; Reza MM; Rahman A; Beheshti A; Band SS; Alinejad-Rokny H, 2022, 'Four-layer ConvNet to facial emotion recognition with minimal epochs and the significance of data diversity', Scientific Reports, 12, http://dx.doi.org/10.1038/s41598-022-11173-0

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, 23, pp. 298, http://dx.doi.org/10.1186/s12859-022-04840-6

Journal articles | 2022

Grapotte M; Saraswat M; Bessière C; Menichelli C; Ramilowski JA; Severin J; Hayashizaki Y; Itoh M; Tagami M; Murata M; Kojima-Ishiyama M; Noma S; Noguchi S; Kasukawa T; Hasegawa A; Suzuki H; Nishiyori-Sueki H; Frith MC; Abugessaisa I; Aitken S; Aken BL; Alam I; Alam T; Alasiri R; Alhendi AMN; Alinejad-Rokny H; Alvarez MJ; Andersson R; Arakawa T; Araki M; Arbel T; Archer J; Archibald AL; Arner E; Arner P; Asai K; Ashoor H; Astrom G; Babina M; Baillie JK; Bajic VB; Bajpai A; Baker S; Baldarelli RM; Balic A; Bansal M; Batagov AO; Batzoglou S; Beckhouse AG; Beltrami AP; Beltrami CA; Bertin N; Bhattacharya S; Bickel PJ; Blake JA; Blanchette M; Bodega B; Bonetti A; Bono H; Bornholdt J; Bttcher M; Bougouffa S; Boyd M; Breda J; Brombacher F; Brown JB; Bult CJ; Burroughs AM; Burt DW; Busch A; Caglio G; Califano A; Cameron CJ; Cannistraci CV; Carbone A; Carlisle AJ; Carninci P; Carter KW; Cesselli D; Chang JC; Chen JC; Chen Y; Chierici M; Christodoulou J; Ciani Y; Clark EL; Coskun M; Dalby M; Dalla E; Daub CO; Davis CA; de Hoon MJL; de Rie D; Denisenko E; Deplancke B; Detmar M; Deviatiiarov R; Di Bernardo D; Diehl AD; Dieterich LC, 2022, 'Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7)', Nature Communications, 13, pp. 1200, http://dx.doi.org/10.1038/s41467-022-28758-y

Journal articles | 2022

Islam S; Mugdha SBS; Dipta SR; Arafat ME; Shatabda S; Alinejad-Rokny H; Dehzangi I, 2022, 'MethEvo: an accurate evolutionary information-based methylation site predictor', Neural Computing and Applications, http://dx.doi.org/10.1007/s00521-022-07738-9

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, 20, pp. 4975 - 4983, http://dx.doi.org/10.1016/j.csbj.2022.09.001

Journal articles | 2022

Labani M; Beheshti A; Lovell NH; Alinejad-Rokny H; Afrasiabi A, 2022, 'KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition', International Journal of Molecular Sciences, 23, pp. 14418 - 14418, http://dx.doi.org/10.3390/ijms232214418

Journal articles | 2022

MacPhillamy C; Alinejad-Rokny H; Pitchford WS; Low WY, 2022, 'Cross-species enhancer prediction using machine learning', Genomics, 114, pp. 110454, http://dx.doi.org/10.1016/j.ygeno.2022.110454

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, PP, pp. 1 - 9, http://dx.doi.org/10.1109/TCBB.2022.3219032

Journal articles | 2022

Rezaie N; Bayati M; Hamidi M; Tahaei MS; Khorasani S; Lovell NH; Breen J; Rabiee HR; Alinejad-Rokny H, 2022, 'Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer', Communications Biology, 5, http://dx.doi.org/10.1038/s42003-022-03528-0

Journal articles | 2022

Saberi-Movahed F; Mohammadifard M; Mehrpooya A; Rezaei-Ravari M; Berahmand K; Rostami M; Karami S; Najafzadeh M; Hajinezhad D; Jamshidi M; Abedi F; Mohammadifard M; Farbod E; Safavi F; Dorvash M; Mottaghi-Dastjerdi N; Vahedi S; Eftekhari M; Saberi-Movahed F; Alinejad-Rokny H; Band SS; Tavassoly I, 2022, 'Decoding clinical biomarker space of COVID-19: Exploring matrix factorization-based feature selection methods', Computers in Biology and Medicine, 146, pp. 105426, http://dx.doi.org/10.1016/j.compbiomed.2022.105426

Journal articles | 2022

Sharifonnasabi F; Jhanjhi NZ; John J; Obeidy P; Band SS; Alinejad-Rokny H; Baz M, 2022, 'Hybrid HCNN-KNN Model Enhances Age Estimation Accuracy in Orthopantomography', Frontiers in Public Health, 10, http://dx.doi.org/10.3389/fpubh.2022.879418

Journal articles | 2022

Sharifrazi D; Alizadehsani R; Joloudari JH; Band SS; Hussain S; Sani ZA; Hasanzadeh F; Shoeibi A; Dehzangi A; Sookhak M; Alinejad-Rokny H, 2022, 'CNN-KCL: Automatic myocarditis diagnosis using convolutional neural network combined with k-means clustering', Mathematical Biosciences and Engineering, 19, pp. 2381 - 2402, http://dx.doi.org/10.3934/MBE.2022110

Journal articles | 2021

Afrasiabi A; Keane JT; Ik-Tsen Heng J; Palmer EE; Lovell NH; Alinejad-Rokny H, 2021, 'Quantitative neurogenetics: Applications in understanding disease', Biochemical Society Transactions, 49, pp. 1621 - 1631, http://dx.doi.org/10.1042/BST20200732

Journal articles | 2021

Ghareyazi A; Mohseni A; Dashti H; Beheshti A; Dehzangi A; Rabiee HR; Alinejad-Rokny H, 2021, 'Whole-genome analysis of de novo somatic point mutations reveals novel mutational biomarkers in pancreatic cancer', Cancers, 13, http://dx.doi.org/10.3390/cancers13174376

Journal articles | 2021

Grapotte M; Saraswat M; Bessière C; Menichelli C; Ramilowski JA; Severin J; Hayashizaki Y; Itoh M; Tagami M; Murata M; Kojima-Ishiyama M; Noma S; Noguchi S; Kasukawa T; Hasegawa A; Suzuki H; Nishiyori-Sueki H; Frith MC; Abugessaisa I; Aitken S; Aken BL; Alam I; Alam T; Alasiri R; Alhendi AMN; Alinejad-Rokny H; Alvarez MJ; Andersson R; Arakawa T; Araki M; Arbel T; Archer J; Archibald AL; Arner E; Arner P; Asai K; Ashoor H; Astrom G; Babina M; Baillie JK; Bajic VB; Bajpai A; Baker S; Baldarelli RM; Balic A; Bansal M; Batagov AO; Batzoglou S; Beckhouse AG; Beltrami AP; Beltrami CA; Bertin N; Bhattacharya S; Bickel PJ; Blake JA; Blanchette M; Bodega B; Bonetti A; Bono H; Bornholdt J; Bttcher M; Bougouffa S; Boyd M; Breda J; Brombacher F; Brown JB; Bult CJ; Burroughs AM; Burt DW; Busch A; Caglio G; Califano A; Cameron CJ; Cannistraci CV; Carbone A; Carlisle AJ; Carninci P; Carter KW; Cesselli D; Chang JC; Chen JC; Chen Y; Chierici M; Christodoulou J; Ciani Y; Clark EL; Coskun M; Dalby M; Dalla E; Daub CO; Davis CA; de Hoon MJL; de Rie D; Denisenko E; Deplancke B; Detmar M; Deviatiiarov R; Di Bernardo D; Diehl AD; Dieterich LC, 2021, 'Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network', Nature Communications, 12, http://dx.doi.org/10.1038/s41467-021-23143-7

Journal articles | 2021

Heidari R; Akbariqomi M; Asgari Y; Ebrahimi D; Alinejad-Rokny H, 2021, 'A systematic review of long non-coding RNAs with a potential role in breast cancer', Mutation Research - Reviews in Mutation Research, 787, http://dx.doi.org/10.1016/j.mrrev.2021.108375

Journal articles | 2021

Liu N; Low WY; Alinejad-Rokny H; Pederson S; Sadlon T; Barry S; Breen J, 2021, 'Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C', Epigenetics and Chromatin, 14, http://dx.doi.org/10.1186/s13072-021-00417-4

Journal articles | 2021

MacPhillamy C; Pitchford WS; Alinejad-Rokny H; Low WY, 2021, 'Opportunity to improve livestock traits using 3D genomics', Animal Genetics, 52, pp. 785 - 798, http://dx.doi.org/10.1111/age.13135

Journal articles | 2021

Mahmoudi MR; Akbarzadeh H; Parvin H; Nejatian S; Rezaie V; Alinejad-Rokny H, 2021, 'Consensus function based on cluster-wise two level clustering', Artificial Intelligence Review, 54, pp. 639 - 665, http://dx.doi.org/10.1007/s10462-020-09862-1

Journal articles | 2021

Pho KH; Akbarzadeh H; Parvin H; Nejatian S; Alinejad-Rokny H, 2021, 'A multi-level consensus function clustering ensemble', Soft Computing, 25, pp. 13147 - 13165, http://dx.doi.org/10.1007/s00500-021-06092-7

Journal articles | 2021

Rajaei P; Jahanian KH; Beheshti A; Band SS; Dehzangi A; Alinejad-rokny H, 2021, 'VIRMOTIF: A user-friendly tool for viral sequence analysis', Genes, 12, pp. 1 - 9, http://dx.doi.org/10.3390/genes12020186

Journal articles | 2021

Rezaie N; Bayati M; Tahaei MS; Hamidi M; Khorasani S; Lovell NH; Breen J; Rabiee HR; Alinejad-Rokny H, 2021, 'Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer', , http://dx.doi.org/10.1101/2021.07.19.453012

Journal articles | 2021

Shamshirband S; Fathi M; Dehzangi A; Chronopoulos AT; Alinejad-Rokny H, 2021, 'A review on deep learning approaches in healthcare systems: Taxonomies, challenges, and open issues', Journal of Biomedical Informatics, 113, http://dx.doi.org/10.1016/j.jbi.2020.103627

Journal articles | 2021

Walsh K; Gokool A; Alinejad-Rokny H; Voineagu I, 2021, 'NeuroCirc: an integrative resource of circular RNA expression in the human brain', Bioinformatics, 37, pp. 3664 - 3666, http://dx.doi.org/10.1093/bioinformatics/btab230

Journal articles | 2020

Afrasiabi A; Alinejad-Rokny H; Lovell N; Xu Z; Ebrahimi D, 2020, 'Insight into the origin of 5’UTR and source of CpG reduction in SARS-CoV-2 genome', , http://dx.doi.org/10.1101/2020.10.23.351353

Journal articles | 2020

Alinejad-Rokny H; Heng JIT; Forrest ARR, 2020, 'Brain-Enriched Coding and Long Non-coding RNA Genes Are Overrepresented in Recurrent Neurodevelopmental Disorder CNVs', Cell Reports, 33, http://dx.doi.org/10.1016/j.celrep.2020.108307

Journal articles | 2020

Bahrani P; Minaei-Bidgoli B; Parvin H; Mirzarezaee M; Keshavarz A; Alinejad-Rokny H, 2020, 'User and item profile expansion for dealing with cold start problem', Journal of Intelligent & Fuzzy Systems, 38, pp. 4471 - 4483, http://dx.doi.org/10.3233/jifs-191225

Journal articles | 2020

Bayati M; Rabiee HR; Mehrbod M; Vafaee F; Ebrahimi D; Forrest ARR; Alinejad-Rokny H, 2020, 'CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes', Scientific Reports, 10, pp. 1286, http://dx.doi.org/10.1038/s41598-020-58107-2

Journal articles | 2020

Hosseinpoor M; Parvin H; Nejatian S; Rezaie V; Bagherifard K; Dehzangi A; Beheshti A; Alinejad-Rokny H, 2020, 'Proposing a novel community detection approach to identify co-interacting genomic regions', Mathematical Biosciences and Engineering, 17, pp. 2193 - 2217, http://dx.doi.org/10.3934/mbe.2020117

Journal articles | 2020

Khakmardan S; Rezvani M; Pouyan AA; Fateh M; Alinejad-Rokny H, 2020, 'MHiC, an integrated user-friendly tool for the identification and visualization of significant interactions in Hi-C data', BMC Genomics, 21, http://dx.doi.org/10.1186/s12864-020-6636-7

Journal articles | 2020

Niu H; Khozouie N; Parvin H; Alinejad-Rokny H; Beheshti A; Mahmoudi MR, 2020, 'An ensemble of locally reliable cluster solutions', Applied Sciences (Switzerland), 10, pp. 1891 - 1891, http://dx.doi.org/10.3390/app10051891

Journal articles | 2020

Niu H; Xu W; Akbarzadeh H; Parvin H; Beheshti A; Alinejad-Rokny H, 2020, 'Deep feature learnt by conventional deep neural network', Computers and Electrical Engineering, 84, http://dx.doi.org/10.1016/j.compeleceng.2020.106656

Journal articles | 2019

Masoudiasl I; Vahdat S; Hessam S; Shamshirband S; Alinejad-Rokny H, 2019, 'Proposing an Integrated Method based on Fuzzy Tuning and ICA Techniques to Identify the Most Influencing Features in Breast Cancer', Iranian Red Crescent Medical Journal, 21, http://dx.doi.org/10.5812/ircmj.92077

Journal articles | 2019

Woodward KJ; Stampalia J; Vanyai H; Rijhumal H; Potts K; Taylor F; Peverall J; Grumball T; Sivamoorthy S; Alinejad-Rokny H; Wray J; Whitehouse A; Nagarajan L; Scurlock J; Afchani S; Edwards M; Murch A; Beilby J; Baynam G; Kiraly-Borri C; McKenzie F; Heng JIT, 2019, 'Atypical nested 22q11.2 duplications between LCR22B and LCR22D are associated with neurodevelopmental phenotypes including autism spectrum disorder with incomplete penetrance', Molecular Genetics and Genomic Medicine, 7, http://dx.doi.org/10.1002/mgg3.507

Journal articles | 2018

Alinejad-Rokny H; Sadroddiny E; Scaria V, 2018, 'Machine learning and data mining techniques for medical complex data analysis', Neurocomputing, 276, pp. 1, http://dx.doi.org/10.1016/j.neucom.2017.09.027

Journal articles | 2018

Kalantari A; Kamsin A; Shamshirband S; Gani A; Alinejad-Rokny H; Chronopoulos AT, 2018, 'Computational intelligence approaches for classification of medical data: State-of-the-art, future challenges and research directions', Neurocomputing, 276, pp. 2 - 22, http://dx.doi.org/10.1016/j.neucom.2017.01.126

Journal articles | 2018

Poulton C; Baynam G; Yates C; Alinejad-Rokny H; Williams S; Wright H; Woodward KJ; Sivamoorthy S; Peverall J; Shipman P; Ravine D; Beilby J; Heng JIT, 2018, 'A review of structural brain abnormalities in Pallister-Killian syndrome', Molecular Genetics and Genomic Medicine, 6, pp. 92 - 98, http://dx.doi.org/10.1002/mgg3.351

Journal articles | 2018

Vafaee F; Dashti H; Alinejad-Rokny H, 2018, 'Transcriptomic Data Normalization', Encyclopedia of Bioinformatics and Computational Biology, Elsevier, http://dx.doi.org/10.1016/B978-0-12-809633-8.20209-4

Journal articles | 2018

Vafaee F; Diakos C; Kirschner M; Reid G; Michael M; Horvath LISA; Alinejad-Rokny H; Cheng ZJ; Kuncic Z; Clarke S, 2018, 'A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis', npj Systems Biology and Applications, 4, pp. 20 - 20, http://dx.doi.org/10.1038/s41540-018-0056-1

Journal articles | 2017

Alinejad-Rokny H; Parvin H; Ahangarikiasari H, 2017, 'Pattern Mining and Identifying Co-Expressed Genes from RNA-Seq Dataset Using a New Swarm Intelligence-Based Clustering (Advanced Science, Engineering and Medicine, Vol. 9(1), pp. 36–45 (2017))', Advanced Science, Engineering and Medicine, 9, pp. 618 - 618, http://dx.doi.org/10.1166/asem.2017.2064

Journal articles | 2017

Alinejad-Rokny H; Parvin H; Ahangarikiasari H, 2017, 'Pattern Mining and Identifying Co-Expressed Genes from RNA-Seq Dataset Using a New Swarm Intelligence-Based Clustering', Advanced Science, Engineering and Medicine, 9, pp. 36 - 45, http://dx.doi.org/10.1166/asem.2017.1959

Journal articles | 2017

Alinejad-Rokny H, 2017, 'A Method to Avoid Gapped Sequential Patterns in Biological Sequences: Case Study: HIV and Cancer Sequences', Journal of Neuroscience and Neuroengineering, 4, pp. 49 - 53, http://dx.doi.org/10.1166/jnsne.2017.1114

Journal articles | 2017

Baghernia A; Pavin H; Mirnabibaboli M; Alinejad-Rokny H, 2017, 'Clustering High-Dimensional Data Stream: A Survey on Subspace Clustering, Projected Clustering on Bioinformatics Applications (Advanced Science, Engineering and Medicine, Vol. 8(9), pp. 749–757 (2016))', Advanced Science, Engineering and Medicine, 9, pp. 617 - 617, http://dx.doi.org/10.1166/asem.2017.2063

Journal articles | 2016

Alinejad-Rokny H; Anwar F; Waters SA; Davenport MP; Ebrahimi D, 2016, 'Source of CpG depletion in the HIV-1 genome', Molecular Biology and Evolution, 33, pp. 3205 - 3212, http://dx.doi.org/10.1093/molbev/msw205

Journal articles | 2016

Alinejad-Rokny H; Masoud M, 2016, 'A method for hypermutated viral sequences detection in fastq and bam format files', Journal of Medical Imaging and Health Informatics, 6, pp. 1202 - 1208, http://dx.doi.org/10.1166/jmihi.2016.1977

Journal articles | 2016

Alinejad-Rokny H, 2016, 'Proposing on optimized homolographic motif mining strategy based on parallel computing for complex biological networks', Journal of Medical Imaging and Health Informatics, 6, pp. 416 - 424, http://dx.doi.org/10.1166/jmihi.2016.1707

Journal articles | 2016

Baghernia A; Pavin H; Mirnabibaboli M; Alinejad-Rokny H, 2016, 'Clustering High-Dimensional Data Stream: A Survey on Subspace Clustering, Projected Clustering on Bioinformatics Applications', Advanced Science, Engineering and Medicine, 8, pp. 749 - 757, http://dx.doi.org/10.1166/asem.2016.1915

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, 492, pp. 1 - 10, http://dx.doi.org/10.1016/j.virol.2016.02.008

Journal articles | 2015

Alinejad-Rokny H; Ebrahimi D, 2015, 'A method to avoid errors associated with the analysis of hypermutated viral sequences by alignment-based methods', Journal of Biomedical Informatics, 58, pp. 220 - 225, http://dx.doi.org/10.1016/j.jbi.2015.10.008

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, 194, pp. 4112 - 4121, http://dx.doi.org/10.4049/jimmunol.1400793

Journal articles | 2015

Parvin H; Mirnabibaboli M; Alinejad-Rokny H, 2015, 'Proposing a classifier ensemble framework based on classifier selection and decision tree', Engineering Applications of Artificial Intelligence, 37, pp. 34 - 42, http://dx.doi.org/10.1016/j.engappai.2014.08.005

Journal articles | 2014

Ahmadinia M; Alinejad-Rokny H; Ahangarikiasari H, 2014, 'Data Aggregation in Wireless Sensor Networks Based on Environmental Similarity: A Learning Automata Approach', Journal of Networks, 9, http://dx.doi.org/10.4304/jnw.9.10.2567-2573

Journal articles | 2014

Alinejad-Rokny H; Pourshaban H; Orimi AG; Baboli MM, 2014, 'Network motifs detection strategies and using for bioinformatic networks', Journal of Bionanoscience, 8, pp. 353 - 359, http://dx.doi.org/10.1166/jbns.2014.1245

Journal articles | 2014

Ebrahimi D; Alinejad-Rokny H; Davenport MP, 2014, 'Insights into the motif preference of APOBEC3 enzymes', PLoS ONE, 9, http://dx.doi.org/10.1371/journal.pone.0087679

Journal articles | 2014

Gooneratne SL; Alinejad-Rokny H; Ebrahimi D; Bohn PS; Wiseman RW; O'Connor DH; Davenport MP; Kent SJ, 2014, 'Linking pig-tailed macaque major histocompatibility complex class I haplotypes and cytotoxic T lymphocyte escape mutations in simian immunodeficiency virus infection', Journal of Virology, 88, pp. 14310 - 14325, http://dx.doi.org/10.1128/JVI.02428-14

Journal articles | 2014

Jamnejad I; Heidarzadegan A; Parvin H; Alinejad-Rokny H, 2014, 'Localizing program bugs based on program invariant', International Journal of Computing and Digital Systems, 3, pp. 141 - 150, http://dx.doi.org/10.12785/IJCDS/030208

Journal articles | 2014

Jamnejad MI; Parvin H; Alinejad-Rokny H; Heidarzadegan A, 2014, 'Proposing a New Method Based on Linear Discriminant Analysis to Build a Robust Classifier', Journal of Bioinformatics and Intelligent Control, 3, pp. 186 - 193, http://dx.doi.org/10.1166/jbic.2014.1086

Journal articles | 2014

Minaei-Bidgoli B; Parvin H; Alinejad-Rokny H; Alizadeh H; Punch WF, 2014, 'Effects of resampling method and adaptation on clustering ensemble efficacy', Artificial Intelligence Review, 41, pp. 27 - 48, http://dx.doi.org/10.1007/s10462-011-9295-x

Journal articles | 2014

Mokhtari SM; Alinejad-Rokny H; Jalalifar H, 2014, 'Selection of the best well control system by using fuzzy multiple-attribute decision-making methods', Journal of Applied Statistics, 41, pp. 1105 - 1121, http://dx.doi.org/10.1080/02664763.2013.862218

Journal articles | 2013

Ahmadinia M; Meybodi M; Esnaashari M; Alinejad-Rokny H, 2013, 'Energy-efficient and multi-stage clustering algorithm in wireless sensor networks using cellular learning automata', IETE Journal of Research, 59, pp. 774 - 782, http://dx.doi.org/10.4103/0377-2063.126958

Journal articles | 2013

Alinejad-Rokny H; Farzaneh MK; Orimi AG; Pedram MM; Kiasari HA, 2013, 'Proposing a new structure for web mining and personalizing web pages', Journal of Emerging Technologies in Web Intelligence, 5, pp. 287 - 295, http://dx.doi.org/10.4304/jetwi.5.3.287-295

Journal articles | 2013

Javanmard R; JeddiSaravi K; Alinejad-Rokny H, 2013, 'Proposed a new method for rules extraction using artificial neural network and artificial immune system in cancer diagnosis', Journal of Bionanoscience, 7, pp. 665 - 672, http://dx.doi.org/10.1166/jbns.2013.1160

Journal articles | 2013

Parvin H; Alinejad-Rokny H; Minaei-Bidgoli B; Parvin S, 2013, 'A new classifier ensemble methodology based on subspace learning', Journal of Experimental and Theoretical Artificial Intelligence, 25, pp. 227 - 250, http://dx.doi.org/10.1080/0952813X.2012.715683

Journal articles | 2013

Parvin H; Alinejad-Rokny H; Parvin S, 2013, 'A Classifier Ensemble of Binary Classifier Ensembles', International Journal of Learning Management Systems, 1, pp. 37 - 47, http://dx.doi.org/10.12785/ijlms/010204

Journal articles | 2013

Parvin H; Alinejad-Rokny H; Parvin S, 2013, 'A New Clustering Ensemble Framework', International Journal of Learning Management Systems, 1, pp. 19 - 25, http://dx.doi.org/10.12785/ijlms/010103

Journal articles | 2013

Parvin H; Minaei-Bidgoli B; Alinejad-Rokny H; Punch WF, 2013, 'Data weighing mechanisms for clustering ensembles', Computers and Electrical Engineering, 39, pp. 1433 - 1450, http://dx.doi.org/10.1016/j.compeleceng.2013.02.004

Journal articles | 2013

Parvin H; Minaei-Bidgoli B; Alinejad-Rokny H, 2013, 'A new imbalanced learning and dictions tree method for breast cancer diagnosis', Journal of Bionanoscience, 7, pp. 673 - 678, http://dx.doi.org/10.1166/jbns.2013.1162

Journal articles | 2012

Alizadeh H; Alinejad-Rokny H; Parvin H; Sohrabi B, 2012, 'A new inference engine: Surface Matching Degree', Applied Mathematical Modelling, http://dx.doi.org/10.1016/j.apm.2012.02.027

Journal articles | 2012

Esmaeili L; Minaei-Bidgoli B; Alinejad-Rokny H; Nasiri M, 2012, 'Hybrid recommender system for joining virtual communities', Research Journal of Applied Sciences, Engineering and Technology, 4, pp. 500 - 509

Journal articles | 2012

Parvin H; Alinejad-Rokny H; Seyedaghaee NR; Parvin S, 2012, 'A Heuristic Scalable Classifier Ensemble of Binary Classifier Ensembles', Journal of Bioinformatics and Intelligent Control, 1, pp. 163 - 170, http://dx.doi.org/10.1166/jbic.2013.1016

Journal articles | 2012

Sadeghi M; Alinejad-Rokny H, 2012, 'On covering of products of T-generalized state machines', Mathematical Sciences Letters, 1, pp. 43 - 52, http://dx.doi.org/10.12785/msl/010106

Journal articles | 2012

Shirvani MH; Alinejad-Rokny H, 2012, 'Performance Assessment of Feasible Scheduling Multiprocessor Tasks Solutions by using DEA FDH method', Information Sciences Letters, 1, pp. 61 - 66, http://dx.doi.org/10.12785/isl/010106

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

Journal articles | 2011

Parvin H; Alinejad-Rokny H; Asadi M, 2011, 'An ensemble based approach for feature selection', Australian Journal of Basic and Applied Sciences, 5, pp. 1153 - 1163
Conference Papers | 2023

Asgharnezhad H; Shamsi A; Bakhshayeshi I; Alizadehsani R; Chamaani S; Alinejad-Rokny H, 2023, 'Improving PPG Signal Classification with Machine Learning: The Power of a Second Opinion', in International Conference on Digital Signal Processing, DSP, Institute of Electrical and Electronics Engineers (IEEE), pp. 1 - 5, presented at 2023 24th International Conference on Digital Signal Processing (DSP), http://dx.doi.org/10.1109/DSP58604.2023.10167869

Preprints | 2023

Karami M; Alizadehsani R; Khadijeh ; Jahanian ; Argha A; Dehzangi I; Alinejad-Rokny H, 2023, Revolutionizing Genomics with Reinforcement Learning Techniques, , http://dx.doi.org/10.48550/arxiv.2302.13268

Conference Papers | 2023

Montazerin M; Rahimian E; Naderkhani F; Atashzar SF; Alinejad-Rokny H; Mohammadi A, 2023, 'HYDRA-HGR: A Hybrid Transformer-Based Architecture for Fusion of Macroscopic and Microscopic Neural Drive Information', in ICASSP 2023 - 2023 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, presented at ICASSP 2023 - 2023 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 04 June 2023 - 10 June 2023, http://dx.doi.org/10.1109/icassp49357.2023.10096192

Preprints | 2022

Band S; Ardabili S; Yarahmadi A; Pahlevanzadeh B; Kausar Kiani A; Beheshti A; Alinejad Rokny H; Dehzangi I; Chang A; Mosavi A; Moslehpour M, 2022, A Survey on Machine Learning and Internet of Medical Things-Based Approaches for Handling COVID-19: Meta-Analysis, , http://dx.doi.org/10.20944/preprints202202.0083.v2

Preprints | 2022

Band S; Ardabili S; Yarahmadi A; Pahlevanzadeh B; Kausar Kiani A; Beheshti A; Alinejad Rokny H; Dehzangi I; Mosavi A, 2022, Machine Learning and Internet of Medical Things for Handling COVID-19: Meta-Analysis, , http://dx.doi.org/10.20944/preprints202202.0083.v1

Conference Papers | 2022

Danaei S; Bostani A; Moravvej SV; Mohammadi F; Alizadehsani R; Shoeibi A; Alinejad-Rokny H; Nahavandi S, 2022, 'Myocarditis Diagnosis: A Method using Mutual Learning-Based ABC and Reinforcement Learning', in IEEE Joint 22nd International Symposium on Computational Intelligence and Informatics and 8th International Conference on Recent Achievements in Mechatronics, Automation, Computer Science and Robotics, CINTI-MACRo 2022 - Proceedings, IEEE, pp. 265 - 270, presented at 2022 IEEE 22nd International Symposium on Computational Intelligence and Informatics and 8th IEEE International Conference on Recent Achievements in Mechatronics, Automation, Computer Science and Robotics (CINTI-MACRo), 21 November 2022 - 22 November 2022, http://dx.doi.org/10.1109/CINTI-MACRo57952.2022.10029403

Preprints | 2022

Kazemi A; Hamidieh K; Dashti H; Ghareyazi A; 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, , http://dx.doi.org/10.21203/rs.3.rs-1567157/v1

Conference Papers | 2022

Khozeimeh F; Roshanzamir M; Shoeibi A; Darbandy MT; Alizadehsani R; Alinejad-Rokny H; Ahmadian D; Khosravi A; Nahavandi S, 2022, 'Importance of Wearable Health Monitoring Systems Using IoMT; Requirements, Advantages, Disadvantages and Challenges', in IEEE Joint 22nd International Symposium on Computational Intelligence and Informatics and 8th International Conference on Recent Achievements in Mechatronics, Automation, Computer Science and Robotics, CINTI-MACRo 2022 - Proceedings, IEEE, pp. 245 - 250, presented at 2022 IEEE 22nd International Symposium on Computational Intelligence and Informatics and 8th IEEE International Conference on Recent Achievements in Mechatronics, Automation, Computer Science and Robotics (CINTI-MACRo), 21 November 2022 - 22 November 2022, http://dx.doi.org/10.1109/CINTI-MACRo57952.2022.10029528

Preprints | 2022

Montazerin M; Rahimian E; Naderkhani F; Atashzar SF; Alinejad-Rokny H; Mohammadi A, 2022, HYDRA-HGR: A Hybrid Transformer-based Architecture for Fusion of Macroscopic and Microscopic Neural Drive Information, , http://dx.doi.org/10.48550/arxiv.2211.02619

Preprints | 2022

Nasab RZ; Ghamsari MRE; Argha A; Macphillamy C; Beheshti A; Alizadehsani R; Lovell NH; Lotfollahi M; Alinejad-Rokny H, 2022, Deep Learning in Spatially Resolved Transcriptomics: A Comprehensive Technical View, , http://dx.doi.org/10.48550/arxiv.2210.04453

Preprints | 2022

Rahaie Z; Rabiee HR; Alinejad-Rokny H, 2022, DeepGenePrior: A deep learning model to prioritize genes affected by copy number variants, , http://dx.doi.org/10.1101/2022.08.22.504862

Preprints | 2022

Rahman MM; Kamal Nasir M; A-Alam N; Islam Khan S; Band S; Dehzangi I; Beheshti A; Alinejad Rokny H, 2022, Hybrid Feature Fusion and Machine Learning Approaches for Melanoma Skin Cancer Detection, , http://dx.doi.org/10.20944/preprints202201.0258.v1

Conference Papers | 2022

Shahabikargar M; Beheshti A; Khatami A; Nguyen R; Zhang X; Alinejad-Rokny H, 2022, 'Domain Knowledge Enhanced Text Mining for Identifying Mental Disorder Patterns', in Proceedings - 2022 IEEE 9th International Conference on Data Science and Advanced Analytics, DSAA 2022, IEEE, presented at 2022 IEEE 9th International Conference on Data Science and Advanced Analytics (DSAA), 13 October 2022 - 16 October 2022, http://dx.doi.org/10.1109/DSAA54385.2022.10032346

Preprints | 2022

Sharifonnasabi F; Jhanjhi N; John J; Obeidy P; Shamshirband S; Alinejad Rokny H; Baz M, 2022, Hybrid HCNN-KNN Model Enhances Age Estimation Accuracy in Orthopantomography, , http://dx.doi.org/10.20944/preprints202108.0413.v3

Preprints | 2022

Sharifonnasabi F; Jhanjhi N; John J; Obeidy P; Shamshirband S; Alinejad Rokny H, 2022, Hybrid HCNN-KNN Transfer Learning Model Enhances Age Estimation Accuracy in Orthopantomography, , http://dx.doi.org/10.20944/preprints202108.0413.v2

Preprints | 2021

Debnath T; Reza MM; Rahman A; Band S; Alinejad Rokny H, 2021, Four-Layer ConvNet to Facial Emotion Recognition with Minimal Epochs and the Significance of Data Diversity, , http://dx.doi.org/10.20944/preprints202105.0424.v1

Preprints | 2021

Hamidi H; Alinejad-Rokny H; Coorens T; Sanghvi R; Lindsay SJ; Rahbari R; Ebrahimi D, 2021, Signatures of Mutational Processes in Human DNA Evolution, , http://dx.doi.org/10.1101/2021.01.09.426041

Preprints | 2021

Islam Khan MS; Rahman A; Karim MR; Bithi NI; Band SS; Dehzangi A; Alinejad-Rokny H, 2021, CovidMulti-Net: A Parallel-Dilated Multi Scale Feature Fusion Architecture for the Identification of COVID-19 Cases from Chest X-ray Images, , http://dx.doi.org/10.1101/2021.05.19.21257430

Preprints | 2021

Kazemi A; Ghareyazi A; Hamidieh K; Dashti H; Tahaei M; Rabiee H; Alinejad Rokny H; Dehzangi A, 2021, Pan-Cancer Integrative Analysis of Whole-Genome <em>De novo</em> Somatic Point Mutations Reveals 17 Cancer Types, , http://dx.doi.org/10.20944/preprints202111.0266.v1

Preprints | 2020

Alinejad-Rokny H; Modegh RG; Rabiee HR; Rezaie N; Tam KT; Forrest ARR, 2020, MaxHiC: robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments, , http://dx.doi.org/10.1101/2020.04.23.056226

Preprints | 2020

Asgari Y; Heng JIT; Lovell N; Forrest ARR; Alinejad-Rokny H, 2020, Evidence for enhancer noncoding RNAs (enhancer-ncRNAs) with gene regulatory functions relevant to neurodevelopmental disorders, , http://dx.doi.org/10.1101/2020.05.16.087395

Preprints | 2020

Dashti H; Dehzangi A; Bayati M; Breen J; Lovell N; Ebrahimi D; Rabiee HR; Alinejad-Rokny H, 2020, Integrative analysis of mutated genes and mutational processes reveals seven colorectal cancer subtypes, , http://dx.doi.org/10.1101/2020.05.18.101022

Preprints | 2020

Liu N; Low WY; Alinejad-Rokny H; Pederson S; Sadlon T; Barry S; Breen J, 2020, Seeing the forest through the trees: Identifying functional interactions from Hi-C, , http://dx.doi.org/10.1101/2020.11.29.402420

Preprints | 2020

Sharifrazi D; Alizadehsani R; Hassannataj Joloudari J; Shamshirband S; Hussain S; Alizadeh Sani Z; Hasanzadeh F; Shoaibi A; Dehzangi A; Alinejad-Rokny H, 2020, CNN-KCL: Automatic Myocarditis Diagnosis using Convolutional Neural Network Combined with K-means Clustering, , http://dx.doi.org/10.20944/preprints202007.0650.v1

Preprints | 2019

Alinejad-Rokny H; Heng JIT; Forrest ARR, 2019, Brain-enriched coding and long non-coding RNA genes are overrepresented in recurrent autism spectrum disorder CNVs, , http://dx.doi.org/10.1101/539817

Preprints | 2018

Bayati M; Rabiee HR; Mehrbod M; Vafaee F; Ebrahimi D; Forrest A; Alinejad-Rokny H, 2018, CANCERSIGN: a user-friendly and robust tool for identification and classification of mutational signatures and patterns in cancer genomes, , http://dx.doi.org/10.1101/424960

Conference Abstracts | 2015

Gooneratne S; Alinejad-Rokny H; Mohammadi D; Bohn P; Wiseman R; O'Connor D; Davenport M; Kent S, 2015, 'LINKING PIGTAIL MACAQUE MHC I HAPLOTYPES AND CTL ESCAPE MUTATIONS IN SIV INFECTION', in JOURNAL OF MEDICAL PRIMATOLOGY, WILEY-BLACKWELL, Vol. 44, pp. 335 - 335, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000361966000094&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Preprints |

Alinejad-Rokny H; Zarepour E; Khadijeh Jahanian H; Beheshti A; Dehzangi A, A Multivariate Data Analytics Approach Revealed No Footprint of APOBEC3 Proteins in Hepatitis B Virus Genome, , http://dx.doi.org/10.2139/ssrn.3514647

Dr Rokny received extensive research funding support relative to career stage (total of $2.75M as sole/leading Chief Investigator (CI) and $10.6M as co-CI), demonstrating an impressive upward research career trajectory. These include:

· CCFA LITWIN IBD Pioneers Program Grant (leading CIB), ($400K, Feb 2023)
· Australian National Health and Medical Research Council (NHMRC) IDEAS grant (CIB), ($600K, Dec 2022)
· CSIRO Next-Generation Graduate Program (leading CI), ($1.7M including $700K for my Lab, 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:

Ali Vahedi, Internship, 2022-2023, (administered by BML).
Afsin Soeiby, Internship, 2022-2023, (administered by Macquarie University).
Mahdi Hosseini, Internship, 2022-2023, (administered by BML).

PhD & MPhil Students:

Roxana Zahedi Nasab, PhD student, 2023-2027, (administered by UNSW).
Ivan Bakhshayeshi, PhD student, 2023-2027, (administered by UNSW).
Mona (Sedigheh) Abedini, 2023-2027, (administered by UNSW).
Md. Mushahidul Islam Shamim, Master by Research (MPhil), 2023-2026, (administered by UNSW).
Yuheng Liang, Master by Research (MPhil), 2023-2026, (administered by UNSW).
Reza Ghamsari, PhD student, 2022-2026, (administered by UNSW).
Ali Afrasiabi, PhD student, 2020-2024, (administered by UNSW).
Tohid Ghasemnejad, PhD student, 2023-2027, (administered by Monash University, co-supervision with Drs Fabrizzio Horta and Faezeh Marzbanrad).
Afshar Shamsi, PhD student, 2023-2027, (administered by Concordia University, co-supervision with Assoc Prof Arash Mohammadi).
Mahdieh Labani, PhD student, 2021-2025, (administered by Macquarie University, co-supervision with Prof Amin Beheshti).
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 Students:

Gabrielle Younes, Master student, 2023-2024, (administered by UNSW).
Sally Chen, Master student, 2023-2024, (administered by UNSW).
Michael De Francesco, Master student, 2023-2024, (administered by UNSW).
Aryan Bhatla, Master student, 2023-2024, (administered by UNSW).
Ivy Lan Liu, Master student, 2022-2023, (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)

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Dr Hamid Alinejad-Rokny

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