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Dr Hamid Alinejad-Rokny

Dr Hamid Alinejad-Rokny

Senior Lecturer
  • Bachelor: Software Engineering, 2004-2009
  • Master: Artificial Intelligence, 2009-2012.
  • Industry: Data Scientist, 2012-2014.
  • Ph.D: BioMedical Machine Learning, UNSW Sydney, 2014-2018.
  • Post-Doctoral: Harry Perkins Institute of Medical Research, UWA Australia, 2017-2019.
  • Director of UNSW BioMedical Machine Learning Laboratory (BML), 2019-present.
     
Engineering
Sch: Biomedical Engineering

Dr Rokny (PhD, UNSW Sydney, 2018) is the Director of UNSW BioMedical Machine Learning Laboratory (BML), where he leads a team of 25 researchers developing trustworthy artificial intelligence for biology and medicine, spanning medical artificial intelligence, large language models, and bio-machine learning. He supervises a dynamic team of researchers and have successfully led over 60 projects, resulting in 100 high-quality publications in top-tier journals such as Nature Communications, Nature Neuroscience, The Lancet, Cell reports, PLOS Computational Biology, Blood, and A* conferences such as ICLR, NeurIPS, AAAI, and ACL, often as the first or senior author. The impact of my work is evident through a high citation rate [5,250+, h-index 40 Google Scholar] and a high FWCI score (AI= 7.6; Neuroscience= 4.7; Health Informatics= 4.75), which is outstanding considering the career stage. The impact of his leadership is also evidenced by securing significant grants, including a DECRA fellowship, UNSW Scientia fellowship, an NHMRC Ideas grant, and a CSIRO NGGP grant, as well as multiple awards such as Google fellowship, Tour de Cure and MSA fellowships for students under his leadership. Additionally, he actively enhance medical AI and machine learning literacy by collaborating with clinicians and health professionals across Sydney hospitals, including the Gene2Care and PreGen consortia, and NSW Health clinics, demonstrating the practical applications of AI to improve health outcomes. As the Health Theme Leader of the UNSW Data Science Hub, He sets health data science priorities, integrating research with practical health solutions. His organisational skills have led me to orchestrate over 100 seminars on AI in medicine, promoting knowledge sharing and collaboration. Furthermore, He contributes to research direction through roles on panels like NSF-CSIRO influencing funding towards innovative AI and genomics project and HUGO meeting. His commitment to training the next generation is showcased through his leadership in CSIRO’s NGGP, collaborating with industry partners like 23Strands to enhance the capabilities of emerging AI researchers in medical technologies. Notably, He is currently leading several national-level initiatives focused on developing foundation models in AI for Biology and Medicine (ClinAI, OmniST, ARGOS, and Molecular AI). These initiatives represent a significant step forward at the national level and aim to position Australia at the forefront of these emerging GPT-like technologies for individualised medicine.
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 | 2024
    Beheshti A; Alinejad-Rokny H; Suero Molina E; Di Ieva A, 2024, 'Understanding Big Data in Neurosurgery', in Advances in Experimental Medicine and Biology, pp. 157 - 175, http://dx.doi.org/10.1007/978-3-031-64892-2_10
    Book Chapters | 2024
    Roshanzamir M; Alizadehsani R; Moravvej SV; Joloudari JH; Alinejad-Rokny H; Gorriz JM, 2024, 'Enhancing Interpretability in Machine Learning: A Focus on Genetic Network Programming, Its Variants, and Applications', in , pp. 98 - 107, http://dx.doi.org/10.1007/978-3-031-61140-7_10
    Book Chapters | 2024
    Shoeibi A; Jafari M; Sadeghi D; Alizadehsani R; Alinejad-Rokny H; Beheshti A; Gorriz JM, 2024, 'Early Diagnosis of Schizophrenia in EEG Signals Using One Dimensional Transformer Model', in , pp. 139 - 149, http://dx.doi.org/10.1007/978-3-031-61140-7_14
    Book Chapters | 2022
    Shabani N; Beheshti A; Farhood H; Bower M; Garrett M; Rokny HA, 2022, 'iCreate: Mining Creative Thinking Patterns from Contextualized Educational Data', in , pp. 352 - 356, http://dx.doi.org/10.1007/978-3-031-11647-6_68
    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, pp. 384 - 389, http://dx.doi.org/10.1007/978-3-030-78270-2_68
    Book Chapters | 2019
    Vafaee F; Dashti H; Alinejad-Rokny H, 2019, 'Transcriptomic Data Normalization', in Encyclopedia of Bioinformatics and Computational Biology Abc of Bioinformatics, pp. 364 - 371, http://dx.doi.org/10.1016/B978-0-12-809633-8.20209-4
  • Journal articles | 2026
    Argha A; Alinejad-Rokny H; Hajati F; Magdy J; Li J; Lim ZZ; Yu J; Yang M; Butcher K; Ooi SY; Lovell NH, 2026, 'ECG-Adapt: A Novel Framework for Robust Electrocardiogram Classification Across Diverse Populations and Recording Conditions', IEEE Transactions on Biomedical Engineering, pp. 1 - 12, http://dx.doi.org/10.1109/TBME.2026.3653051
    Journal articles | 2026
    Flor LS; Spencer CN; Cagney J; Gil GF; Aalruz H; Abd ElHafeez S; Abdelwahab SI; Abdoun M; Abebe M; Abebe Y; Abedi A; Abeldaño Zuñiga RA; Abie A; Abiodun O; Aboagye RG; Abreu LG; Abu Farha RK; Abubakar B; Abuhammad S; Achore M; Adams LC; Adebiyi BO; Adedokun KA; Adegbile OE; Adegoke NA; Adeleke OT; Adeniyi MA; Adesina MA; Adewuyi HO; Adnani QES; Adzigbli LA; Afolabi AA; Afolabi RF; Afzal MS; Afzal S; Agyemang-Duah W; Ahinkorah BO; Ahmad A; Ahmad D; Ahmad MM; Ahmed A; Ahmed A; Ahmed H; Ahmed MS; Ahmed O; Akin-Odanye EO; Akosile W; Akpabio IU; Alam Z; Al-Amer RM; Alansari AN; Alanzi TM; Aleidi SM; Alemu MB; Alhalaiqa FN; Al-Iede M; Alinejad Rokny H; Almagharbeh WT; Al-Mamun M; Almazan JU; Alnaeem MM; Alrimawi I; Alshahrani NZ; Alyahya MSI; Amin TT; Amini S; Amiri S; Amu H; Amzat J; Anderson DB; Anuoluwa BS; Anvari S; Anyasodor AE; Aravkin AY; Arias de la Torre J; Armocida B; Arrieta A; Arumuganainar D; Ashraf T; Aslam B; Asri Y; Athari SS; Atorkey P; Atre SR; Atsbaha AH; Atta JA; Atteraya MS; Azzam AY; Sheeba B; Baghlaf KK; Baig AA; Balcha WF; Balmori-de-la-Miyar J; Bandyopadhyay S; Barik M; Barker-Collo SL; Bashar MA; Bashir S; Bashiri A; Bastan MM, 2026, 'Disease burden attributable to intimate partner violence against females and sexual violence against children in 204 countries and territories, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023', Lancet, 407, pp. 31 - 52, http://dx.doi.org/10.1016/S0140-6736(25)02503-6
    Journal articles | 2026
    Guo ZZ; Wu R; Li W; Yang K; Ying X; Alinejad-Rokny H; Ye Y, 2026, 'Mapping biology in space: from spatial transcriptomics platforms to analytical tools and databases', Science Bulletin, http://dx.doi.org/10.1016/j.scib.2026.01.034
    Journal articles | 2026
    Intarak N; Ghasemnejad T; Fakhruddin KS; Kamal A; Prommanee S; Jahanian KH; Lovell NH; Alinejad-Rokny H; Porntaveetus T, 2026, 'LRP6 β-Propeller Destabilization: Novel Variant, Phenotype and Diagnostic Implications in Tooth Agenesis', International Dental Journal, 76, http://dx.doi.org/10.1016/j.identj.2025.109367
    Journal articles | 2026
    Li W; Zhang D; Peng E; Shen S; Alinejad-Rokny H; Liu Y; Zheng J; Jiang C; Ye Y, 2026, 'HiST: Histological Images Reconstruct Tumor Spatial Transcriptomics via MultiScale Fusion Deep Learning', Advanced Science, http://dx.doi.org/10.1002/advs.202514351
    Journal articles | 2025
    Ahmadi-Dastgerdi N; Hosseini-Nejad H; Alinejad-Rokny H, 2025, 'A hardware-efficient on-implant spike compression processor based on VQ-DAE for brain-implantable microsystems', Medical and Biological Engineering and Computing, 63, pp. 2047 - 2056, http://dx.doi.org/10.1007/s11517-025-03317-x
    Journal articles | 2025
    Argha A; Alinejad-Rokny H; Baumgartner M; Schreier G; Celler BG; Redmond SJ; Butcher K; Ooi SY; Lovell NH, 2025, 'A Novel Deep Ensemble Method for Selective Classification of Electrocardiograms', IEEE Transactions on Biomedical Engineering, 72, pp. 833 - 842, http://dx.doi.org/10.1109/TBME.2024.3476088
    Journal articles | 2025
    Collaborators GBDLRIAAR; Sirota SB; Bender RG; Dominguez R-MV; Movo A; Swetschinski LR; Araki DT; Han C; Wool EE; He J; Carter A; Jabbar AAJ; Aalipour MA; Aalruz H; Dolatabadi ZA; Abbastabar H; ElHafeez SA; Abdalla AN; Abdalla MA; Abdullah ; Abdallah EM; Razeq NMIA; Abdelkader A; Abd-Elsalam S; Abdelwahab SI; Abdoun M; Abdous A; Abdrabou MM; Aziz JMA; Abdulah DM; Abdullahi A; Abdul-Rahman T; Abdykerimova K; Getahun HA; Abedi A; Abejew AA; Abidi SH; Abil OZ; Abiodun O; Aboagye RG; Abolhassani H; Abonie US; Aborode AT; Abourashed NM; Abtahi D; Abu Z; Abu Farha RK; Abuadas FHA; Abubakar AK; Abubakar U; Abu-Elala N; Abu-Gharbieh E; Abuhelwa AY; Abukhadijah HJ; Abushanab D; Acharya AB; Acharya KP; Acharya S; Achore M; Adal O; Adams LC; Addo IY; Adebisi TA; Adedia D; Adedokun KA; Adegoke NA; Adekanmbi V; Adeleke OT; Adesina MA; Adesola RO; Adetunji CO; Adetunji JB; Adewumi IP; Adhana MT; Adhikary RK; Adiba A; Adiga U; Adnan M; Adnani QES; Affinito G; Afzal S; Agafari GB; Aggarwal N; Agordoh PD; Agrawal A; Agyemang-Duah W; Ahadi M; Ahinkorah BO; Ahmad AA; Ahmad A; Ahmad D; Ahmad F; Ahmad I; Ahmad K; Ahmad MM; Ahmad R; Ahmad S; Ahmad T; Ahmadi A; Ahmadi M; Ahmed A; Ahmed A; Ahmed GS; Ahmed H; Ahmed MS; Ahmed MS; Ahmed M; Ahmed N; Ahmed S; Ahmed SA; El-Imam IA; Akeju O; Akhigbe RE; Akhtar MN; Akinosoglou K; Akram H; Al Awaidy S; Al Hasan SM; Al Zoubi MAM; Al-Abbadi MA; Alajlani MM; Al-Aly Z; Alam K; Alam MK; Alanezi FM; Alanzi TM; Alao JO; Alarifi A; Al-Ashwal FY; Alavi SMA; Albashtawy M; AlBataineh MT; Al-Dewik N; Aldhaleei WA; Aleidi SM; Alemnew F; Alfalki AM; Algammal AM; Alhumaidi A; Alhumaydhi FA; Ali HM; Ali K; Ali L; Ali M; Ali MD; Ali MU; Ali R; Ali S; Ali SS; Al-Iede M; Alif M; Alimohammadi M; Rokny HA; Alipour M; Al-Jabi SW; Aljofan M; Aljunid SM; Allemailem KS; Al-Marwani S; Almazan JU; Al-Mekhlafi HM; Almobayed A; Alnaeem MM; Alnakshabandie WMY; Alniss HY; Alomari MA; Alqahtani JS; Al-Qudimat AR; Al-Raddadi RM; Alrimawi I; Alrousan SM; Alsabri MA; Alshahrani NZ; Alshetaiwi H; Alsowaida YS; Altaany Z; Altaf A; Al-Tammemi AB; Al-Tawfiq JA; Althobiani MA; Altirkawi KA; Alvis-Guzman N; Alvis-Zakzuk NJ; Alwafi H; Al-Wardat M; Al-Worafi YM; Aly H; Alyahya MSI; Alzoubi KH; Al-Zubairi AS; Al-Zubayer A; Al-Zyoud WA; Amafah EJ; Mohammadi MA; Amhare AF; Amini S; Aminu K; Aminu N; Aminzare M; Amiri S; Amirtharaj AD; Amugsi DA; Amusa GA; Anagnostakis F; Anbesu EW; Ancuceanu R; Anderlini D; Anil A; Anjana P; Anjorin A-AA; Annadurai K; Anuoluwa BS; Anuoluwa IA; Anvari S; Anwer R; Anyasodor AE; Apostol GLC; Appati W; Arabloo J; Arockiaraj J; Arooj M; Artamonov AA; Arumuganainar D; Arystan N; Asdaq SMB; Asebot MT; Asefa SM; Asemahagn MAA; Ashraf SA; Ashraf T; Ashrafi M; Aslam MS; Asri Y; Assefa DZ; Assembekov B; Atac O; Athari SS; Atre SR; Atta JA; Atwan ZA; Augello M; Aujayeb A; Aurangzeb K; Awan SJ; Awoke AA; Awosile BB; Ayele HM; Ayipo YO; Ayyoubzadeh SM; Azad AKM; Azadi D; Azami H; Aziz SA; Azizan A; Babatope AE; Babu GR; Bacha IT; Badar M; Badran AA; Baghizadeh F; Baghlaf KK; Bahreini R; Baig AA; Bakhshali MA; Balakrishnan S; Hasankhani MB; Barac A; Barik M; Barqawi HJ; Bashir MI; Bashir S; Bashiri A; Basri R; Bassat Q; Bastan M-M; Batiha A-M; Batra K; Batra R; Bayat M; Bayleyegn ZW; Bazaid AS; Bedi N; Beeraka NM; Behzadi P; Belay BM; Belayneh AG; Belayneh M; Bele S; Belgaumi UI; Bell ML; Bello MB; Bello OO; Bello UM; Tune SNBK; Bera OPP; Berihun AA; Bermudez ANC; Bettencourt PJG; Bhargava A; Bhaskar S; Bhattacharjee P; Bhattacharjee S; Bhatti JS; Bhatti MS; Binsaleh NK; Birru EM; Biswas B; Biswas MS; Bitar AN; Bitew M; Bizzozero-Peroni B; Bodhare T; Bogale EK; Boloor A; Bolourinejad P; Borran M; Bosoka SA; Carvajal AB; Bouaoud S; Boxe C; Briko NI; Bui LP; Busch F; Bustanji Y; Calina D; Capodici A; Carugno A; Carvalho F; Castañeda-Orjuela CA; Cegolon L; Cenderadewi M; Cernigliaro A; Cevik M; Chadwick J; Chakraborty C; Chakraborty S; Chattu VK; Chau LD; Chaudhary AA; Chaudhuri S; Chaurasia A; Chen H; Chen H; Chen H; Chen R; Chen X; Chew NWS; Ching PR; Chisti MJ; Cho WCS; Chong B; Chopra D; Chopra S; Chowdhury EK; Christopher DJ; Chu D-T; Chuang T-W; Chukwu IS; Chung E; Chung S; Chutiyami M; Conti S; Corlateanu A; Cosma C; Cruz-Martins N; Dabbagh A; Dadras O; Dagnew EM; Dai X; Dang AK; Daniel RA; Danpanichkul P; Danso SE; Darcho SD; Darouei B; Darwesh AM; Das JK; Das S; Davletov D; de Souza WM; Deekonda S; Del Riccio M; Delgado-Enciso I; Demeke D; Derese TN; Dervišević E; Dervišević M; Desalegn G; Devanbu VGC; Devegowda D; Dewan SMR; Dhali A; Dhane AS; Dhimal ML; Dhimal M; Dhungel B; Di Bella S; Di Paolo A; Di Pumpo M; Ding G; Thi H; Ngoc M; Phuong TH; Dokova KG; Dolatkhah N; Dorostkar F; Doshi OP; Dourado PMM; Dowou RK; Duraisamy S; Durojaiye OC; Dutta S; Ebohon O; Ebrahimi MH; Ed-Dra A; Edeh C; Edinur HA; Efendi F; Eghbali F; Eini E; Ekholuenetale M; Eko SM; Arab RAE; Sayed IE; Zaki MES; Eldaboush A; El-Deyarbi M; Elhadi M; Elhadi YAM; Elhoumed M; Elmeligy OAA; Elmonem MA; Elnaem MH; Elshaer M; Eltahawy AS; Eshetie S; Eshrati B; Eshun G; Eslami M; Fadavian H; Fagbamigbe AF; Fakhradiyev IR; Fally M; Fan Q; Farahmand M; Farasani A; Fareed M; Farhana A; Farooq SMY; Fasina FO; Fasina MM; Fatehizadeh A; Fatima Z; Fekadu G; Ferrara P; Ferreira N; Fetensa G; Feyisa BR; Firew BS; Fischer F; Fonzo M; Rodrigues CF; Fowotade OD; Gaal PA; Gad AG; Gaihre S; Gajdács M; Ganesh B; Gangachannaiah S; Gao X; Garcia FJB; Garcia-Azorin D; Garlasco J; Gatzioufas Z; Gautam RK; Gebremeskel TG; Geremew GW; Gessner BD; Getahun GK; Getaneh G; Gete KY; Ghadiri K; Ghaffari K; Ghamkhar A; Gharaibeh L; Ghasemi M; Ghatee MA; Ghazy RM; Ghimire S; Ghoba S; Gil AU; Gilani SA; Giri BR; Girombelli A; Göbölös L; Gohari K; Goleij P; Golmohammadi M; Gong W; Goshu YA; Guadie HA; Guan S-Y; Guarducci G; Gubari MIM; Gulma KA; Gunawardane DA; Gupta AK; Gupta G; Gupta L; Gupta S; Gupta S; Gupta VB; Gupta VK; Gutiérrez-Murillo RS; Guzman-Esquivel J; Habteyohannes AD; Hadei M; Hadi NR; Hadian Z; Hafiz A; Nam NH; Haile A; Hailu KT; Haller S; Hamad IM; Hamed M; Hammoud A; Yekdeş DH; Hanif A; Hanifi N; Hanna F; Haque A; Harapan H; Harboe ZB; Harsini S; Has EMM; Hasan I; Hasan K; Hasani H; Haselbeck AH; Zadeh AH; Hashempur MH; Hasnain A; Hasnain S; Hassan A; Hassan IN; Hassan I; Hassan I; Hassan MA; Hassan N; Hassani S; Hathagoda LW; Hayat K; He Q; Heibati B; Heidari M; Helmy YA; Hendy A; Herteliu C; Hezam K; Hiraike Y; Holla R; Holler JGG; Hossain A; Hossain S; Hosseinzadeh M; Hostiuc M; Hostiuc S; Huang J; Huang Y; Hushmandi K; Hussain J; Hussein AM; Hussein D; Hussein MA; Hussein NR; Husseiny MI; Ibitoye SE; Ibragimova L; Ibrahim AA; Ibrahim KS; Ibrayeva A; Ikiroma A; Ikram A; Ikuta KS; Ilesanmi OS; Ilic IM; Ilic MD; Ilyas MH; Ilyasu S; Imam MT; Immurana M; Irham LM; Isa MA; Ishaqui AA; Islam R; Islam S; Islam MS; Ismael SS; Ismail F; Ismail NE; Ismoldayev Y; Iwagami M; Iwu-Jaja CJ; Iyasu AN; Jaafari J; Jadidi A; Jahrami H; Jain A; Jakovljevic M; Jalloh M; Jamal A; Jamal QMS; Jamaluddin J; James J; Jamora RDG; Jarrahi E; Mamaghani AJ; Javidnia J; Jawaid T; Jayaram S; Jayasinghe RD; Jayasinghe YA; Jeon JJ; Jeong S; Jiang M; Jin W; Johnston I; Jomehzadeh N; Jonas JB; Jose J; Joseph AP; Joseph N; Joshi K; Joshua CE; Vaishali K; Kaambwa B; Kadashetti V; Kadir DHH; Kadir MF; Kaibullayeva J; Kalavani K; Kalra S; Kamal MA; Kamorudeen RT; Kamyshnyi O; Kang J; Kanmodi KK; S SK; Kant S; Kar D; Kar D; Karajizadeh M; Karakasis P; Karami J; Karch A; Behnagh AK; Karkhah S; Karobari MI; Karpiński TMM; Kashoo FZ; Kashyap MK; Kassahun NBB; Kausar MA; Kazemi F; Kebede AZ; Kebede HK; Kebede YT; Keivanlou M-H; Kempen JH; Keshwani A; Khader YS; Khajuria H; Khalifa HO; Khalil AA; Khalili P; Khamesipour F; Khan A; Khan FUU; Khan IW; Khan IH; Khan M; Khan MI; Khan MU; Khan S; Khan YS; Khan Z; Khasbage SU; Khatatbeh H; Khatatbeh MM; Kheirallah KA; Khezeli M; Khoshvaght P; Khoshvaght S; Khosravi F; Khosravi S; Kim G; Kim HJ; Kim MS; Kimokoti RW; B SK; Kisa A; Kisa S; Kishore L; Klu D; Shivakumar KM; Kochhar S; Koh SWC; Kolahi A-A; Kompani F; Korma WE; Kormoker T; Korshunov VA; Korzh O; Kostev K; Koul PA; Kretchy J-P; Krishan K; Kuddus M; Kuehni CE; Kuitunen I; Kulimbet M; Kulshreshtha S; Kumah E; Kumar D; Kumar J; Kumar K; Kumar N; Kumar R; Kumar T; Kumar V; Kumaran S; Kundu S; Kunjavara J; Kunutsor SK; Kurmi OP; Kurniasari MD; Kushawaha PK; Kusuma D; Kuttybayev A; Kuwornu JP; Kytö V; La Vecchia A; Lahariya C; Lai H; Lajunen T; Lakanova B; Lal DK; Lanfranchi F; Lau CL; Lawanson T; Le DH; Le TTT; Ledda C; Lee SV; Lee SW; Lee W-C; Leivaditis V; Lemma DA; Lewis MSS; Li C; Li X; Lin J; Liu G; Liu H; Liu J; Liu X; Liu Y; Liu Z; Llanaj E; Lodhi MS; Loftus MJ; Lu K; Lubinda J; Lucchetti G; Luo P; Lutambi AM; Lv H; Lytras MD; Lytvyak E; Amin HIM; Sheng-Kai K; Feei Z; Mabrok M; Madadi F; Madadizadeh F; Maffia P; Maghool F; Magwe EA; Mahamed SA; Mahmood NH; Mahmoudi S; Malik AA; Malik S; Malik T; Malinga LA; Malkamu B; Manilal A; Mansoor F; Manzoor S; Maqbool T; Marateb HR; Margetis K; Marks-Hultström M; Martinez-Guerra BA; Martins-Melo FR; Martorell M; Marzo RR; Marzouk S; Matei CN; Mathangasinghe Y; Mathur N; Matozinhos FP; Mattiello R; Maude RJ; Mavrovounis G; McPhail SM; Mediratta RP; Mehari M; Mehboob R; Mehrotra R; Mekonnen LB; Meles HN; Melese A; Memary E; Memish ZA; Mendoza W; Menezes GA; Mengistie EA; Menon TP; Meo A; Mercogliano M; Meretoja TJ; Merza MA; Mestrovic T; Mettananda CDK; Mettananda S; Metwally MMM; Mewoabi SDD; Miazgowski B; Michalek IM; Minervini G; Ming W-K; Mini GK; Mirrakhimov EM; Mirshahvalad SA; Mishra A; Mishra S; Mishra V; Mohamed MG; Mohamed NS; Ahmed KAHM; Mohammad T; Mohammadi A; Mohammadi MK; Mohammadi MR; Mohammadi S; Mohammadi S; Mohammed O; Mohammed S; Mohammed Y; Mohan S; Mohanta YK; Mohseni M; Mohsenzadeh A; Mokdad AH; Mollaei A; Monasta L; Moni MA; Montalti M; Moraga P; Morais DF; Morawska L; Morovvati M; Morsy MM; Mosquera FEC; Mosser JF; Motappa R; Mousavi SA; Khaneghah AM; Kiasary FM; Kiasary SMSM; Mousnad MAA; Mowafy HL; Yousefi KM; Mubarik S; Muhammad JS; Mukherjee S; Mukhopadhyay A; Mulatu S; Mulita F; Muniyandi M; Munjal K; Murillo-Zamora E; Musa S; Musaigwa F; Muthu S; Muthusamy R; Muvunyi CM; Muzaffar M; Nafei A; Nagarajan AJ; Nagarajan K; Naguib G; Naik GR; Naik H; Nainu F; Nair S; Najmuldeen HHR; Nangia V; Naqid IA; Nargus S; Nashwan AJ; Nasiri H; Nassar M; Natto ZS; Naureen Z; Nayak BP; Nazari J; Nchanji GT; Nega AT; Negash AA; Negoi I; Negoi RI; Nematollahi MH; Nepal S; Netsere HB; Ngabonziza JCS; Nguyen CT; Nguyen CT; Nguyen HT; Nguyen HLT; Nguyen L; Nguyen NP; Nguyen TT; Nguyen T; Nguyen VT; Niazi RK; Nikoobar A; Niyonsenga JMV; Nkrumah-Boateng A; Nnaji CA; Nnyanzi LA; Nomura S; Noreen S; Nriagu VC; Nri-Ezedi CA; Nshimiyimana JC; Nugen F; Nunemo MH; Nwakama CN; Nzoputam CI; Nzoputam OJ; Oancea B; Oddi FM; Oduro MS; Ofakunrin AOD; Ogundijo OA; Ojedoyin OO; Okati-Aliabad H; Okeke SR; Okekunle AP; Okonji OC; Okunlola OA; Okwute PG; Olagunju AT; Olusanya BO; Onyedibe KI; Opitz M; Oradova AS; Ordak M; Orish VN; Orscelik A; Ortiz-Prado E; Osborne A; Osei E; Othman EH; Otorkpa OJ; Ouyahia A; Owusu IA; Oyebanji OA; Oyebola K; Oyelade T; Oyeniran KA; Oyeyemi OT; Ozsahin I; Mahesh PA; Padubidri JR; Paija DM; Palicz T; Pana A; Panda SK; Pandey A; Pandi-Perumal SRR; Panos GD; Pantazopoulos I; Paolino G; Papa MV; Papadimopoulos I; Paranjkhoo P; Pardhan S; Parida A; Park C; Pashaei A; Pasovic M; Passera R; Patel J; Patel M; Patel NN; Patel S; Patil S; Patoulias D; Pawar S; Pawar S; Toroudi HP; Pekarcikova J; Peprah ; Pereira G; Perera N; Chacon GP; Perna S; Petcu I-R; Peter OJ; Pham HQ; Pham TT; Philip AK; Piracha ZZ; Pirera E; Plotnikov E; Poddighe D; Polibin RV; Poluru R; Postma MJ; Pourasghary S; Pourbabaki R; Poursadeqiyan M; Pourtaheri N; Prada SI; Pradhan PMS; Prashant A; Prates EJS; Purkait T; Puvvula J; Qanash H; Qasim NH; Qi X; Qi Z; Qiu J-Y; Rabiee N; Rabiu AGG; Rachmat B; Radhakrishnan RA; Radhakrishnan V; Raghav YS; Raghuveer P; Rahamon SK; Rahim HM-A; Rahimi-Movaghar V; Rahman FM; Rahman M; Rahman O; Rahman MA; Rahmati M; Raina SK; Raj JP; Raja A; Rajaa S; Rajendran G; Rajendran J; Rajindrajith S; Rajizadeh MA; Rakhimov KD; Ramadan MM; Ramasamy C; Ramasamy SK; Ramazanu S; Ramzan M; Ranabhat CL; Noei FR; Rao AG; Rao M; Rao SJ; Rasouli-Saravani A; Rath RS; Rathi I; Rathish D; Rauniyar SK; Rawaf DL; Rawaf S; Ray A; Reddy MMRK; Redwan E; Reta MA; Reyes LF; Rezaei N; Rezaeian M; Rizvi MR; Roever L; Rohilla R; Rony MKK; Ross AGP; Rout HS; Roy A; Roy P; Roy P; Roy S; Roy S; Chowdhury SR; Rubeshkumar P; de Andrade Ruela G; Chandan SN; Saad AMA; Sabbatucci M; Saber-Ayad MM; Rafiei SKS; Saddique MN; Sadee BA; Sadeghi E; Sadeghi E; Sadek B; Sadr H; Saeed M; Saeed S; Saeed U; Saeedi M; Sagharichi M; Saghazadeh A; Sah AK; Saha I; Rafsanjani AS; Sharif-Askari FS; Sharif-Askari NS; Sahebkar A; Sahu M; Sahu SK; Saki M; Sakshaug JW; Salami B; Saleem Z; Saleh MA; Salehi ; Sallam M; Kafil HS; Samodra YL; Samy AM; Sanjari E; Sanjeev RK; Sankar S; Santric-Milicevic MM; Jose BPS; Saravanan A; Sarma H; Sarmadi M; Sarode GS; Sarode SC; Sassano M; Sathian B; Satpathy M; Far MS; Saya GK; Sedighi M; Seifmanesh H; Sekaran S; Selvaraj B; Selvaraj S; Selvaraj V; Semenova Y; Senthilkumaran S; Serban D; Sethi Y; Alshohadaei SMS; Seyedi D; Seylani A; Shaalan YKFS; Shahbaz K; Shahid S; Shahid SA; Shahini E; Shahwan MJ; Shaikh MA; Shaikh N; Shakeri A; Shakerimoghaddam A; Shakoor S; Sham S; Shamim MA; Shams AH; Shams-Beyranvand M; Shamsi A; Shan D; Shannawaz M; Sharifan A; Rad JS; Jazi FS; Sharma A; Sharma B; Sharma K; Sharma M; Sharma M; Sharma RK; Sharma V; Shastry RP; Shastry S; Shawahna R; Sheidaei A; Shenoy RR; Shenoy SM; Sherchan SP; Shetty M; Shetty PH; Shetty PK; Shi W; Shiferaw D; Shimul MH; Shin JI; Shittu A; Shiue I; Shivamallu C; Shivarov V; Shoaib A; Shokri A; Shool S; Shorofi SA; Shrestha S; Shuaibu SA; Sibuyi NRS; Siddig EE; Silva LMLR; Simkhada PP; Simpson CR; Singer MK; Singh A; Singh A; Singh H; Singh H; Singh JA; Singh K; Singh P; Singh PS; Singh P; Singh S; Singh S; Singh S; Singh S; Singh V; Sinha MK; Sinto R; Skryabin VY; Skryabina AA; SobhZahedi M; Sohel ; Sokhan A; Soliman AM; Soliman MMS; Soliman NS; Soliman SSM; Soltaninejad H; Song W; Sood P; Soraneh S; Sorensen RJD; Soriano JB; Sorrentino M; Spagnolo AM; Spahic E; Sreeramareddy CT; Sridharan K; Srinivasan M; Sriram S; Stanikzai MH; Steiropoulos P; Stergachis A; Stubbs B; Su C-Y; Subasi O; Subramanian B; Subramaniyan V; Sujon H; Sulaiman SK; Sullman MJM; Sundaram T; Swain CK; Szarpak L; Y SST; Tabatabaei SM; Tabatabaeizadeh S-A; Tabatabai S; Tabche C; Taha ZM-A; Soodejani MT; Taiba J; Talaat IM; Tampa M; Tanashat M; Tanveer M; Tareke AA; Tariku MK; Tariq S; Tat NY; Tat VY; Taveira N; Tedla MG; Tefera YM; Tekulu TG; Temedie-Asogwa T; Temsah M-H; Tesfu AA; Tessema B; Thakur CK; Thangaraju P; Thapar R; Tharwat I; Tharwat S; Thienemann F; Thind MK; Thiruvengadam M; Ticoalu JHV; Tiwari K; Tiwari VK; Tleshev M; Tomo S; Tovani-Palone MR; Tran AT; Tran NH; Tran QTH; Tran TH; Duc NTM; Le Trinh VT; Tristan CD; Tromans SJ; Truppa C; Tse G; Tseriotis V-S; Tuglo LS; Ullah A; Ullah H; Ullah R; Ullah S; Umar L; Umar M; Umar UM; Upadhyay E; Usman JS; Ozsahin DU; Uzunçıbuk H; Uzzaman N; Vaithinathan AG; Valdez PR; Vaman RS; Van den Eynde J; Vasankari TJ; Vasudevan SS; Venkidasamy B; Verma AK; Verma P; Veroux M; Villa S; Villafañe JH; Vitiello A; Vu L; Waheed Y; Walia M; Wander A; Wang L; Wang X; Wang Y; Wang Y; Wassie YA; Weerasekara I; Wei X; Wickramasinghe DP; Wickramasinghe ND; Wieckiewicz M; Wilandika A; Wireko AA; Wiysonge CSS; Wojewodzic MW; Wonde TE; Wondmeneh YC; Wongnaah FG; Wu F; Wu JF; Wu Z; Wubie YM; Xia Z; Xiao L; Xiao N; Xie W; Xu H; Xu S; Yadav MK; Yahoo S; Yahya G; Yakubu Y; Yang H; Yang K; Yang X; Yao H; Yao L; Yassin MA; YektaKooshali MH; Yesuf SA; Yewodiaw TK; Yezli S; Yi S; Yismaw MB; Yismaw YE; Yon DK; Yonemoto N; Yu Y; Yuan H; Yuan Q; Yunusa U; Yuwanati M; Zafar M; Zafar MS; Zaghampour M; Zakham F; Zamagni G; Zaman BA; Zamora N; Zar HJ; Zastrozhin M; Zeariya MGM; Zeb J; Zemariam AB; Zensen S; Zeru EM; Zhang H; Zhang J; Zhang P; Zhang X; Zhang Z; Zhanuzakov M; Zhao C; Zhao L; Zhu B; Zhu Z; Zhumagaliuly A; Zielińska M; Zumla A; Zyoud AH; Zyoud SH; Zyoud SH; Hay SI; Naghavi M; Murray CJL; Kyu HH, 2025, 'Global burden of lower respiratory infections and aetiologies, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023', The Lancet Infectious Diseases, pp. S1473-3099(25)00689-9, http://dx.doi.org/10.1016/s1473-3099(25)00689-9
    Journal articles | 2025
    Du Y; Zhao Y; Li J; Wang J; You S; Zhang Y; Zhang L; Yang J; Alinejad-Rokny H; Cheng S; Shao C; Zou D; Ye Y, 2025, 'PLXDC1+ Tumor-Associated Pancreatic Stellate Cells Promote Desmoplastic and Immunosuppressive Niche in Pancreatic Ductal Adenocarcinoma', Advanced Science, 12, http://dx.doi.org/10.1002/advs.202415756
    Journal articles | 2025
    Farbehi N; Alinejad-Rokny H; Chtanova T; Rnjak-Kovacina J, 2025, 'Spatial and single-cell transcriptomics unravel the complex interplay between the body and medical implants', Cell Biomaterials, 1, http://dx.doi.org/10.1016/j.celbio.2025.100099
    Journal articles | 2025
    Green NFO; Sutton GJ; Pérez-Burillo J; Wang J; Bagot S; Danon HG; Walsh K; Gokool A; Miles SA; Yang G; Herring CA; Liang Y; Pfundstein G; Sytnyk V; Alinejad-Rokny H; Lister R; Rosenbluh J; Gagnon-Bartsch JA; Voineagu I, 2025, 'CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer’s disease', Nature Neuroscience, http://dx.doi.org/10.1038/s41593-025-02154-3
    Journal articles | 2025
    Hansun S; Argha A; Alinejad-Rokny H; Alizadehsani R; Gorriz JM; Liaw ST; Celler BG; Marks GB, 2025, 'A New Ensemble Transfer Learning Approach with Rejection Mechanism for Tuberculosis Disease Detection', IEEE Transactions on Radiation and Plasma Medical Sciences, 9, pp. 433 - 446, http://dx.doi.org/10.1109/TRPMS.2024.3474708
    Journal articles | 2025
    Hansun S; Argha A; Bakhshayeshi I; Wicaksana A; Alinejad-Rokny H; Fox GJ; Liaw ST; Celler BG; Marks GB, 2025, 'Diagnostic Performance of Artificial Intelligence–Based Methods for Tuberculosis Detection: Systematic Review', Journal of Medical Internet Research, 27, http://dx.doi.org/10.2196/69068
    Journal articles | 2025
    Hosseinzadeh M; Tanveer J; Rahmani AM; Alanazi A; Zaidi MM; Aurangzeb K; Alinejad-Rokny H; Porntaveetus T; Lee SW, 2025, 'A comprehensive survey of golden jacal optimization and its applications', Computer Science Review, 56, http://dx.doi.org/10.1016/j.cosrev.2025.100733
    Journal articles | 2025
    Lee SW; Tanveer J; Rahmani AM; Alinejad-Rokny H; Khoshvaght P; Zare G; Malekpour Alamdari P; Hosseinzadeh M, 2025, 'SFGCN: Synergetic fusion-based graph convolutional networks approach for link prediction in social networks', Information Fusion, 114, http://dx.doi.org/10.1016/j.inffus.2024.102684
    Journal articles | 2025
    Naghavi M; Kyu HH; Bhoomadevi A; Aalipour MA; Aalruz H; Ababneh HS; Abafita BJ; Abaraogu UO; Abbafati C; Abbasi M; Abbaspour F; Abbastabar H; Abd Al Magied AHA; Elhafeez SA; Abdalla AN; Abdalla MA; Abdallah EM; Abdeeq BA; Abdel Razeq NMI; Abdelgalil AA; Abdel-Hameed R; Abdelmasseh M; Abdelnabi M; Abdel-Rahman WM; Abdous A; Abdrabou MM; Aziz JMA; Abdulah DM; Abdullahi A; Abdul-Rahman T; Getahun HA; Abedi A; Abedi A; Abedi P; Abejew AA; Zuñiga RAA; Abid SUA; Abidi SH; Abie A; Abiodun OO; Aboagye RG; Abohashem S; Abolhassani H; Abonie US; Abourashed NM; Abouzid M; Abramov D; Abreu LG; Abtahi D; Farha RKA; Abuadas FHA; Abubakar AK; Abu-Elala N; Abu-Gharbieh E; Abuhammad S; Abuhelwa AY; Abukhadijah HJ; Abu-Rmeileh NME; Aburuz S; Abushanab D; Accrombessi MMK; Acharya AB; Acharya A; Adal O; Adams LC; Adamu AA; Addo IY; Adeagbo OA; Adebisi TA; Adedeji IA; Adedokun KA; Adegbile OE; Adegoke NA; Adeleke OT; Adema BG; Aden B; Adesina IA; Adesina MA; Adetunji JB; Adewuyi HO; Adeyeoluwa TE; Adhana MT; Adhikary RK; Adiga U; Parvar TA; Adnan M; Adnani QES; Adoma PO; Adzigbli LA; Adzrago D; Affinito G; Afifi AM; Afoakwah C; Afolabi AA; Afolabi RF; Afrăsânie VA; Afzal S; Agafari GB; Agampodi SB; Agampodi TC; Mitra S; Schutte A; Lin J; Sachdev P; Dai-Keller Z; Sundstorm J; Boufous S; Degenhardt L; Alinejad-Rokny H; Onie S; Maulik PK; Okeke S; Cullen P; Haghdoost F; Pesudovs K; Peden A; Keshri V; Akbarialiabad H; Roehr S; Perez Chacon G; Hunter J; Lennon M; Xu L; Mitchell P; Bhaskar S; Peprah P; Jha V; Saddik B; Ye P, 2025, 'Global burden of 292 causes of death in 204 countries and territories and 660 subnational locations, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023', Lancet, 406, pp. 1811 - 1872, http://dx.doi.org/10.1016/S0140-6736(25)01917-8
    Journal articles | 2025
    Pushpakumara B; Becirovic R; van Dorst J; Coffey M; Halim J; Beheshti B; Argha A; Alinejad-Rokny H; Ooi C, 2025, '16 Artificial intelligence integrating gut microbiome multi-omics to predict clinical outcomes in children with cystic fibrosis', Journal of Cystic Fibrosis, 24, pp. S9 - S9, http://dx.doi.org/10.1016/s1569-1993(25)01636-4
    Journal articles | 2025
    Schumacher AE; Zheng P; Barber RM; Bhoomadevi A; Aalipour MA; Aalruz H; Ababneh HS; Abaraogu UO; Abbafati C; Abbas N; Abbasifard M; Abbaspour F; Abd Al Magied AHA; Elhafeez SA; Abdalla MA; Abdallah EM; Abdel Razeq NMI; Abdel-Hameed R; Abdel-Rahman WM; Abd-Elsalam S; Abdelwahab OA; Abdi P; Abdollahi A; Abdoun M; Abdous A; Abdulah DM; Abdulkader RS; Abdullahi A; Abdulraheem AS; Getahun HAA; Abedi P; Abedi A; Abejew AA; Zuñiga RAA; Abidi SH; Abie A; Abiodun O; Abiodun OO; Aboagye RG; Abohashem S; Abonie US; Abourashed NM; Abouzid M; Abramov D; Abreu LG; Abtahi D; Farha RKA; Abuadas FHA; Abubakar AK; Abubakar B; Abu-Gharbieh E; Abuhammad S; Abuhelwa AY; Abukhadijah HJ; Aburuz S; Abushanab D; Zaid AA; Acharya AB; Achore M; Acuna JM; Adair T; Adams LC; Adebayo OM; Adebisi TA; Adedia D; Adedokun KA; Adegbile OE; Adegoke NA; Adeleke OT; Adesina MA; Adesina IA; Adetokunboh OO; Adeyeoluwa TE; Adhana MT; Adhikari K; Adhikary RK; Adiga U; Parvar TA; Adnan M; Adnani QES; Adzigbli LA; Adzrago D; Affinito G; Afolabi AA; Afolabi RF; Afzal S; Agafari GB; Aggarwal N; Aghaalikhani M; Aghajanian S; Aghamir SMK; Agide FD; Agoi MD; Sobrinho CA; Agrawal A; Agyemang-Duah W; Ahinkorah BO; Ahmad R; Ahmad D; Ahmad F; Mitra S; Schutte A; Arnlov J; Lin J; Sachdev P; Sitas F; Feng X; Boufous S; Degenhardt L; Alinejad-Rokny H; Onie S; Biswas RK; Maulik PK; Okeke S; Haghdoost F; Peden A; Akbarialiabad H; Roehr S; Xu L; Vella A; Mitchell P; Bhaskar S; Peprah P; Saddik B; Ye P, 2025, 'Global age-sex-specific all-cause mortality and life expectancy estimates for 204 countries and territories and 660 subnational locations, 1950–2023: a demographic analysis for the Global Burden of Disease Study 2023', Lancet, 406, pp. 1731 - 1810, http://dx.doi.org/10.1016/S0140-6736(25)01330-3
    Journal articles | 2025
    Shamsi A; Becirovic R; Alinejad-Rokny H; Mohammadi A; Argha A, 2025, 'Gradient surgery: A necessity for robust test-time adaptation for detecting casting defects', Engineering Applications of Artificial Intelligence, 161, http://dx.doi.org/10.1016/j.engappai.2025.112039
    Journal articles | 2025
    Stark BA; DeCleene NK; Desai EC; Hsu JM; Johnson CO; Lara-Castor L; LeGrand KE; A PB; Aalipour MA; Aalruz H; Abafita BJ; Abaraogu UO; Abavisani M; Abbas N; Abbasi M; Abbasian M; Abbastabar H; Abd Al Magied AHA; ElHafeez SA; Abdelalim PA; Abdelfattah OM; Abdel-Hameed PR; Abdelnabi M; Wael M Abdel-Rahman P; Abdi P; Abdisa WM; Abdissa D; Abdous A; Abdullah M; Abdullahi A; Abdykerimova K; Abebe M; Abedi A; Abedi A; Abejew AA; Abhilash ES; Abiodun OO; Abiodun PO; Kasem RA; Aboagye RG; Abohashem S; Abolhassani H; Abonie US; Aborode AT; Abourashed NM; Abramov D; Abreu LG; Abtahi D; Abu Farha RK; Kende Abubakar AK; Abubakar IJ; Abu-Elala N; Abu-Gharbieh E; Abukhadijah HJ; Aburuz S; Abushanab D; Acharya AB; Acharya A; Acharya S; Achore M; Adal O; Adams LC; Adamu LH; Adão R; Addo IY; Adebayo OM; Adebisi TA; Adedia D; Adedokun KA; Adegbile OE; Adegboye OA; Adegoke NA; Adekanmbi V; Adeleke OT; Oluwaseun Adetunji C; Adeyomoye OI; Adha R; Adhikari K; Adhikary RK; Adikusuma W; Parvar TA; Adnan M; Sakilah Adnani QE; Adoma PO; Adzigbli LA; Adzrago D; Afifi AM; Afolabi HA; Afrashteh F; Afrooghe A; Afzal MS; Afzal S; Agampodi SB; Agarwal DM; Agarwal G; Agarwal P; Ageru TA; Aggarwal N; Aghajanian S; Sobrinho CA; Alinejad-Rokny H; Biswas RK; Okeke S; Haghdoost F; Burley C; Wang N; Schutte A; Sachdev P; Lin J; Si Y; Sundstorm J; Peprah P; Bhaskar S; Neal B; Feng X; Xu L; Si L; Saddik B; Ye P, 2025, 'Global, Regional, and National Burden of Cardiovascular Diseases and Risk Factors in 204 Countries and Territories, 1990-2023', Journal of the American College of Cardiology, 86, pp. 2167 - 2243, http://dx.doi.org/10.1016/j.jacc.2025.08.015
    Journal articles | 2025
    Wang F; Lin J; Alinejad-Rokny H; Ma W; Meng L; Huang L; Yu J; Chen N; Wang Y; Yao Z; Xie W; Wong KC; Li X, 2025, 'Unveiling Multi-Scale Architectural Features in Single-Cell Hi-C Data Using scCAFE', Advanced Science, 12, http://dx.doi.org/10.1002/advs.202416432
    Journal articles | 2025
    Wangsanut T; Khamto N; Alinejad-Rokny H; Pongpom M, 2025, 'Regulatory functions of AcuK and AcuM transcription factors in fungal metabolic adaptation, stress response, and virulence', Frontiers in Cellular and Infection Microbiology, 15, http://dx.doi.org/10.3389/fcimb.2025.1717070
    Journal articles | 2025
    Yu Z; Chen R; Gui P; Wang W; Razzak I; Alinejad-Rokny H; Zeng X; Shang X; Zhang L; Yang X; Yu H; Huang W; Lu H; van Wijngaarden P; He M; Zhu Z; Ge Z, 2025, 'A cross population study of retinal aging biomarkers with longitudinal pre-training and label distribution learning', Npj Digital Medicine, 8, http://dx.doi.org/10.1038/s41746-025-01751-7
    Journal articles | 2025
    Zobeiri A; Rezaee A; Hajati F; Argha A; Alinejad-Rokny H, 2025, 'Post-Cardiac arrest outcome prediction using machine learning: A systematic review and meta-analysis', International Journal of Medical Informatics, 193, http://dx.doi.org/10.1016/j.ijmedinf.2024.105659
    Journal articles | 2024
    Abedini SS; Akhavantabasi S; Liang Y; Heng JIT; Alizadehsani R; Dehzangi I; Bauer DC; Alinejad-Rokny H, 2024, 'A critical review of the impact of candidate copy number variants on autism spectrum disorder', Mutation Research Reviews in Mutation Research, 794, http://dx.doi.org/10.1016/j.mrrev.2024.108509
    Journal articles | 2024
    Ahmadi-Dastgerdi N; Hosseini-Nejad H; Alinejad-Rokny H, 2024, 'A Hardware-Efficient Novelty-Aware Spike Sorting Approach for Brain-Implantable Microsystems', International Journal of Neural Systems, 34, http://dx.doi.org/10.1142/S0129065724500679
    Journal articles | 2024
    Hosseinzadeh M; Haider A; Malik MH; Adeli M; Mzoughi O; Gemeay E; Mohammadi M; Alinejad-Rokny H; Khoshvaght P; Porntaveetus T; Rahmani AM, 2024, 'Enhanced heart sound classification using Mel frequency cepstral coefficients and comparative analysis of single vs. ensemble classifier strategies', Plos One, 19, http://dx.doi.org/10.1371/journal.pone.0316645
    Journal articles | 2024
    Islam S; Mugdha SBS; Dipta SR; Arafat ME; Shatabda S; Alinejad-Rokny H; Dehzangi I, 2024, 'MethEvo: an accurate evolutionary information-based methylation site predictor', Neural Computing and Applications, 36, pp. 201 - 212, http://dx.doi.org/10.1007/s00521-022-07738-9
    Journal articles | 2024
    Jafari M; Sadeghi D; Shoeibi A; Alinejad-Rokny H; Beheshti A; García DL; Chen Z; Acharya UR; Gorriz JM, 2024, 'Empowering precision medicine: AI-driven schizophrenia diagnosis via EEG signals: A comprehensive review from 2002–2023', Applied Intelligence, 54, pp. 35 - 79, http://dx.doi.org/10.1007/s10489-023-05155-6
    Journal articles | 2024
    MacPhillamy C; Chen T; Hiendleder S; Williams JL; Alinejad-Rokny H; Low WY, 2024, 'DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era', Gigascience, 13, http://dx.doi.org/10.1093/gigascience/giae061
    Journal articles | 2024
    Rahaie Z; Rabiee HR; Alinejad-Rokny H, 2024, 'CNVDeep: deep association of copy number variants with neurocognitive disorders', BMC Bioinformatics, 25, http://dx.doi.org/10.1186/s12859-024-05874-8
    Journal articles | 2024
    Razzak I; Naz S; Alinejad-Rokny H; Nguyen TN; Khalifa F, 2024, '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, 21, pp. 573 - 581, http://dx.doi.org/10.1109/TCBB.2022.3219032
    Journal articles | 2024
    Sadeghi A; Hajati F; Rezaee A; Sadeghi M; Argha A; Alinejad-Rokny H, 2024, '3DECG-Net: ECG fusion network for multi-label cardiac arrhythmia detection', Computers in Biology and Medicine, 182, http://dx.doi.org/10.1016/j.compbiomed.2024.109126
    Journal articles | 2024
    Taylor R; Taylor J; Denisenko E; Jones M; Clayton J; Laing N; Forrest A; Alinejad-Rokny H; Ravenscroft G, 2024, 'Mapping human skeletal muscle enhancers to increase rates of genetic diagnosis', NEUROMUSCULAR DISORDERS, 43, http://dx.doi.org/10.1016/j.nmd.2024.07.096
    Journal articles | 2024
    Truong P; Shen S; Joshi S; Islam MI; Zhong L; Raftery MJ; Afrasiabi A; Alinejad-Rokny H; Nguyen M; Zou X; Bhuyan GS; Sarowar CH; Ghodousi ES; Stonehouse O; Mohamed S; Toscan CE; Connerty P; Kakadia PM; Bohlander SK; Michie KA; Larsson J; Lock RB; Walkley CR; Thoms JAI; Jolly CJ; Pimanda JE, 2024, 'TOPORS E3 ligase mediates resistance to hypomethylating agent cytotoxicity in acute myeloid leukemia cells', Nature Communications, 15, pp. 7360, http://dx.doi.org/10.1038/s41467-024-51646-6
    Journal articles | 2024
    Xue J; Alinejad-Rokny H; Liang K, 2024, 'Navigating micro- and nano-motors/swimmers with machine learning: Challenges and future directions', Chemphysmater, 3, pp. 273 - 283, http://dx.doi.org/10.1016/j.chphma.2024.06.001
    Journal articles | 2024
    Zahedi R; Ghamsari R; Argha A; Macphillamy C; Beheshti A; Alizadehsani R; Lovell NH; Lotfollahi M; Alinejad-Rokny H, 2024, 'Deep learning in spatially resolved transcriptfomics: A comprehensive technical view', Briefings in Bioinformatics, 25, http://dx.doi.org/10.1093/bib/bbae082
    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, http://dx.doi.org/10.3390/s23031466
    Journal articles | 2023
    Argha A; Li J; Magdy J; Alinejad-Rokny H; Celler BG; Butcher K; Ooi SY; Lovell NH, 2023, 'Assessing the Generalizability of a Deep Learning-based Automated Atrial Fibrillation Algorithm', Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS, http://dx.doi.org/10.1109/EMBC40787.2023.10341108
    Journal articles | 2023
    Azim SM; Sabab NHN; Noshadi I; Alinejad-Rokny H; Sharma A; Shatabda S; Dehzangi I, 2023, 'Accurately predicting anticancer peptide using an ensemble of heterogeneously trained classifiers', Informatics in Medicine Unlocked, 42, http://dx.doi.org/10.1016/j.imu.2023.101348
    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, http://dx.doi.org/10.3390/cancers15143566
    Journal articles | 2023
    Hansun S; Argha A; Alinejad-Rokny H; Liaw ST; Celler BG; Marks GB, 2023, 'Revisiting Transfer Learning Method for Tuberculosis Diagnosis', Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBS, http://dx.doi.org/10.1109/EMBC40787.2023.10340441
    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, 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, 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, 35, pp. 22179 - 22188, 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
    Subramanian S; Thoms JAI; Huang Y; Cornejo-Páramo P; Koch FC; Jacquelin S; Shen S; Song E; Joshi S; Brownlee C; Woll PS; Chacon-Fajardo D; Beck D; Curtis DJ; Yehson K; Antonenas V; O'Brien T; Trickett A; Powell JA; Lewis ID; Pitson SM; Gandhi MK; Lane SW; Vafaee F; Wong ES; Göttgens B; Alinejad-Rokny H; Wong JWH; Pimanda JE, 2023, 'Genome-wide transcription factor–binding maps reveal cell-specific changes in the regulatory architecture of human HSPCs', Blood, 142, pp. 1448 - 1462, http://dx.doi.org/10.1182/blood.2023021120
    Journal articles | 2023
    Wang F; Alinejad-Rokny H; Lin J; Gao T; Chen X; Zheng Z; Meng L; Li X; Wong KC, 2023, 'A Lightweight Framework For Chromatin Loop Detection at the Single-Cell Level', Advanced Science, 10, http://dx.doi.org/10.1002/advs.202303502
    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, 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, 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, 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, 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, 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, http://dx.doi.org/10.1038/s41467-022-28758-y
    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, 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, http://dx.doi.org/10.1016/j.ygeno.2022.110454
    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, 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 | 2022
    Subramanian S; Thoms JA; Huang Y; Jacquelin S; Shen S; Song E; Joshi S; Brownlee C; Woll PS; Fajardo DC; Beck D; Curtis DJ; Yehson K; Antonenas V; O' Brien T; Trickett A; Powell J; Pitson SM; Gandhi MK; Cornejo P; Wong E; Lane SW; Gottgens B; Rokny HA; Wong JWH; Pimanda JE, 2022, 'Comparative Analysis of Genome-Scale Gene Regulatory Networks in Human Hematopoietic Stem and Myeloid Progenitor Fractions', BLOOD, 140, pp. 2846 - 2848, http://dx.doi.org/10.1182/blood-2022-165620
    Journal articles | 2022
    Truong P; Shen S; Joshi S; Afrasiabi A; Zhong L; Raftery MJ; Larsson J; Lock RB; Walkley CR; Rokny HA; Thoms JAI; Jolly CJ; Pimanda JE, 2022, 'Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and Sumoylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia', BLOOD, 140, http://dx.doi.org/10.1182/blood-2022-165713
    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 N; Breen J; Rabiee H; 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 and 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, pp. 225, 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, 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, pp. 106656, 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, pp. e00507, 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; Ebrahimi Mohammadi D, 2014, 'Insights into the motif preference of APOBEC3 enzymes', Plos One, 9, pp. e87679, 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
    Journal articles | 2011
    Parvin H; Helmi H; Minaei B; Rokny HA; Shirgahi H, 2011, 'Linkage learning based on differences in local optimums of building blocks with one optima', International Journal of Physical Sciences, 6, pp. 3419 - 3425
    Journal articles | 2011
    Rokny HA; Pedram MM; Shirgahi H, 2011, 'Discovered motifs with using parallel Mprefixspan method', Scientific Research and Essays, 6, pp. 4220 - 4226, http://dx.doi.org/10.5897/sre11.212
  • Preprints | 2026
    Chen D; Liu Z; Fang F; Leong CT; Ni S; Argha A; Alinejad-Rokny H; Yang M; Li C, 2026, Expanding before Inferring: Enhancing Factuality in Large Language Models through Premature Layers Interpolation, http://dx.doi.org/10.48550/arxiv.2506.02973
    Preprints | 2026
    Karami M; Khadijeh ; Jahanian ; Alizadehsani R; Dehzangi I; Gorriz JM; Zhang Y; Wang J; Hajati F; Yang M; Porntaveetus T; Alinejad-Rokny H, 2026, Revolutionizing Genomics with Reinforcement Learning Techniques, http://dx.doi.org/10.48550/arxiv.2302.13268
    Preprints | 2026
    Yang Z; Xu A; Li J; Yan L; Zhou J; Qin Z; Chang H; Chen Y; Chen L; Argha A; Alinejad-Rokny H; Tan M; Cai Y; Yang M, 2026, Structuring Reasoning for Complex Rules Beyond Flat Representations, http://dx.doi.org/10.48550/arxiv.2510.05134
    Preprints | 2025
    Asgharnezhad H; Shamsi A; Alizadehsani R; Mohammadi A; Alinejad-Rokny H, 2025, Enhancing Monte Carlo Dropout Performance for Uncertainty Quantification, http://dx.doi.org/10.48550/arxiv.2505.15671
    Conference Papers | 2025
    Chen D; Liu Z; Fang F; Leong CT; Ni S; Argha A; Alinejad-Rokny H; Yang M; Li C, 2025, 'Expanding before Inferring: Enhancing Factuality in Large Language Models through Premature Layers Interpolation', in Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing, Association for Computational Linguistics, pp. 12781 - 12796, presented at Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing, - , http://dx.doi.org/10.18653/v1/2025.emnlp-main.645
    Conference Papers | 2025
    Chen G; Fan L; Gong Z; Xie N; Li Z; Liu Z; Li C; Qu Q; Alinejad-Rokny H; Ni S; Yang M, 2025, 'AgentCourt: Simulating Court with Adversarial Evolvable Lawyer Agents', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 5850 - 5865, http://dx.doi.org/10.18653/v1/2025.findings-acl.304
    Conference Papers | 2025
    Chen L; Shan R; Wang H; Wang L; Liu Z; Luo R; Wang J; Alinejad-Rokny H; Yang M, 2025, 'CLaSp: In-Context Layer Skip for Self-Speculative Decoding', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 31608 - 31618, http://dx.doi.org/10.18653/v1/2025.acl-long.1525
    Conference Papers | 2025
    Doan BG; Shamsi A; Guo XY; Mohammadi A; Alinejad-Rokny H; Sejdinovic D; Teney D; Ranasinghe DC; Abbasnejad E, 2025, 'Bayesian Low-Rank Learning (Bella): A Practical Approach to Bayesian Neural Networks', in Proceedings of the Aaai Conference on Artificial Intelligence, pp. 16298 - 16307, http://dx.doi.org/10.1609/aaai.v39i15.33790
    Preprints | 2025
    Gao Y; Luo Y; Li W; Lan Y; Jiang H; Chen Y; Yi X; Li B; Alinejad-Rokny H; Wang T; Fu L; Yang M; Si T, 2025, Autonomous Liquid-handling Robotics Scripting for Accessible and Responsible Protein Engineering, http://dx.doi.org/10.1101/2025.09.30.679666
    Preprints | 2025
    Ghamsari R; de Graaf C; Thijssen R; You Y; Lovell N; Alinejad-Rokny H; Ritchie M, 2025, Comparative Analysis of Single-Nucleus and Single-Cell RNA Sequencing in Human Bone Marrow Mononuclear Cells: Methodological Insights and Trade-offs, http://dx.doi.org/10.1101/2025.09.08.675012
    Preprints | 2025
    Lee S; Ni S; Wei C; Li S; Fan L; Argha A; Alinejad-Rokny H; Xu R; Gong Y; Yang M, 2025, xJailbreak: Representation Space Guided Reinforcement Learning for Interpretable LLM Jailbreaking, http://dx.doi.org/10.48550/arxiv.2501.16727
    Conference Papers | 2025
    Lee S; Zhou J; Ao C; Li K; Du X; He S; Wu H; Liu T; Liu J; Alinejad-Rokny H; Yang M; Liang Y; Wen Z; Ni S, 2025, 'Quantification of Large Language Model Distillation', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 4985 - 5004, http://dx.doi.org/10.18653/v1/2025.acl-long.248
    Conference Papers | 2025
    Li J; Chen Y; Liu Z; Tan M; Zhang L; Li Y; Luo R; Chen L; Luo J; Argha A; Alinejad-Rokny H; Zhou W; Yang M, 2025, 'STORYTELLER: An Enhanced Plot-planning Framework for Coherent and Cohesive Story Generation', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 20818 - 20846, http://dx.doi.org/10.18653/v1/2025.findings-acl.1071
    Preprints | 2025
    Li J; Chen Y; Liu Z; Tan M; Zhang L; Li Y; Luo R; Chen L; Luo J; Argha A; Alinejad-Rokny H; Zhou W; Yang M, 2025, STORYTELLER: An Enhanced Plot-Planning Framework for Coherent and Cohesive Story Generation, http://dx.doi.org/10.48550/arxiv.2506.02347
    Conference Papers | 2025
    Luo R; Li Y; Chen L; He W; Lin TE; Liu Z; Zhang L; Song Z; Alinejad-Rokny H; Xia X; Liu T; Hui B; Yang M, 2025, 'DEEM: DIFFUSION MODELS SERVE AS THE EYES OF LARGE LANGUAGE MODELS FOR IMAGE PERCEPTION', in 13th International Conference on Learning Representations Iclr 2025, pp. 72484 - 72511
    Preprints | 2025
    Luo R; Lin T-E; Zhang H; Wu Y; Liu X; Yang M; Li Y; Chen L; Li J; Zhang L; Xia X; Alinejad-Rokny H; Huang F, 2025, OpenOmni: Advancing Open-Source Omnimodal Large Language Models with Progressive Multimodal Alignment and Real-Time Self-Aware Emotional Speech Synthesis, http://dx.doi.org/10.48550/arxiv.2501.04561
    Conference Papers | 2025
    Luo R; Zhang H; Chen L; Lin TE; Liu X; Wu Y; Yang M; Li Y; Wang M; Zeng P; Gao L; Shen HT; Li Y; Alinejad-Rokny H; Xia X; Huang F; Song J, 2025, 'MMEvol: Empowering Multimodal Large Language Models with Evol-Instruct', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 19655 - 19682, http://dx.doi.org/10.18653/v1/2025.findings-acl.1009
    Preprints | 2025
    Sadeghi A; Hajati F; Argha A; Lovell NH; Yang M; Alinejad-Rokny H, 2025, Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking, http://arxiv.org/abs/2505.01696v1
    Conference Papers | 2025
    Sun Y; Chen G; Alinejad-Rokny H; Bao J; Huang Y; Liang B; Wong KF; Yang M; Xu R, 2025, 'Learning First-Order Logic Rules for Argumentation Mining', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 14133 - 14148, http://dx.doi.org/10.18653/v1/2025.acl-long.691
    Preprints | 2025
    Wang Q; Chen G; Wang H; Liu H; Zhu M; Qin Z; Li L; Yue Y; Wang S; Li J; Wu Y; Liu Z; Chen L; Luo R; Fan L; Li J; Zhang L; Xu K; Li C; Alinejad-Rokny H; Ni S; Lin Y; Yang M, 2025, IPBench: Benchmarking the Knowledge of Large Language Models in Intellectual Property, http://dx.doi.org/10.48550/arxiv.2504.15524
    Preprints | 2025
    Zahedi R; Argha A; Farbehi N; Bakhshayeshi I; Ye Y; Lovell NH; Alinejad-Rokny H, 2025, SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics, http://dx.doi.org/10.48550/arxiv.2506.11491
    Preprints | 2025
    Zhao J; Xu L; Tan M; Zhang L; Argha A; Alinejad-Rokny H; Yang M, 2025, RxSafeBench: Identifying Medication Safety Issues of Large Language Models in Simulated Consultation, http://dx.doi.org/10.48550/arxiv.2511.04328
    Conference Papers | 2025
    Zhu J; Tan M; Yang M; Li R; Alinejad-Rokny H, 2025, 'CollectiveSFT: Scaling Large Language Models for Chinese Medical Benchmark with Collective Instructions in Healthcare', in Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, pp. 51 - 60, http://dx.doi.org/10.1007/978-981-96-1151-5_6
    Conference Papers | 2025
    Zhu K; Zang Q; Jia S; Wu S; Fang F; Li Y; Guo S; Zheng T; Li B; Wu H; Qu X; Yang J; Liu Z; Yue X; Liu J; Lin C; Yang M; Alinejad-Rokny H; Ni S; Huang W; Zhang G, 2025, 'LIME: Less Is More for MLLM Evaluation', in Proceedings of the Annual Meeting of the Association for Computational Linguistics, pp. 9086 - 9121, http://dx.doi.org/10.18653/v1/2025.findings-acl.474
    Preprints | 2024
    Chen D; Fang F; Ni S; Liang F; Hu X; Argha A; Alinejad-Rokny H; Yang M; Li C, 2024, Lower Layers Matter: Alleviating Hallucination via Multi-Layer Fusion Contrastive Decoding with Truthfulness Refocused, http://dx.doi.org/10.48550/arxiv.2408.08769
    Preprints | 2024
    Doan BG; Shamsi A; Guo X-Y; Mohammadi A; Alinejad-Rokny H; Sejdinovic D; Teney D; Ranasinghe DC; Abbasnejad E, 2024, Bayesian Low-Rank LeArning (Bella): A Practical Approach to Bayesian Neural Networks, http://dx.doi.org/10.48550/arxiv.2407.20891
    Conference Papers | 2024
    Hansun S; Argha A; Alinejad-Rokny H; Liaw ST; Celler BG; Marks GB, 2024, 'Pulmonary Tuberculosis Detection Using an Ensemble of ConvNeXts', in Ibiomed 2024 Proceedings of the 5th International Conference on Biomedical Engineering 2024, pp. 29 - 33, http://dx.doi.org/10.1109/iBioMed62485.2024.10875706
    Preprints | 2024
    Hansun S; Argha A; Bakhshayeshi I; Wicaksana A; Alinejad-Rokny H; Fox GJ; Liaw S-T; Celler BG; Marks GB, 2024, Diagnostic Performance of Artificial Intelligence–Based Methods for Tuberculosis Detection: Systematic Review (Preprint), http://dx.doi.org/10.2196/preprints.69068
    Preprints | 2024
    Javed S; Khan TM; Qayyum A; Alinejad-Rokny H; Sowmya A; Razzak I, 2024, Advancing Medical Image Segmentation with Mini-Net: A Lightweight Solution Tailored for Efficient Segmentation of Medical Images, http://dx.doi.org/10.48550/arxiv.2405.17520
    Preprints | 2024
    Liang Y; Abedini S; Farbehi N; Alinejad-Rokny H, 2024, How chromatin interactions shed light on interpreting non-coding genomic variants: opportunities and future direc-tions, http://dx.doi.org/10.48550/arxiv.2411.17956
    Preprints | 2024
    Luo J; Chen L; Luo R; Zhu L; Ao C; Li J; Chen Y; Cheng X; Yang W; Su J; Argha A; Alinejad-Rokny H; Li C; Ni S; Yang M, 2024, PersonaMath: Boosting Mathematical Reasoning via Persona-Driven Data Augmentation, http://dx.doi.org/10.48550/arxiv.2410.01504
    Preprints | 2024
    Ni S; Wu H; Yang D; Qu Q; Alinejad-Rokny H; Yang M, 2024, Small Language Model as Data Prospector for Large Language Model, http://dx.doi.org/10.48550/arxiv.2412.09990
    Preprints | 2024
    Rahmani AM; Haider A; Adeli M; Mzoughi O; Gemeay E; Mohammadi M; Alinejad-Rokny H; Khoshvaght P; Hosseinzadeh M, 2024, Enhanced Heart Sound Classification Using Mel Frequency Cepstral Coefficients and Comparative Analysis of Single vs. Ensemble Classifier Strategies, http://dx.doi.org/10.48550/arxiv.2406.00702
    Preprints | 2024
    Rahmani AM; Khoshvaght P; Alinejad-Rokny H; Sadeghi S; Asghari P; Arabi Z; Hosseinzadeh M, 2024, A Diagnostic Model for Acute Lymphoblastic Leukemia Using Metaheuristics and Deep Learning Methods, http://dx.doi.org/10.48550/arxiv.2406.18568
    Preprints | 2024
    Shamsi A; Becirovic R; Argha A; Abbasnejad E; Alinejad-Rokny H; Mohammadi A, 2024, ETAGE: Enhanced Test Time Adaptation with Integrated Entropy and Gradient Norms for Robust Model Performance, http://dx.doi.org/10.48550/arxiv.2409.09251
    Conference Abstracts | 2024
    Taylor R; Taylor J; Denisenko E; Jones M; Clayton J; Laing N; Forrest A; Alinejad-Rokny H; Ravenscroft G, 2024, 'Mapping human skeletal muscle enhancers to increase rates of genetic diagnosis', in NEUROMUSCULAR DISORDERS, PERGAMON-ELSEVIER SCIENCE LTD, CZECH REPUBLIC, Prague, Vol. 43, presented at 29th International Congress of the World-Muscle-Society (WMS), CZECH REPUBLIC, Prague, 08 October 2024 - 12 October 2024, http://dx.doi.org/10.1016/j.nmd.2024.07.096
    Preprints | 2024
    Truong P; Shen S; Joshi S; Islam MI; Zhong L; Raftery M; Afrasiabi A; Alinejad-Rokny H; Nguyen M; Zou X; Bhuyan GS; Sarowar C; Ghodousi E; Stonehouse O; Mohamed S; Toscan C; Connerty P; Kakadia P; Bohlander S; Michie K; Larsson J; Lock R; Walkley C; Thoms J; Jolly C; Pimanda J, 2024, Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML, http://dx.doi.org/10.1101/2024.04.17.589858
    Preprints | 2024
    Wang F; Lin J; Alinejad-Rokny H; Ma W; Meng L; Huang L; Yu J; Chen N; Wang Y; Yao Z; Xie W; Li X; Wong K-C, 2024, Unveiling multi-scale architectural features in single-cell Hi-C data using scCAFE, http://dx.doi.org/10.1101/2024.09.10.611762
    Preprints | 2024
    Wang Q; Ni S; Liu H; Lu S; Chen G; Feng X; Wei C; Qu Q; Alinejad-Rokny H; Lin Y; Yang M, 2024, AutoPatent: A Multi-Agent Framework for Automatic Patent Generation, http://dx.doi.org/10.48550/arxiv.2412.09796
    Preprints | 2024
    Zhu J; Tan M; Yang M; Li R; Alinejad-Rokny H, 2024, CollectiveSFT: Scaling Large Language Models for Chinese Medical Benchmark with Collective Instructions in Healthcare, http://dx.doi.org/10.48550/arxiv.2407.19705
    Preprints | 2023
    Abedini SS; Akhavan S; Heng J; Alizadehsani R; Dehzangi I; Bauer DC; Rokny H, 2023, A Critical Review of the Impact of Candidate Copy Number Variants on Autism Spectrum Disorders, http://dx.doi.org/10.48550/arxiv.2302.03211
    Conference Papers | 2023
    Argha A; Li J; Magdy J; Alinejad-Rokny H; Celler BG; Butcher K; Ooi SY; Lovell NH, 2023, 'Assessing the Generalizability of a Deep Learning-based Automated Atrial Fibrillation Algorithm', in Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBS, http://dx.doi.org/10.1109/EMBC40787.2023.10341108
    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, http://dx.doi.org/10.1109/DSP58604.2023.10167869
    Preprints | 2023
    Jafari M; Sadeghi D; Shoeibi A; Alinejad-Rokny H; Beheshti A; García DL; Chen Z; Acharya UR; Gorriz JM, 2023, Empowering Precision Medicine: AI-Driven Schizophrenia Diagnosis via EEG Signals: A Comprehensive Review from 2002-2023, http://dx.doi.org/10.48550/arxiv.2309.12202
    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 IEEE International Conference on Acoustics Speech and Signal Processing Proceedings, http://dx.doi.org/10.1109/ICASSP49357.2023.10096192
    Preprints | 2023
    Roshanzamir M; Shamsi A; Asgharnezhad H; Alizadehsani R; Hussain S; Moosaei H; Mohammadi A; Acharya UR; Alinejad H, 2023, Quantifying Uncertainty in Automated Detection of Alzheimer’s Patients Using Deep Neural Network, http://dx.doi.org/10.20944/preprints202301.0148.v1
    Preprints | 2023
    Subramanian S; Subramanian S; Thoms JAI; Huang Y; Cornejo P; Koch F; Jacquelin S; Shen S; Song E; Joshi S; Brownlee C; Woll P; Fajardo DC; Beck D; Curtis D; Yehson K; Antonenas V; Brien TO; Trickett A; Powell J; Lewis I; Pitson S; Gandhi M; Lane S; Vafaee F; Wong E; Göttgens B; Rokny HA; Wong JWH; Pimanda J, 2023, Cell Type-Specific Regulation by a Heptad of Transcription Factors in Human Hematopoietic Stem and Progenitor Cells, http://dx.doi.org/10.1101/2023.04.18.537282
    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, pp. 265 - 270, http://dx.doi.org/10.1109/CINTI-MACRo57952.2022.10029403
    Preprints | 2022
    Jafari M; Shoeibi A; Ghassemi N; Heras J; Ling SH; Beheshti A; Zhang Y-D; Wang S-H; Alizadehsani R; Gorriz JM; Acharya UR; Rokny HA, 2022, Automatic Diagnosis of Myocarditis Disease in Cardiac MRI Modality using Deep Transformers and Explainable Artificial Intelligence, http://dx.doi.org/10.48550/arxiv.2210.14611
    Preprints | 2022
    Jafari M; Shoeibi A; Khodatars M; Ghassemi N; Moridian P; Delfan N; Alizadehsani R; Khosravi A; Ling SH; Zhang Y-D; Wang S-H; Gorriz JM; Rokny HA; Acharya UR, 2022, Automated Diagnosis of Cardiovascular Diseases from Cardiac Magnetic Resonance Imaging Using Deep Learning Models: A Review, http://dx.doi.org/10.48550/arxiv.2210.14909
    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, pp. 245 - 250, 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://arxiv.org/abs/2210.04453v3
    Preprints | 2022
    Parhami P; Fateh M; Rezvani M; Rokny HA, 2022, A benchmarking of deep neural network models for cancer subtyping using single point mutations, http://dx.doi.org/10.1101/2022.07.24.501264
    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, 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
    Conference Abstracts | 2022
    Truong P; Shen S; Joshi S; Afrasiabi A; Zhong L; Raftery MJ; Larsson J; Lock RB; Walkley CR; Rokny HA; Thoms JAI; Jolly CJ; Pimanda JE, 2022, 'Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and Sumoylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia', in BLOOD, ELSEVIER, LA, New Orleans, Vol. 140, presented at 64th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH), LA, New Orleans, 10 December 2022 - 13 December 2022, http://dx.doi.org/10.1182/blood-2022-165713
    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 | 2021
    Rezaie N; Bayati M; Tahaei MS; Hamidi M; Khorasani S; Lovell N; Breen J; Rabiee H; 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
    Preprints | 2021
    Rezaie N; Bayati M; Tahaei MS; Hamidi M; Khorasani S; Lovell N; Breen J; Rabiee H; Rokny HA, 2021, Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer, http://dx.doi.org/10.21203/rs.3.rs-827525/v1
    Preprints | 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
    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 A; 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 H; 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 $3.5M as sole/leading Chief Investigator (CI) and $10.6M as co-CI), demonstrating an impressive upward research career trajectory. These include:

  • Australia's Economic Accelerator, (CIA, Dec 2025, $499K).
  • UNSW-Mahidol Joint Seed Grant, (CIA, Nov 2025, $20K).
  • Australia's Economic Accelerator, (CIB, March 2025, $200K).
  • GESA Paediatric Research Grant (CIB, Nov, 2024)
  • UNSW GRIP Award (CIA, Nov, 2024)
  • UNSW-SJTU Collaborative Research Grant, (CIA, Nov, 2024)
  • Trustworthy Digital Society Grant, (CIA, Oct, 2024)
  • Garvan Cellular Genomics Futures Institute Award (CIA, Sep, 2024).
  • UNSW Scientia Program Fellowship (variation award) (sole CI), ($800K, Sep 2023).
  • 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)
  • GROW Funding (CIA), a competitive internal funding form USNW SYDNEY, Jun 2022, ($40K)
  • 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)
  • 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
  • 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)

 

Dr. Rokny has been named on several industry funding in collaboration with Macquarie University), These include:

  • Industry research partnership funding (CID), from PORSPA advance company, 750K for my Lab, May 2024, ($4.7M).
  • Industry research partnership funding (CID), Australian Digital Domains Group, 600K for my Lab, Nov 2022, ($3.6M).
  • Industry research partnership funding (CIE), from Australian digital companies Truuth/Locii, May 2022, ($3.2M).
  • Industry research partnership funding (CIC), from PORSPA advance company, May 2021, ($2.1M).

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:

  • ·     Millennium Prize for Outstanding EMCR, Lorne Genome, Feb 2025.
  • ·     Adjunct Research Scientist, CSIRO, Aug 2022-2023
  • ·     Honorary Lecturer Fellow, University of Macquarie, Oct 2020-2023
  • ·     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

 

PhD & MPhil Students:

  • Rejisa Becirovic, PhD student, 2026-2030, (administered by UNSW), co-supervision with Dr. Reza Argha.
  • Liting Huang, PhD student, 2026-2030, (administered by UNSW), co-supervision with with Dr. Reza Argha and dr. Nona Farbehi.
  • Amir Hossein Zobeiri, PhD student, 2026-2030, (administered by UNSW), co-supervision with Dr. Reza Argha.
  • Mohammadreza Taghimohammadi, PhD student, 2026-2030, (administered by UNSW), co-supervision with Dr. Reza Argha.
  • Sally Chen, PhD student, 2025-2029, (administered by UNSW), co-supervision with Assoc. Prof Fatemeh Vafaee and Mr Mark Grosser (23Strands company).
  • Yuheng Liang, PhD student, 2025-2029, (administered by UNSW), co-supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Caleb The-Tjoean, Master by Research (MPhil), (administered by UNSW), co-supervision with Prof Irina Voineagu.
  • Lucy Chhua, Master by Research (MPhil), 2025-2028, (administered by UNSW), co-supervision with Assoc. Prof Ankur Sharma and Prof Nigel Lovell.
  • Ellie Shalbafian, Master by Research (MPhil), 2024-2027, (administered by UNSW), joint supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Jonathan Williams, Master by Research (MPhil), 2024-2028, (administered by UNSW), co-supervision with Dr Reza Argha and Prof Nigel Lovell.
  • Coco Xiaoge Huang, PhD student, 2024-2028, (administered by UNSW), co-supervision with Dr Fatemeh Vafaee and Mr Mark Grosser (23Strands company).
  • Rebecca Browne, PhD student, 2024-2028, (administered by UNSW), co-supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Tohid Ghasemnejad, PhD student, 2023-2027, (administered by UNSW), co-supervision with Drs Fabrizzio Horta, Faezeh Marzbanrad, and Mr Mark Grosser (23Strands company).
  • Roxana Zahedi Nasab, PhD student, 2023-2027, (administered by UNSW), co-supervision with Prof Nigel Lovell, Dr Reza Argha, and Dr Mo Lotfollahi.
  • Ivan Bakhshayeshi, PhD student, 2023-2027, (administered by UNSW), co-supervision with Prof Nigel Lovell and Dr Reza Argha.
  • Mona (Sedigheh) Abedini, 2023-2027, (administered by UNSW), co-supervision with Dr Fatemeh Vafaee and A/Prof Orazio Vittorio.
  • Md. Mushahidul Islam Shamim, Ph.D student, 2023-2027, (administered by UNSW), co-supervision with A/Prof Nadeem Kaakoush.
  • Reza Ghamsari, PhD student, 2022-2026, (administered by UNSW), co-supervision with Prof Nigel Lovell and Prof Matthew Ritchie (WEHI).
  • Afshar Shamsi, PhD student, 2023-2027, (administered by Concordia University), co-supervision with Assoc Prof Arash Mohammadi.

 

Master Students:

  • Morgan Wong, Master student, 2026-2027, (administered by UNSW).
  • Anish Sinha, Master student, 2026-2027, (administered by UNSW).
  • Evan Watson,  Master student, 2026-2027, (administered by UNSW).
  • Hannah Veitch, Master student, 2025-2026, (administered by UNSW)

 

Previous supervision and mentoring:

  • Mehran Piran, PhD student, 2020-2024, (administered by Monash University), co-supervision with Dr Alex Combes.
  • Mahdieh Labani, PhD student, 2021-2025, (administered by Macquarie University), co-supervision with Prof Amin Beheshti.
  • Ali Afrasiabi, PhD student, 2020-2024, (administered by UNSW).
  • 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).
  • Sunday Offor, PhD student, 2019-2023, (administered by UNSW), co-supervision with Assoc Prof Irina Voineagu.
  • Yuheng Liang, Master by Research (MPhil), 2022-2024, (administered by UNSW).
  • Sally Chen, Master student, 2023-2024, (administered by UNSW).
  • Michael De Francesco, Master student, 2023-2024, (administered by UNSW).
  • Gabrielle Younes, 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).
  • 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)