Javad Zahiri

Title(s)Postdoctoral Scholar, Neurosciences
SchoolVc-health Sciences-schools
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Transcriptomic Analysis of Cyclamen persicum to Identify Invovled Genes in Triterpene Secondary Metabolites Pathway. Biochem Genet. 2024 Apr 05. Hekmati Z, Solouki M, Emamjomeh A, Zahiri J, Mirzaie-Asl A. PMID: 38578589.
      View in: PubMed   Mentions:    Fields:    
    2. Predictive three-biomarker panel in peripheral blood mononuclear cells for detecting hepatocellular carcinoma. Sci Rep. 2024 03 29; 14(1):7527. Fayazzadeh S, Ghorbaninejad M, Rabbani A, Zahiri J, Meyfour A. PMID: 38553531; PMCID: PMC10980807.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    3. 123VCF: an intuitive and efficient tool for filtering VCF files. BMC Bioinformatics. 2024 Feb 14; 25(1):68. Eidi M, Abdolalizadeh S, Moeini S, Garshasbi M, Zahiri J. PMID: 38350858; PMCID: PMC10865685.
      View in: PubMed   Mentions:    Fields:    
    4. AI-Enhanced Detection of Clinically Relevant Structural and Functional Anomalies in MRI: Traversing the Landscape of Conventional to Explainable Approaches. J Magn Reson Imaging. 2024 Jan 19. Khosravi P, Mohammadi S, Zahiri F, Khodarahmi M, Zahiri J. PMID: 38243677.
      View in: PubMed   Mentions:    Fields:    
    5. Reconstructing the cell-cell interaction network among mouse immune cells. Biotechnol Bioeng. 2023 09; 120(9):2756-2764. Azadian S, Doustmohammadi A, Naseri M, Khodarahmi M, Arab SS, Yazdanifar M, Zahiri J, Lewis NE. PMID: 37227044; PMCID: PMC10524935.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    6. Correction to: Efficiency of monolayers in evaporation suppression from water surface considering meteorological parameters. Environ Sci Pollut Res Int. 2023 Apr; 30(17):50795. Karimzadeh M, Zahiri J, Nobakht V. PMID: 36843172.
      View in: PubMed   Mentions:    Fields:    
    7. Efficiency of monolayers in evaporation suppression from water surface considering meteorological parameters. Environ Sci Pollut Res Int. 2023 Apr; 30(17):50783-50794. Karimzadeh M, Zahiri J, Nobakht V. PMID: 36808536.
      View in: PubMed   Mentions:    Fields:    
    8. Level of Attention to Motherese Speech as an Early Marker of Autism Spectrum Disorder. JAMA Netw Open. 2023 02 01; 6(2):e2255125. Pierce K, Wen TH, Zahiri J, Andreason C, Courchesne E, Barnes CC, Lopez L, Arias SJ, Esquivel A, Cheng A. PMID: 36753277; PMCID: PMC9909502.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    9. Language, Social, and Face Regions Are Affected in Toddlers with Autism and Predictive of Language Outcome. Res Sq. 2023 Jan 31. Duan K, Eyler L, Pierce K, Lombardo M, Datko M, Hagler D, Taluja V, Zahiri J, Campbell K, Barnes C, Arias S, Nalabolu S, Troxel J, Courchesne E. PMID: 36778379; PMCID: PMC9915795.
      View in: PubMed   Mentions:
    10. Discovering Common Pathogenic Mechanisms of COVID-19 and Parkinson Disease: An Integrated Bioinformatics Analysis. J Mol Neurosci. 2022 Nov; 72(11):2326-2337. Jahanimoghadam A, Abdolahzadeh H, Rad NK, Zahiri J. PMID: 36301487; PMCID: PMC9607846.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    11. A predictive ensemble classifier for the gene expression diagnosis of ASD at ages 1 to 4 years. Mol Psychiatry. 2023 02; 28(2):822-833. Bao B, Zahiri J, Gazestani VH, Lopez L, Xiao Y, Kim R, Wen TH, Chiang AWT, Nalabolu S, Pierce K, Robasky K, Wang T, Hoekzema K, Eichler EE, Lewis NE, Courchesne E. PMID: 36266569; PMCID: PMC9908553.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    12. Identifying Key Lysosome-Related Genes Associated with Drug-Resistant Breast Cancer Using Computational and Systems Biology Approach. Iran J Pharm Res. 2022 Dec; 21(1):e130342. Shiralipour A, Khorsand B, Jafari L, Salehi M, Kazemi M, Zahiri J, Jajarmi V, Kazemi B. PMID: 36915401; PMCID: PMC10007991.
      View in: PubMed   Mentions: 1  
    13. Editorial: Artificial Intelligence in Environmental Microbiology. Front Microbiol. 2022; 13:944242. Sarrafzadeh MH, Mansouri SS, Zahiri J, Mussatto SI, Asgharnejad H. PMID: 35770174; PMCID: PMC9234568.
      View in: PubMed   Mentions:
    14. PSSMCOOL: a comprehensive R package for generating evolutionary-based descriptors of protein sequences from PSSM profiles. Biol Methods Protoc. 2022; 7(1):bpac008. Mohammadi A, Zahiri J, Mohammadi S, Khodarahmi M, Arab SS. PMID: 35388370; PMCID: PMC8977839.
      View in: PubMed   Mentions: 2  
    15. Large scale validation of an early-age eye-tracking biomarker of an autism spectrum disorder subtype. Sci Rep. 2022 03 11; 12(1):4253. Wen TH, Cheng A, Andreason C, Zahiri J, Xiao Y, Xu R, Bao B, Courchesne E, Barnes CC, Arias SJ, Pierce K. PMID: 35277549; PMCID: PMC8917231.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    16. Investigation and characterization of human gut phageome in advanced liver cirrhosis of defined etiologies. Gut Pathog. 2022 Feb 15; 14(1):9. Naseri M, Palizban F, Yadegar A, Khodarahmi M, Asadzadeh Aghdaei H, Houri H, Zahiri J. PMID: 35168645; PMCID: PMC8845349.
      View in: PubMed   Mentions: 1  
    17. Investigation of etiology-specific alterations in the gut microbiota in liver cirrhosis. Expert Rev Gastroenterol Hepatol. 2021 Dec; 15(12):1435-1441. Naseri M, Houri H, Yadegar A, Asadzadeh Aghdaei H, Zahiri J. PMID: 34632902.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    18. Drug repositioning based on gene expression data for human HER2-positive breast cancer. Arch Biochem Biophys. 2021 11 15; 712:109043. Khanjani F, Jafari L, Azadiyan S, Roozbehi S, Moradian C, Zahiri J, Hasannia S, Sajedi RH. PMID: 34597657.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    19. Correction to: Moonlighting protein prediction using physico‑chemical and evolutional properties via machine learning methods. BMC Bioinformatics. 2021 Jul 09; 22(1):366. Shirafkan F, Gharaghani S, Rahimian K, Sajedi RH, Zahiri J. PMID: 34243708; PMCID: PMC8272308.
      View in: PubMed   Mentions:    Fields:    
    20. Filtering of the Gene Signature as the Predictors of Cisplatin-Resistance in Ovarian Cancer. Iran J Biotechnol. 2021 Jul; 19(3):e2643. Ataei A, Arab SS, Zahiri J, Rajabpour A, Kletenkov K, Rizvanov A. PMID: 34825010; PMCID: PMC8590720.
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    21. Moonlighting protein prediction using physico-chemical and evolutional properties via machine learning methods. BMC Bioinformatics. 2021 May 24; 22(1):261. Shirafkan F, Gharaghani S, Rahimian K, Sajedi RH, Zahiri J. PMID: 34030624; PMCID: PMC8142502.
      View in: PubMed   Mentions: 6     Fields:    
    22. Proteomic profiling of the rat hippocampus from the kindling and pilocarpine models of epilepsy: potential targets in calcium regulatory network. Sci Rep. 2021 04 15; 11(1):8252. Sadeghi L, Rizvanov AA, Dabirmanesh B, Salafutdinov II, Sayyah M, Shojaei A, Zahiri J, Mirnajafi-Zadeh J, Khorsand B, Khajeh K, Fathollahi Y. PMID: 33859251; PMCID: PMC8050094.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    23. Posttranslational modifications in proteins: resources, tools and prediction methods. Database (Oxford). 2021 04 07; 2021. Ramazi S, Zahiri J. PMID: 33826699; PMCID: PMC8040245.
      View in: PubMed   Mentions: 144     Fields:    Translation:Cells
    24. Bioinformatic tools for DNA methylation and histone modification: A survey. Genomics. 2021 05; 113(3):1098-1113. Chenarani N, Emamjomeh A, Allahverdi A, Mirmostafa S, Afsharinia MH, Zahiri J. PMID: 33677056.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    25. Reconstruction of Intercellular Signaling Network by Cytokine-Receptor Interactions. Iran J Biotechnol. 2021 Jan; 19(1):e2560. Azadian S, Zahiri J, Shahriar Arab S, Hassan Sajedi R. PMID: 34179188; PMCID: PMC8217541.
      View in: PubMed   Mentions:
    26. RepCOOL: computational drug repositioning via integrating heterogeneous biological networks. J Transl Med. 2020 10 02; 18(1):375. Fahimian G, Zahiri J, Arab SS, Sajedi RH. PMID: 33008415; PMCID: PMC7532104.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    27. Alpha influenza virus infiltration prediction using virus-human protein-protein interaction network. Math Biosci Eng. 2020 04 15; 17(4):3109-3129. Khorsand B, Savadi A, Zahiri J, Naghibzadeh M. PMID: 32987519.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    28. Estimation of transverse mixing coefficient in streams using M5, MARS, GA, and PSO approaches. Environ Sci Pollut Res Int. 2020 May; 27(13):14553-14566. Zahiri J, Nezaratian H. PMID: 32048189.
      View in: PubMed   Mentions:    Fields:    
    29. Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders. J Biosci. 2020; 45. Ramazi S, Allahverdi A, Zahiri J. PMID: 33184251.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    30. Digging deeper into volatile organic compounds associated with cancer. Biol Methods Protoc. 2019; 4(1):bpz014. Janfaza S, Khorsand B, Nikkhah M, Zahiri J. PMID: 32161807; PMCID: PMC6994028.
      View in: PubMed   Mentions: 35  
    31. Novel BDNF-regulatory microRNAs in neurodegenerative disorders pathogenesis: An in silico study. Comput Biol Chem. 2019 Dec; 83:107153. Khani-Habibabadi F, Askari S, Zahiri J, Javan M, Behmanesh M. PMID: 31751881.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    32. iMet: A graphical user interface software tool to merge metabolic networks. Heliyon. 2019 Jun; 5(6):e01766. Mohammadi R, Zahiri J, Niroomand MJ. PMID: 31286073; PMCID: PMC6587100.
      View in: PubMed   Mentions: 1  
    33. Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development. Genomics. 2020 01; 112(1):820-830. Shiri Y, Solouki M, Ebrahimie E, Emamjomeh A, Zahiri J. PMID: 31136791.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    34. AntAngioCOOL: computational detection of anti-angiogenic peptides. J Transl Med. 2019 03 04; 17(1):71. Zahiri J, Khorsand B, Yousefi AA, Kargar M, Shirali Hossein Zade R, Mahdevar G. PMID: 30832671; PMCID: PMC6399940.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    35. OligoCOOL: A mobile application for nucleotide sequence analysis. Biochem Mol Biol Educ. 2019 03; 47(2):201-206. Khorsand B, Khammari A, Shirvanizadeh N, Zahiri J, Arab SS. PMID: 30681253.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    36. Protein complex prediction: A survey. Genomics. 2020 01; 112(1):174-183. Zahiri J, Emamjomeh A, Bagheri S, Ivazeh A, Mahdevar G, Sepasi Tehrani H, Mirzaie M, Fakheri BA, Mohammad-Noori M. PMID: 30660789.
      View in: PubMed   Mentions: 16     Fields:    
    37. Identification, Prediction and Data Analysis of Noncoding RNAs: A Review. Med Chem. 2019; 15(3):216-230. Emamjomeh A, Zahiri J, Asadian M, Behmanesh M, Fakheri BA, Mahdevar G. PMID: 30484409.
      View in: PubMed   Mentions: 3     Fields:    
    38. Identification of the Molecular Events Involved in the Development of Prefrontal Cortex Through the Analysis of RNA-Seq Data From BrainSpan. ASN Neuro. 2019 Jan-Dec; 11:1759091419854627. Najafi H, Naseri M, Zahiri J, Totonchi M, Sadeghizadeh M. PMID: 31213068; PMCID: PMC6582306.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    39. Performance evaluation measures for protein complex prediction. Genomics. 2019 12; 111(6):1483-1492. Ivazeh A, Zahiri J, Rahgozar M, Srihari S. PMID: 30312661.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    40. afpCOOL: A tool for antifreeze protein prediction. Heliyon. 2018 Jul; 4(7):e00705. Eslami M, Shirali Hossein Zade R, Takalloo Z, Mahdevar G, Emamjomeh A, Sajedi RH, Zahiri J. PMID: 30094375; PMCID: PMC6074609.
      View in: PubMed   Mentions: 6  
    41. Unraveling the transcriptional complexity of compactness in sistan grape cluster. Plant Sci. 2018 May; 270:198-208. Shiri Y, Solouki M, Ebrahimie E, Emamjomeh A, Zahiri J. PMID: 29576073.
      View in: PubMed   Mentions: 2     Fields:    Translation:Animals
    42. Cancer Odor Database (COD): a critical databank for cancer diagnosis research. Database (Oxford). 2017 01 01; 2017. Janfaza S, Banan Nojavani M, Khorsand B, Nikkhah M, Zahiri J. PMID: 29220448; PMCID: PMC5737198.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    43. A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production. Mol Biosyst. 2016 07 19; 12(8):2552-61. Mohammadi R, Fallah-Mehrabadi J, Bidkhori G, Zahiri J, Javad Niroomand M, Masoudi-Nejad A. PMID: 27265370.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    44. rpiCOOL: A tool for In Silico RNA-protein interaction detection using random forest. J Theor Biol. 2016 08 07; 402:1-8. Akbaripour-Elahabad M, Zahiri J, Rafeh R, Eslami M, Azari M. PMID: 27134008.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    45. Computational Detection of piRNA in Human Using Support Vector Machine. Avicenna J Med Biotechnol. 2016 Jan-Mar; 8(1):36-41. Seyeddokht A, Aslaminejad AA, Masoudi-Nejad A, Nassiri M, Zahiri J, Sadeghi B. PMID: 26855734; PMCID: PMC4717465.
      View in: PubMed   Mentions: 2  
    46. LocFuse: human protein-protein interaction prediction via classifier fusion using protein localization information. Genomics. 2014 Dec; 104(6 Pt B):496-503. Zahiri J, Mohammad-Noori M, Ebrahimpour R, Saadat S, Bozorgmehr JH, Goldberg T, Masoudi-Nejad A. PMID: 25458812.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    47. Predicting protein-protein interactions between human and hepatitis C virus via an ensemble learning method. Mol Biosyst. 2014 Dec; 10(12):3147-54. Emamjomeh A, Goliaei B, Zahiri J, Ebrahimpour R. PMID: 25230581.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    48. Analysis of candidate genes has proposed the role of y chromosome in human prostate cancer. Iran J Cancer Prev. 2014; 7(4):204-11. Khosravi P, Zahiri J, Gazestani VH, Mirkhalaf S, Akbarzadeh M, Sadeghi M, Goliaei B. PMID: 25628841; PMCID: PMC4307103.
      View in: PubMed   Mentions: 2  
    49. Computational Prediction of Protein-Protein Interaction Networks: Algo-rithms and Resources. Curr Genomics. 2013 Sep; 14(6):397-414. Zahiri J, Bozorgmehr JH, Masoudi-Nejad A. PMID: 24396273; PMCID: PMC3861891.
      View in: PubMed   Mentions: 33  
    50. PPIevo: protein-protein interaction prediction from PSSM based evolutionary information. Genomics. 2013 Oct; 102(4):237-42. Zahiri J, Yaghoubi O, Mohammad-Noori M, Ebrahimpour R, Masoudi-Nejad A. PMID: 23747746.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansCells
    51. Scatter-search with support vector machine for prediction of relative solvent accessibility. EXCLI J. 2013; 12:52-63. Kashefi AH, Meshkin A, Zargoosh M, Zahiri J, Taheri M, Ashtiani S. PMID: 26417216; PMCID: PMC4531788.
      View in: PubMed   Mentions: 1  
    52. A novel efficient dynamic programming algorithm for haplotype block partitioning. J Theor Biol. 2010 Nov 21; 267(2):164-70. Zahiri J, Mahdevar G, Nowzari-Dalini A, Ahrabian H, Sadeghi M. PMID: 20728452.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    53. Tag SNP selection via a genetic algorithm. J Biomed Inform. 2010 Oct; 43(5):800-4. Mahdevar G, Zahiri J, Sadeghi M, Nowzari-Dalini A, Ahrabian H. PMID: 20546935.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
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