Esmaeil Ebrahimie
School of Animal and Veterinary Science
Faculty of Sciences, Engineering and Technology
-
Journals
Year Citation 2024 Ranjbar, S., Emamjomeh, A., Ebrahimi, M., Ghorbani, A., Ebrahimie, E., & Shiri, Y. (2024). Comparative analysis of bioinformatic tools to predict and quantify active circular RNAs during grape cluster development. Biologia Plantarum, 68, 1-11.
2024 Li, J., Li, X. H., Ebrahimie, E., & Huang, L. (2024). Editorial: Exploring genetic characteristics and molecular mechanisms of host adaptation of viruses with artificial intelligence (AI) or (and) biological (BIO) approaches. Frontiers in Cellular and Infection Microbiology, 14, 3 pages.
2024 Pashaei-Asl, R., Motaali, S., Ebrahimie, E., Mohammadi-Dehcheshmeh, M., Ebrahimi, M., & Pashaiasl, M. (2024). Delivery of doxorubicin by Fe<sub>3</sub>O<sub>4</sub> nanoparticles, reduces multidrug resistance gene expression in ovarian cancer cells.. Pathology, research and practice, 263, 155667.
2024 Moghadam, A., Taghizadeh, M. S., Haghi, R., Tahmasebi, A., Niazi, A., & Ebrahimie, E. (2024). Exploring novel insights: Methyl jasmonate treatment reveals novel lncRNA-mediated regulation of secondary metabolite biosynthesis pathways in Echinacea purpurea. Food Bioscience, 57, 10 pages.
Scopus32024 Vassileff, N., Spiers, J. G., Lee, J. D., Woodruff, T. M., Ebrahimie, E., Mohammadi Dehcheshmeh, M., . . . Cheng, L. (2024). A Panel of miRNA Biomarkers Common to Serum and Brain-Derived Extracellular Vesicles Identified in Mouse Model of Amyotrophic Lateral Sclerosis. Molecular Neurobiology, 61(8), 5901-5915.
Scopus3 Europe PMC12024 Samandari-Bahraseman, M. R., Ismaili, A., Esmaeili-Mahani, S., Ebrahimie, E., & Loit, E. (2024). Bunium persicum Seeds Extract in Combination with Vincristine Mediates Apoptosis in MCF-7 Cells through Regulation of Involved Genes and Proteins Expression. Anti-Cancer Agents in Medicinal Chemistry, 24(3), 213-223.
Scopus2 Europe PMC22024 Zhao, K., Ebrahimie, E., Mohammadi-Dehcheshmeh, M., Lewsey, M. G., Zheng, L., & Hoogenraad, N. J. (2024). Transcriptomic signature of cancer cachexia by integration of machine learning, literature mining and meta-analysis. Computers in Biology and Medicine, 172, 108233.
Scopus1 Europe PMC12024 Tabatabeipour, S. N., Shiran, B., Ravash, R., Niazi, A., & Ebrahimie, E. (2024). Meta-analysis of RNA-seq data of the medicinal plant Catharanthus roseus under some biotic and abiotic stresses. Agricultural Biotechnology Journal, 16(1), 209-234.
2024 Tabatabaeipour, S. N., Shiran, B., Ravash, R., Niazi, A., & Ebrahimie, E. (2024). Comprehensive transcriptomic meta-analysis unveils new responsive genes to methyl jasmonate and ethylene in Catharanthus roseus. Heliyon, 10(5), e27132.
Scopus1 Europe PMC12023 Shamloo-Dashtpagerdi, R., Razi, H., Alemzadeh, A., & Ebrahimie, E. (2023). Further insights into the association of the protein phosphatase gene ABI1 with drought and salinity stress responses in Brassica species. Journal of Plant Biochemistry and Biotechnology, 32(1), 106-120.
Scopus3 WoS32023 Neisi, M., Fakheri, B. A., Ebrahimie, E., Emamjomeh, A., Zahiri, J., & Parvizi Almani, M. (2023). RNA-Seq Analyzing Reveals the Key Role of SVR3 Gene in Tolerating the Freezing Stress in Saccharum spontaneum. Journal of Plant Growth Regulation, 42(4), 2613-2625.
2023 Shariatzadeh, M., Karami, A., Moghadam, A., Lotfi, M., Maggi, F., & Ebrahimie, E. (2023). The Essential Oil from Oliveria decumbens Vent. (Apiaceae) as Inhibitor of Breast Cancer Cell (MCF-7) Growth. Pharmaceuticals, 16(1), 59.
Scopus3 WoS22023 Homer, B., Judd, J., Mohammadi Dehcheshmeh, M., Ebrahimie, E., & Trott, D. J. (2023). Gut Microbiota and Behavioural Issues in Production, Performance, and Companion Animals: A Systematic Review. Animals, 13(9), 1458.
Scopus6 Europe PMC62023 Pezeshkian, Z., Mirhoseini, S. Z., Ghovvati, S., & Ebrahimie, E. (2023). Phenotypic evaluation of feed efficiency, growth and carcass traits inative turkeys. Journal of Central European Agriculture, 24(1), 85-94.
Scopus12023 Esmaeili, F., Farhadpour, M., Abbas-Mohammadi, M., Alilou, M., Morshedi, D., Ebrahimie, E., & Lohrasebi, T. (2023). Appraisals on the anticancer properties of Mentha species using bioassays and docking studies. Industrial Crops and Products, 203, 13 pages.
Scopus32023 Pashaei-Asl, R., Pashaiasl, M., Ebrahimie, E., Lale Ataei, M., & Paknejad, M. (2023). Apoptotic effects of human amniotic fluid mesenchymal stem cells conditioned medium on human MCF-7 breast cancer cell line. BioImpacts, 13(3), 191-206.
Scopus1 WoS12023 Piryaei, Z., Salehi, Z., Ebrahimie, E., Ebrahimi, M., & Kavousi, K. (2023). Meta-analysis of integrated ChIP-seq and transcriptome data revealed genomic regions affected by estrogen receptor alpha in breast cancer. BMC Medical Genomics, 16(1), 19 pages.
2023 Esfahani, E. D., Ebrahimie, E., Niazi, A., & Dehcheshmeh, M. M. (2023). Pattern discovery of long non-coding RNAs associated with the herbal treatments in breast and prostate cancers. Quantitative Biology, 11(3), 343-358.
2023 Hazi, A., Ebrahimie, E., Levay, E. A., Mohammadi-Dehcheshmeh, M., Zelko, M., Govic, A., & Nasser, H. (2023). Crosstalk between short- and long-term calorie restriction transcriptomic signatures with anxiety-like behavior, aging, and neurodegeneration: implications for drug repurposing. Frontiers in Behavioral Neuroscience, 17, 13 pages.
2023 Nezamivand-Chegini, M., Metzger, S., Moghadam, A., Tahmasebi, A., Koprivova, A., Eshghi, S., . . . Ebrahimie, E. (2023). Integration of transcriptomic and metabolomic analyses provides insights into response mechanisms to nitrogen and phosphorus deficiencies in soybean. Plant science : an international journal of experimental plant biology, 326, 111498.
Scopus15 WoS10 Europe PMC42022 Govic, A., Nasser, H., Levay, E. A., Zelko, M., Ebrahimie, E., Mohammadi Dehcheshmeh, M., . . . Hazi, A. (2022). Long-Term Calorie Restriction Alters Anxiety-like Behaviour and the Brain and Adrenal Gland Transcriptomes of the Ageing Male Rat. Nutrients, 14(21), 1-18.
Scopus10 WoS4 Europe PMC62022 Shojaee, S., Ravash, R., Shiran, B., & Ebrahimie, E. (2022). Meta-analysis highlights the key drought responsive genes in genes: PEPC and TaSAG7 are hubs response networks. Journal of Genetic Engineering and Biotechnology, 20(1), 18 pages.
Scopus2 WoS2 Europe PMC12022 Piryaei, Z., Salehi, Z., Tahsili, M. R., Ebrahimie, E., Ebrahimi, M., & Kavousi, K. (2022). Agonist/antagonist compounds' mechanism of action on estrogen receptor-positive breast cancer: A system-level investigation assisted by meta-analysis. Informatics in Medicine Unlocked, 31, 100985.
Scopus32022 Mondol, R. K., Truong, N. D., Reza, M., Ippolito, S., Ebrahimie, E., & Kavehei, O. (2022). AFExNet: An Adversarial Autoencoder for Differentiating Breast Cancer Sub-Types and Extracting Biologically Relevant Genes. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19(4), 2060-2070.
Scopus4 WoS22022 Xie, S., Trott, D. J., Saputra, S., Ebrahimie, E., Mohammadi Dehcheshmeh, M., Page, C., . . . Govendir, M. (2022). Pharmacokinetic profile and effect on the faecal microbiome of a single dose of pradofloxacin oral suspension in the rabbit (Oryctolagus cuniculus). Journal of Veterinary Pharmacology and Therapeutics, 45(2), 203-212.
Scopus1 Europe PMC12022 Sharifi, S., Shahreza, M. L., Pakdel, A., Reecy, J. M., Ghadiri, N., Atashi, H., . . . Ebrahimie, E. (2022). Systems biology–derived genetic signatures of mastitis in dairy cattle: A new avenue for drug repurposing. Animals, 12(1), 11 pages.
Scopus5 WoS2 Europe PMC42022 Dorostkar, S., Dadkhodaie, A., Ebrahimie, E., Heidari, B., & Ahmadi-Kordshooli, M. (2022). Comparative transcriptome analysis of two contrasting resistant and susceptible Aegilops tauschii accessions to wheat leaf rust (Puccinia triticina) using RNA-sequencing. Scientific Reports, 12(1), 19 pages.
Scopus13 WoS10 Europe PMC82022 Ghasemi, E., Ebrahimi, M., & Ebrahimie, E. (2022). Machine learning models effectively distinguish attention-deficit/hyperactivity disorder using event-related potentials. Cognitive Neurodynamics, 16(6), 1335-1349.
Scopus102022 Shakoori, Z., Pashaei-Asl, R., Pashaiasl, M., Davaran, S., Ghanbari, H., Ebrahimie, E., & Rezayat, S. M. (2022). Biocompatibility study of P (N-isopropylacrylamide)-based nanocomposite and its cytotoxic effect on HeLa cells as a drug delivery system for Cisplatin. Journal of Drug Delivery Science and Technology, 71, 11 pages.
Scopus1 WoS12022 Alanazi, I. O., Alamery, S. F., Ebrahimie, E., & Mohammadi-Dehcheshmeh, M. (2022). Splice-disrupt genomic variants in prostate cancer. Molecular Biology Reports, 49(6), 4237-4246.
Scopus3 WoS1 Europe PMC32022 Nezamivand-Chegini, M., Metzger, S., Moghadam, A., Tahmasebi, A., Koprivova, A., Eshghi, S., . . . Ebrahimie, E. (2022). Nitrogen and phosphorus deficiencies alter primary and secondary metabolites of soybean roots.
2022 Pezeshkian, Z., Mirhoseini, S. Z., Ghovvati, S., & Ebrahimie, E. (2022). Transcriptome Analysis of Breast Muscle Reveals Pathways Related to Protein Deposition in High Feed Efficiency of Native Turkeys. Animals, 12(10), 20 pages.
Scopus3 WoS3 Europe PMC22021 Nezamivand-Chegini, M., Ebrahimie, E., Tahmasebi, A., Moghadam, A., Eshghi, S., Mohammadi-Dehchesmeh, M., . . . Niazi, A. (2021). New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean. BMC Genomics, 22(1), 21 pages.
Scopus8 WoS3 Europe PMC52021 Tabrizi, A. E., Tahmoorespur, M., & Ebrahimie, E. (2021). Resensitizing resistant Escherichia Coli ST131 to Macrolide using Fluoroquinolones. Journal of Advanced Pharmacy Education and Research, 11(4), 29-34.
2021 Ahsan, R., Tahsili, M. R., Ebrahimi, F., Ebrahimie, E., & Ebrahimi, M. (2021). Image processing unravels the evolutionary pattern of SARS-CoV-2 against SARS and MERS through position-based pattern recognition. Computers in Biology and Medicine, 134, 11 pages.
Scopus2 WoS12021 Ebrahimie, E., Mohammadi-Dehcheshmeh, M., Laven, R., & Petrovski, K. (2021). Rule Discovery in Milk Content towards Mastitis Diagnosis: Dealing with Farm Heterogeneity over Multiple Years through Classification Based on Associations. Animals, 11(6), 1-13.
Scopus8 WoS6 Europe PMC52021 Panahi, R., Ebrahimie, E., Niazi, A., & Afsharifar, A. (2021). Integration of meta-analysis and supervised machine learning for pattern recognition in breast cancer using epigenetic data. Informatics in Medicine Unlocked, 24, 100629.
Scopus82021 Ghabeshi, S., Ebrahimie, E., Yavarian, J., Salimi, V., Shafiei-Jandaghi, N. Z., Rezaie, F., . . . Azad, T. M. (2021). Molecular characterization of low pathogenic avian influenza H9N2 virus during co-circulation with newly-emerged highly pathogenic avian influenza H5N8 virus in Iran. Acta virologica, 65(2), 200-211.
2021 Kharrati-Koopaee, H., Ebrahimie, E., Dadpasand, M., Niazi, A., Tian, R., & Esmailizadeh, A. (2021). Gene network analysis to determine the effect of hypoxia-associated genes on brain damages and tumorigenesis using an avian model. Journal of Genetic Engineering and Biotechnology, 19(1), 24 pages.
Scopus2 WoS2 Europe PMC22021 Sahranavardfard, P., Madjd, Z., Razavi, A. E., Ghanadan, A., Firouzi, J., Khosravani, P., . . . Ebrahimi, M. (2021). An integrative analysis of the micro-RNAs contributing in stemness, metastasis and B-Raf pathways in malignant melanoma and melanoma stem cell. Cell Journal, 23(3), 261-272.
Scopus5 WoS2 Europe PMC22021 Yip, S., Mohammadi Dehcheshmeh, M., McLelland, D. J., Boardman, W. S. J., Saputra, S., Ebrahimie, E., . . . Trott, D. J. (2021). Porphyromonas spp., Fusobacterium spp., and Bacteroides spp. dominate microbiota in the course of macropod progressive periodontal disease. Scientific reports, 11(1), 17775-1-17775-10.
Scopus13 WoS5 Europe PMC82021 Ebrahimie, E., Zamansani, F., Alanazi, I. O., Sabi, E. M., Khazandi, M., Ebrahimi, F., . . . Ebrahimi, M. (2021). Advances in understanding the specificity function of transporters by machine learning. Computers in Biology and Medicine, 138, 1-8.
Scopus7 WoS3 Europe PMC12021 Ataei, M. L., Karimipour, M., Shahabi, P., Pashaei-Asl, R., Ebrahimie, E., & Pashaiasl, M. (2021). The restorative effect of human amniotic fluid stem cells on spinal cord injury. Cells, 10(10), 15 pages.
Scopus5 WoS4 Europe PMC52021 Esmaeili, F., Lohrasebi, T., Mohammadi-Dehcheshmeh, M., & Ebrahimie, E. (2021). Evaluation of the effectiveness of herbal components based on their regulatory signature on carcinogenic cancer cells. Cells, 10(11), 3139.
Scopus5 WoS2 Europe PMC32021 Ebrahimie, E., Rahimirad, S., Tahsili, M., & Mohammadi Dehcheshmeh, M. (2021). Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.. World J Stem Cells, 13(10), 1394-1416.
Scopus7 WoS3 Europe PMC42021 Liyaghatdar, Z., Pezeshkian, Z., Mohammadi Dehcheshmeh, M., & Ebrahimie, E. (2021). Fast school closures correspond with a lower rate of COVID-19 incidence and deaths in most countries. Informatics in Medicine Unlocked, 27, 100805-1-100805-6.
Scopus3 Europe PMC22021 Tabrizi, A. E., Tahmoorespur, M., & Ebrahimie, E. (2021). ABC Transporters are Hub Genes in Response of Resistant E. Coli ST131 to Ciprofloxacin. ARCHIVES OF PHARMACY PRACTICE, 12(3), 82-88.
WoS12021 Hemmatzadeh, F., Sumarningsih, S., Tarigan, S., Indriani, R., Dharmayanti, N. L. P., & Ebrahimie, E. (2021). Expression of Concern: Recombinant M2e Protein-Based ELISA: A Novel and Inexpensive Approach for Differentiating Avian Influenza Infected Chickens from Vaccinated Ones. PLOS ONE, 16(4), 2 pages.
2021 Ansari, E., Karami, A., & Ebrahimie, E. (2021). Isolation of 2-phenylethanol biosynthesis related gene and developmental patterns of emission of scent compounds in Persian musk rose (Rosa moschata Herrm.) (vol 19C. 101176, 2019). BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY, 31, 1 page. 2021 Saedi, S., Jafarzadeh Shirazi, M. R., Niazi, A., Tahmasebi, A., & Ebrahimie, E. (2021). Prepubertal exposure to a high dose of cadmium induces hypothalamic injury through transcriptome profiling alteration and neuronal degeneration in female rats. Chemico-Biological Interactions, 337, 1-15.
Scopus9 WoS6 Europe PMC42021 Hickey, T. E., Selth, L. A., Chia, K. M., Laven-Law, G., Milioli, H. H., Roden, D., . . . Tilley, W. D. (2021). The androgen receptor is a tumor suppressor in estrogen receptor-positive breast cancer. Nature Medicine, 27(2), 310-320.
Scopus135 WoS89 Europe PMC982021 Mohammadi-Dehcheshmeh, M., Moghbeli, S. M., Rahimirad, S., Alanazi, I. O., Shehri, Z. S. A., & Ebrahimie, E. (2021). A Transcription Regulatory Sequence in the 5' Untranslated Region of SARS-CoV-2 Is Vital for Virus Replication with an Altered Evolutionary Pattern against Human Inhibitory MicroRNAs.. Cells, 10(2), 319.
Scopus23 WoS14 Europe PMC232021 Farhadi, S., Ghias, J. S., Hasanpur, K., Mohammadi, S. A., & Ebrahimie, E. (2021). Molecular mechanisms of fat deposition: IL-6 is a hub gene in fat lipolysis, comparing thin-tailed with fat-tailed sheep breeds. Archives Animal Breeding, 64(1), 53-68.
Scopus9 WoS2 Europe PMC62020 Farhadian, M., Rafat, S. A., Panahi, B., & Ebrahimie, E. (2020). Transcriptome signature of two lactation stages in Ghezel sheep identifies using RNA-Sequencing.. Animal Biotechnology, 33(2), 223-233.
Scopus9 WoS6 Europe PMC92020 Ghabeshi, S., Ebrahimie, E., Salimi, V., Ghanizadeh, A., Khodakhah, F., Yavarian, J., . . . Azad, T. M. (2020). Experimental direct-contact transmission of influenza A/H9N2 virus in the guinea pig model in Iran. Future Virology, 15(5), 277-292.
WoS12020 Rafiepour, M., Ebrahimie, E., Vahidi, M. F., Salekdeh, G. H., Niazi, A., Dadpasand, M., . . . Qanbari, S. (2020). Whole genome re-sequencing reveals adaptation prior to the divergence of buffalo subspecies.. Genome biology and evolution, 13(1), 1-14.
Scopus8 WoS4 Europe PMC42020 Sharifi, S., Pakdel, A., Jahanbakhsh, J., Aryan, Y., Mahdavi, A., & Ebrahimie, E. (2020). Molecular mechanisms of resistance to bovine mastitis. Livestock Science, 239, 5 pages.
Scopus4 WoS22020 Khelghatibana, F., Javan-Nikkhah, M., Safaie, N., Fotouhifar, K. B., Vahdati, K., & Ebrahimie, E. (2020). Comparative study of virulence of ophiognomonia leptostyla. Journal of Crop Protection, 9(2), 307-318. 2020 Butcher, R. G., Pettett, L. M., Fabijan, J., Ebrahimie, E., Mohammadi-Dehcheshmeh, M., Speight, K. N., . . . Trott, D. J. (2020). Periodontal disease in free-ranging koalas (Phascolarctos cinereus) from the Mount Lofty Ranges, South Australia, and its association with koala retrovirus infection.. Australian veterinary journal, 98(5), 200-206.
Scopus8 WoS7 Europe PMC52020 Kidsley, A. K., O'Dea, M., Ebrahimie, E., Mohammadi Dehcheshmeh, M., Saputra, S., Jordan, D., . . . Trott, D. J. (2020). Genomic analysis of fluoroquinolone-susceptible phylogenetic group B2 extraintestinal pathogenic Escherichia coli causing infections in cats. Veterinary Microbiology, 245(-), 108685-1-108685-7.
Scopus12 WoS10 Europe PMC92020 Len, J., Beehan, D., Eilts, B., Ebrahimie, E., & Lyle, S. (2020). Stallion Sperm Integrity After Centrifugation to Reduce Seminal Plasma Concentration and Cool Storage for 4 days. Journal of Equine Veterinary Science, 85, 3 pages.
Scopus5 WoS42020 Shiri, Y., Solouki, M., Ebrahimie, E., Emamjomeh, A., & Zahiri, J. (2020). Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development. Genomics, 112(1), 820-830.
Scopus14 WoS11 Europe PMC52020 Tilley, W., Hickey, T., Selth, L., Chia, K. M., Milioli, H., Laven-Law, G., . . . Carroll, J. (2020). The Androgen Receptor is a Tumour Suppressor in Estrogen Receptor Positive Breast Cancer.
2019 Sharifi, S., Pakdel, A., Ebrahimie, E., Aryan, Y., Ghaderi Zefrehee, M., & Reecy, J. M. (2019). Prediction of key regulators and downstream targets of E. coli induced mastitis. Journal of Applied Genetics, 60(3-4), 367-373.
Scopus15 WoS10 Europe PMC92019 Ansari, E., Karami, A., & Ebrahimie, E. (2019). Isolation of 2-phenylethanol biosynthesis related gene and developmental patterns of emission of scent compounds in Persian musk rose (Rosa moschata Herrm.). Biocatalysis and Agricultural Biotechnology, 19, 6 pages.
Scopus4 WoS22019 Kharrati-Koopaee, H., Ebrahimie, E., Dadpasand, M., Niazi, A., & Esmailizadeh, A. (2019). Genomic analysis reveals variant association with high altitude adaptation in native chickens. Scientific Reports, 9(1), 22 pages.
Scopus12 WoS10 Europe PMC102019 Ebrahimi, M., Mohammadi-Dehcheshmeh, M., Ebrahimie, E., & Petrovski, K. R. (2019). Comprehensive analysis of machine learning models for prediction of sub-clinical mastitis: Deep Learning and Gradient-Boosted Trees outperform other models. Computers in Biology and Medicine, 114, 9 pages.
Scopus102 WoS63 Europe PMC302019 Farhadian, M., Rafat, S. A., Hasanpur, K., Ebrahimi, M., & Ebrahimie, E. (2019). Corrigendum: Cross-Species Meta-Analysis of Transcriptomic Data in Combination With Supervised Machine Learning Models Identifies the Common Gene Signature of Lactation Process.. Front Genet, 10, 1034.
Scopus1 WoS1 Europe PMC12019 Moore, N. L., Hanson, A. R., Ebrahimie, E., Hickey, T. E., & Tilley, W. D. (2019). ANTI-proliferative transcriptional effects of medroxyprogesterone acetate in Estrogen receptor positive breast cancer cells are predominantly mediated by ThE progesterone receptor.. Journal of Steroid Biochemistry and Molecular Biology, 199, 105548.
Scopus14 WoS7 Europe PMC52019 Alanazi, I. O., Al Shehri, Z. S., Ebrahimie, E., Giahi, H., & Mohammadi-Dehcheshmeh, M. (2019). Non-coding and coding genomic variants distinguish prostate cancer, castration-resistant prostate cancer, familial prostate cancer, and metastatic castration-resistant prostate cancer from each other. Molecular Carcinogenesis, 58(6), 13 pages.
Scopus11 WoS8 Europe PMC72019 Kargarfard, F., Sami, A., Hemmatzadeh, F., & Ebrahimie, E. (2019). Identifying mutation positions in all segments of influenza genome enables better differentiation between pandemic and seasonal strains. Gene, 697, 78-85.
Scopus8 WoS7 Europe PMC82019 Tahmasebi, A., Ashrafi-Dehkordi, E., Shahriari, A. G., Mazloomi, S. M., & Ebrahimie, E. (2019). Integrative meta-analysis of transcriptomic responses to abiotic stress in cotton. Progress in Biophysics and Molecular Biology, 146, 112-122.
Scopus58 WoS41 Europe PMC352019 Tahmasebi, A., Ebrahimie, E., Pakniyat, H., Ebrahimi, M., & Mohammadi-Dehcheshmeh, M. (2019). Insights from the Echinacea purpurea (L.) Moench transcriptome: Global reprogramming of gene expression patterns towards activation of secondary metabolism pathways. Industrial Crops and Products, 132, 365-376.
Scopus11 WoS62019 Speight, K. N., Houston-Francis, M., Mohammadi Dehcheshmeh, M., Ebrahimie, E., Saputra, S., & Trott, D. J. (2019). Oxalate-degrading bacteria, including Oxalobacter formigenes, colonise the gastrointestinal tract of healthy koalas (Phascolarctos cinereus) and those with oxalate nephrosis. Australian Veterinary Journal, 97(5), 166-170.
Scopus5 WoS5 Europe PMC12019 Rahmatizadeh, F., Aziz, S. G. G., Khodadadi, K., Ataei, M. L., Ebrahimie, E., Rad, J. S., & Pashaiasl, M. (2019). Bidirectional and opposite effects of naïve mesenchymal stem cells on tumor growth and progression. Advanced Pharmaceutical Bulletin, 9(4), 539-558.
Scopus15 WoS13 Europe PMC122019 Tahmasebi, A., Ebrahimie, E., Pakniyat, H., Ebrahimi, M., & Mohammadi Dehcheshmeh, M. (2019). Tissue-specific transcriptional biomarkers in medicinal plants: Application of large-scale meta-analysis and computational systems biology. Gene, 691, 114-124.
Scopus13 WoS7 Europe PMC82019 Godini, R., Fallahi, H., & Ebrahimie, E. (2019). A comparative system-level analysis of the neurodegenerative diseases. Journal of Cellular Physiology, 234(4), 5215-5229.
Scopus5 WoS4 Europe PMC42018 Mohammadi Dehcheshmeh, M., Niazi, A., Ebrahimi, M., Tahsili, M., Nurollah, Z., Ebrahimi Khaksefidi, R., . . . Ebrahimie, E. (2018). Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots of Medicago truncatula by Integration of Machine Learning, Promoter Analysis, and Direct Merging Meta-Analysis. Frontiers in Plant Science, 9, 24 pages.
Scopus23 WoS16 Europe PMC132018 Pashaei-Asl, F., Pashaei-Asl, R., Khodadadi, K., Akbarzadeh, A., Ebrahimie, E., & Pashaiasl, M. (2018). Enhancement of anticancer activity by silibinin and paclitaxel combination on the ovarian cancer. Artificial Cells, Nanomedicine and Biotechnology, 46(7), 1483-1487.
Scopus52 WoS41 Europe PMC242018 Alanazi, I., AlYahya, S., Ebrahimie, E., & Mohammadi-Dehcheshmeh, M. (2018). Computational systems biology analysis of biomarkers in lung cancer; unravelling genomic regions which frequently encode biomarkers, enriched pathways, and new candidates. Gene, 659, 29-36.
Scopus14 WoS8 Europe PMC72018 Baharlou Houreh, M., Ghorbani Kalkhajeh, P., Niazi, A., Ebrahimi, F., & Ebrahimie, E. (2018). SpliceDetector: A software for detection of alternative splicing events in human and model organisms directly from transcript IDs. Scientific Reports, 8(1), 11 pages.
Scopus8 WoS6 Europe PMC62018 Rahimi, T., Niazi, A., Deihimi, T., Taghavi, S., Ayatollahi, S., & Ebrahimie, E. (2018). Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil. Functional and Integrative Genomics, 18(5), 533-543.
Scopus18 WoS13 Europe PMC52018 Azizi, F., Jalil, H., Nasiri, Z., Moshtaghian, J., Esmaeili, F., Doostmohammadi, A., . . . Ebrahimie, E. (2018). The combined effects of three dimensional cell culture and natural tissue extract on neural differentiation of P19 embryonal carcinoma stem cells. Journal of tissue engineering and regenerative medicine, 12(9), 1909-1924.
Scopus7 WoS4 Europe PMC32018 Farhadian, M., Rafat, S., Hasanpur, K., & Ebrahimie, E. (2018). Transcriptome signature of the lactation process, identified by meta-analysis of microarray and RNA-Seq data. Biotechnologia, 99(2), 153-163.
Scopus102018 Farhadian, M., Rafat, S., Hasanpur, K., Ebrahimi, M., & Ebrahimie, E. (2018). Cross-species meta-analysis of transcriptomic data in combination with supervised machine learning models identifies the common gene signature of lactation process. Frontiers in Genetics, 9(JUL), 1-17.
Scopus28 WoS26 Europe PMC162018 Shamloo-Dashtpagerdi, R., Razi, H., Ebrahimie, E., & Niazi, A. (2018). Molecular characterization of Brassica napus stress related transcription factors, BnMYB44 and BnVIP1, selected based on comparative analysis of Arabidopsis thaliana and Eutrema salsugineum transcriptomes. Molecular Biology Reports, 45(5), 1111-1124.
Scopus20 WoS15 Europe PMC72018 Godini, R., Fallahi, H., & Ebrahimie, E. (2018). Network analysis of inflammatory responses to sepsis by neutrophils and peripheral blood mononuclear cells. PLoS ONE, 13(8), e0201674.
Scopus21 WoS15 Europe PMC172018 Helal, S., Li, J., Liu, L., Ebrahimie, E., Dawson, S., Murray, D., & Long, Q. (2018). Predicting academic performance by considering student heterogeneity. Knowledge-Based Systems, 161, 134-146.
Scopus148 WoS832018 Helal, S., Li, J., Liu, L., Ebrahimie, E., Dawson, S., & Murray, D. J. (2018). Identifying key factors of student academic performance by subgroup discovery. International Journal of Data Science and Analytics, 7(3), 227-245.
Scopus36 WoS252018 Ebrahimie, E., Ebrahimi, F., Ebrahimi, M., Tomlinson, S., & Petrovski, K. R. (2018). A large-scale study of indicators of sub-clinical mastitis in dairy cattle by attribute weighting analysis of milk composition features: highlighting the predictive power of lactose and electrical conductivity. Journal of Dairy Research, 85(2), 193-200.
Scopus54 WoS35 Europe PMC242018 Alanazi, I., Ebrahimie, E., Hoffmann, P., & Adelson, D. (2018). Correction to: Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis (Apoptosis, (2013), 18, 11, (1291-1305), 10.1007/s10495-013-0887-6). Apoptosis, 23(1), 92.
Scopus1 WoS12018 Tarigan, S., Wibowo, M., Indriani, R., Sumarningsih, S., Artanto, S., Idris, S., . . . Ignjatovic, J. (2018). Field effectiveness of highly pathogenic avian influenza H5N1 vaccination in commercial layers in Indonesia. PLoS ONE, 13(1), e0190947-1-e0190947-15.
Scopus21 WoS14 Europe PMC122018 Alisoltani, A., Shiran, B., Sarvestani, N., Fallahi, H., Feto, N., & Ebrahimie, E. (2018). Changes in microsatellite motifs in response to abiotic stresses: a case study using wheat and rice RNA-sequencing data. Asian Journal of Scientific Research, 11(1), 12-21.
Scopus12018 Sharifi, S., Pakdel, A., Ebrahimi, M., Reecy, J., Farsani, S., & Ebrahimie, E. (2018). Integration of machine learning and metaanalysis identifies the transcriptomic bio-signature of mastitis disease in cattle. PLoS ONE, 13(2), 18 pages.
Scopus83 WoS63 Europe PMC462018 Ebrahimie, E., Ebrahimi, F., Ebrahimi, M., Tomlinson, S., & Petrovski, K. (2018). Hierarchical pattern recognition in milking parameters predicts mastitis prevalence. Computers and Electronics in Agriculture, 147, 6-11.
Scopus51 WoS39 Europe PMC42018 Ricciardelli, C., Bianco-Miotto, T., Jindal, S., Butler, L., Leung, S., McNeil, C., . . . Tilley, W. (2018). The magnitude of androgen receptor positivity in breast cancer is critical for reliable prediction of disease outcome. Clinical Cancer Research, 24(10), 2328-2341.
Scopus65 WoS53 Europe PMC522018 Centenera, M., Selth, L., Ebrahimie, E., Butler, L., & Tilley, W. (2018). New opportunities for targeting the androgen receptor in prostate cancer. Cold Spring Harbor Perspectives in Medicine, 10(12), 1-19.
Scopus22 WoS18 Europe PMC152018 Shiri, Y., Solouki, M., Ebrahimie, E., Emamjomeh, A., & Zahiri, J. (2018). Unraveling the transcriptional complexity of compactness in sistan grape cluster. Plant Science, 270, 198-208.
Scopus10 WoS6 Europe PMC32017 Fruzangohar, M., Ebrahimie, E., & Adelson, D. (2017). A novel hypothesis-unbiased method for gene ontology enrichment based on transcriptome data. PLoS ONE, 12(2), e0170486-1-e0170486-14.
Scopus17 WoS13 Europe PMC132017 Knight, E., Trott, D., Page, S., Garg, S., Zhang, Q., Song, Y., . . . Shipstone, M. (2017). In vitro comparison of the dermal penetration of three different topical formulations containing lasalocid. Veterinary Dermatology, 28(4), 342-347.
Scopus1 WoS12017 Kakeshpour, T., Monfared, S., Ebrahimi, A., Beyraghdar Kashkooli, A., & Ebrahimie, E. (2017). Expression analyses of salinity stress- associated ESTs in Aeluropus littoralis. Gene Expression Patterns, 25-26, 76-84.
Scopus2 WoS1 Europe PMC22017 Pashaei-Asl, R., Pashaei-Asl, F., Gharabaghi, P., Khodadadi, K., Ebrahimi, M., Ebrahimie, E., & Pashaiasl, M. (2017). The inhibitory effect of ginger extract on Ovarian cancer cell line; Application of systems biology. Advanced Pharmaceutical Bulletin, 7(2), 241-249.
Scopus48 WoS38 Europe PMC202017 Moazzzam Jazi, M., Seyedi, S., Ebrahimie, E., Ebrahimi, M., De Moro, G., & Botanga, C. (2017). A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery. BMC Genomics, 18(1), 1-21.
Scopus38 WoS32 Europe PMC152017 Ebrahimie, E., Fruzangohar, M., Moussavi Nik, S. H., & Newman, M. (2017). Gene Ontology-based analysis of zebrafish’ omics data using the web tool Comparative Gene Ontology. Zebrafish, 14(5), 492-494.
Scopus13 WoS11 Europe PMC72017 Rahbar, S., Novin, M., Alizadeh, E., Shahnazi, V., Pashaei-Asl, F., AsrBadr, Y., . . . Pashaiasl, M. (2017). New insights into the expression profile of MicroRNA-34c and P53 in infertile men spermatozoa and testicular tissue. Cellular and Molecular Biology, 63(8), 77-83.
Scopus23 WoS18 Europe PMC102017 Das, R., Gregory, P. A., Fernandes, R. C., Denis, I., Wang, Q., Townley, S. L., . . . Selth, L. A. (2017). MicroRNA-194 promotes prostate cancer metastasis by inhibiting SOCS2. Cancer Research, 77(4), 1021-1034.
Scopus97 WoS88 Europe PMC672017 Shirzad, H., Esmaeili, F., Bakhshalizadeh, S., Ebrahimie, M., & Ebrahimie, E. (2017). Production of stable GFP-expressing neural cells from P19 embryonal carcinoma stem cells. Molecular and Cellular Probes, 32, 46-54.
Scopus1 WoS1 Europe PMC12016 Mansouri, A., Esmaeili, F., Nejatpour, A., Houshmand, F., Shabani, L., & Ebrahimie, E. (2016). Differentiation of P19 embryonal carcinoma stem cells into insulin-producing cells promoted by pancreas-conditioned medium. Journal of Tissue Engineering and Regenerative Medicine, 10(7), 600-612.
Scopus8 WoS7 Europe PMC62016 Mehrfarjam, Z., Esmaeili, F., Shabani, L., & Ebrahimie, E. (2016). Induction of pancreatic β cell gene expression in mesenchymal stem cells. Cell Biology International, 40(5), 486-500.
Scopus13 WoS12 Europe PMC92016 Pashaiasl, M., Khodadadi, K., Kayvanjoo, A., Pashaei-asl, R., Ebrahimie, E., & Ebrahimi, M. (2016). Unravelling evolution of Nanog, the key transcription factor involved in self-renewal of undifferentiated embryonic stem cells, by pattern recognition in nucleotide and tandem repeats characteristics. Gene, 578(2), 194-204.
Scopus18 WoS16 Europe PMC122016 Hasan, N., Ebrahimie, E., Ignjatovic, J., Tarigan, S., Peaston, A., & Hemmatzadeh, F. (2016). Antigenic mapping for determining the immunoreactivity of different regions of M2e protein of H5N1 influenza using overlapping peptides-based ELISA. PLoS One. 2016 Jamali, A., Ferdousi, R., Razzaghi, S., Li, J., Safdari, R., & Ebrahimie, E. (2016). DrugMiner: comparative analysis of machine learning algorithms for prediction of potential druggable proteins. Drug Discovery Today, 21(5), 718-724.
Scopus76 WoS65 Europe PMC462016 Ebrahimie, E., Moussavi Nik, S., Newman, M., Van Der Hoek, M., & Lardelli, M. (2016). The Zebrafish equivalent of Alzheimer's disease-associated PRESENILIN Isoform PS2V regulates inflammatory and other responses to hypoxic stress. Journal of Alzheimer's Disease, 52(2), 581-608.
Scopus14 WoS12 Europe PMC122016 Alanazi, I., & Ebrahimie, E. (2016). Computational systems biology approach predicts regulators and targets of microRNAs and their genomic hotspots in apoptosis process. Molecular Biotechnology, 58(7), 460-479.
Scopus13 WoS11 Europe PMC92016 Hasan, N., Ebrahimie, E., Ignjatovic, J., Tarigan, S., Peaston, A., & Hemmatzadeh, F. (2016). Epitope mapping of avian influenza m2e protein: different species recognise various epitopes. PLoS One, 11(6), e0156418-1-e0156418-15.
Scopus8 WoS8 Europe PMC42016 Pashaiasl, M., Ebrahimi, M., & Ebrahimie, E. (2016). Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis. Molecular Biology Reports, 43(9), 923-937.
Scopus29 WoS23 Europe PMC142016 Kargarfard, F., Sami, A., Mohammadi-Dehcheshmeh, M., & Ebrahimie, E. (2016). Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments. BMC Genomics, 17(1), 925-1-925-10.
Scopus20 WoS17 Europe PMC132015 Ebrahimi, M., Ebrahimie, E., & Bull, C. (2015). Minimizing the cost of translocation failure with decision-tree models that predict species' behavioral response in translocation sites. Conservation Biology, 29(4), 1208-1216.
Scopus16 WoS13 Europe PMC42015 Rafiei, F., Torabi, Z., & Ebrahimie, E. (2015). "Type A" response regulators are involved in the plant-microbe interaction. Plant Omics Journal, 8(2), 178-182.
Scopus22015 Moussavi Nik, S., Newman, M., Wilson, L., Ebrahimie, E., Wells, S., Musgrave, I., . . . Lardelli, M. (2015). Alzheimer's disease-related peptide PS2V plays ancient, conserved roles in suppression of the unfolded protein response under hypoxia and stimulation of γ-secretase activity. Human Molecular Genetics, 24(13), 3662-3678.
Scopus26 WoS22 Europe PMC142015 Fruzangohar, M., Ebrahimie, E., Ogunniyi, A. D., Mahdi, L. K., Paton, J. C., & Adelson, D. L. (2015). Correction: Comparative GO: A web application for comparative gene ontology and gene ontology-based gene selection in bacteria. PLoS ONE, 10(4), 1 page.
Scopus6 WoS4 Europe PMC32015 Lim, A., Moussavi Nik, S., Ebrahimie, E., & Lardelli, M. (2015). Analysis of nicastrin gene phylogeny and expression in zebrafish. Development Genes and Evolution, 225(3), 171-178.
Scopus5 WoS4 Europe PMC32015 Bidabadi, M., Shiran, B., Fallahi, H., Rafiei, F., Esmaeili, F., & Ebrahimie, E. (2015). Identification of differential expressed transcripts of almond (Prunus dulcis ‘Sefied’) in response to water-deficit stress by cDNA-AFLP. Journal of Forest Research, 20(4), 403-410.
Scopus2 WoS12015 Shamloo-Dashtpagerdi, R., Razi, H., & Ebrahimie, E. (2015). Mining expressed sequence tags of rapeseed (Brassica napus L.) to predict the drought responsive regulatory network. Physiology and Molecular Biology of Plants, 21(3), 329-340.
Scopus18 WoS13 Europe PMC82015 Khazandi, M., Eats, P., Trott, D., Ebrahimie, E., Perry, J., Hickey, E., . . . Petrovski, K. (2015). Development of an improved Streptococcus uberis experimental mastitis challenge model using different doses and strains in lactating dairy cows. Journal of Dairy Research, 82(4), 470-477.
Scopus8 WoS8 Europe PMC32015 Ebrahimie, E., Nurollah, Z., Ebrahimi, M., Hemmatzadeh, F., & Ignjatovic, J. (2015). Unique ability of pandemic influenza to downregulate the genes involved in neuronal disorders. Molecular Biology Reports, 42(9), 1377-1390.
Scopus14 WoS11 Europe PMC92015 Kargarfard, F., Sami, A., & Ebrahimie, E. (2015). Knowledge discovery and sequence-based prediction of pandemic influenza using an integrated classification and association rule mining (CBA) algorithm. Journal of Biomedical Informatics, 57, 181-188.
Scopus34 WoS24 Europe PMC122015 Gharaghani, F., Rafiei, F., Mirakhorli, N., & Ebrahimie, E. (2015). Differential expression of TLP, ERF1, and R2R3MYB in annual Medicago species under salinity conditions. Genetics and Molecular Research, 14(3), 10152-10164.
Scopus5 WoS5 Europe PMC42015 Tavizi, A., Javaran, M., Moieni, A., Mohammadi-Dehcheshmeh, M., Mohebodini, M., & Ebrahimie, E. (2015). Root and shoot parts of strawberry: factories for production of functional human pro-insulin. Molecular Biology Reports, 42(5), 1013-1023.
Scopus8 WoS8 Europe PMC22015 Parvini, F., Zeinanloo, A. A., Ebrahimie, E., Tahmasebi-Enferadi, S., & Hosseini-Mazinani, M. (2015). Differential expression of fatty acid desaturases in Mari and Shengeh olive cultivars during fruit development and ripening. European Journal of Lipid Science and Technology, 117(4), 523-531.
Scopus19 WoS172015 Alisoltani, A., Fallahi, H., Shiran, B., Alisoltani, A., & Ebrahimie, E. (2015). RNA-Seq SSRs and small RNA-Seq SSRs: new approaches in cancer biomarker discovery. Gene, 560(1), 34-43.
Scopus9 WoS7 Europe PMC52015 Shamloo-Dashtpagerdi, R., Razi, H., Aliakbari, M., Lindlöf, A., Ebrahimi, M., & Ebrahimie, E. (2015). A novel pairwise comparison method for in silico discovery of statistically significant cis-regulatory elements in eukaryotic promoter regions: application to Arabidopsis. Journal of Theoretical Biology, 364, 364-376.
Scopus12 WoS8 Europe PMC62015 Hemmatzadeh, F., Keyvanfar, H., Hasan, N., Niap, F., Bani Hassan, E., Hematzade, A., . . . Ignjatovic, J. (2015). Interaction between Bovine leukemia virus (BLV) infection and age on telomerase misregulation. Veterinary Research Communications, 39(2), 97-103.
Scopus7 WoS5 Europe PMC52015 Panahi, B., Mohammadi, S., Khaksefidi, R., Fallah Mehrabadi, J., & Ebrahimie, E. (2015). Genome-wide analysis of alternative splicing events in Hordeum vulgare: highlighting retention of intron-based splicing and its possible function through network analysis. FEBS Letters, 589(23), 3564-3575.
Scopus33 WoS25 Europe PMC242015 Khaksefidi, R., Mirlohi, S., Khalaji, F., Fakhari, Z., Shiran, B., Fallahi, H., . . . Ebrahimie, E. (2015). Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus. Frontiers in Plant Science, 6(Sep), 741-1-741-14.
Scopus67 WoS49 Europe PMC272015 Khaksar, G., Tabatabaei, B., Arzani, A., Ghobadi, C., & Ebrahimie, E. (2015). Functional analysis of a pomegranate (Punica granatum L.) MYB transcription factor involved in the regulation of anthocyanin biosynthesis. Iranian Journal of Biotechnology, 13(1), 104517-104525.
Scopus12 WoS9 Europe PMC62015 Alisoltani, A., Shiran, B., Fallahi, H., & Ebrahimie, E. (2015). Gene regulatory network in almond (Prunus dulcis Mill.) in response to frost stress. Tree Genetics and Genomes, 11(5), 100-1-100-15.
Scopus21 WoS142015 Mahdi, L., Van der Hoek, M., Ebrahimie, E., Paton, J., & Ogunniyi, A. (2015). Characterization of pneumococcal genes involved in bloodstream invasion in a mouse model. PLoS One, 10(11), e0141816-1-e0141816-15.
Scopus19 WoS18 Europe PMC172015 Torkzaban, B., Kayvanjoo, A., Ardalan, A., Mousavi, S., Mariotti, R., Baldoni, L., . . . Hosseini-Mazinani, M. (2015). Machine learning based classification of microsatellite variation: an effective approach for phylogeographic characterization of olive populations. PLoS One, 10(11), e0143465-1-e0143465-17.
Scopus19 WoS10 Europe PMC92014 Delavari, A., Zare, S., Ghaemi, M., Kashfi, R., Ebrahimi, M., Tahmasebi, A., . . . Ebrahimie, E. (2014). Determining the structural amino acid attributes which are important in both protein thermostability and alkalophilicity: a case study on xylanase. Biotechnologia, 95(2), 161-173.
Scopus22014 Hadifar, F., Ignjatovic, J., Tarigan, S., Indriani, R., Ebrahimie, E., Haliza Hasan, N., . . . Hemmatzadeh, F. (2014). Multimeric recombinant M2e protein-based ELISA: A significant improvement in differentiating avian influenza infected chickens from vaccinated ones. PLoS One, 9(10), e108420-1-e108420-8.
Scopus13 WoS17 Europe PMC92014 Pourkhorshid, Z., Dadkhodaie, A., Niazi, A., Heidari, B., & Ebrahimi, E. (2014). Identification of wheat stripe rust resistance genes in Iranian wheat cultivars using molecular markers. Annual Research & Review in Biology, 4(17), 2766-2778.
2014 Mahdi, L., Deihimi, T., Zamansani, F., Fruzangohar, M., Adelson, D., Paton, J., . . . Ebrahimie, E. (2014). A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease. BMC Genomics, 15(1), 769-1-769-15.
Scopus16 WoS14 Europe PMC142014 Zinati, Z., Zamansani, F., Hossein KayvanJoo, A., Ebrahimi, M., Ebrahimi, M., Ebrahimie, E., & Mohammadi Dehcheshmeh, M. (2014). New layers in understanding and predicting α-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase. Computers in Biology and Medicine, 54, 14-23.
Scopus17 WoS13 Europe PMC62014 Zamani Babgohari, M., Ebrahimie, E., & Niazi, A. (2014). In silico analysis of high affinity potassium transporter (HKT) isoforms in different plants. Aquatic Biosystems, 10(1), 9-1-9-14.
Europe PMC72014 Ebrahimie, M., Esmaeili, F., Cheraghi, S., Houshmand, F., Shabani, L., & Ebrahimie, E. (2014). Efficient and simple production of insulin-producing cells from embryonal carcinoma stem cells using mouse neonate pancreas extract, as a natural inducer. PLOS One, 9(3), 1-12.
Scopus34 WoS30 Europe PMC232014 Ebrahimi, M., Aghagolzadeh, P., Shamabadi, N., Tahmasebi, A., Alsharifi, M., Adelson, D., . . . Ebrahimie, E. (2014). Understanding the undelaying mechanism of HASubtyping in the level of physic-chemal characteristics of protein. PLoS One, 9(5), e96984-1-e96984-14.
Scopus26 WoS18 Europe PMC152014 Mousavi, S., Alisoltani, A., Shiran, B., Fallahi, H., Ebrahimie, E., Imani, A., & Houshmand, S. (2014). De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress. PLoS One, 9(8), e104541-1-e104541-13.
Scopus53 WoS43 Europe PMC332014 Hosseinpour, B., Bakhtiarizadeh, M., Mirabbassi, S., & Ebrahimie, E. (2014). Comparison of hematopoietic cancer stem cells with normal stem cells leads to discovery of novel differentially expressed SSRs. Gene, 550(1), 10-17.
Scopus2 WoS2 Europe PMC22014 Newman, M., Ebrahimie, E., & Lardelli, M. (2014). Using the zebrafish model for Alzheimer's disease research. Frontiers in Genetics, 5(JUN), 189-1-189-10.
Scopus112 WoS92 Europe PMC552014 Panahi, B., Abbaszadeh, B., Taghizadeghan, M., & Ebrahimie, E. (2014). Genome-wide survey of alternative splicing in sorghum bicolor. Physiology and Molecular Biology of Plants, 20(3), 323-329.
Scopus30 WoS25 Europe PMC202014 Shekoofa, A., Emam, Y., Shekoufa, N., Ebrahimi, M., & Ebrahimie, E. (2014). Determining the most important physiological and agronomic traits contributing to maize grain yield through machine learning algorithms: a new avenue in intelligent agriculture. PLoS One, 9(5), e97288-1-e97288-9.
Scopus69 WoS51 Europe PMC152014 Bakhtiarizadeh, M., Moradi-Shahrbabak, M., Ebrahimi, M., & Ebrahimie, E. (2014). Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology. Journal of Theoretical Biology, 356, 213-222.
Scopus53 WoS43 Europe PMC232014 Alisoltani, A., Fallahi, H., Ebrahimi, M., Ebrahimi, M., & Ebrahimie, E. (2014). Prediction of potential cancer-risk regions based on transcriptome data: towards a comprehensive view. PLoS One, 9(5), e96320-1-e96320-13.
Scopus22 WoS19 Europe PMC152014 Bakhtiarizadeh, M., Moradi-Shahrbabak, M., & Ebrahimie, E. (2014). Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue. Genes and Genomics, 36(1), 105-117.
Scopus15 WoS142014 Mohammadi Dehcheshmeh, M., Ebrahimie, E., Tyerman, S., & Kaiser, B. (2014). A novel method based on combination of semi-in vitro and in vivo conditions in Agrobacterium rhizogenes-mediated hairy root transformation of Glycine species. In Vitro Cellular & Developmental Biology-plant, 50(2), 282-291.
Scopus10 WoS112013 Alanazi, I., Ebrahimie, E., Hoffmann, P., & Adelson, D. (2013). Combined gene expression and proteomic analysis of EGF induced apoptosis in A431 cells suggests multiple pathways trigger apoptosis. Apoptosis, 18(11), 1291-1305.
Scopus23 WoS19 Europe PMC152013 Hosseinpour, B., Bakhtiarizadeh, M., Khosravi, P., & Ebrahimie, E. (2013). Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network. Gene, 531(2), 212-219.
Scopus25 WoS23 Europe PMC252013 Panahi, B., Mohammadi, S., & Ebrahimie, E. (2013). Identification of miRNAs and their potential targets in halophyte plant Thellungiella halophila. Biotechnologia: przeglad informacyjny, 94(3), 285-290.
Scopus122013 Mahdi, L., Ebrahimie, E., Adelson, D., Paton, J., & Ogunniyi, A. (2013). A transcription factor contributes to pathogenesis and virulence in streptococcus pneumoniae. PLoS One, 8(8), 1-9.
Scopus14 WoS13 Europe PMC122013 Alimohammadi, M., Shiran, B., Martinez-Gomez, P., & Ebrahimie, E. (2013). Identification of water-deficit resistance genes in wild almond Prunus scoparia using cDNA-AFLP. Scientia Horticulturae, 159, 19-28.
Scopus20 WoS202013 Deihimi, T., Niazi, A., & Ebrahimie, E. (2013). Identification and expression analysis of TLPs as candidate genes promoting the responses to both biotic and abiotic stresses in wheat. Plant Omics, 6(2), 107-115.
Scopus5 WoS22013 Moghadam, A., Ebrahimie, E., Taghavi, S., Niazi, A., Babgohari, M., Deihimi, T., . . . Ramezani, A. (2013). How the nucleus and mitochondria communicate in energy production during stress: nuclear MtATP6, an early-stress responsive gene, regulates the mitochondrial F1F0-ATP synthase complex. Molecular Biotechnology, 54(3), 756-769.
Scopus30 WoS25 Europe PMC142013 Bakhtiarizadeh, M., Moradi-Shahrbabak, M., & Ebrahimie, E. (2013). Underlying functional genomics of fat deposition in adipose tissue. Gene, 521(1), 122-128.
Scopus58 WoS54 Europe PMC412013 Fruzangohar, M., Ebrahimie, E., Ogunniyi, A., Mahdi, L., Paton, J., & Adelson, D. (2013). Comparative GO: a web application for comparative Gene Ontology and Gene Ontology-based gene selection in bacteria. PLoS One, 8(3), 1-8.
Scopus58 WoS53 Europe PMC442013 Babgohari, M., Niazi, A., Moghadam, A., Deihimi, T., & Ebrahimie, E. (2013). Genome-wide analysis of key salinity-tolerance transporters (HKT1;5) in wheat and wild wheat relatives (A and D genomes). In Vitro Cellular & Developmental Biology-plant, 49(2), 97-106.
Scopus31 WoS282013 Hemmatzadeh, F., Sumarningsih, S., Tarigan, S., Indriani, R., Dharmayanti, N., Ebrahimie, E., & Igniatovic, J. (2013). Recombinant M2e protein-based ELISA: A novel and inexpensive approach for differentiating avian influenza infected chickens from vaccinated ones. PLoS One, 8(2), 1-9.
Scopus23 WoS28 Europe PMC162013 Shamloo-Dashtpagerdi, R., Razi, H., Lindlof, A., Niazi, A., Dadkhodaie, A., & Ebrahimie, E. (2013). Comparative analysis of expressed sequence tags (ESTs) from Triticum monococcum shoot apical meristem at vegetative and reproductive stages. Genes and Genomics, 35(3), 365-375.
Scopus7 WoS52013 Ramezani, A., Niazi, A., Abolimoghadam, A., Babgohari, M., Deihimi, T., Ebrahimi, M., . . . Ebrahimie, E. (2013). Quantitative expression analysis of TaSOS1 and TaSOS4 genes in cultivated and wild wheat plants under salt stress. Molecular Biotechnology, 53(2), 189-197.
Scopus38 WoS29 Europe PMC132012 Bakhtiarizadeh, M., Arefnejad, B., Ebrahimie, E., & Ebrahimi, M. (2012). Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus). Genetics and Molecular Research, 11(2), 1558-1574.
Scopus14 WoS11 Europe PMC62012 Tahmasebi, A., Aram, F., Ebrahimi, M., Mohammadi Dehcheshmeh, M., & Ebrahimie, E. (2012). Genome-wide analysis of cytosolic and chloroplastic isoforms of glutathione reductase in plant cells. Plant Omics, 5(2), 94-102.
Scopus16 WoS132012 Hosseinpour, B., HajiHoseini, V., Kashfi, R., Ebrahimie, E., & Hemmatzadeh, F. (2012). Protein interaction network of Arabidopsis thaliana female gametophyte development identifies novel proteins and relations. PLoS One, 7(12), 1-12.
Scopus22 WoS20 Europe PMC142012 Abolimoghadam, A., Taghavi, S., Niazi, A., Djavaheri, M., & Ebrahimie, E. (2012). Isolation and in silico functional analysis of MtATP6, a 6-kDa subunit of mitochondrial F₁F₀-ATP synthase, in response to abiotic stress. Genetics and Molecular Research, 11(4), 3547-3567.
Scopus19 WoS17 Europe PMC82012 Bijanzadeh, E., Emam, Y., Ebrahimie, E., & Ebrahimi, M. (2012). Application of unsupervised weighting algorithms for identifying important attributes and factors contributing to grain and biological yields of wheat. Crop Breeding Journal, 2(2), 111-117. 2012 Deihimi, T., Niazi, A., Ebrahimi, M., Kajbaf, K., Fanaee, S., Bakhtiarizadeh, M., & Ebrahimie, E. (2012). Finding the undiscovered roles of genes: an approach using mutual ranking of coexpressed genes and promoter architecture-case study: dual roles of thaumatin like proteins in biotic and abiotic stresses. SpringerPlus, 1(30), 1-10.
Scopus25 WoS23 Europe PMC182012 Borji, H., Azizzadeh, M., Ebrahimi, M., & Asadpour, M. (2012). Study on small ruminant lungworms and associated risk factors in northeastern Iran. ASIAN PACIFIC JOURNAL OF TROPICAL MEDICINE, 5(11), 853-856.
WoS7 Europe PMC52012 Hosseinzadeh, F., Ebrahimi, M., Goliaei, B., & Shamabadi, N. (2012). Classification of Lung Cancer Tumors Based on Structural and Physicochemical Properties of Proteins by Bioinformatics Models. PLOS ONE, 7(7), 8 pages.
WoS23 Europe PMC132012 Beiki, A. H., Saboor, S., & Ebrahimi, M. (2012). A new avenue for classification and prediction of olive cultivars using supervised and unsupervised algorithms. PLoS ONE, 7(9), e44164-1-e44164-9.
WoS20 Europe PMC162011 Ebrahimi, M. (2011). Comparing various attributes of prolactin hormones in different species: application of bioinformatics tools. IRANIAN JOURNAL OF VETERINARY RESEARCH, 12(3), 205-213.
WoS32011 Ebrahimi, M., & Taherianfard, M. (2011). Pathological and Hormonal Changes in Freshwater Fishes Due to Exposure to Heavy Metals Pollutants. WATER AIR AND SOIL POLLUTION, 217(1-4), 47-55.
WoS42011 Lakizadeh, A., Agha-Golzadeh, P., Ebrahimi, M., Ebrahimie, E., & Ebrahimi, M. (2011). Engineering thermostable enzymes; application of unsupervised clustering algorithms. Advanced Studies in Biology, 3(2), 63-78. 2011 Ebrahimie, E., Ebrahimi, M., & Ebrahimi, M. (2011). Amino acid features: a missing compartment of prediction of protein function. Nature Precedings, Online, 1-16.
2011 Ebrahimi, M., Lakizadeh, A., Agha-Golzadeh, P., Ebrahimie, E., & Ebrahimi, M. (2011). Prediction of thermostability from amino acid attributes by combination of clustering with attribute weighting: A new vista in engineering enzymes. PLoS One, 6(8), e23146-1-e23146-11.
Scopus58 WoS44 Europe PMC322011 Ashrafi, E., Alemzadeh, A., Ebrahimi, M., Ebrahimie, E., Dadkhodaei, N., & Ebrahimi, M. (2011). Amino acid features of P1B-ATPase heavy metal transporters enabling small numbers of organisms to cope with heavy metal pollution. Bioinformatics and Biology Insights, 5, 59-82.
Scopus28 WoS24 Europe PMC152011 Baseri, S., Towhidi, M., & Ebrahimie, E. (2011). A modified efficient empirical Bayes regression model for predicting phenomena with a large number of independent variables and fewer observations; examples of its application in human disease, protein bioinformatics, and microarray gene expression profiling. Advanced Studies in Biology, 3(4), 181-204. 2011 Shekoofa, A., Emam, Y., Ebrahimi, M., & Ebrahimie, E. (2011). Application of supervised feature selection methods to define the most important traits affecting maximum kernel water content in maize. Australian Journal of Crop Science, 5(2), 162-168.
Scopus6 WoS42011 Ebrahimie, E., Ebrahimi, M., Sarvestani, N., & Ebrahimi, M. (2011). Protein attributes contribute to halo-stability, bioinformatics approach. Aquatic Biosystems, 7(1), 1-14.
Scopus44 Europe PMC282011 Tahrokh, E., Ebrahimi, M., Zamansani, F., Ebrahimi, M., Sarvestani, N., Mohammadi Dehcheshmeh, M., . . . Ebrahimie, E. (2011). Comparative study of ammonium transporters in different organisms by study of a large number of structural protein features via data mining algorithms. Genes and Genomics, 33(5), 565-575.
Scopus11 WoS112011 Bakhtiarizadeh, M., Ebrahimi, M., & Ebrahimie, E. (2011). Discovery of EST-SSRs in lung cancer: Tagged ESTs with SSRs lead to differential amino acid and protein expression patterns in cancerous tissues. PLoS One, 6(11), 1-11.
Scopus14 WoS12 Europe PMC72010 Ebrahimi, M., & Ebrahimie, E. (2010). Sequence-based prediction of enzyme thermostability through bioinformatics algorithms. Current Bioinformatics, 5(3), 195-203.
Scopus26 WoS212010 Ebrahimi, M., Ebrahimie, E., Shamabadi, N., & Ebrahimi, M. (2010). Are there any differences between features of proteins expressed in malignant and benign breast cancers?. Journal of Research in Medical Sciences (JRMS), 15(6), 299-309.
Scopus27 WoS24 Europe PMC172010 Ebrahimie, E., Ebrahimi, M., & Sarvestani, N. (2010). Investigating protein features contribute to salt stability of halolysin proteins. Journal of Cell and Molecular Research, 2(1), 15-28. 2010 Bijanzadeh, E., Emam, Y., & Ebrahimie, E. (2010). Determining the most important features contributing to wheat grain yield using supervised feature selection model. Australian Journal of Crop Science, 4(6), 402-407.
Scopus21 WoS132010 Boskabadi, H., Maamouri, G., Ebrahimi, M., Ghayour-Mobarhan, M., Esmaeily, H., Sahebkar, A., & Ferns, G. A. A. (2010). Neonatal hypernatremia and dehydration in infants receiving inadequate breastfeeding. ASIA PACIFIC JOURNAL OF CLINICAL NUTRITION, 19(3), 301-307.
WoS33 Europe PMC242010 Ebrahimie, E., Mohammadi-Dehcheshmeh, M., Ebrahimi, M., & Ebrahimi, M. (2010). A study on functional modulations of genome in somatic embryogenesis pathway using EST analysis. NEW BIOTECHNOLOGY, 27, S43.
WoS22009 Ebrahimi, M., Ebrahimie, E., & Ebrahimi, M. (2009). Searching for patterns of thermostability in proteins and defining the main features contributing to enzyme thermostability through screening, clustering, and decision tree algorithms. EXCLI Journal, 8, 218-233.
Scopus19 WoS172009 Shirazi, M., & Ebrahimie, E. (2009). Evidence that estrogen mediates the positive feedback effect on GnRH. Advances in Environmental Biology, 3(3), 244-248. 2008 Mohammadi-Dehcheshmeh, M., Khalighi, A., Naderi, R., Sardari, M., & Ebrahimie, E. (2008). Petal: a reliable explant for direct bulblet regeneration of endangered wild populations of Fritillaria imperialis L.. Acta Physiologiae Plantarum, 30(3), 395-399.
Scopus22 WoS162007 Ebrahimie, E., Naghavi, M. R., Hosseinzadeh, A., Behamta, M. R., Mohammadi-Dehcheshmeh, M., Sarrafi, A., & Spangenberg, G. (2007). Induction and comparison of different in vitro morphogenesis pathways using embryo of cumin (Cuminum cyminum L.) as a model material. Plant Cell, Tissue and Organ Culture, 90(3), 293-311.
Scopus19 WoS142007 Ebrahimie, E., Hosseinzadeh, A., Nagavi, M. R., Ghannadha, M. R., & Mohammadie-Dehcheshmeh, M. (2007). Combined direct regeneration protocols in tissue culture of different cumin genotypes based on pre-existing meristems. Pakistan Journal of Biological Sciences, 10(9), 1360-1370.
Scopus12007 Mohammadi-Dehcheshmeh, M., Khalighi, A., Naderi, R., Ebrahimie, E., & Sardari, M. (2007). Indirect somatic embryogenesis from petal explant of endangered wild population of Fritillaria imperialis. Pakistan Journal of Biological Sciences, 10(11), 1875-1879.
Scopus122006 Ebrahimie, E., Habashy, A. A., Mohammadie-Dehcheshmeh, M., Ghannadha, M. R., Ghareyazie, B., & Yazdi-Amadi, B. (2006). Direct shoot regeneration from mature embryo as a rapid and genotype-independent pathway in tissue culture of heterogeneous diverse sets of cumin (Cuminum cyminum L.) genotypes. In Vitro Cellular and Developmental Biology - Plant, 42(5), 455-460.
Scopus24 WoS232003 Ebrahimie, E., Habashi, A. A., Ghareyazie, B., Ghannadha, M., & Mohammadie, M. (2003). A rapid and efficient method for regeneration of plantlets from embryo explants of cumin (Cuminum cyminum). Plant Cell, Tissue and Organ Culture, 75(1), 19-25.
Scopus32 WoS23 -
Conference Papers
Year Citation 2023 Perov, I., Petrovski, K., & Ebrahimie, E. (2023). Differences in Milk Production Curves on Ten Dairy Farms with Automated and Conventional Milking System in South-East Australia. In A. Ronzhin, & A. Kostyaev (Eds.), Proceedings of the Third International Conference on Agriculture Digitalization and Organic Production (ADOP 2023) Vol. 362 (pp. 215-224). St Petersburg, Russia: Springer Nature Singapore.
DOI2015 Lardelli, M., Ebrahimie, E., Newman, M., Nik, S. M., & Hoek, M. V. D. (2015). Transcriptome analyses using human and zebrafish brain data reveal hypoxia as an important element in Alzheimer's disease. In JOURNAL OF NEUROCHEMISTRY Vol. 134 (pp. 324). Cairns, AUSTRALIA: WILEY-BLACKWELL. 2011 Ebrahimie, E., Ebrahimi, M., Deihimi, T., & Ebrahimi, M. (2011). Using neural networks expert system to predict protein thermostbility. In 2009 International Conference on Machine Learning and Computing - IPCSIT vol 3 (pp. 368-373). Singapore: IPCSIT. 2011 Ebrahimi, M., Ebrahimie, E., Tahmasebi, A., Sarvestani, N., & Deihimi, T. (2011). Bioinformatics and protein engineering; presenting a few applications employed in our labs. In 2009 International Conference on Machine Learning and Computing - vol 3 (pp. 516-520). Singapore: IPCSIT. 2010 Ebrahimi, M., & Ebrahimie, E. (2010). Application of bioinformatics algorithms to define the most important protein features contribute to GABA receptors diversity. In 2010 2nd International Conference on Chemical, Biological and Environmental Engineering (ICBEE 2010) (pp. 207-211). USA: IEEE.
DOI2010 Baseri, S., Ebrahimi, M., Ebrahimie, E., & Ebrahimi, M. (2010). Comparison of classical statistical, bayes, and empirical bayes methods in analysis of microarray data; which method can deal with large number of variables (genes) and small number of replications?. In NEW BIOTECHNOLOGY Vol. 27 (pp. S21). ELSEVIER SCIENCE BV.
DOI2010 Dehkordi, E. A., Alemzadeh, A., Ebrahimie, E., Agagolzadeh, P., & Ebrahimi, M. (2010). Bioinformatics study on P<sub>1B</sub>-ATPase; an important hyperaccumulator heavy metal transporter in phytoremediation. In NEW BIOTECHNOLOGY Vol. 27 (pp. S22). ELSEVIER SCIENCE BV.
DOI2009 Ebrahimi, M., Ebrahimie, E., Ebrahimi, M., Deihimi, T., Delavari, A., & Mohammadi-Dehcheshmeh, M. (2009). Application of neural networks methods to define the most important features contributing to xylanase enzyme thermostability. In IEEE Congress on Evolutionary Computation, 2009. CEC '09 Vol. 406 (pp. 2885-2891). USA: IEEE.
DOI Scopus5 WoS12006 Mohammadi-Dehcheshmeh, M., Khalighi, A., Ebrahimie, E., Sardari, M., & Naderi, R. (2006). Direct bulblet regeneration from mature embryo:: A rapid, efficient and genotype-independent in vitro morphogenesis pathway for preservation of endangered wild populations of <i>Fritillaria imperialis</i> and <i>Fritillaria persica</i>. In HORTSCIENCE Vol. 41 (pp. 1066). AMER SOC HORTICULTURAL SCIENCE.
WoS32006 Ebrahimie, E., Mohammadi-Dehcheshmeh, M., & Sardari, M. (2006). <i>Fritillaria</i> species are at risk of extinction in Iran:: Study on effective factors and necessity of international attention. In HORTSCIENCE Vol. 41 (pp. 1002). AMER SOC HORTICULTURAL SCIENCE.
WoS52006 Khalighi, A., Dehcheshmeh, M. M., Ebrahimie, E., Sardari, M., Naderi, R., & Naderi, R. (2006). Different developmental stages of mother plants induct different morphogenesis pathways in in vitro culture of <i>Fritillaria imperialis</i> and <i>Fritillaria persica</i>. In HORTSCIENCE Vol. 41 (pp. 984-985). AMER SOC HORTICULTURAL SCIENCE. 2004 Ebrahimie, E., Dehcheshmeh, M. M., Taleie, A., Gannadha, M. R., & Habashi, A. A. (2004). PLANT REGENERATION AND TRANSIENT GUS REPORTER GENE EXPRESSION IN CUM IN (CUMINIUM CYMINNIUM) EMBRYOS FOLLOWING PARTICLE BOMBARDMENT AND AGROBACTERIUM-MEDIATED TRANSFORMATION: ROLES OF PLANT GROWTH REGULATORS COMBINATIONS OF INOCULATION AND BOMBARDMENT MEDIUM. In ACTA PHYSIOLOGIAE PLANTARUM Vol. 26 (pp. 61). SPRINGER HEIDELBERG. -
Conference Items
Year Citation 2020 Lim, E., Hickey, T. A., Selth, L. A., Chia, K. M., Milioli, H. H., Roden, D., . . . Tilley, W. D. (2020). The androgen receptor is a tumour suppressor in estrogen receptor positive breast cancer. Poster session presented at the meeting of CANCER RESEARCH. San Antonio, TX: AMER ASSOC CANCER RESEARCH.
DOI
Connect With Me
External Profiles
