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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.
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PubMed Mentions: Fields:
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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.
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PubMed Mentions: Fields:
Translation:
HumansCells
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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.
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PubMed Mentions: Fields:
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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.
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PubMed Mentions: Fields:
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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.
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PubMed Mentions:
2 Fields:
Translation:
Animals
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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.
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PubMed Mentions: Fields:
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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.
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PubMed Mentions: Fields:
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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.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
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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.
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PubMed Mentions:
4 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
1
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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.
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PubMed Mentions:
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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.
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PubMed Mentions:
3
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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.
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PubMed Mentions:
12 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
2
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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.
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PubMed Mentions:
2 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
4 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions: Fields:
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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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PubMed Mentions:
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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.
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PubMed Mentions:
6 Fields:
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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.
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PubMed Mentions:
5 Fields:
Translation:
Animals
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Posttranslational modifications in proteins: resources, tools and prediction methods. Database (Oxford). 2021 04 07; 2021.
Ramazi S, Zahiri J. PMID: 33826699; PMCID: PMC8040245.
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PubMed Mentions:
155 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
6 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
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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.
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PubMed Mentions:
5 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
11 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions: Fields:
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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.
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PubMed Mentions:
46 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
40
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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.
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PubMed Mentions:
6 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
1
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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.
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PubMed Mentions:
4 Fields:
Translation:
AnimalsCells
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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.
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PubMed Mentions:
5 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
2 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
19 Fields:
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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.
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PubMed Mentions: Fields:
Translation:
Humans
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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.
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PubMed Mentions:
3 Fields:
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Performance evaluation measures for protein complex prediction. Genomics. 2019 12; 111(6):1483-1492.
Ivazeh A, Zahiri J, Rahgozar M, Srihari S. PMID: 30312661.
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PubMed Mentions:
1 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
6
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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.
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PubMed Mentions:
2 Fields:
Translation:
Animals
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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.
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PubMed Mentions:
8 Fields:
Translation:
Humans
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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.
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PubMed Mentions:
5 Fields:
Translation:
Cells
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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.
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PubMed Mentions:
14 Fields:
Translation:
HumansAnimalsCells
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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.
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PubMed Mentions:
2
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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.
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PubMed Mentions:
27 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
14 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
2
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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.
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PubMed Mentions:
33
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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:
53 Fields:
Translation:
HumansCells
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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.
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PubMed Mentions:
1
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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.
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PubMed Mentions:
4 Fields:
Translation:
Humans
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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:
7 Fields:
Translation:
Humans