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Software

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OOgenesis_Pred  is a Support Vector Machine-based classifier to predict the oogenesis related proteins based on 1920

meaningful protein sequence features. It takes protein FASTA sequences as input, and generate output about the

potential of a protein to be involved in oogenesis. OOgenesis_pred depends on two programs (libsvm and protr package

in R) and can be run on Linux. You can download it here or Github.

Please cite:

OOgenesis_Pred: A sequence-based method for predicting oogenesis proteins by six different modes of Chous pseudo

amino acid composition. Maryam Rahimi, Mohammad Reza Bakhtiarizadeh, Abdollah Mohammadi Sangcheshmeh.

(2017). Journal of theoretical biology. 414: 128–136. 

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PrESOgenesis is a  Support Vector Machine-based classifier  to predict the spermatogenesis/embryogenesis/oogenesis

relatedproteins  based on  1920  meaningful protein sequence features. It takes protein/DNAFASTA sequences as  input, 

and generate  output  about the potential of a protein to be involved  in spermatogenesis/embryogenesis/oogenesis.

PrESOgenesisdepends on  two programs (libsvm and protr  package in R) and can berun on Linux. Also,  it  use  TransDecoder

software to convert the DNA sequences (mRNA transcripts that converted to DNA) to protein. You can download it in Github.

Please cite:

PrESOgenesis: A two-layer multi-label predictor for identifying fertility-related proteins using support vector machine and

pseudo amino acid composition approach. Mohammad Reza Bakhtiarizadeh, Maryam Rahimi, Abdollah Mohammadi

Sangcheshmeh, Vahid Shariati J, Seyed Alireza Salami. (2018). Scietific Reports. 8:9025.

 

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B.Sc

    Animal Genetics

    Experimental Designs in Agriculture

M.Sc

    Molecular Genetics

    Bioinformatics

Ph.D

     Advanced Experimental Designs in Agriculture

     Advanced Bioinformatics

   Bioinformatics:

         Gene expression data analysis (EST, SAGE and Microarray data)

         Promoter analysis

         Protein and DNA sequence data mining (Software development)

         Non-coding RNA prediction (miRNA, lncRNA, circRNA, tRNA-derived RNA and piwiRNA)

         Integrative Gene regulatory Network

         And ... 

                                         

   NGS data analysis:

         RNA-seq data analysis (Expression, SNP calling, RNA-editing detection, APA detection and ...)

         DNA-seq and Exome-seq data anlysis (SNP calling, De novo assembly and ...)

         miRNA-seq data analysis (Expression, novel miRNA detection, Isomir detection and ...)

         De novo transcriptome assembly

         And ...

a) International papers

  1. Bakhtiarizadeh MR, 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): e27118.

  1. Bakhtiarizadeh MR, Arefnejad B, Ebrahimie E, Ebrahimi M. (2012). Application of functional genomic information to develop efficient EST-SSRs for the chicken (Gallus gallus). Genet Mol Res. 11 (2): 1558-1574.

  1. Deihimi T, Niazi A, Ebrahimi M, Kajbaf K, Fanaee S, Bakhtiarizadeh MR and 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. Bakhtiarizadeh MR, Moradi-Shahrbabak M, Ebrahimie E. (2013). Underlying functional genomics of fat deposition in adipose tissue. Gene. 521: 122-128.

  1. Hosseinpour B, Bakhtiarizadeh MR*, 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: 212-219.

  1. Najafpanah MJ, Sadeghi M, Bakhtiarizadeh MR. (2013). Reference genes selection for quantitative real-time PCR using RankAggreg method in different tissues of Capra hircus. PLoS One. 8: e83041.

  1. Bakhtiarizadeh MR, 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.

  1. Bakhtiarizadeh MR, Moradi-Shahrbabak M, Ebrahimie E. (2014). Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue. Genes & Genomics. 36: 105-117.

  1. Hosseinpour B, Bakhtiarizadeh MR*, Mirabbassi SM, Ebrahimie E. (2014). Comparison of hematopoietic cancer stem cells with normal stem cells leads to discovery of novel differentially expressed SSRs. Gene. 550: 10-17.

  1. Sadeghi M, Najaf Panah MJ, Bakhtiarizadeh MR, Emami A. (2015). Transcription analysis of genes involved in lipid metabolism reveals the role of chromium in reducing body fat in animal models. J Trace Elem Med Biol. 32: 45-51.

  1. Bakhtiarizadeh MR*, Hosseinpour B, Arefnezhad B, Shamabadi N, Salami SA. (2016). In silico prediction of long intergenic non-coding RNAs in sheep. Genome. 59: 263-275.

  1. Bakhtiarizadeh MR, Najaf-Panah MJ, Mousapour H, Salami SA. (2016). Versatility of different melting temperature (T m) calculator software for robust PCR and real-time PCR oligonucleotide design: A practical guide. Gene Reports. 2: 1-3.

  1. Rahimi M, Bakhtiarizadeh MR*, Mohammadi Sangcheshmeh A. (2017). OOgenesis_Pred:A sequence-based method for predicting oogenesis proteins by six different modes of Chous pseudo amino acid composition Journal of theoretical biology. 414: 128–136.

  1. Sadr AS, Nassiri M, Salami SA, Bakhtiarizadeh MR, Tahmoorespur M, Shafeinia A. RNASeq reveals novel and differentially expressed isoforms in native and commercial poultry.  (2016).   Journal of Cell and Molecular Research. 9 (1): 16-22.

  1. Behdani E, Bakhtiarizadeh MR*. Construction of an integrated gene regulatory network link to stress-related immune system in cattle. (2017). Genetica. 145: 441-454.

  1. Hosseinpour B, Sepahvand S, Kamali Aliabad K, Bakhtiarizadeh MR, Imani A, Assareh R, Salami SA. Transcriptome profiling of fully open flowers in a frost-tolerant almond genotype in response to freezing stress. (2017). Molecular Genetics and Genomics. 293: 151–163.

  1. Mozduri Z, Bakhtiarizadeh MR*, Salehi A. Integrated regulatory network reveals novel candidate regulators in the development of negative energy balance in cattle. (2017). Animal. 12 (6): 1196-1207.

  1. Bakhtiarizadeh MR*, Salehi A, Rivera RM. Genome-wide identification and analysis of A-to-I RNA editing events in bovine by transcriptome sequencing. (2018). PLOS ONE. 13 (2): e0193316.

  1. Bakhtiarizadeh MR*, Rahimi M, Mohammadi Sangcheshmeh A, Shariati J V, Salami SA. PrESOgenesis: A two-layer multi-label predictor for identifying fertility-related proteins using support vector machine and pseudo amino acid composition approach. (2018). Scientific Reports. 8:9025.

  1. Izadnia H, Tahmoorespur M, Bakhtiarizadeh MR, Nassiry MR, Saeid Esmaeilkhanian S. Gene Expression Profile Analysis of Residual Feed Intake (RFI) for Isfahan Native Chickens Using RNA-SEQ Data. (2018). Italian Journal of Animal Science.

  1. Khalkhali-Evrigh R, Hafezian SH, Hedayat-Evrigh N, Farhadi A, Bakhtiarizadeh MR. Genetic variants analysis of three dromedary camels using whole genome sequencing data. (2018). PLOS ONE. 13 (9): e0204028.

  1. Bakhtiarizadeh MR, Hosseinpour B, Shahhoseini M, Korte A, Gifani P. (2018). Weighted Gene Co-expression Network Analysis of Endometriosis and Identification of Functional Modules Associated With Its Main Hallmarks. Frontiers in Genetics. 9 (453). 1-15.

 

b) Persian papers

  1. Bakhtiarizadeh MR, Moradi-Shahrbabak M, Pakdel A, Moghimi A. (2010). Genetic Relationships between Linear Type Traits, Milk Yield and Open Day in Holstein Cows of Iran. Iraninal Journal of Animal Science. 40 (4): 13-19.

  1. Bakhtiarizadeh MR, Moradi-Shahrbabak M. (2011). An Estimation of the Lactation Curve Parameters through Incomplete Gamma Function and a Determination of the Genetic Relationship between these Parameters and udder Traits, in Holstein Population of Iran. Iraninal Journal of Animal Science. 41 (1): 1-10.

  1. Bakhtiarizadeh MR, Moradi-Shahrbabak M, Pakdel A. (2011).  Genetic relationships between linear type traits, somatic cell score and longevity in Holstein cows of Iran. Animal Sciences Journal (Pajouhesh & Sazandegi). 84 (3): 30-38.

  1. Bakhtiarizadeh MR, Moradi-Shahrbabak M, Pakdel A. (2012). Use Of Principal Components Analysis to Prediction Fat-tail Weight Trait in Lori-Bakhtiari Sheep. Iraninal Journal of Animal Science. 43 (1): 103-111.

  1. Raana J, Yazdanshenas P,; Amin Afshar M, Mohammadi Sangcheshmeh A, Varnaseri; H, Chamani M, Nazaran MH, Bakhtiyarizadeh MR. (2015). Effect of zinc nano-complex on bull semen quality after freeze-thawing process. Journal of Animal Production. 17 (2): 371-380.

  1. Mouzdori Z, Bakhtiarizadeh MR*. (2016).  Promoter analysis of effective genes in negative energy balance in dairy cows. Journal of Animal Production. 18 (1): 13-26.

  1. Behdani E, Roshanfekr H, Ghaderi Zefrehei M, Fayazi J, Bakhtiarizadeh MR. (2016). Identifying Regulatory genes affected on Immune system by using Bos Taurus leukocyte RNA-Seq data. Genetics novin. 11 (2): 207-215.

  1. Mozduri Z, Bakhtiarizadeh MR* and Salehi A. (2017). Identification of new miRNAs and isomirs in liver tissue of dairy cows. Iraninal Journal of Animal Science. 47 (4): 557-569.

  1. Bazrafshan M, Bakhtiarizadeh MR*, Mahdavi F, Salehi A. (2017). Identification of novel regulatory elements involved in growth rate reduction in mammals. Genetics novin. 12 (1): 101-114.

  1. Jaefari E, Bakhtiarizadeh MR* and Salehi A. (2017). Identification and analysis of new miRNAs and isomirs and their targets in cows exposed to mastitis. Journal of Animal Production. 18 (4): 647-659.

  1. Bakhtiarizadeh MR*, Mozduri Z and Shakeri P. (2017). Prediction of novel pseudogenes in ovine reference genome. Iranian Journal of Animal Science Research. 9 (4): 484-497.

  1. Khalkhali Evriq R, Hafezian SH, Hedayat N, Farhadi A, Bakhtiarizadeh MR. (2018). Detection and analysis of deletions and insertions in genome of Iranian dromedary camels using whole genome sequencing data. Journal of Animal Production. 20 (1): 109-120.

  1. Hesani Z, Nassiri MR, Bakhtiarizadeh MR, Tahmoorespur M, Javadmanesh A. (2018). Gene Expression Analysis on Apoptosis network and Depict it in EsfahaniAndRoss Breeds. Iranian Journal of Animal Science Research. 10 (1): 117-130.

  1. Sadeghi D, Mortazavian SMM, Bakhtiarizadeh MR. (2018). Transcriptome analysis of cumin (Cuminum cyminum L.) using RNA-Seq. Journal of Agricultural Biotechnology. 9 (4): 101-116.

  1. Alboshekeh SN, Tahmoorespur M, Bakhtiarizadeh MR, Nassiri MR, Esmaeilkhanian S. (2018). Study of the genetic network that affecting the growth of pectoralis muscle in Ross chickens under RNA-Seq data. Genetic Engineering and Biosafety Journal. 6 (2): 189-203.

  1. Alboshekeh SN, Bakhtiarizadeh MR, Tahmoorespur M. (2018). Identification of RNA isoforms expressed in skeletal muscle of native and commercial chickens by sequencing method. Iraninal Journal of Animal Science. 49 (2): 179-191.

  1. Izadnia HR, Tahmoorespur M, Bakhtiarizadeh MR, Nassiri MR, Esmaeilkhanian S. (2018). Isoform Expression Profile Analysis of Residual Feed Intake for Isfahan Native Chickens Using RNA-Seq Data. Iranian Journal of Animal Science Research (In press).

  1. Taghizadeh V, Nassiri MR, Tahmoorespur M, Bakhtiarizadeh MR, Javadmanesh A. (2018). Gene expression network analysis on angiogenesis pathway in low temperature-induced ascites susceptible chickens in B-line pedigree of Iranian meat-type strain,Arian. Iranian Journal of Animal Science Research. (In press).

  1. Alboshekeh SN, Tahmoorespur M, Bakhtiarizadeh MRNassiri MR, Esmaeilkhanian S. (2018). Effect of the mitoproteum genes on skeletal muscle growth of chicken indigenous Isfahan province by RNA-seq data. Iranian Journal of Animal Science Research. (In press).

Education:

                 2008-2011: Ph.D  in Genetic and Animal Breeding From University of Tehran.

                 2006-2008: M.Sc  in Genetic and Animal Breeding From University of Tehran.

                 2002-2006: B. Sc  in Animal Scien

 

Visiting scholar: June 22 (2018) to 19 September (2018)

           University of Missouri, USA

 

Work experience: 2011- Till now:

           Faculty Member of Department of Animal and Poultry Science, College of Aburaihan, University of Tehran.

Title: Assistant Professor

Address: College Of Aburaihan, University Of Tehran, Pakdasht,Tehran, Iran.

Tel/Fax: 021 36040907

Academic Email:  mrbakhtiari@ut.ac.ir

Gmail:                   mrb20045@gmail.com 

Gitub adress:        https://github.com/mrb20045

Google Scholar:   https://scholar.google.com/citations?user=ZtpFeUgAAAAJ&hl=en

Researchgate:       https://www.researchgate.net/profile/Mohammad_Reza_Bakhtiarizadeh‚Äč

ORCID iD:           0000-0001-5336-6987

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Supervisor:

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1- Nsder Alboshekeh:

    Thesis: Gene expression profile analysis of skeletal muscle development of chicken indigenous

                 Isfahan province by RNA-seq data (2017). (Completed)

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2- Hamid Reza Izadnia:

   Thesis: Gene expression profile analysis of residual feed intake of chicken indigenous Isfahan

                Province by RNA-seq data (2018). (Completed)

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3- Zahra Taherian

Thesis: Expression profile analysis of long noncoding RNAs in invasive-ductal carcinoma breast

             cancer by next-generation sequencing. (Current)

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4- Sepideh Dashti

Thesis: High throughput expression profiling of Circular RNA in ductal invasive breast carcinoma

             tissues. (Current)

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5- Mohammad Mahdi Taghvaei

Thesis: Analysis of cold strees responsive microRNAs in Rapeseed (Brassica napus). (Current)

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Advisor:

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1- Ayeh sadat Sadr:

     Thesis: Comparison and differentioal expression of immune system genes of local and commercial

                   poultry by RNASeq analysis (2017). (Completed)

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2- Elham Behdani:

    Thesis: Bayesian network constructing using bovine leukocytes RNA-seq data (2017). (Completed)

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3- Vahid Taghizadeh:

    Thesis: Transcriptom and pathway analysis of angiogenesis in resistant and susceptible

                chickens for ascites in Iranian Paternal meat type line, Arian, by NGS technology (2017).

                (Completed)

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4- Reza Khalkhali:

   Thesis: Whole genome resequencing of Iranian dromedary camels for genetic variants analysis (2018).

                (Completed)

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5- Mohammad Sadat Hosseini:

    Thesis:  Patterns of gene expression in response to drought stress and isolation of drought-inducible

                 promoter in Persian walnut drought-inducible promoter in Persian walnut. (Current)

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6- Mahsa Rasekhi:

    Thesis: Investigation effect of LPS-derived Escherichia coli on ovine reproductive organs via

                 RNA-Seq data. (Current)

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7- Atefeh Berenjian:

    Thesis: A study on the effects of omega-3 supplementation on alleviates physiologic stresses and

                expression of lipid metabolism- involved genes in laying hens (using RNA-seq). (Current)

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8- Jamshid Azimian

    Thesis:  Transcriptome Analysis of Bread Wheat (Triticum aestivum) In Response To Salinity Stress.

                  (Current)

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9- Pegah Javid

    Thesis:  Differential transcript analysis of tolerant vs. suseptible Persian Gulf corals to heat shock.

                  (Current)

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Supervisor:

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1- Zohreh Mozdouri:

    Thesis: Gene regulatory networks involved in the liver tissue of dairy cows in negative energy balance

                 during the early postpartum period using RNA-Seq and miRNA data (2016). (Completed)

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2- Elham Jaefari:

    Thesis: Investigation of gene regulatory network involved in mastitis disease, using RNA-Seq and

                 miRNA-Seq data (2016). (Completed)

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3- Shabnam Mirzaei:

    Thesis: Study of gene regulatory mechanisms of mastitis using weighted genes co-expressed network

                 (2017). (Completed)

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4- Hamid Shafiei:

    Thesis: Study of RNA editing in various tissues in chickens using RNA-Seq (2017). (Completed)

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5- Sadeghi Darioush:

    Thesis: Assessment of selection response and heritability some of traits and transcriptome

                 evaluation using NGS in cumin (Cuminum ceminum L.) (2017). (Completed)
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6- Parastoo Karimi:

    Thesis: Investigation of gene expression profile of long non-coding RNA in liver tissue of native and commercial chicken. (Current) 

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Advisor:

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1- Somayeh Golshahian:

    Thesis: Genetic polymorphism in exon2 of GDF9 and exon1of BMP15 gene using RFLP-PCR in Zandi

                  sheep (2016). (Completed)
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2- Pedram Shakeri:

    Thesis:

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3- Fatemeh Rasouli:

    Thesis:

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4- Farnoos Rostami:

    Thesis:

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