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My 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 related proteins based on 1920
meaningful protein sequence features. It takes protein/DNA FASTA sequences
as input, and generate output about the potential of a protein to be
involved in spermatogenesis/embryogenesis/oogenesis. PrESOgenesis depends
on two programs (libsvm and protr package in R) and can be run 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.

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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: 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: 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. Ayeh Sadat Sadr, Mohammadreza Nassiri, Seyed Alireza Salami, Mohammad Reza Bakhtiarizadeh, Mojtaba Tahmoorespur, Alireza Shafeinia. RNASeq reveals novel and differentially expressed isoforms in native and commercial poultry.  (2016).   Journal of Cell and Molecular Research (In press).

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

  1. Batool Hosseinpour, Sadegh Sepahvand, Kazem Kamali Aliabad, MohammadReza Bakhtiarizadeh, Ali Imani, Reza Assareh, Seyed Alireza Salami. Transcriptome profiling of fully open flowers in a frost-tolerant almond genotype in response to freezing stress. (2017). Molecular Genetics and Genomics

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: 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: 1-10.

  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: 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: 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: 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: 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: 207-215.

  1. Zohre Mozduri, Mohammad Reza Bakhtiarizadeh and Abdolreza Salehi. (2017). Identification of new miRNAs and isomirs in liver tissue of dairy cows. Iraninal Journal of Animal Science 47: 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: 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 (In press).

  1. Zohre Mozduri, Mohammad Reza Bakhtiarizadeh and Pedram Shakeri. (2017). Prediction of novel pseudogenes in ovine reference genome. Iranian Journal of Animal Science Research (In press).

  1. Vahid Taghizadeh, Mohammad Reza Nassiri, Mojtaba Tahmoorespur, Mohammad Reza Bakhtiarizadeh. (2017). 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. Nader Alboshekeh, Mojtaba Tahmoorespur, Mohammad Reza Bakhtiarizadeh, Mohammad Reza Nassiri, Saeud Esmaeilkhanian. (2017). 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

 

 

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

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Supervisor:

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1- Hamid Reza Izadnia:

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

                Province by RNA-seq data.

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2- Nsder Alboshekeh:

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

                 Isfahan province by RNA-seq data.

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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).

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2- Elham Behdani:

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

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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.

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4- 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.

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4- Reza Khalkhali:

   Thesis: 

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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).

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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).

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3- Shabnam Mirzaei:

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

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4- Hamid Shafiei:

    Thesis: Study of RNA editing in various tissues in chickens using RNA-seq.

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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).

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