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My software


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.

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. 



    Animal Genetics

    Experimental Designs in Agriculture


    Molecular Genetics



     Advanced Experimental Designs in Agriculture

     Advanced 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.
  2. 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.
  3. 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.
  4. Bakhtiarizadeh MR, Moradi-Shahrbabak M, Ebrahimie E (2013) Underlying functional genomics of fat deposition in adipose tissue. Gene 521: 122-128.
  5. 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.
  6. 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.
  7. Bakhtiarizadeh MR, Moradi-Shahrbabak M, Ebrahimi M, Ebrahimie E (2014) Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology. J Theor Biol 356: 213-222.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. Rahimi M, Bakhtiarizadeh MR, Mohammadi Sangcheshmeh A (2017) OOgenesis_Pred:A sequence-based method for predicting oogenesis proteins by six different 

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.
  2. 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.
  3. 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.
  4. 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.

  5. 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.
  6. Mouzdori Z, Bakhtiarizadeh MR (2016)  Promoter analysis of effective genes in negative energy balance in dairy cows. Journal of Animal Production 18: 13-26.
  7. 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.


                 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

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


Tel/Fax:  021 36040907
Email: mrbakhtiari@ut.ac.ir

1- Ayeh sadat Sadr.

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

                        by RNASeq analysis

2- Elham Behdani.

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

3- Hamid Reza Izadnia.


4- Nsder Alboshekeh.


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.

2- Elham Jaefari.

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