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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.

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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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.
  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.

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
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.

   Thesis:

4- Nsder Alboshekeh.

    Thesis:

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.