انتشارات

انتشارات:

  1. Najme Khorasani, Mehdi Sadeghi, Abbas Nowzari-Dalini (2020) A computational model of stem cell molecularmechanism to maintain tissue homeostasis, PLoS ONE 15(7): e0236519
  2. Seyed Amir Malekpour, Amir Reza Alizad-Rahvar and Mehdi Sadeghi (2020) LogicNet: probabilistic continuous logics inreconstructing gene regulatory networks, BMC Bioinformatics, 21:318, https://doi.org/10.1186/s12859-020-03651-x
  3. C. Razavi Pashabayg, N. Momenifar, S. A. Malekpour, M. Sadeghi, A. Rahimi Foroushani, H. Rafatpanah, N. Valizadeh, F. Sabet, S. M. Jazayeri, H. Keyvani, S. A. Rezaee and M. Norouzi (2020) Phylogenetic and phylodynamic study of Human T-cell lymphotropic virus Type 1 (HTLV-1) in Iran, Infection, Genetics and Evolution, 85, 104426
  4. Nasim Ejlali, Hamid Pezeshk, Yogendra P Chaubey, Mehdi Sadeghi, Ali Ebrahimi, Abbas Nowzari-Dalini (2020) Parrondo’s paradox for games with three players and its potential application in combination therapy for type II diabetes, Physica A: Statistical Mechanics and its Applications, 556, 124707
  5. Hadiseh Safdari, Ata Kalirad, Cristian Picioreanu, Rouzbeh Tusserkani, Bahram Goliaei, Mehdi Sadeghi (2020) Noise-driven cell differentiation and the emergence of spatiotemporal patterns, Plos one, e0232060
  6. Safar Vafadar, Kaveh Kavousi, Hadiseh Safdari, Ata Kalira, Mehdi Sadeghi (2020) From indication to decision: A hierarchical approach to model the chemotactic behavior of Escherichia coli, Journal of Theoretical Biology, 495, 110253
  7. Farzaneh Salari, Fatemeh Zare Mirakabad, Mehdi Sadeghi (2020) A new hash function and its use in read mapping on genome, AUT Journal of Mathematics and Computing,
  8. Fazeleh S Mohseni-Salehi, Fatemeh Zare-Mirakabad, Mehdi Sadeghi, Soudeh Ghafouri-Fard (2020) A Stochastic Model of DNA Double-Strand Breaks Repair Throughout the Cell Cycle, Bulletin of Mathematical Biology, 82, 1-36
  9. Masomeh Askari, Razieh Karamzadeh, Naser Ansari-Pour, Mohammad Hossein Karimi-Jafari, Navid Almadani, Mohammad Ali Sadighi Gilani, Hamid Gourabi, Ahmad Vosough Taghi Dizaj, Anahita Mohseni Meybodi, Mehdi Sadeghi, Anu Bashamboo, Ken McElreavey, Mehdi Totonch (2019) Identification of a missense variant in CLDN2 in obstructive azoospermia, Journal of human genetics, 64, 1023-1032
  10. Maryam Shahdoust ; Hossein Mahjub ; Hamid Pezeshk ; Mehdi Sadeghi (2019) A Network-based Comparison between Molecular Apocrine Breast Cancer Tumor and Basal and Luminal Tumors by Joint Graphical Lasso, IEEE/ACM Trans Comput Biol Bioinform. 2019 Apr 15. doi: 10.1109/TCBB.2019.2911074
  11. Najmeh Salehi, Bahareh Attaran, Negin Eskini, Maryam Esmaeili, Atefeh Sharifirad, Mehdi Sadeghi, Marjan Mohammadi (2019) New insights into resistance of Helicobacter pylori against thirdand fourth‐generation fluoroquinolones: A molecular docking study of prevalent GyrA mutations,  Helicobacter. 2019, DOI: 10.1111/hel.12628
  12. Mostafa Taheri, Kazem Nouri, Yazdan Asgari, Zahra Zabihinpour, MehdiSadeghi (2019) The Significance of Noise in the Evolution of Negative and Positive Cooperativity in Protein Complexes, MATCH Commun. Math. Comput. Chem. 81 , 177-192
  13. Farzaneh Salari, Fatemeh Zare-Mirakabad, MehdiSadeghi and Hassan Rokni-Zadeh (2018) Assessing the impact of exact reads on reducing the error rate of read mapping, BMC Bioinformatics (2018) 19:406
  14. Amir Reza Alizad-Rahvar, Mehdi Sadeghi (2018) Ambiguity in logic-based models of gene regulatory networks: An integrative multiperturbation analysis, PLoS ONE 13(11): e0206976.
  15. Seyed Amir Malekpour, Hamid Pezeshk,Mehdi Sadeghi ( 2018) MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples, SCIENTIFIC REPORTS , 8:4009 | DOI:10.1038/s41598-018-22323-8
  16. Atiyeh Fotoohinasab a, Emad Fatemizadeh b, Hamid Pezeshk c,d, Mehdi Sadeghi, (2018) Denoising of genetic switches based on Parrondo’s paradox, Physica A, 493, 410–420
  17. Sayed‑Hamidreza Mozhgani et al (2018) Molecular evolution and phylodynamics of hepatitis B virus infection circulating in Iran, Archives of Virology , doi.org/10.1007/s00705-018-3764-3
  18. Seyed Amir Malekpour, Parsa Pakzad, Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Ruzbeh Tusserkani, Bahram Goliaei and Mehdi Sadeghi (2018) Modeling the probability distribution of the bacterial burst size via a game-theoretic approach, Journal of Bioinformatics and Computational Biology VOL. 16, NO. 04. doi: 10.1142/S0219720018500129
  19. M. Sadeghi, H. Pezeshk, R. Tusserkani, A. Sharifi Zarchi, A. Malekpour, M. Foroughmand, S. Goliaei, M. Totonchi, N. Ansari–Pour, (2017) The Role and Importance of Genome Sequencing in Prediction of Cancer Risk, International Journal of Biotechnology and Bioengineering, Vol:11, No:8, 460-465
  20. J. Salimi Sartakhti, M. H. Manshaei ,S. Bateni, M. Sadeghi, (2017)  Evolutionary Emergence of Angiogenesis in Avascular Tumors using a Spatial Public Goods Game, PLoS ONE, Volume 12, Issue 4,.
  21. Nasim Ejlali, Mohammad Reza Faghihi and Mehdi Sadeghi (2017) Bayesian comparison of protein structures using partial Procrustes distance, Stat. Appl. Genet. Mol. Biol. 2017; 16(4): 243–257
  22. Fazeleh S. Mohseni-Salehi, Fatemeh Zare-Mirakabad, Soudeh Ghafouri-Fard, Mehdi Sadeghi (2017) The effect of stochasticity on repair of DNA double strand breaks throughout non-homologous end joining pathway, Mathematical Medicine and Biology (2017) 00, 1–23
  23. Maryam Shahdoust, Hamid Pezeshk, Hossein Mahjub, Mehdi Sadeghi (2017) F-MAP: A Bayesian approach to infer the gene regulatory network using external hints,PLoS ONE 12(9): e0184795.
  24. Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand and Marcos J. Araúzo-Bravo (2017) DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism, BMC Genomics (2017) 18:964, DOI 10.1186/s12864-017-4353-7
  25. Bahareh Khazaei, Javad Salimi Sartakhti, Mohammad Hossein Manshaei, Quanyan Zhu, Mehdi Sadeghi, Seyed Rasoul Mousavi )2017) HIV-1-infected T-cells dynamics and prognosis: An evolutionary game model, Computer Methods and Programs in Biomedicine, Volume 152, 1-14
  26. Dorri F, Pezeshk , Sadeghi M (2017) Stochastic Cell Fate and Longevity of Offspring, Cell J.;19(3):343-351
  27. zahra zamanzadeh; Mitra Ataei; Seyed Massood Nabavi; Ghasem Ahangaria; Mehdi Sadeghi; Mohammad Hosein Sanati, (2017) In Silico Perspectives on the Prediction of the PLP’s Epitopes involved in Multiple Sclerosis, Iranian J. Biotechnology, 15, 10-12
  28. Fereshteh Chitsazian, Mehdi Sadeghi and Elahe Elahi (2017) Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines, BMC Bioinformatics
  29. Javad Salimi Sartakhtia, Mohammad Hossein Manshaeia, Mehdi Sadeghi (2017) MMP–TIMP interactions in cancer invasion: An evolutionary game-theoretical framework, Journal of Theoretical Biology, Volume 412, 17–26
  30. Seyed Amir Malekpour, Hamid Pezeshk and Mehdi Sadeghi (2017) PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities, BMC Bioinformatics
  31. Samiie Pouragahi  ; Mohammad Hossein Sanati ; Mehdi Sadeghi; and Marjan Nassiri-Asl (2016) Bioinformatics Approach for Pattern of Myelin-Specific Proteins and Related Human Disorders,Biotechnology and Health Sciences. 3(4)
  32.  Zahra Zamanzadeh, Ghasem Ahangari, Mitra Ataei, Samie Pouragahi, Seyed Massood Nabavi, Mehdi Sadeghi, Mohammad Hossein Sanati (2016) Association of New Putative Epitopes of Myelin Proteolipid Protein (58-74) with Pathogenesis of Multiple Sclerosis, Iranian Journal of Allergy, Asthma and Immunology,  15(5):394-402
  33. Katayoun Samimi-Rad1, Ramin Rahimnia, Mahdi Sadeghi, Seyed Amir Malekpour, Mona Marzban, Maryam Keshvari, Seyed Jalal Kiani, Seyed-Moayed Alavian (2016) Epidemic History of Hepatitis C Virus amongPatients with Inherited Bleeding Disorders inIran, PLOS ONE, 11(9)
  34. Seyed Amir Malekpour , Hamid Pezeshk , Mehdi Sadeghi (2016)  MGP-HMM: Detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts, Mathematical Biosciences, 279 (2016) 53–62
  35. Rahim Jafari, Mehdi Sadeghi, Mehdi Mirzaie (2016) Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein–protein docking results, Journal of Molecular Graphics and Modelling, 66, 108–114
  36. Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz and Mehdi Sadeghi (2015) Increased robustness of early embryogenesisthrough collective decision-making by keytranscription factors, BMC Systems Biology, 9:23
  37. Vajiheh Eskandari, Bagher Yakhchali, Mehdi Sadeghi, Ali Asghar Karkhane, Houra Ahmadi-Danesh1(2015) Efficient Cadmium Bioaccumulation by Displayed HybridCS3 Pili: Effect of Heavy Metal Binding Motif InsertionSite on Adsorption Capacity and Selectivity, Appl Biochem Biotechnol, 177(8):1729-41
  38. Mohieddin Jafari, Mehdi Mirzaie and Mehdi Sadeghi (2015) Interlog protein network: an evolutionarybenchmark of protein interaction networksfor the evaluation of clustering algorithms, BMC Bioinformatics , 16:319
  39. Pegah Khosravi, Vahid H Gazestani, Leila Pirhaji, Brian Law, Mehdi Sadeghi, Bahram Goliaeiand Gary D Bader (2015) Inferring interaction type in generegulatory networks using co‑expression data , Algorithms Mol Biol , 10:23
  40. Mohammad-Hadi Foroughmand-Araabi, Bahram Goliaei, Kasra Alishahi, Mehdi Sadeghi, Sama Goliaei (2015) Codon usage and protein sequence pattern dependency in different organisms: a Bioinformatics approach, Journal of Bioinformatics and Computational Biology, Vol. 13, No. 2
  41. Maryam PourkamaliAnarakiand Mehdi Sadeghi (2015) Honey bee-inspired algorithms for SNP haplotype reconstruction problem, Journal of Experimental & Theoretical Artificial Intelligence, May 12, 2015
  42. Pegah Khosravi, Vahid H. Gazestani , Mohammad Akbarzadeh , Samira Mirkhalaf , Mehdi Sadeghi, Bahram Goliaei (2015) Comparative Analysis of Prostate Cancer Gene Regulatory Networks via Hub Type Variation, Avicenna J Med Biotech; 7(1): 8-15
  43. M Norouzi, F Ramezani, A Khedive,........, M Sadeghi,.........., (2014) Hepatitis B Virus Genotype D is the Only Genotype Circulating in Iranian Chronic Carriers, the Unique Pattern of Genotypic Homogeneity, Journal of Gastroenterology and Hepatology Research, 213(9): 1238-1243
  44. Pegah Khosravi, Javad Zahiri, Vahid H. Gazestani, Samira Mirkhalaf, Mohammad Akbarzadeh, Mehdi Sadeghi, Bahram Goliaei (2014) Analysis of Candidate Genes Has ... of Y Chromosome in Human Prostate Cancer, Iranian Journal of Cancer Prevention, 7(4), 204-211
  45. Maryam Pourkamali Anaraki, Mehdi Sadeghi (2014) Efficient fast heuristic algorithms for minimum error correction haplotyping from SNP fragments, Int. J. Computational Biology and Drug Design, 7(4)358-368
  46. Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Mehdi Sadeghi(2014)ARYANA: Aligning Reads by Yet AnotherApproach, BMC Bioinformatics, 15(Suppl 9):S12
  47. Mahdi Heidari , Sayed-Amir Marashi, Ruzbeh Tusserkani, Mehdi Sadeghi, (2014) Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals, Biosystems, 124, 86–94
  48. Pegah Khosravi, Vahid H. Gazestani, Yazdan Asgari, Brian Law, Mehdi Sadeghi, Bahram Goliaei (2014) Network-based approach reveals Y chromosome influences prostate cancer susceptibility, Computers in Biology and Medicine,  54,  24–31
  49. Faezeh Dorri, Hamid Mahini, Ali Sharifi-Zarchi, Mehdi Totonchi, Ruzbeh Tusserkani,Hamid Pezeshk, Mehdi Sadeghi (2014) Natural Biased Coin Encoded in the Genome DeterminesCell Strategy, Plos One, Volume 9 , Issue 8,  e103569
  50. Alireza Vazifedoost, Maseud Rahgozar, Behzad Moshiri, Mehdi Sadeghi, Chua Hon Nian, See Kiong Ng, and Limsoon Wong (2014) Using data fusion for scoring reliability of protein–protein interactions,Journal of Bioinformatics and Computational BiologyVol. 12, No. 4,
  51. Maryam Pourkamali Anaraki, Mehdi Sadeghi (2014)Efficient fast heuristicalgorithms for minimum errorcorrection haplotyping from SNP fragments, Int. J. Computational Biology and Drug Design,In press
  52. Zeinalzadeh N, Ahangari G, Sadeghi M, Amani J, Bathaie SZ, Jafari M (2014) Design and characterization a chimeric multi-epitope construct containing CfaB, ST toxoid, CssA, CssB and LTB of Enterotoxigenic E. coli: bioinformatics approach, Biotechnol Appl Biochem. 2013 Dec 24. doi: 10.1002/bab.1196.
  53. Samaneh Saadat , Zhaleh Safikhani , Kambiz Badie , Mehdi Sadeghi (2014)  Clustering of Short Read Sequences for de novo Transcriptome Assembly Progress in Biological Sciences, Vol. 4, Number 1, 43-52
  54. E. S. Ansari. , H. Pezeshk. , M. Sadeghi. and C. Eslahchi. (2014) ProDomAs; Protein Domain Assignment Algorithm using Centre-Based Clustering and Independent Dominating Set,Proteins: Structure, Function and Bioinformatics,  82, 1937–1946
  55. Mahdi Pakdaman Naeini, Behzad Moshiri, Babak Nadjar Araabi, Mehdi Sadeghi (2014) Learning by abstraction: Hierarchical classification model using evidential theoretic approach and Bayesian ensemble model, Neurocomputing, 130, 73–82
  56. Mohammad-Hadi Foroughmand-Araabi, Bahram Goliaei, Kasra Alishahi and MehdiSadeghi(2014) Dependency of codon usage on protein sequence patterns: a statistical study, Theoretical Biology and Medical Modelling 2014, 11:2
  57.  Ghasem Mahdevar, AbbasNowzari-Dalini, Mehdi Sadeghi (2013) Inferring gene correlation networks from transcriptionfactor binding sites, Genes Genet. Syst., 88, 301–309
  58. Haghighi Mohamad Ali; Mobarez Ashraf Mohabati; Salmanian Ali Hatef; Moazeni,Mohamad; Zali Mohamad Reza; Sadeghi Mehdi; Amani Jafar (2013) In silico experiment with an antigen-toll-like receptor-5 agonist fusion construct for immunogenic application to Helicobacter pylori, Indian J Hum Genet. 19(1):43-53
  59. Zhaleh Safikhani , Mehdi Sadeghi , Hamid Pezeshk , Changiz Eslahchi (2013) SSP: An interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads, Genomics 102, 507–514
  60. Mohieddin Jafari, Mehdi Sadeghi, Mehdi Mirzaie, Sayed-Amir Marashi, Mostafa Rezaei-Tavirani (2013) Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks, Mitochondrion, 13, 668–675
  61. Mehdi Mirzaie, Mehdi Sadeghi(2013)Delaunay-based non-local interactions are sufficient and accurate in protein fold recognition,Proteins: Structure, Function and Bioinformatics,82, 415–423
  62. Seyedeh-Nafiseh Hassani & Mehdi Totonchi & Ali Sharifi-Zarchi Sepideh Mollamohammadi & Mohammad Pakzad & Sharif Moradi & Azam Samadian &Najmehsadat Masoudi & Shahab Mirshahvaladi & Ali Farrokhi & Boris Greber &Marcos J. Araúzo-Bravo & Davood Sabour &Mehdi Sadeghi& Ghasem Hosseini Salekdeh &Hamid Gourabi & Hans R. Schöler & Hossein Baharvand (2013) Inhibition of TGFβSignaling Promotes GroundState Pluripotency, Stem Cell Rev and Rep10,16-30
  63. Mohammad-Hadi Foroughmand-Araabi, Bahram Goliaei, MehdiSadeghi(2013)iProsite: an improved prosite database achieved by replacing ambiguous positions with more informative representations, Progress in Biological Sciences, 3(1), 67-81
  64. Vahed M, Motalebi E, Rigi G, Akbari Noghabi K, Soudi MR, Sadeghi M, Ahmadian G. (2013) Improving chitinolytic activity of Bacillus pumilus SG2 by random mutagenesis. J Microbiol Biotechnol. 23,1519-28
  65. Eskandari V, Yakhchali B, Sadeghi M, Karkhane AA. (2013) In silico design and construction of metal binding hybrid proteins for specific removal of cadmium based on CS3 pili display on the surface of Escherichia coli. Biotechnol Appl Biochem. Jun 7. doi: 10.1002/bab.1132. [Epub ahead of print]
  66. Mohieddin Jafari , Mehdi Mirzaie, Mehdi Sadeghi , Sayed-Amir Marashi , Mostafa Rezaei-Tavirani (2013) Exploring biological processes involved in embryonic stem cell differentiation by analyzing proteomic data, Biochimica et Biophysica Acta,  1834 , 1063–1069
  67. V. Rezaei, H. Pezeshk, M. Sadeghi and C. Eslahchi (2013)Assignment of protein sequences to protein family profiles using spatial statistics, MATCH Communications in Mathematical and Computer Chemistry, 69(1), 7-24
  68. Mitra Mirzarezaei, Mehdi Sadeghi, Babak N. Araabi (2012) Construction and analysis of tissue-specific protein-protein interaction network in humans, Progress in Biological Sciences, 2(2), 1-13
  69. Vahid Rezaei, Sima Naghizadeh, Hamid Pzeshk, Mehdi Sadeghi, Changiz Eslahchi (2012) Comparison of the bidirectional Baum-Welch algorithm and the Baum-Welch algorithm on regular lattice, Progress in Biological Sciences, 2(2), 14-22
  70. Ensieh Salehghamari, Javad Hamedi, Elahe Elahi, Zargham Sepehrizadeh, Mehdi Sadeghi, Guenther Muth (2012) Prediction of the pho regulonin Streptomyces clavuligerus DSM 738, New Microbiologica,35, 447-457
  71. Rosa Aghdam, Hamid Pezeshk, Seyed AmirMalekpour, Soudabeh Shemehsavar, Mehdi Sadeghi and Changiz Eslahchi (2012) A Clustering Approach for Estimating Parameters of a Profle Hidden Markov Model, To apper in International Journal of Data Mining and Bioinformatics
  72. Ghasem Mahdevar , Mehdi Sadeghi , AbbasNowzari-Dalini (2012) Transcription factor binding sites detection by using alignment-based approach, Journal of Theoretical Biology 304,  96–102
  73. Changiz Eslahchi , Reza Hassanzadeha, Ehsan Mottaghib, Mahnaz Habibi, Hamid Pezeshk ,Mehdi Sadeghi (2012) Constructing circular phylogenetic networks from weighted quartets usingsimulated annealing, Mathematical Biosciences, 235, 123–127
  74. Kaveh Kavousi, Mehdi Sadeghi, Behzad Moshiri , BabakN. Araabi , Ali Akbar Moosavi-Movahedi (2012) Evidence theoretic protein fold classification based on the concept of hyperfold, Mathematical Biosciences, 240, 148-60
  75. Mehdi Mirzaei, Mehdi Sadeghi (2012) Distance-dependent atomic knowledge-based force in protein fold recognition, Proteins, 80, 683-690
  76. M. Habibi, C. Eslahchi, H. Pezeshk, M. Sadeghi. (2011) An Information Theoretic Approach to Secondary Structure Assignment,MATCH Communications in Mathematical and Computer Chemistry,65 (1): 5–20.
  77. Mitra Mirzarezaee, Mehdi Sadeghi, and Babak N. Araabi (2011) Dynamical Analysis of Yeast Protein Interaction Network During the Sake Brewing Process, The Journal of Microbiology., 49, pp.965-973
  78. Pooya Zakeri , Behzad Moshiri, Mehdi Sadeghi , (2011) Prediction ofproteinsubmitochondrialocations basedondatafusionofvariousfeatures ofsequences, Journal of Theoretical Biology, 269, 208-216
  79. Kaveh Kavousi, Behzad Moshiri, Mehdi Sadeghi, Babak N. Araabi, Ali Akbar Moosavi-Movahedi, (2011) A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM, Computational Biology and Chemistry 35, 1-9
  80. Rosa Aghdam, Hamid Pezeshk, Seyed Amir Malekpour, Soudabeh Shemehsavar, MehdiSadeghiand Changiz Eslahchi (2010) A Bidirectional Bayesian Monte Carlo Approach for Estimating Parameters of a Profile Hidden Markov Model, Applied Science Segment: 1(2) APS/1531
  81. Mitra Mirzarezaee, Babak N. Araabi,, Mehdi Sadeghi(2010)Comparison of Hubs in Effective Normal and Tumor Protein Interaction Networks, Basic And Clinical Neuroscience, 2 (1) :44-50
  82. Mirzaei, Mehdi and Sadeghi, Mehdi (2010) Knowledge-based potentials in protein fold recognition, Journal of Paramedical Sciences,Vol.1, No.4,65-75
  83. Mitra Mirzarezaee, Babak N Araabi,Mehdi Sadeghi, (2010) Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae, BMC Systems Biology 2010, 4:172
  84. Changiz Eslahchi, Hamid Pezeshk, Mehdi Sadeghi, Philippe Giabbanelli, Fateme Movahedi, Vahid Dabbaghian, (2010) A probabilistic model for the spread of HIV infection among injection drug Users, World Journal of Modelling and Simulation,  6,  267-273
  85. Seyedhadi Ghasemi, GholamrezaAhmadian, Mehdi Sadeghi, DanielR.Zeigler, HeshmatollahRahimian, SoheilaGhandili, NedaNaghibzadeh, AliDehestani (2010) First reportofabifunctionalchitinase/lysozymeproducedby Bacillus pumilus SG2, Enzyme andMicrobialTechnology, 48,225–231
  86. Alireza Meshkin, Nasser Ghasem Aghaee , Mehdi Sadeghi (2010) Modeling and implementing an agent-based system for prediction of protein3 relative solvent accessibility, Expert Systems with Applications 38, 6324–6332
  87. Mehdi Sadeghi, Hamid Pezeshk, Changiz eslahchi,, Sara Ahmadian, Sepideh Mah Abadi, (2010) Construction of random perfect phylogeny matrix, Advances and Applications in Bioinformatics and Chemistry, 3 89–96
  88. Mahnaz Habibi, changiz eslahchi, Mehdi sadeghi, Hamid Pezashk (2010) The interpretation of protein structuresbased on graph theory and contact map, Open Access Bioinformatics, 2 127–137
  89. J. Zahiri, G.Mahdevar, A.Nowzari-dalini, H.Ahrabian, M.Sadeghi (2010) A novel efficient dynamic programming algorithm for haplotype block partitioning, Journal of Theoretical Biology, 267, 164-170
  90. Ghasem Mahdevar, Javad Zahiri, Mehdi Sadeghi, Abbas Nowzari-Dalini, Hayedeh Ahrabian (2010) Tag SNP selection via a genetic algorithm, Journal of Biomedical Informatics, 43, 800-804
  91. Gholam Ali Kardar, Alireza Zomorodipour, Mostafa Moin, Zahra Pourpak, Mehdi Sadeghi, Fariba Ataei (2010) The effects of novel mutations in A1 domain of humancoagulation factor VIII on its secretion level in culturedmammalian cells,Iranian Journal of Biotechnology,  8, 139-149
  92. Shahriar Arab, Mehdi Sadeghi, Changiz Eslahchi, Hamid Pezeshk, Armita Sheari (2010) A pairwise residue contact area-based mean force potential for discrimination of native protein structure, BMC Bioinformatics , 11:16
  93. Ali Katanforoush, Mehdi Sadeghi, Hamid Pezeshk and Elahe Elahi (2009) Global haplotype partitioning for maximal associated SNP pairs, BMC Bioinformatics , 10:269
  94. Seyed Amir Malekpour , Sima Naghizadeh , Hamid Pezeshk , Mehdi Sadeghi, Changiz Eslahchi (2009) A Segmental Semi Markov Model for protein secondary structure prediction, Mathematical Biosciences 221, 130–135
  95. Alireza Meshkin1, , Mehdi Sadeghi, Nasser Ghasem-Aghaee (2009) Prediction of Relative Solvent Accessibility using Pace Regression, EXCLI Journal; 8: 211-217
  96. Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdei Sadeghi, Abbas Nowzari-Dalini, Bahram Goliaei, (2009) New scoring schema for finding motifs in DNA Sequences, BMC Bioinformatics, 10:93
  97. Mehdi Mirzaie, Changiz Eslahchi, Hamid Pezeshk, and Mehdi Sadeghi (2009) A distance-dependent atomic knowledge based potential and force for discrimination of native structures from decoys, Proteins, Volume 77: 454-463
  98. Changiz Eslahchi, Hamid Pezeshk, Mehdi Sadeghi, and Alireza Sheikh attar (2009) LIBRA: A de Novo Motif Finding in Promoter Sequences Based on Linear Algebra, Proceedings of World Academy of Science, Engineering and Technology, Volume 37, 506-512
  99. F. Zare-Mirakabad, M. Sadeghi, H. Ahrabiana, and A. Nowzari-Dalini (2009) RNAComp: A new method for RNA secondary structure alignment, MATCH Communications in Mathematical and in Computer Chemistry, 61(3),789-816
  100. H. Mirzaei, S. Ahmadian, S. Mahabadi, M. Sadeghi, C. Eslahchi, H. Pezeshk (2009) An Algorithm for Construction of All Perfect Phylogeny Matrices, MATCH Communications in Mathematical and in Computer Chemistry, 62 (2) 251-259
  101. M. Kargar, H. Poormohammadi, L. Pirhaji, M. Sadeghi, H. Pezeshk, C. Eslahchi: Enhanced Evolutionary and Heuristic Algorithms for Haplotype Reconstruction Problem Using Minimum Error Correction Model, MATCH Communications in Mathematical and in Computer Chemistry,  62 (2) 261-274
  102. F. Zare-Mirakabad, P. Davoodi, H. Ahrabian , A. Nowzari-Dalini,M. Sadeghi, B. Goliaei (2009) Finding Motifs Based on Suffix Trie, Advanced Modeling and Optimization, 11(2), 177-194
  103. Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdi Sadeghi, Somaieh Hashemifar, Abbas Nowzari-Dalini, Bahram Goliaei (2009) Genetic algorithm for dyad pattern finding in DNA sequences, Genes Genet. Syst. 84, 81-93
  104. Changiz Eslahchi, Hamid Pezeshk, Mehdi Sadeghi, Amir Massoud Rahimi, Heydar Maboudi Afkham, ShahriarArab (2009) STON: Anovel method for protein three-dimensional structure comparison, Computers in Biology and Medicine, 39,166-172
  105. Seyed Amir Malekpour, Sima Naghizadeh, Hamid Pezeshk, Mehdi Sadeghi , Changiz Eslahchi (2009)  Protein secondary structure prediction using three neural networks and a segmental semi Markov model, Mathematical Biosciences, 217 ,145–150
  106. Sayed-Rzgar Hosseinia, Mehdi Sadeghib, Hamid Pezeshk, Changiz Eslahchi, Mahnaz Habibi (2008) PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive Cα atoms, Computational Biology and Chemistry, 32, 406–411
  107. Amir Momen-Roknabadi, Mehdi Sadeghi, Hamid Pezeshk and Sayed-Amir Marashi (2008) Impact of residue accessible surface area on the prediction of protein secondary structures, BMC Bioinformatics, 9:357
  108. Armita Sheari, Mehdi Kargar, Ali Katanforoush, Shahriar Arab, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi and Sayed- Amir Marashi (2008) A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins, BMC Bioinformatics., 9:274
  109. Leila Pirhaji , Mehdi Kargar , Armita Shearic, Hadi Poormohammadi, Mehdi Sadeghi, Hamid Pezeshk, Changiz Eslahchi (2008) The performances of the chi-square test and complexity measures for signal recognition in biological sequences, Journal of Theoretical Biology,251, 380-387
  110. Eslahchi C, Sadeghi M, Pezeshk H, Kargar M, Poormohamadi H. (2007) Haplotyping Problem, A Clustering Approach.American Institute of Physics Conference Proceedings – September, 936:185-190.
  111. Sayed-Amir Marashi, Mehdi Kargar, Ali Katanforoush, Hassan Abolhassani and Mehdi Sadeghi (2007) Evolution of ‘Ligand-Diffusion Chreods’ on Protein-Surface Models:A Genetic Algorithm Study, Chemistry and Biodiversity, vol 4, 2766-2771
  112. Shahriar Arab, Farzad Didehvar, Changiz Eslahchi, Mehdi Sadeghi(2007) Helix segment assignment in proteins using fuzzy logic, Iranain Journal of Biotechnology, Vol. 5, 93-99
  113. Roghayeh Zarei, Shahriar Arab and Mehdi Sadeghi (2007) A Method for Protein Accessibility Prediction based on Residue Types and ConformationalStates, Computational Biology and Chemistry, Vol. 31, 384–388
  114. Fereshteh Chitsazian, Betsabeh Khoramian Tusi, Elahe Elahi,‡ Heidar Amini Saroei, Mohammad H. Sanati, Shahin Yazdani, Mohammad Pakravan, Navid Nilforooshan,_ Yadollah Eslami, Mohammad Ali Zare Mehrjerdi, Reza Zareei, Mahmood Jabbarvand, Ali Abdolahi, Ali R. Lasheyee, Arash Etemadi, Behnaz Bayat, Mehdi Sadeghi, Mohammad M. Banoei, Behnam Ghafarzadeh, Mohammad R. Rohani, Akram Rismanchian, Yvonne Thorstenson, and Mansoor Sarfarazi (2007) "CYP1B1 Mutation Profile of Iranian Primary Congenital Glaucoma Patients and Associated Haplotypes". Journal of Molecular Diagnostics, Vol. 9, No. 3, 382-392
  115. Khosrow Khalifeh, Bijan Ranjbar, Khosro Khajeh, Hossein Naderi-Manesh, Mehdi Sadeghi and Sara Gharavi (2007) "A stopped-flow fluorescence study of the native and modified lysozyme", Biologia, volum 62,No.3: 258—264
  116. Narges Kh. Tafreshi, Saman Hosseinkhani, Majid Sadeghizadeh, Mehdi Sadeghi, Bijan Ranjbar and Hossein Naderi-Manesh (2007) "The Influence of Insertion of a Critical Residue (Arg356) in Structure and Bioluminescence Spectra of Firefly Luciferase", The Journal of Biological Chemistry, Vol. 282, 8641–8647
  117. Z Moosavi-Movahedi, S Safarian, M Zahedi, M Sadeghi, AA Saboury, J Chamani, H Bahrami, A Ashraf-Modarres and AA Moosavi-Movahedi (2006) "Calorimetric and Binding    Dissections of HAS Upon Interaction with Bilirubin", The Protein Journal, 25(3), 193-201
  118. Moosavi-Movahedi AA, Gharanfoli M, Jalili S, Ahmad F, Chamani J, Hakimelahi GH, Sadeghi M, Amani M, Saboury AA. (2006) "The correlation of Rnase A enzymatic activity with the changes in the distance between Nd2-His12 and Nd1-His119 upon addition of stabilizing and destabilizing salts", The Protein Journal, 25(2), 117 – 125
  119. Marashi SA, Eslahchi C, Pezeshk H, Sadeghi M. (2006) "Impact of RNA structure on the prediction of donor and acceptor splice sites" BMC Bioinformatics. 13;7(1):297
  120. Maryam Monsef Shokri , Khosro Khajeh , Jahan Alikhajeh , Ahmad Asoodeh ,  Bijan Ranjbar , Saman Hosseinkhani , Mehdi Sadeghi (2006) " Comparison of the molten globule states of thermophilic and mesophilic α-amylases ", Biophysical Chemistry, Volume 122, Issue 1:58-65
  121. Sayed-Amir Marashi , Hani Goodarzi , Mehdi Sadeghi , Changiz                                              Eslahchi ,Hamid Pezeshk (2006) "Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks" Computational Biology and Chemistry, 30: 50-57
  122. Leila Hassani , Bijan Ranjbar , Khosro Khajeh , Hossein Naderi-Manesh , Mehdi Naderi-Manesh, Mehdi Sadeghi (2006) "Horseradish peroxidase thermostabilization:The combinatorial effects of the surface modification and the polyols" Enzyme and Microbial Technology,  38: 118-125
  123. Khosro Khajeh, Maryam Monsef Shokri , S. Mohsen Asghari , Fatemeh Moradian, Atiah Ghasemi, Mehdi Sadeghi, Bijan Ranjbar, Saman Hosseinkhani, Sara Gharavi, Hossein Naderi-Manesh (2006) "Acidic and proteolytic digestion of α-amylases from Bacilluslicheniformis and Bacillus amyloliquefaciens:Stability and flexibility analysis" Enzyme and Microbial Technology, 38: 422-428
  124. Mehdi Sadeghi, Hossein Naderi-Manesh, mahbobeh Zarrabi and Bijan Ranjbar (2006)   "Effective factors in thermostability of thermophilic proteins", Biophysical Chemistry, 119: 256-270 
  125. Ali Akbar Saboury, Malihe Sadat Atri, Mohammad Hossein Sanati and Mehdi Sadeghi (2005) "Application of a simple calorimetric data analysis on the binding study of calcium ions by human growth hormone" Journal of Thermal analysis and calorimetry, 83:175 - 179
  126. Saboury AA, Atri MS, Sanati MH, Moosavi-Movahedi AA, Hakimelahi GH, Sadeghi M(2006) "A thermodynamic study on the interaction between magnesium ion and human growth hormone."Biopolymers, 81:120-126
  127. Saber Zahri, Mohammad Reza Zamani*, Mostafa Motallebi, Mehdi Sadeghi (2005)   “Cloning and characterization of cbhII gene from Trichoderma parceramosum and its expression in Pichia pastoris” Iranian Journal of Biotechnology, Vol. 3, No. 4, 204-215
  128. M. S. Atri, A. A. Saboury, M. Rezaei-Tavirani, M. H. Sanati, A. A. Moosavi-Movahedi, M. Sadeghi, H. Mansuri-Torshizi, M. Khodabandeh(2005) "Binding Properties and Conformational Change of Human Growth Hormone upon Interaction with Fe+3 ", Thermochimica Acta. 438: 178-183
  129. Mehdi Sadeghi, Sahar Parto, Shahriar Arab and Bijan Ranjbar (2005) "Prediction of protein secondary structure based on residue pair types and    conformational states using dynamic programming algorithm", FEBS Letters, 579: 3397-3400
  130. Seyed-omid ranaei, Gholam-Hossein Riazi, Mehdi Sadeghi and et al (2004) "Modification of substrate inhibition of synaptosomal acetylcholinesterase by cardiotoxin", J. Biochem. Mol. Biol., 37: 330-338
  131. Davood Ajloo, Ali akbar Moosavi Movahedi, mehdi Sadeghi and Housain Gharibi (2002)"Comparative structural and functional studies of avian and mammalian hemoglobin", Acta Biochemica Polonica, 49: 459-470
  132. Hossein Naderi-Manesh, Mehdi Sadeghi, Shahriar Arab and Ali Akbar Moosavi movahedi (2001) "Prediction of protein surface accessibility with information theory", PROTEINS, 42: 452-459
  133. B. Goliaei , A. Rabbani , F. Assadion, H. Keshavarzi , and M.Sadeghi (1991) “ Effcts of
  134. environmental pH on the production of hematopoietic growth factors” , J.Sci.I.R.Iran , 2: 5-10
  1. مهدی صادقی، علی اکبر موسوی موحدی " پایداری حرارتی پروتئین ها و کاربرد آن در بیوتکنولوژی"، فصل 7 ، 263-287، شیمی فیزیک ماکرو ملکول های حیاتی، انتشارات دانشگاه تهران
  2. مهدی صادقی، علی اکبر موسوی موحدی " سنتز ژن" ، نشریه شیمی و مهندسی شیمی، سال دوازدهم، شماره یک، 51-59 ، 1372
  3. مهدی صادقی، علی اکبر موسوی موحدی " RNAهای کاتالیتیک"،، نشریه شیمی و مهندسی شیمی، سالیازدهم، شماره یک،75-82، 1371
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  5. مهناز حبيبي، چنگيز اصلاحچي، حميد پزشك، مهدي صادقي " روشي تحليلي براي نسبت دادن ساختمان دوم پروتئين" مجله علوم دانشگاه تهران، جلد سي و چهارم شماره 3، 41-48، 1387
  6. نارسيس آفتاب كياني، مهدي صادقي، چنگيز اصلاحچي " نقشه هاي تماس 1روتئيني اسيد آمينه محور" مجله علوم دانشگاه تهران، جلد سي و چهارم شماره 3، 49-54، 1387
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  9. مهدی صادقی، صفر وفادار دولق " ماده تاریخ و استفاده از رایانه در ساختن آن" فصلنامه تخصصی سبک شناسی نظم و نثر فارسی، سال سوم، شماره چهارم،231-243، 1389
  10.  سید شهریار عرب، مهدی صادقی،  چنگیز اصلاح چی، حمید پزشک " پیش گویی انعطاف پذیری قطعات پروتئینی با استفاده از پروفایل انرژی" علوم وفناوری زیستی مدرس، دوره 1، شماره 1،1-7 1389
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