2012

·        V. Rezaei, H. Pezeshk, M. Sadeghi and C. Eslahchi. Assignment of protein sequences to protein family profiles using spatial statistics, To appear in MATCH Communications in Mathematical and Computer Chemistry, 2012.

·        C. Eslahchi, F. Movahedi. Calculation of Transition Probabilities in the Birth and Death Markov process in the epidemic model, Mathematical and Computer Modelling, 2012, 55, 810-815.

2011

·        C. Eslahchi, R. Hassanzadeh, E. Mottaghi, M. Habibi, H. Pezeshk, M. Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing, Mathematical Biosciences In Press, Accepted Manuscript.

·        C. Eslahchi, H. Pezeshk, N. Afzaly, A. Katanforoush. Haplotype block partitioning and tagSNP selection under the perfect phylogeny model, Iranian Journal of Biotechnology (IJB), 2011, 9, 4

·        M. Mirzarezaee, M. Sadeghi, B. N. Araabi. Dynamical Analysis of Yeast Protein Interaction Network During the Sake Brewing Process, The Journal of Microbiology 2011, 49, pp.

·        P. Zakeri , B. Moshiri, M. Sadeghi. Prediction of protein submitochondria locations based on data fusion of various features of sequences, Journal of Theoretical Biology 2011, 269, 208-216

·        K. Kavousi, B. Moshiri, M. Sadeghi, B. N. Araabi, A. A. Moosavi-Movahedi, A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM, Computational Biology and Chemistry 2011, 35, 1-9

·        R. Aghdam, H. Pezeshk, A. Malekpour, S.Shemehsavar, M. Sadeghi, C. Eslahchi. A Clustering Approach for Estimating Parameters of a Profile Hidden Markov Model, To appear in International Journal of Data Mining and Bioinformatics

·        M. Habibi, C. Eslahchi, H. Pezeshk, M. Sadeghi. An Information Theoretic Approach to Secondary Structure Assignment, MATCH Communications in Mathematical and Computer Chemistry 2011,65 (1): 5–20.

·        Pezeshk H, Nematollahi N, Maroufy V, Marriott P, and Gittins J.  Bayesian Sample Size Calculation For Estimation Of The Difference Between Two Binomial Proportions. Statistical Method in Medical Research (Published on line in March 2011) DOI: 10.1177/0962280211399562.

2010

·        M. Mirzaei, M. Sadeghi. Knowledge-based potentials in protein fold recognition, Journal of Paramedical Sciences 2010, Vol.1, No.4, 65-75

·        Aghdam R, Pezeshk H, Malekpour S. M., Shemehsavar S, Sadeghi M and Eslahchi C.  A Bidirectional Bayesian Monte Carlo Approach for Estimating Parameters of a Profile Hidden Markov Model. Applied Science Segment 1(2) APS/1531, 2010

·        M. Mirzarezaee, B. N. Araabi, M. Sadeghi. Comparison of Hubs in Effective Normal and Tumor Protein Interaction Networks, Basic and Clinical Neuroscience 2010, Volume 2, Number 1: 44-50

·        M. Mirzarezaee, B. N. Araabi, M. Sadeghi, Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae, BMC Systems Biology 2010, 4:172

·        A. Meshkin, N. Ghasem Aghaee , M. Sadeghi. Modeling and implementing an agent-based system for prediction of protein 3 relative solvent accessibility, Expert Systems with Applications 2010, 38, 6324–6332

·        Eslahchi C, Pezeshk H, Sadeghi M, Giabbanelli P, Movahedi F, Dabbaghian V. A Probabilistic Model for the Spread of HIV Infection among Injection Drug Users. World Journal of Modelling and Simulation (WJMS), volume 6, number 4, pp. 267-273, 2010. [7 pp.]

·        Ayati M, Taheri G, Arab S, Wong L, Eslahchi C. Overcoming Drug Resistance by Co-Targeting. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 198--201, Hong Kong, December 2010

·        Aghdam R, Ejlali N, Pezeshk H. A New Method for Estimating Parameters of a Profile Hidden Markov Model. Biostatistics, Bioinoformatics and Biomathematics. 2010 Nov; 2(1): 33-43.

·        Sadeghi M, Pezeshk H, Eslahchi C, Ahmadian S, Mah Abadi S. Construction of Random Perfect Phylogeny Matrix. Advances and Applications in Bioinformatics and Chemistry 2010, 3,89,96.

·        Habibi M, Eslahchi C, Sadeghi M, Pezeshk H. The interpretation of protein structures based on graph theory and contact map. Open Access Bioinformatics 2010:2 1–11.

·        Mahdevar G, Zahiri J, Sadeghi M, Nowzari-Dalini A, Ahrabian H. Tag SNP selection via a genetic algorithm. J Biomed Inform. 2010 Oct;43(5):800-4.

·        Ejlali N, Pezeshk H. A Bidirectional Hidden Markov Model in Linear Memory. Journal of Statistical Science 2010, 4:129

·        Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: A method for the construction of phylogenetic networks based on the Monte-Carlo method.  BMC Evolutionary Biology, 2010, 10:254.

·        Pezeshk H, Naghizadeh S, Malekpour S. A, Eslahchi C, Sadeghi M. A Modified Bidirectional Hidden Markov Model and its Application in Protein Secondary Structure Prediction. Proceeding of the Second Interaction Conference on Advanced Computer Control (ICACC 2010), Shenyang, China 27th-29th March 2010, pp 535-538.  

·         Arab S, Sadeghi M, Eslahchi C, Pezeshk H. A pairwise residue contact area-based mean force potential for discrimination of native protein structure. BMC Bioinformatics, 2010;  11:16 doi:10.1186/1471-2105-11-16

2009

·         Katanforoush A, Sadeghi M, Pezeshk H, Elahi E. Global haplotype partitioning for maximal associated SNP pairs. BMC Bioinformatics, 2009; 10(1): 269.

·         Malekpour S. A., Naghizadeh S., Pezeshk, H., Sadeghi, M., Eslahchi, C. A Segmental Semi Markov Model for Protein Secondary Structure Prediction. Mathematical Biosciences, 2009; 221: 130-135

·         Mirzaee M., Eslahchi C., Pezeshk H., Sadeghi M. A Distance Dependent Atomic Knowledge Based Potential and Force for Discrimination of Native Structures from Decoys. PROTEINS, 2009; 77: 454-463

·         Zare-Mirakabad F., Ahrabian H., Sadeghi M., Nowzari-Dalini A., Goliaei B. New scoring schema for finding motifs in DNA Sequences, BMC Bioinformatics 2009, 10:93

·         Zare-Mirakabad F., Davoodi P., Ahrabian H., Nowzari-Dalini A., Sadeghi M.,  Goliaei B. Finding Motifs Based on Suffix Trie, Advanced Modeling and Optimization, 2009, 11(2), 177-194

·         Eslahchi C., Pezeshk H., Sadeghi M., Sheikh attar A. LIBRA: A de Novo Motif Finding in Promoter Sequences Based on Linear Algebra. Proceedings of world Academy of Science, Engineering and Technology, 2009, 37: 507-512

·         Mirzaei H., Ahmadian S., Mahabadi S., Sadeghi M., Eslahchi C., Pezeshk H. An Algorithm for Construction of all Perfect Phylogeny Matrices. Match, 2009, 62, 2: 251-259

·         Kargar M., Poormohammadi H., Pirhaji L., Sadeghi M., Pezeshk H., Eslahchi C. Enhanced Evolutionary and Heuristic Algorithms for Haplotype Reconstruction Problem Using Minimum Error Correction Model. Match, 2009, 62, 2: 261-274

·         Eslahchi C., Pezeshk H., Sadeghi M., Rahimi A. M., Maboudi Afkham H., Arab S. Ston: A Novel Method for Protein three-dimensional Structure Comparison. Computers in Biology and Medicine 2009, 39, 2: 166-172.

·         Malekpour S. A., Naghizadeh S., Pezeshk, H., Sadeghi, M., Eslahchi, C. Protein Secondary Structure Prediction Using three Neural Networks and a Segmental Semi Markov Model. Mathematical Biosciences 2009, 217, 2: 145-150.

·         Zare-Mirakabad F., Sadeghi M., Ahrabian H., Nowzari-Dalini. RNAComp: A New Method for RNA Secondary Structure Alignment. MATCH Communications in Mathematical and Computer Chemistry 2009, 61, 3: 789-816.

2008

·         Hosseini S. R., Sadeghi, M., Pezeshk H., Eslahchi C., Habibi M. PROSIGN: A Method for Protein Secondary Structure Assignment Based on Three-Dimensional Coordinates of Cosecutive Ca atoms. Computational Biology and Chemistry 2008, 32, 6: 406-411.

·         Naghizadeh S., Pezeshk H., Sadeghi M., Mohammadzadeh M., Eslahchi C.  A Modification on a Left-to-Right and Right-to-Left Dependency Model for Secondary Structure Prediction. Journal of Science, University of Tehran 2008, 34, 3, 61-66.

·         Habibi M., Eslahchi C., Pezeshk H., Sadeghi M. An Information theoritical Approch to Secondary Structure Assignment. Journal of Science, University of Tehran 2008, 34, 3, 41-48.

·         Momen-Roknabadi A., Sadeghi M., Pezeshk H., Marashi S. A. Impact of Residue Accessible Surface Area on the Prediction of Protein Secondary Structures. BMC Bioinformatics 2008, 9:357.

·         Sheari A, Kargar M, Katanforoush A, Arab S, Sadeghi M, Pezeshk H, Eslahchi C, Marashi S.A. A Tale of two Symmetrical Tails: Structural and Functional Charateristics of Palindroms in Proteins. BMC Bioinformatics 2008,9:274.

·         Pirhaji L, Kargar M, Sheari A, Poormohamadi H, Sadeghi M, Pezeshk H, Eslahchi C. The Performance of chi-square Test and complexity Measures for Signal Recognition in Biological Sequences. Journal of Theoretical Biology. (2008) vol. 251, 380-387.

·         Farzadfard F, Gharaei N, Pezeshk H, Marashi SA. β-sheet Capping: Signals that Initiate and Terminate β-sheet Formation. Journal of Structural Biology. 2008, 101-110.

2007

·         Shahriar Arab, Farzad Didehvar, Changiz Eslahchi, Mehdi Sadeghi Helix segment assignment in proteins using fuzzy logic , IRANIAN JOURNAL of BIOTECHNOLOGY, 2007, Vol. 5, 93-99.

·         Eslahchi C, Sadeghi M, Pezeshk H, Kargar M, Poormohamadi H. Haplotyping Problem, A Clustering Approach. American Institute of Physics Conference Proceedings – September 2007, 936:185-190.

·         Zarei R, Arab S, Sadeghi M. A Method for Protein Accessibility Prediction Based on Residue types and Conformational States. Computational Biology and Chemistry 2007, 31: 384-388.

·         Marashi SA, Kargar M, Katanforoush A, Abolhasani H, Sadeghi M. Evolution of ‘Ligand-Diffusion Chreodes’ on protein – surface Models: A Genetic Algorithm study. Chemistry and Biodivrsity. 2007, 4: 2766-2771.

·         Goodarzi H, Katanforoush A, Torabi N, Shateri Najafabadi H. Solvent Accessibility, Residue Charge and Residue Volume, the three Ingredients of a Robust Amino Acid Substitution Matrix. Journal of Theoretical Biology 2007, 245: 715-725.

·         Marashi SA, Behrouzi R, Pezeshk H.  Adaptation of proteins to different environments: A comparison of proteome structural properties in Bacillus subtilis and Escherichia coli. J Theor Biol. 2007; 244(1):127-32.

·         Marashi SA, Eslahchi C, Pezeshk H, Sadeghi M.  Impact of RNA structure on the prediction of donor and acceptor splice sites. BMC Bioinformatics. 2006; 7:297.

·         Marashi SA, Goodarzi H, Sadeghi M, Eslahchi C, Pezeshk H.  Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. Comput Biol Chem. 2006; 30(1):50-7.