IPM Positions

Professor, School of Biological Sciences Senior Researcher, School of Biological Sciences (2006 - 2020 )

Non IPM Affiliations

Professor of University of Tehran

Related Papers

1.	Y. Panahi, F. Salasar Moghaddam, Kh. Babaei, M. Eftekhar, R. Shervin Badv, M. Eskandari, M. Vafaee-Shahi, H. Pezeshk and M. Pedram Sexual Dimorphism in Telomere Length in Childhood Autism Autism and Developmental Disorders (2022), 10.1007/s10803-022-05486-2  [abstract]

2.	S. salmanian, H. Pezeshk and M. Sadeghi Inter protein residue covariation information unravels physically interacting protein dimers BMC Bioinformatics 21 (2020), 1-21 https://doi.org/10.1186/s12859-020-03930-7  [abstract]

3.	M. Ghamghami, N. Ghahreman, P. Irannejad and H. Pezeshk A parametric empirical Bayes (PEB) approach for estimating maize progress percentage at field scale Agricultural and Forest Meteorology 281 (2020), https://doi.org/10.1016/j.agrformet.2019.107829  [abstract]

4.	N. Ejlali, H. Pezeshk, Y. P. Chaubey, M. Sadeghi, A. Ebrahimi and A. Nowzari-Dalini Parrondos Paradox for Games with Three Players and Its Potential Application in Combination Therapy for Type II Diabetes Physica A 556 (2020), https://doi.org/10.1016/j.physa.2020.124707  [abstract]

5.	S. Hosseinian, E. Arefian, H. Rakhsh-Khorshid, M. Eivani, A. Rezayof, H. Pezeshk and S. A. Marashi A meta-analysis of gene expression data highlights synaptic dysfunction in the hippocampus of brains with Alzheimers disease Scientific Reports 10 (2020), 1-9 https://doi.org/10.1038/s41598-020-64452-z  [abstract]

6.	M. Shahdoust, H. Mahjub, H. Pezeshk and M. Sadeghi A Network-based Comparison between Molecular Apocrine Breast Cancer Tumors and Basal and Luminal Tumors by Joint Graphical Lasso computational biology and bioinformatics DOI: 10.1109/TCBB.2019.2911074 (2019),   [abstract]

7.	R. Aghdam, V. Rezaei Tabar and H. Pezeshk Some Node Ordering Methods for the K2 Algorithm Computational Intelligence DOI: 10.1111/coin.12182 (2018), 1-17  [abstract]

8.	N. Ejlali, H. Pezeshk, Y. P. Chaubey and M. Sadeghi Parrondo's Paradox for Games with Three Players Technical Report 983832/1/ report No. 1/18 (2018) (2018), Spectrum: Concordia University, https://spectrum.library.concordia.ca/983832/1/report1-18.pdf  [abstract]

9.	A. Malekpour, H. Pezeshk and M. Sadeghi MSeq-CNV: accurate detection of Copy Number Variation from Sequencing of Multiple samples Scientific Reports 8 (2018), doi:10.1038/s41598-018-22323-8  [abstract]

10.	M. Sadeghi, H. Pezeshk, R. Tusserkani, A. Sharifi Zarchi, S.A. Malekpour-Nargesi, Mehdi. Foroughmand, S. Goliaei, M. Totonchi and N. Ansari-Pour The Role and Importance of Genome Sequencing in Prediction of Cancer Risk Bioengineering and Pharmaceutical Engineering 11 (2017), 455-460  [abstract]

11.	A. Sharifi-Zarchi, D. Gerovska, K. Adachi, M. Totonchi, H. Pezeshk, R. J. Taft, H. R. Schöler, . Chitsaz, M. Sadeghi, B. Baharvand and M. J. Araúzo-Bravo DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism BMC Genomics 18 (2017), 964  [abstract]

12.	A. Fotoohinasab, E. Fatemizadeh, H. Pezeshk and M. Sadeghi Denoising of genetic switches based on Parrondos paradox Physica A: Statistical Mechanics and its Applications 493 (2017), 410-420  [abstract]

13.	M. Shahdoust, H. Pezeshk, H. Mahjub and M. Sadeghi F-MAP: A Bayesian approach to infer the gene regulatory network using external hints PlosOne 19 (2017), https://doi.org/10.1371/journal.pone.0184795  [abstract]

14.	F. Dorri, H. Pezeshk and M. Sadeghi Stochastic Cell Fate and Longevity of Offspring Cell Journal 19 (2017), 343-350  [abstract]

15.	H. Seidkhani, A. R. Nikolaev, R. N. Meghanathan, H. Pezeshk, A. Masoudi-Nejad and C. van Leeuwen Task modulates functional connectivity networks in free viewing behavior NeuroImage 159 (2017), 289 - 301 https://doi.org/10.1016/j.neuroimage.2017.07.066  [abstract]

16.	A. Malekpour, H. Pezeshk and M. Sadeghi PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities BMC Bioinformatics https://doi.org/10.1186/s12859-016-1296-y (2016), 1-30  [abstract]

17.	S. A. Malekpour, H. Pezeshk and M. Sadeghi MGP-HMM: detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts Mathematical Biosciences (2016), 53-62  [abstract]

18.	V. Rezaei Tabar and H. Pezeshk Generalized Profile Hidden Markov Model (PHMM) based on the Dependency between sequences Progress in Biological Sciences 6 (2016), 117-127 10.22059/PBS.2016.590014  [abstract]

19.	M. Bideli. , J. Gittins. and H. Pezeshk A Mixed Bayesian/Frequentist Approach to Sample Size Determination Problem for Clinical Trials Progress in Biological Sciences 6 (2016), 1-9  [abstract]

20.	N. Ejlali. , H. Pezeshk. and M. Sadeghi. A Note on the Parrondo's Paradox The 10th Seminar on Probabilty and Stochastic Processes (2015), 140  [abstract]

21.	A. Sharifi-Zarchi. , M. Totonchi. , K. Khaloughi. , R. Karamzadeh. , M. J. Araúzo-Bravo. , H. Baharvand. , R. Tusserkani. , H. Pezeshk. , H. R. Chitsaz. and M. Sadeghi. Increased robustness of early embryogenesis through collective decision-making by key transcription factors BMC Systems Biology DOI:10.1186/s12918-015-0169-8 (2015),   [abstract]

22.	A. Kazemi-Pour. , B. Goliaei. and H. Pezeshk. Protein Complex Discovery by Interaction Filtering from Protein Interaction Networks Using Mutual Rank Coexpression and Sequence Similarity BioMed Research International 2015 (2015), 7  [abstract]

23.	F, Dorri. , H. Mahini. , A. Sharifi-Zarchi. , M. Totonchi. , R. Tusserkani. , H. Pezeshk. and M. Sadeghi. Natural Biased Coin Encoded in the Genome Determines Cell Strategy Plos One 9 (2014), e103569  [abstract]

24.	V. Maroufy. , P. Marriott. and H. Pezeshk. An Optimization Approach To Calculating Sample Sizes For Trials With Binary Responses Biopharmaceutical Statistics 24 (2014), 715-731  [abstract]

25.	E. S. Ansari. , H. Pezeshk. , M. Sadeghi. and C. Eslahchi. ProDomAs; Protein Domain Assignment Algorithm using Centre-Based Clustering and Independent Dominating Set Proteins: Structure, Function and Bioinformatics 82 (2014), 1937â??1946  [abstract]

26.	V.Rezaei. , S. Naghizadeh. , H. Pezeshk. , M. Sadeghi. and C. Eslahchi. Comparison of the bidirectional Baum-Welch algorithm and the Baum-Welch algorithm on regular lattice Progress in Biological Sciences 2 (2013), 14-22  [abstract]

27.	H. Pezeshk. , N. Nematollahi. , V. Maroufy. , P. Marriott. and J. Gittins. Bayesian Sample Size Calculation For Estimation Of The Difference Between Two Binomial Proportions Statistical Methods in Medical Research 22 (2013), 598-611  [abstract]

28.	V.Rezaei. , H. Pezeshk. , M. Sadeghi. and C. Eslahchi. Assignment Of Protein Sequences To Protein Family Profiles Using Spatial Statistics. MATCH Communication in Methematical and in Computer Chemistry 69 (2013), 7-24  [abstract]

29.	V.Rezaei. Rezaie, H. Pezeshk and H.Pérez-Sa'nchez. Generalized Baum-Welch Algorithm Based On The Similarity Between Sequences. Plos One 8 (2013), e80565  [abstract]

30.	Z. Safikhani. , M. Sadeghi. , H. Pezeshk. and C. Eslahchi. SSP: An interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads Genomics 102 (2013), 507-514  [abstract]

31.	R. Aghdam. , H. Pezeshk. and M. Ganjali. A New Method for Estimating parameters of A Profile Hidden Markov models Based on Phylogenetic tree Iranian Statistical Conference (2012),   [abstract]

32.	R. Aghdam. , H. Pezeshk. , S.A. Malekpour. , S. Shemehsavar. , M. Sadeghi. and C. Eslahchi. A Clustering Approach for Estimating Parameters of a Profle Hidden Markov Model International Journal of Data Mining and Bioinformatics 8 (2012), 66-82  [abstract]

33.	V.Rezaei. , M. Mohamadzadeh. and H.Pezeshk. Comparison Between Spatial Statistics Model And Bidirectional Hidden Markov Model For Assignment Of Protein Sequences Iranian Statistical Conference (2012), 511-517  [abstract]

34.	H. Pezeshk. and V. Maroufy. Shannon Information For Expected Net Gain Of Sampling Iranian Statistical Conference (2012), 465-472  [abstract]

35.	C. Eslahchi. , R. Hassanzadeh. , E. Mottaghi. , M. Habibi. , H. Pezeshk. and M. Sadeghi. Constructing Circular Phylogenetic Networks From Weighted Quartets Using Simulated Annealing Mathematical Biosciences 235 (2012), 123-127  [abstract]

36.	S. Naghizadeh. , V. Rezaei. , H.Pezeshk. and D. Matthews. A Modified Hidden Markov Model And Its Application In Protein Secondary Structure Prediction Proteomics Bioinform 5 (2012),   [abstract]

37.	M. Habibi. , C. Eslahchi. , H. Pezeshk. and M. Sadeghi. An Information Theoretic Approach To Secondary Structure Assignment MATCH Communications in Mathematical and in Computer Chemistry 65 (2011), 5-20  [abstract]

38.	C. Eslahchi. , A. Katanforoush. , H. Pezeshk. and N. Afzaly. Haplotype Block Partitioning And TagSNP Selection Under The Perfect Phylogeny Model IRANIAN JOURNAL of BIOTECHNOLOGY 9 (2011),   [abstract]

39.	H. Pezeshk (Joint with N. Nematollahi, V. Maroufy, P. Marriott and J. Gittins) Bayesian sample size calculation for estimation of the difference between two binomial proportions Statistical Methods in Medical Research (Accepted) [abstract]

40.	S.Arab. , C. Eslahchi. , M. Sadeghi. , H. Pezeshk. and A. Sheari. A Pairwise Residue Contact Area-Based Mean Force Potential For Discrimination Of Native Protein Structure BMC Bioinformatics 11 (2010), 16  [abstract]

41.	H. Pezeshk. , S. Naghizadeh. , S. A. Malekpour. , C. Eslahchi. and M. Sadeghi. A Modified Bidirectional Hidden Markov Model And Its Application In Protein Secondary Structure Prediction Proceeding of the Second International Conference on Advanced Computer Control 3 (2010), 535-538  [abstract]

42.	N. Ejlali. and H. Pezeshk. A Bidirectional Hidden Markov Model In Linear Memory Journal of Statistical Science 2 (2010), 131-148  [abstract]

43.	M. Habibi. , C. Eslahchi. , M. Sadeghi. and H. Pezeshk. The Interpretation Of Protein Structures Based On Graph Theory And Contact Map Open Access Bioinformatics 2 (2010), 127-137  [abstract]

44.	M. Sadeghi. , H. Pezeshk. , C. Eslahchi. , S. Ahmadian. and S. Mah Abadi. Construction Of Random Perfect Phylogeny Matrix Advances and Applications in Bioinformatics and Chemistry 3 (2010), 89-96  [abstract]

45.	C. Eslahchi. , H. Pezeshk. , M. Sadeghi. , P. Giabbanelli. , F. Movahedi. and V.A. Dabbaghian. A Probabilistic Model For The Spread Of HIV Infection Among Injection Drug Users World Journal of Modelling and Simulation 6 (2010), 267-273  [abstract]

46.	R. Aghdam. , H. Pezeshk. , S.A. Malekpour. , S. Shemehsavar. , M. Sadeghi. and C. Eslahchi. A Bidirectional Bayesian Monte Carlo Approach For Estimating Parameters Of A Profile Hidden Markov Model Applied Science Segment 1 (2010),   [abstract]

47.	H. Pezeshk (Joint with Ch. Eslahchi, M. Sadeghi, Ph. Giabbanelli, F. Movahedi, and V. Dabbaghian) A probabilistic model for the spread of HIV infection among injection drug users World Journal of Modelling and Simulation 6 (2010), 267-273  [abstract]

48.	H. Mirzaei. , S. Ahmadian. , S. Mahabadi. , M. Sadeghi. , C. Eslahchi. and H. Pezeshk. An Algorithm for Construction of All Perfect Phylogeny Matrices MATCH Communication in Methematical and in Computer Chemistry 62 (2009), 251  [abstract]

49.	M. Mirzaie. , C. Eslahchi. , H. Pezeshk. and M. Sadeghi. A distance-dependent atomic knowledge based potential and force for discrimination of native structures from decoys Proteins: Structure, Function and Bioinformatics 77 (2009), 454-463  [abstract]

50.	S. A. Malekpour. , S. Naghizadeh . , H. Pezeshk. , M. Sadeghi. and C. Eslahchi. Protein secondary structure prediction using three neural networks and a segmental semi Markov model Mathematical Biosciences 217 (2009), 145-150  [abstract]

51.	C. Eslahchi. , H. Pezeshk. , M. Sadeghi. , A. M. Rahimi. , H. Maboudi Afkham. and S. Arab. STON: Anovel method for protein three-dimensional structure comparison Computers in Biology and Medicine 39 (2009), 166-172  [abstract]

52.	M. Kargar. , H. Poormohammadi. , L. Pirhaji. , M. Sadeghi. , H. Pezeshk. and C. Eslahchi. Enhanced Evolutionary And Heuristic Algorithms For Haplotype Reconstruction Problem Using Minimum Error Correction Model Match 62 (2009), 261-274  [abstract]

53.	C. Eslahchi. , H. Pezeshk. , M. Sadeghi. and A. S. Attar. LIBRA: A de Novo Motif Finding In Promoter Sequences Based On Linear Algebra. Proceedings of world Academy of Science Engineering and Technology 37 (2009), 507-512  [abstract]

54.	M. Mirzaie. , C. Eslahchi. , H. Pezeshk. and M. Sadeghi. A Distance Dependent Atomic Knowledge Based Potential And Force For Discrimination Of Native Structures From Decoys Protein Journal 77 (2009), 454-463  [abstract]

55.	S. A. Malekpour. , S. Naghizadeh. , H. Pezeshk. , M. Sadeghi. and C. Eslahchi. A Segmental Semi Markov Model For Protein Secondary Structure Prediction Mathematical Biosciences 221 (2009), 130-135  [abstract]

56.	A. Katanforoush. , M. Sadeghi. , H. Pezeshk. and E. Elahi. Global Haplotype Partitioning For Maximal Associated SNP Pairs BMC Bioinformatics 10 (2009), 269  [abstract]

57.	F. Farzadfard. , N. Gharaei. , H. Pezeshk. and S. A. Marashi. β-Sheet capping: Signals that initiate and terminate β-sheet formation Journal of Structural Biology 161 (2008), 101-110  [abstract]

58.	L. Pirhaji. , M. Kargar. , A. Sheari. , H. Poormohamadi. , M. Sadeghi. , H. Pezeshk. and C. Eslahchi. The Performance Of Chi-Square Test And Complexity Measures For Signal Recognition In Biological Sequences Journal of Theoretical Biology 251 (2008), 380-387  [abstract]

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

60.	A. Momen-Roknabadi. , M. Sadeghi. , H. Pezeshk. and S. A. Marashi. Impact of Residue Accessible Surface Area on the Prediction of Protein Secondary Structures BMC Bioinformatics 9 (2008), 357  [abstract]

61.	M. Habibi. , C. Eslahchi. , H. Pezeshk. and M. Sadeghi. An Information Theoritical Approch To Secondary Structure Assignment Iran. Int. J. Sci. 34 (2008), 41-48  [abstract]

62.	S. Naghizadeh. , H. Pezeshk. , M. Sadeghi. , M. Mohammadzadeh. and C. Eslahchi. A MODIFICATION ON A LEFT-TO-RIGHT AND RIGHT-TO-LEFT DEPENDENCY MODEL FOR SECONDARY STRUCTURE PREDICTION Iran. Int. J. Sci. 34 (2008), 61-66  [abstract]

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

64.	C. Eslahchi. , M. Sadeghi. , H. Pezeshk. , M. Kargar. and H. Poormohammadi. Haplotyping Problem, A Clustering Approach AIP 936 (2007), 185-190  [abstract]

65.	S. A. Marashi. , R. Behrouzi. and H. Pezeshk. Adaptation Of Proteins To Different Environments: A Comparison Of Proteome Structural Properties In Bacillus Subtilis And Escherichia Coli Journal of Theoretical Biology 244 (2007), 127-132  [abstract]

66.	C. Eslahchi. , M. Sadeghi. , H. Pezeshk. , M. Kargar. and H. Poormohamadi. American Institute of Physics Conference Proceedings AIP CONF PROC 936 (2007),   [abstract]