Impact of RNA structure on the prediction of donor and acceptor splice sites. - Sayed-Amir Marashi; Changiz Eslahchi; Hamid Pezeshk; Mehdi Sadeghi (BMC Bioinform., 2006)

Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks. - Sayed-Amir Marashi; Hani Goodarzi; Mehdi Sadeghi; Changiz Eslahchi; Hamid Pezeshk (Comput. Biol. Chem., 2006)

A method for protein accessibility prediction based on residue types and conformational states. - Roghayeh Zarei; Shahriar Arab; Mehdi Sadeghi (Comput. Biol. Chem., 2007)

Impact of residue accessible surface area on the prediction of protein secondary structures. - Amir Momen-Roknabadi; Mehdi Sadeghi; Hamid Pezeshk; Sayed-Amir Marashi (BMC Bioinform., 2008)

A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins. - Armita Sheari; Mehdi Kargar; Ali Katanforoush; Shahriar Arab; Mehdi Sadeghi; Hamid Pezeshk; Changiz Eslahchi; Sayed-Amir Marashi (BMC Bioinform., 2008)

PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive Calpha atoms. - Sayed-Rzgar Hosseini; Mehdi Sadeghi; Hamid Pezeshk; Changiz Eslahchi; Mahnaz Habibi (Comput. Biol. Chem., 2008)

F.C.A: Designing a fuzzy clustering algorithm for haplotype assembly. - M-Hossein Moeinzadeh; Ehsan Asgarian; Morteza Mohammad Noori; Mehdi Sadeghi; Sara Sharifian-R (FUZZ-IEEE, 2009)

Global haplotype partitioning for maximal associated SNP pairs. - Ali Katanforoush; Mehdi Sadeghi; Hamid Pezeshk; Elahe Elahi (BMC Bioinform., 2009)

New scoring schema for finding motifs in DNA Sequences. - Fatemeh Zare-Mirakabad; Hayedeh Ahrabian; Mehdi Sadeghi; Abbas Nowzari-Dalini; Bahram Goliaei (BMC Bioinform., 2009)

STON: A novel method for protein three-dimensional structure comparison. - Changiz Eslahchi; Hamid Pezeshk; Mehdi Sadeghi; Amir Massoud Rahimi; Heydar Maboudi Afkham; Shahriar Arab (Comput. Biol. Medicine, 2009)

A pairwise residue contact area-based mean force potential for discrimination of native protein structure. - Shahriar Arab; Mehdi Sadeghi; Changiz Eslahchi; Hamid Pezeshk; Armita Sheari (BMC Bioinform., 2010)

Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae. - Mitra Mirzarezaee; Babak Nadjar Araabi; Mehdi Sadeghi (BMC Syst. Biol., 2010)

Tag SNP selection via a genetic algorithm. - Ghasem Mahdevar; Javad Zahiri; Mehdi Sadeghi; Abbas Nowzari-Dalini; Hayedeh Ahrabian (J. Biomed. Informatics, 2010)

A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM. - Kaveh Kavousi; Behzad Moshiri; Mehdi Sadeghi; Babak Nadjar Araabi; Ali Akbar Moosavi-Movahedi (Comput. Biol. Chem., 2011)

Modeling and implementing an agent-based system for prediction of protein relative solvent accessibility. - Alireza Meshkin; Nasser Ghasem-Aghaee; Mehdi Sadeghi (Expert Syst. Appl., 2011)

Evaluation of Fuzzy Linear Programming Application in Energy Models. - Mehdi Sadeghi; Hossein Mirshojaeian Hosseini (Int. J. Energy Optim. Eng., 2013)

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals. - Mahdi Heydari; Sayed-Amir Marashi; Ruzbeh Tusserkani; Mehdi Sadeghi (Biosyst., 2014)

ARYANA: Aligning Reads by Yet Another Approach. - Milad Gholami; Aryan Arbabi; Ali Sharifi-Zarchi; Hamidreza Chitsaz; Mehdi Sadeghi (BMC Bioinform., 2014)

Network-based approach reveals Y chromosome influences prostate cancer susceptibility. - Pegah Khosravi; Vahid H. Gazestani; Yazdan Asgari; Brian Law; Mehdi Sadeghi; Bahram Goliaei (Comput. Biol. Medicine, 2014)

Using artificial immunity network for face verification. - Mehdi Sadeghi; Keivan Maghooli; Mohammad Shahram Moein (Int. Arab J. Inf. Technol., 2014)

Efficient fast heuristic algorithms for minimum error correction haplotyping from SNP fragments. - Maryam Pourkamali Anaraki; Mehdi Sadeghi (Int. J. Comput. Biol. Drug Des., 2014)

Learning by abstraction: Hierarchical classification model using evidential theoretic approach and Bayesian ensemble model. - Mahdi Pakdaman Naeini; Behzad Moshiri; Babak Nadjar Araabi; Mehdi Sadeghi (Neurocomputing, 2014)

Using data fusion for scoring reliability of protein-protein interactions. - Alireza Vazifedoost; Maseud Rahgozar; Behzad Moshiri; Mehdi Sadeghi; Hon Nian Chua; See-Kiong Ng; Limsoon Wong (J. Bioinform. Comput. Biol., 2014)

Erratum to: Inferring interaction type in gene regulatory networks using co-expression data. - Pegah Khosravi; Vahid H. Gazestani; Leila Pirhaji; Brian Law; Mehdi Sadeghi; Gary D. Bader; Bahram Goliaei (Algorithms Mol. Biol., 2015)

Inferring interaction type in gene regulatory networks using co-expression data. - Pegah Khosravi; Vahid H. Gazestani; Leila Pirhaji; Brian Law; Mehdi Sadeghi; Bahram Goliaei; Gary D. Bader (Algorithms Mol. Biol., 2015)

Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. - Mohieddin Jafari; Mehdi Mirzaie; Mehdi Sadeghi (BMC Bioinform., 2015)

Increased robustness of early embryogenesis through collective decision-making by key transcription factors. - Ali Sharifi-Zarchi; Mehdi Totonchi; Keynoush Khaloughi; Razieh Karamzadeh; Marcos J. Araúzo-Bravo; Hossein Baharvand; Ruzbeh Tusserkani; Hamid Pezeshk; Hamidreza Chitsaz; Mehdi Sadeghi (BMC Syst. Biol., 2015)

Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach. - Mohammad-Hadi Foroughmand-Araabi; Bahram Goliaei; Kasra Alishahi; Mehdi Sadeghi; Sama Goliaei (J. Bioinform. Comput. Biol., 2015)

Seismic vulnerability assessment and risk modelling of telecommunication systems. - Naghmeh Pakdel-Lahiji; Morteza Bastami; Mehdi Sadeghi (Int. J. Crit. Infrastructures, 2016)

Honey bee-inspired algorithms for SNP haplotype reconstruction problem. - Maryam Pourkamali Anaraki; Mehdi Sadeghi (J. Exp. Theor. Artif. Intell., 2016)

Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines. - Fereshteh Chitsazian; Mehdi Sadeghi; Elahe Elahi (BMC Bioinform., 2017)

PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities. - Seyed Amir Malekpour; Hamid Pezeshk; Mehdi Sadeghi (BMC Bioinform., 2017)

HIV-1-infected T-cells dynamics and prognosis: An evolutionary game model. - Bahareh Khazaei; Javad Salimi Sartakhti; Mohammad Hossein Manshaei; Quanyan Zhu; Mehdi Sadeghi; Seyed Rasoul Mousavi (Comput. Methods Programs Biomed., 2017)

Assessing the impact of exact reads on reducing the error rate of read mapping. - Farzaneh Salari; Fatemeh Zare-Mirakabad; Mehdi Sadeghi; Hassan Rokni-Zadeh (BMC Bioinform., 2018)

Visualization in the integrated SimPhoNy multiscale simulation framework. - Joan Adler; Sampo Kulju; Jari Hyväluoma; Keijo Mattila; Kit Choi; Ioannis Tziakos; Didrik Pinte; G. A. García; Y. Makushok; V. Makushok; J. Lama; G. Román-Pérez; et al. (Comput. Phys. Commun., 2018)

Modeling the probability distribution of the bacterial burst size via a game-theoretic approach. - Seyed Amir Malekpour; Parsa Pakzad; Mohammad-Hadi Foroughmand-Araabi; Sama Goliaei; Ruzbeh Tusserkani; Bahram Goliaei; Mehdi Sadeghi (J. Bioinform. Comput. Biol., 2018)

LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks. - Seyed Amir Malekpour; Amir Reza Alizad-Rahvar; Mehdi Sadeghi (BMC Bioinform., 2020)

Inter-protein residue covariation information unravels physically interacting protein dimers. - Sara Salmanian; Hamid Pezeshk; Mehdi Sadeghi (BMC Bioinform., 2020)

A Network-Based Comparison Between Molecular Apocrine Breast Cancer Tumor and Basal and Luminal Tumors by Joint Graphical Lasso. - Maryam S. Daneshpour; Hossein Mahjub; Hamid Pezeshk; Mehdi Sadeghi (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Prospects and challenges of cancer systems medicine: from genes to disease networks. - Mohammad Reza Karimi; Amir-Hossein Karimi; Shamsozoha Abolmaali; Mehdi Sadeghi; Ulf Schmitz (Briefings Bioinform., 2022)

Determining the adjusted initial treatment dose of warfarin anticoagulant medicine using kernel-based support vector regression. - Rouhollah Maghsoudi; Mitra Mirzarezaee; Mehdi Sadeghi; Babak Nadjar Araabi (Comput. Methods Programs Biomed., 2022)

A new survival analysis model in adjuvant Tamoxifen-treated breast cancer patients using manifold-based semi-supervised learning. - Ramazan Teimouri Yansari; Mitra Mirzarezaee; Mehdi Sadeghi; Babak Nadjar Araabi (J. Comput. Sci., 2022)

wpLogicNet: logic gate and structure inference in gene regulatory networks. - Seyed Amir Malekpour; Maryam Shahdoust; Rosa Aghdam; Mehdi Sadeghi (Bioinform., 2023)

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms. - Seyed Amir Malekpour; Laleh Haghverdi; Mehdi Sadeghi (Briefings Bioinform., 2024)