Published / Accepted Papers


  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011 & EALIER

2019


Differential network analysis and protein-protein interaction study reveals active protein modules in glucocorticoid resistance for infant acute lymphoblastic leukemia, Z Mousavian, A Nowzari-Dalini, Y Rahmatallah, A Masoudi-Nejad, Molecular Medicine 25 (1), 36

Active repurposing of drug candidates for melanoma based on GWAS, PheWAS and a wide range of omics data. A Khosravi, B Jayaram, B Goliaei, A Masoudi-Nejad, Molecular Medicine 25 (1), 30

‎FeatureSelect: a software for feature selection based on machine learning approaches, Y Masoudi-Sobhanzadeh, H Motieghader, A Masoudi-Nejad, BMC bioinformatics 20 (1), 170

 

Network-based expression analyses and experimental validations revealed high co-expression between Yap1 and stem cell markers compared to differentiated cells, F Dehghanian, Z Hojati, F Esmaeili, A Masoudi-Nejad, Genomics 111 (4), 831-839

GPS: Identification of disease genes by rank aggregation of multi-genomic scoring schemes, A Meshkin, A Shakery, A Masoudi-Nejad, Genomics 111 (4), 612-618

Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues, N Barjaste, M Shahhoseini, P Afsharian, A Sharifi-Zarchi, ... , Journal of assisted reproduction and genetics, 1-10

Trader as a new optimization algorithm predicts drug-target interactions efficiently, Y Masoudi-Sobhanzadeh, Y Omidi, M Amanlou, A Masoudi-Nejad, Scientific Reports 9 (1), 9348

Drug databases and their contributions to drug repurposing, Y Masoudi-Sobhanzadeh, Y Omidi, M Amanlou, A Masoudi-Nejad, Genomics

Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis, M Kouhsar, SA Jamalkandi, A Moeini, A Masoudi-Nejad, Scientific reports 9 (1), 8434

DrugR+: A comprehensive relational database for drug repurposing, combination therapy, and replacement therapy, Y Masoudi-Sobhanzadeh, Y Omidi, M Amanlou, A Masoudi-Nejad, Computers in biology and medicine 109, 254-262

Systematic analysis of genes and diseases using PheWAS-associated networks, A Khosravi, M Kouhsar, B Goliaei, B Jayaram, A Masoudi-Nejad, Computers in biology and medicine 109, 311-321

Novel putative drugs and key initiating genes for neurodegenerative disease determined using network‐based genetic integrative analysis, Z Mortezaei, JB Cazier, AA Mehrabi, C Cheng, A Masoudi‐Nejad, Journal of cellular biochemistry 120 (4), 5459-5471

CatbNet: A Multi Network Analyzer for Comparing and Analyzing the Topology of Biological Networks, E Pournoor, N Elmi, A Masoudi-Nejad, Current genomics 20 (1), 69-75

LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma, S Alaei, B Sadeghi, A Najafi, A Masoudi-Nejad, Genomics 111 (1), 76-89

2018


Block alignment: New representation and comparison method to study evolution of genomes, MNA Lanjanian H, Nowzari A, Hosseinkhan N, Masoudi-Nejad A, Genomics, https://www.ncbi.nlm.nih.gov/pubmed/3044

Cattle infection response network and its functional modules, H Beiki, A Pakdel, AN Javaremi, A Masoudi-Nejad, JM Reecy, BMC immunology 19 (1), 2

‎Reconstruction of the genome-scale co-expression network for the Hippo signaling pathway in colorectal cancer, F Dehghanian, Z Hojati, N Hosseinkhan, Z Mousavian, A Masoudi-Nejad, Computers in biology and medicine 99, 76-84

 

SCAN-Toolbox: Structural COBRA Add-oN (SCAN) for Analysing Large Metabolic Networks, Y Asgari, Z Zabihinpour, A Masoudi-Nejad, Current Bioinformatics 13 (1), 100-107

Comparison of gene co-expression networks in Pseudomonas aeruginosa and Staphylococcus aureus reveals conservation in some aspects of virulence, N Hosseinkhan, Z Mousavian, A Masoudi-Nejad, Gene 639, 1-10

Link prediction potentials for biological networks, S Sulaimany, M Khansari, A Masoudi-Nejad, International Journal of Data Mining and Bioinformatics 20 (2), 161-184

The importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation, M Dehghan-Shasaltaneh, H Lanjanian, GH Riazi, A Masoudi-Nejad, Iranian journal of pharmaceutical research: IJPR 17 (1), 63

2017


Sequence-based 5-mers highly correlated to epigenetic modifications in genes interactions, D Salimi, A Moeini, A Masoudi-Nejad, Genes & genomics 40 (12), 1363-1371

Task modulates functional connectivity networks in free viewing behavior, H Seidkhani, AR Nikolaev, RN Meghanathan, H Pezeshk, ..., NeuroImage 159, 289-301

Biogeography, distribution and conservation status of maples (Acer L.) in Iran, M Mohtashamian, F Attar, K Kavousi, A Masoudi-Nejad, Trees 31 (5), 1583-1598

 

Inhibitory effects of lactic acid bacteria isolated from traditional fermented foods against aflatoxigenic Aspergillus spp., M Ebrahimi, M Khomeiri, A Masoudi-Nejad, A Sadeghi, B Sadeghi, ..., Comparative Clinical Pathology 26 (5), 1083-1092

Candidate novel long noncoding RNAs, MicroRNAs and putative drugs for Parkinson's disease using a robust and efficient genome-wide association study, Z Mortezaei, H Lanjanian, A Masoudi-Nejad, Genomics 109 (3-4), 158-164

Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis, E Khodadadi, AA Mehrabi, A Najafi, S Rastad, A Masoudi-Nejad, Physiology and molecular biology of plants 23 (2), 331-342

Micromorphological studies of leaf epidermal features in populations of maples (Acer L.) from Iran, M Mohtashamian, F Attar, K Kavousi, A Masoudi-Nejad, Phytotaxa 299 (1), 36-54

Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data, Z Narimani, H Beigy, A Ahmad, A Masoudi-Nejad, H Fröhlich, PloS one 12 (2), e0171240

Network-based expression analysis reveals key genes related to glucocorticoid resistance in infant acute lymphoblastic leukemia, Z Mousavian, A Nowzari-Dalini, RW Stam, Y Rahmatallah, ..., Cellular Oncology 40 (1), 33-45

A hybrid gene selection algorithm for microarray cancer classification using genetic algorithm and learning automata, H Motieghader, A Najafi, B Sadeghi, A Masoudi-Nejad, Informatics in Medicine Unlocked 9, 246-254

mRNA–miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation, H Motieghader, M Kouhsar, A Najafi, B Sadeghi, A Masoudi-Nejad, Molecular BioSystems 13 (10), 2168-2180

Sequential and mixed genetic algorithm and learning automata (SGALA, MGALA) for feature selection in QSAR, H MotieGhader, S Gharaghani, Y Masoudi-Sobhanzadeh, ..., Iranian journal of pharmaceutical research: IJPR 16 (2), 533

Predicting brain network changes in Alzheimer's disease with link prediction algorithms, S Sulaimany, M Khansari, P Zarrineh, M Daianu, N Jahanshad, ..., Molecular BioSystems 13 (4), 725-735

2016


Network-based expression analysis reveals key genes related to glucocorticoid resistance in infant acute lymphoblastic leukemia. Cellular Oncology.

A systems biology approach to reconcile metabolic network models with application to Synechocystis sp. PCC 6803 for biofuel production. Molecular Biosystems.

‎Large-scale Gene Co-expression Network as a Source of Functional Annotation for Bovine Genes. BMC Genomics.

 

Information Theory in Systems Biology: Signaling and Metabolic Networks. Seminars in Cell and Developmental Biology.

CeFunMO: a centrality based method for discovering functional motifs with application in biological networks. Computers in Biology and Medicine.

Information Theory in Systems Biology: Gene Regulatory and Protein-Protein Interaction Networks. Seminars in Cell and Developmental Biology.

Drug-Target Interaction Prediction from PSSM based Evolutionary Information. Journal of Pharmacological and Toxicological Methods.

Flow of Information in Biological Systems. Seminars in Cell and Developmental Biology

Determination of the Best Concentration of Streptozotocin to Create a Diabetic Brain Using Histological Techniques. J Mol Neurosci.

Computational Detection of piRNA in Human Using Support Vector Machine. Avicenna J Med Biotechnol.

Protein Clustering and Interactome Analysis in Parkinson and Alzheimer's Diseases.Arch Iran Med.

Large-scale Gene Co-expression Network as a Source of Functional Annotation for Bovine Genes. BMC Genomics. ACCEPTED

The importance of α-CT and salt bridges in the formation of insulin and its receptor complex by computational simulation. Iranian Journal of Pharmaceutical Research. ACCEPTED.

Predicting Brain Network Changes in Alzheimer’s Disease with Link Prediction Algorithms. Molecular Biosystems. REVISED.

SCAN-Toolbox : Structural COBRA Add-oN (SCAN) for Metabolic Networks. Current Bioinformatics. ACCEPTED.

NetCentra: A Program for Analyzing the Network Centrality in Biological, Social and Other Networks. SUBMITTED.

Sensitivity Analysis of the Brain's Signaling Network Flow: finding the optimal region of the systems for perturbation. SUBMITTED.

LuCaSim: a toolbox for Lung Cancer Modeling and Simulation. SUBMITTED.

Cattle Bacterial Stress Response Network and its Functional Modules. BMC Immunology. SUBMITTED.

2015


Cancer Modeling and Network Biology: accelerating toward personalized medicine. Seminar in Cancer Biology.

Metabolic Cancer Biology: structural-based analysis of cancer as a metabolic disease, new sights and opportunities for disease treatment. Seminar in Cancer Biology.

Predictive Genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data. Seminar in Cancer Biology.

 

Alterations in cancer cells metabolism: the Warburg effect and metabolic adaptation. Genomics.

Computational modeling of core regulatory elements controlling airway remodeling pathway in chronic lung diseases. PLOS ONE. Accepted

Co-expressional conservation in virulence and stress related genes of three Gamma Proteobacterial species: Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa. Molecular Biosystems.

Reconstruction of gene regulatory network reveals key apoptotic pathways and candidate survival genes after traumatic spinal cord injury. Genomics. Under Review

Novel hybrid Algorithms using Learning Automata and Genetic Algorithm for feature selection in QSAR: anti cancer case study.

Feature selection in QSAR using Cuckoo Optimization Algorithm on anti-cancer data.

2014


Cuckoo Search Epistasis: a new method for exploring significant genetic interactions. Nature's Heredity

Informative Bayesian Model Selection‎: ‎A‎ Method for Identifying Interactions in Genome-Wide Data. Molecular Biosystems.

‎Microarray gene expression analysis of human airway in patients exposed to sulfur mustard. Journal of Receptors and Signal Transduction.

 

Drug-Target Interaction Prediction via Chemogenomic Space: Learning-Based Methods. Expert Opinion on Drug Metabolism and Toxicology.

Cancer Systems Biology and Modeling: microscopic scale and multiscale approaches. Seminar in Cancer Biology.

BosFinder: a Novell Pre-MicroRNA Gene Prediction algorithm in Bos taurus. Animal Genetics.

Genome Scale Modeling in Systems Biology: algorithms and resources. Current Genomics.

Pathway Reconstruction of Airway Remodeling in Chronic Lung Diseases: a systems biology approach. PLOS ONE.

Genome-scale co-expression network comparison between Escherichia coli, Bacillus subtilis, and Salmonella enetica serovar Typhimurium reveals conservation and divergence in their regulatory networks and explains their dissimilar lifestyles. PLOS ONE

Weighted-Directed Networks: merging weight and direction into scale free biological network. Current Bioinformatics

LocFuse: Human Protein-Protein Interaction Prediction via Classifier Fusion Using Localization Information. Genomics.

Computational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach. PLOS ONE.

Integrative Systems Biology: Integration of epigenetics data into kinetics modeling in Yeast. Functional & Integrative Genomics.

Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung. Current Genomics.

2013


Controllability in metabolic cancer networks according to drug targets as driver nodes.

Human RNAi Pathway: crosstalk with organelles and cells. Functional and Integrative Genomics.

‎Drug-Target and Disease Networks: polypharmacology in the post-genomic era. In Silico Pharmacology.

 

Reconstruction of integrated genome-scale coexpression network revealed key modules in lung adenocarcinoma. PLOS ONE.

Computational Prediction of Protein–Protein Interaction Networks: algorithms and resources. Current Genomics.

Centrality Measures in Biological Networks. Current Bioinformatics.

C-element: a New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks.

QuateXelero: an accelerated exact network motif detection algorithm.

Discovering dominant pathways and signal–response relationships in signaling networks. Genomics.

Discovering dominant pathways and signal–response relationships in signaling networks. Genomics.

PPIevo: Protein-Protein Interaction Prediction from Evolutionary Information. Genomics.

Computational Structure Analysis of Biomacromolecule Complexes by Interface Geometry. Computational Biology and Chemistry.

Co-Occurrence: a Gene Reference Resource for Coincidental Patterns of Gene Mutations in Human Cancers. Journal of Proteomics and Bioinformatics.

A Sequence Motif Associated with Intrinsic Mutation Hot-Spots in Human Cancers. Journal of Proteomics and Bioinformatics.

Extracting a Cancer Model by Ant Colony Optimization Algorithm. International Journal of Data Mining and Bioinformatics.

2012


Modeling of tumor progression in non-small-cell lung cancer (NSCLC) and intrinsic resistance to TKI in loss of PTEN expression.

HomoTarget: a New Algorithm for Prediction of MicroRNA Targets in Homo sapiens. Genomics.

‎Normalized Similarity Index: An adjusted index to prioritize article citations. Journal of Informetrics.

 

Nonparametric Simulation of Signal Transduction Networks with Semi-Synchronized Update

CytoKavosh: a Cytoscape Plug-in for Finding Network Motifs in Large Biological Networks.

Modeling and Analysis of Abnormality Detection in Biomolecular Nano-Networks. Nano Communication Networks.

Building Blocks of Biological Networks: A Review on Major Network Motif Discovery Algorithms. IET Systems Biology.

Computational Analysis of RNA-Protein Interaction interfaces via the Voronoi Diagram. Journal of Theoretical Biology.

Bioinformatics Study of the 3-hydroxy-3-methylglotaryl-Coenzyme A Reductase (HMGR) Gene in Gramineae. Molecular Biology Reports.

Molecular epidemiology of hepatitis C virus among injection drug users in Iran. Archives of Virology.

2011 & EALIER


Genome-scale computational analysis of DNA curvature and repeats in Arabidopsis and rice uncovers plant-specific genomic properties. BMC Genomics.

Emerging Roles of Epigenetic Mechanisms in Parkinson's disease. Functional and Integrative Genomics.

RNAi Pathway Integration in Caenorhabditis elegans Development. Functional and Integrative Genomics

 

Computational methodologies for analyzing, modeling and controlling gene regulatory networks. Biomedical Engineering and Computational Biology.

Reconstruction of Arabidopsis thaliana Fully-Integrated Small RNA Pathway. Functional & Integrative Genomics.

Kavosh: A New Algorithm for Finding Network Motifs. BMC Bioinformatics.

MODA: An Efficient Algorithm for Network Motif Discovery in Biological Networks. Genes and Genetic Systems.

N4: A Precise and Highly Sensitive Promoter Predictor Using Neural Network fed by Nearest Neighbors. Genes and Genetic Systems.

Genotyping of Fusarium verticillioides strains producing fumonisin B1 in feed associated with animal health problems. Iranian Journal of Veterinary Research (IJVR).

Bioinformatics Resources for Plant Genomics Research. Methods Mol Biol

A New Approach for Touching Cells Segmentation. IEEE BioMedical Engineering and Informatics.

EGENES: Transcriptome-based plant database of genes with metabolic pathway information and EST indices in KEGG. Plant Physiology.

EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Research.

an alternative to radiation hybrid mapping for large-scale genome analysis in barley. Molecular Genetics and Genomics.

Diabetes and Systems Biology. JICS

Application of near-infrared spectroscopy and support vector machine in detection of HIV-1 infection. Kowsar Medical Journal

gpALIGNER: a fast algorithm for global pairwise alignment of DNA sequences

Effect of expression of chalcone synthase gene on flavonoids content and rooting ability in Juglans regia L. Plant Cell, Tissue and Organ Culture.

Integration and Reduction of Microarray Data Using Information Theory Approach. IJCCE.

Genotyping of Fusarium verticillioides strains producing fumonisin B1 in feed associated with animal health problems. Iranian Journal of Veterinary Research.

Mining Biological Repetitive Sequences Using Support Vector Machines and Fuzzy SVM. IJCCE.

Finding Exact and Solo LTR-Retrotransposons in Biological Sequences Using SVM. IJCCE.

Recognition Protein-RNA Interaction interfaces via the Voronoi Diagram. JICS.

Molecular typing of Epidermophyton floccosum isolated from patients with dermatophytosis by RAPD-PCR. J Basic Microbiol.

Effect of endogenous phenols and some antioxidant enzyme activities on rooting of Persian walnut. African Journal of Plant Science.

Quantitative Study of Seed Storage Proteins (HMW-GS) in Wheat Using Electrophoresis and Laser Scanning Densitometry. Physiology and Molecular Biology of Plants.

Dissection of rye chromosome 1R in common wheat. Genes and Genetics System

Molecular Typing of Iranian Cladosporium Isolates Using RAPD-PCR. Journal of Biotechnology.

Importance of 273rd residue in proteolytic processing for production of functional TSGA10 protein. Bioscience Hypotheses.

Molecular cloning, sequencing and chromosomal mapping of a 1A-encoded omega-gliadin gene from wheat. Genome.

Transfer of rye chromosome segments to wheat by a gametocidal system. Chromosome Research.

Separation of rust resistance genes from Sec-1 on rye chromosome 1R by the gametocidal recombination. Chromosome Research.

Wheat storage protein. Wheat Information Service.