| YEAR |
TITLE |
| 2022 |
Extracting potential new targets for treatment of Adenoid Cystic Carcinoma
using bioinformatic methods
TF Pordanjani, B Dabirmanesh, P Choopanian, M Mirzaie, S Mohebbi,
...
|
| 2022 |
Bipartite network models to design combination therapies in acute myeloid
leukaemia
M Jafari, M Mirzaie, J Bao, F Barneh, S Zheng, J Eriksson, CA Heckman,
...
Nature communications 13 (1), 1-12
|
| 2022 |
Monitoring Functional Post-Translational Modifications Using a Data-Driven
Proteome Informatic Pipeline Based on PEIMAN2
P Nickchi, M Mirzaie, M Baumann, AS Dibavar, M Jafari
bioRxiv
|
| 2022 |
NIMAA: an R/CRAN package to accomplish NomInal data Mining AnAlysis
M Jafari, C Chen, M Mirzaie, J Tang
bioRxiv
|
| 2021 |
Publisher Correction: Nkx3-1 and Fech genes might be switch genes involved
in pituitary non-functioning adenoma invasiveness
N Khayer, M Jalessi, A Jahanbakhshi, M Mirzaie
Scientific Reports 11 (1), 1-1
|
| 2021 |
IrGO: Iranian traditional medicine General Ontology and knowledge base
A Naghizadeh, M Salamat, D Hamzeian, S Akbari, H Rezaeizadeh, ...
Journal of Biomedical Semantics 12 (1), 1-11
|
| 2021 |
Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning
adenoma invasiveness
N Khayer, M Jalessi, A Jahanbakhshi, M Mirzaie
Scientific reports 11 (1), 1-13
|
| 2021 |
Metabolomic signature of amino acids in plasma of patients with non-segmental
Vitiligo
R Marzabani, H Rezadoost, P Choopanian, S Kolahdooz, N Mozafari,
...
Metabolomics 17 (10), 1-11
|
| 2021 |
A compartmental model that predicts the effect of social distancing
and vaccination on controlling COVID-19
M Dashtbali, M Mirzaie
Scientific Reports 11 (1), 1-11
|
| 2021 |
Serum metabolomics study of women with different annual decline rates
of anti-Müllerian hormone: an untargeted gas chromatography–mass spectrometry-based
study
N Moslehi, P Mirmiran, R Marzbani, H Rezadoost, M Mirzaie, F Azizi,
...
Human Reproduction 36 (3), 721-733
|
| 2021 |
Identification of key genes and convergent pathways disrupted in autism
spectrum disorder via comprehensive bioinformatic analysis
M Rahnama, HA Tehrani, M Mirzaie
Informatics in Medicine Unlocked 24, 100589
|
| 2021 |
Amino acids targeted based metabolomics study in non-segmental Vitiligo:
a pilot study
R Marzabani, H Rezadoost, P Chopanian, N Mozafari, M Jafari, M Mirzaie,
...
bioRxiv
|
| 2020 |
Rps27a might act as a controller of microglia activation in
triggering neurodegenerative diseases
N Khayer, M Mirzaie, SA Marashi, M Jalessi
Plos one 15 (9), e0239219
|
| 2020 |
Optimal control and differential game solutions for social distancing
in response to epidemics of infectious diseases on networks
MM Mohammadali Dashtbali, Alaeddin Malek
Optimal Control, Applications and Methods
|
| 2020 |
Molecular Network Analysis in Rabies Pathogenesis Using Cooperative
Game Theory
R Bostani, M Mirzaie
Iranian Journal of Biotechnology 18 (3), e2551
|
| 2020 |
Can we assume the gene expression profile as a proxy for signaling network
activity?
M Piran, R Karbalaei, M Piran, J Aldahdooh, M Mirzaie, N Ansari-Pour,
...
Biomolecules 10 (6), 850
|
| 2020 |
UNaProd: a universal natural product database for Materia Medica of
Iranian traditional medicine
A Naghizadeh, D Hamzeheian, S Akbari, F Mohammadi, T Otoufat, ...
Evidence-Based Complementary and Alternative Medicine 2020
|
| 2020 |
Research Article UNaProd: A Universal Natural Product Database for Materia
Medica of Iranian Traditional Medicine
A Naghizadeh, D Hamzeheian, S Akbari, F Mohammadi, T Otoufat, ...
medicine 23, 25
|
| 2020 |
Protein complex prediction: A survey
J Zahiri, A Emamjomeh, S Bagheri, A Ivazeh, G Mahdevar, HS Tehrani,
...
Genomics 112 (1), 174-183
|
| 2019 |
An insight to HTLV-1-associated myelopathy/tropical spastic paraparesis
(HAM/TSP) pathogenesis; evidence from high-throughput data integration
and meta-analysis
SH Mozhgani, M Piran, M Zarei-Ghobadi, M Jafari, SM Jazayeri, ...
Retrovirology 16 (1), 1-11
|
| 2019 |
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction,
mapping and mining analysis
M Ashtiani, P Nickchi, S Jahangiri-Tazehkand, A Safari, M Mirzaie,
...
BMC bioinformatics 20 (1), 1-4
|
| 2019 |
A mathematical model of honey bee colony dynamics to predict the effect
of pollen on colony failure
S Bagheri, M Mirzaie
PLoS One 14 (11), e0225632
|
| 2019 |
Revisiting temperaments with a fine-tuned categorization using Iranian
traditional medicine general ontology
A Naghizadeh, D Hamzeheian, S Akbari, H Rezaeizadeh, MA Vaghasloo,
...
Preprints
|
| 2019 |
Modeling seasonal changes and death rate of hive bee in honey bee colony
S Bagheri, M Mirzaie, R Salehi
Journal of Advanced Mathematical Modeling 9 (2), 77-92
|
| 2019 |
Impact of Hydrophobic Amino Acids in Protein Fold Recognition
M Mirzaie
Modares Journal of Biotechnology 10 (3), 433-440
|
| 2019 |
Discrimination power of knowledge-based potential dictated by the dominant
energies in native protein structures
M Mirzaie
Amino acids 51 (7), 1029–1038
|
| 2019 |
CINNA: an R/CRAN package to decipher Central Informative Nodes in Network
Analysis
M Ashtiani, M Mirzaie, M Jafari
Bioinformatics 35 (8), 1436-1437
|
| 2019 |
Integrated use of bioinformatic resources reveals that co-targeting
of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal
transition in cancer
F Barneh, M Mirzaie, P Nickchi, TZ Tan, JP Thiery, M Piran, M Salimi,
...
Briefings in bioinformatics 20 (2), 717-731
|
| 2019 |
Three-way interaction model with switching mechanism as an effective
strategy for tracing functionally-related genes
N Khayer, M Mirzaie, SA Marashi, M Rezaei-Tavirani, F Goshadrou
Expert review of proteomics 16 (2), 161-169
|
| 2019 |
Identification of native protein structures captured by principal interactions
M Mirzaie
BMC Bioinformatics 20 (604)
|
| 2018 |
A systematic survey of centrality measures for protein-protein interaction
networks
M Ashtiani, A Salehzadeh-Yazdi, Z Razaghi-Moghadam, H Hennig, ...
BMC systems biology 12 (1), 1-17
|
| 2018 |
Valproic acid inhibits the protective effects of stromal cells against
chemotherapy in breast cancer: Insights from proteomics and systems
biology
F Barneh, M Salimi, F Goshadrou, M Ashtiani, M Mirzaie, H Zali,
M Jafari
Journal of cellular biochemistry 119 (11), 9270-9283
|
| 2018 |
IrGO 1.0: Iranian traditional medicine general ontology
A Naghizadeh, S Akbari, D Hamzeian, H Rezaeizadeh, MA Vaghasloo,
...
F1000Research 7, 1319
|
| 2018 |
Quantitative HPLC-based metabolomics of some Iranian saffron (Crocus
sativus L.) accessions
M Vahedi, M Kabiri, SA Salami, H Rezadoost, M Mirzaie, MR Kanani
Industrial Crops and Products 118, 26-29
|
| 2018 |
Human T‐lymphotropic virus 1 (HTLV‐1) pathogenesis: A systems virology
study
SH Mozhgani, M Zarei‐Ghobadi, M Teymoori‐Rad, T Mokhtari‐Azad, ...
Journal of cellular biochemistry 119 (5), 3968-3979
|
| 2018 |
Hydrophobic residues can identify native protein structures
M Mirzaie
Proteins: Structure, Function, and Bioinformatics 86 (4), 467-474
|
| 2018 |
Game theory approach in analyzing biological networks
R Bostani, M Jafari, M Mirzaie
|
| 2017 |
A logic-based dynamic modeling approach to explicate the evolution of
the central dogma of molecular biology
M Jafari, N Ansari-Pour, S Azimzadeh, M Mirzaie
PloS one 12 (12), e0189922
|
| 2017 |
Three-way interaction model to trace the mechanisms involved in Alzheimer’s
disease transgenic mice
N Khayer, SA Marashi, M Mirzaie, F Goshadrou
PloS one 12 (9), e0184697
|
| 2017 |
A systematic survey of centrality measures for protein-protein interaction
networks
M Ashtiani, A Salehzadeh-Yazdi, Z Razaghi-Moghadam, H Hennig, ...
bioRxiv, 149492
|
| 2017 |
CINNA: An R package for deciphering Central Informative Nodes in Network
Analysis
M Ashtiani, M Mirzaie, M Jafari
BioRxiv, 168757
|
| 2017 |
Selection of most relevant centrality measures: A systematic survey
on protein-protein interaction networks
M Ashtiani, A Salehzadeh, Z Razaghi-Moghadam, H Hennig, ...
bioRxiv, 149492
|
| 2017 |
A Rational Drug Combination Design to Inhibit Epithelial-Mesenchymal
Transition in a Three-Dimensional Microenvironment
F Barneh, M Mirzaie, P Nickchi, TZ Tan, JP Thiery, M Piran, M Salimi,
...
bioRxiv, 148767
|
| 2016 |
Systems biomedicine of rabies delineates the affected signaling pathways
S Azimzadeh Jamalkandi, SH Mozhgani, H Gholami Pourbadie, ...
Frontiers in microbiology 7, 1688
|
| 2016 |
Updates on drug–target network; facilitating polypharmacology and data
integration by growth of DrugBank database
F Barneh, M Jafari, M Mirzaie
Briefings in bioinformatics 17 (6), 1070-1080
|
| 2016 |
Polarity‐based fractionation in proteomics: hydrophilic interaction
vs reversed‐phase liquid chromatography
M Jafari, M Mirzaie, M Khodabandeh, H Rezadoost, A Ghassempour,
...
Biomedical Chromatography 30 (7), 1036-1041
|
| 2016 |
Investigating the importance of Delaunay-based definition of atomic
interactions in scoring of protein–protein docking results
R Jafari, M Sadeghi, M Mirzaie
Journal of Molecular Graphics and Modelling 66, 108-114
|
| 2015 |
Interlog protein network: an evolutionary benchmark of protein interaction
networks for the evaluation of clustering algorithms
M Jafari, M Mirzaie, M Sadeghi
BMC bioinformatics 16 (1), 1-9
|
| 2015 |
Signaling network of lipids as a comprehensive scaffold for omics data
integration in sputum of COPD patients
SA Jamalkandi, M Mirzaie, M Jafari, H Mehrani, P Shariati, ...
Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of
Lipids …
|
| 2015 |
Erratum: bioactive lipids in emphysema: decoding fat to reveal COPD
phenotypes
M Mirzaie, F Kheradmand
American journal of respiratory and critical care medicine 191 (10),
1210
|
| 2015 |
Bioactive lipids in emphysema. Decoding fat to reveal COPD phenotypes
M Mirzaie, F Kheradmand
American journal of respiratory and critical care medicine 191 (3),
241-243
|
| 2015 |
Signaling network of lipids as a comprehensive scaffold for omics data
integration in sputum of COPD patients Molecular and cell biology of
lipids
S Azimzadeh, M Mirzaie, M Jafari, H Mehrani, P Shariati, M Khodabandeh
|
| 2014 |
Relationship between B-factor and average shortest path in the protein
structure
KM Badrabadi, M Mirzaie
Archives of Advances in Biosciences 5 (3)
|
| 2014 |
Delaunay‐based nonlocal interactions are sufficient and accurate in
protein fold recognition
M Mirzaie, M Sadeghi
Proteins: Structure, Function, and Bioinformatics 82 (3), 415-423
|
| 2014 |
Book Review・Buchbesprechung
P Heusser, S Eberhard, J Weinzirl, P Orlow, B Berger, M Jafari,
...
Complementary Medicine Research 21 (4), 267-269
|
| 2014 |
Tagungen und Kongresse・Meetings and Conferences
P Heusser, S Eberhard, J Weinzirl, P Orlow, B Berger, M Jafari,
...
Complementary Medicine Research 21 (4), 272-274
|
| 2014 |
Daniel Kaiser-† Juli 2014
P Heusser, S Eberhard, J Weinzirl, P Orlow, B Berger, M Jafari,
...
Complementary Medicine Research 21 (4), 222-222
|
| 2014 |
News/Ticker
P Heusser, S Eberhard, J Weinzirl, P Orlow, B Berger, M Jafari,
...
Complementary Medicine Research 21 (4), 271-271
|
| 2014 |
Contents of Forthcoming Issues・Themenvorschau
P Heusser, S Eberhard, J Weinzirl, P Orlow, B Berger, M Jafari,
...
Complementary Medicine Research 21 (4), 276-276
|
| 2014 |
Proteomics and traditional medicine: new aspect in explanation of temperaments
M Jafari, H Rezadoost, M Karimi, M Mirzaie, M Rezaie-Tavirani, ...
Complementary Medicine Research 21 (4), 250-253
|
| 2013 |
Cell Survival Entropy and Cellular Resistance Activation Dose: Effect
of Calprotectin on Gastric Adenocarcinoma Cell Line
M Rezaei‐Tavirani, M Rahmati‐Roodsari, M Mirzaie, PA Geram, S Sobhi
International Journal of Cancer Management 6 (Supplement)
|
| 2013 |
Evolutionarily conserved motifs and modules in mitochondrial protein–protein
interaction networks
M Jafari, M Sadeghi, M Mirzaie, SA Marashi, M Rezaei-Tavirani
Mitochondrion 13 (6), 668-675
|
| 2013 |
Exploring biological processes involved in embryonic stem cell differentiation
by analyzing proteomic data
M Jafari, M Mirzaie, M Sadeghi, SA Marashi, M Rezaei-Tavirani
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1834
(6), 1063-1069
|
| 2013 |
Ranked k-medoids: A fast and accurate rank-based partitioning algorithm
for clustering large datasets
SMR Zadegan, M Mirzaie, F Sadoughi
Knowledge-Based Systems 39, 133-143
|
| 2012 |
Distance‐dependent atomic knowledge‐based force in protein fold recognition
M Mirzaie, M Sadeghi
Proteins: Structure, Function, and Bioinformatics 80 (3), 683-690
|
| 2012 |
Identifying native structures with scoring function based on Delaunay
Tessellation.
M Mirzaie
|
| 2010 |
Knowledge-based potentials in protein fold recognition
M Mirzaie, M Sadeghi
Archives of Advances in Biosciences 1 (4)
|
| 2009 |
A distance‐dependent atomic knowledge‐based potential and force for
discrimination of native structures from decoys
M Mirzaie, C Eslahchi, H Pezeshk, M Sadeghi
Proteins: Structure, Function, and Bioinformatics 77 (2), 454-463
|
| |
A Rational Drug Combination Design Proves to Inhibit Epithelial-Mesenchymal
Transition in a Three-Dimensional Microenvironment
F Barneh, M Mirzaie, P Nickchi, M Piran, M Salimi, F Goshadrou,
AR Aref, ...
|
| |
Harmonic Centrality
M Ashtiani, M Mirzaie, M Jafari
|
| |
Centrality measure calculation
M Ashtiani, M Mirzaie, M Jafari
|
| |
Cell survival entropy and cellular resistance activation dose: Effect
of calprotectin on gastric adenocarcinoma cell line
MR Tavirani, MR Roodsari, M Mirzaie, PA Geram, S Sobhi
|
| |
Identification of native protein structures captured by principal interactions
|
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