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1

Cancer systems biology and modeling: Microscopic scale and multiscale approaches

Masoudi-Nejad, Ali, Bidkhori, Gholamreza, Hosseini Ashtiani, Saman, Najafi, Ali, Bozorgmehr, Joseph H., Wang, Edwin

Journal:

Seminars in Cancer Biology

Year:

2015

Language:

english

File:

PDF, 1.80 MB

english, 2015

2

Kavosh: a new algorithm for finding network motifs

Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabian, Elahe Elahi, Abbas Nowzari-Dalini, Elnaz Saberi Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber, Ali Masoudi-Nejad

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.17 MB

english, 2009

3

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

Masoudi-Nejad, Ali, Asgari, Yazdan

Journal:

Seminars in Cancer Biology

Year:

2015

Language:

english

File:

PDF, 1.96 MB

english, 2015

4

Molecular typing of Epidermophyton floccosum isolated from patients with dermatophytosis by RAPD-PCR

Alireza Khosravi, Forough Behzad, Azar Sabokbar, Hojjatollah Shokri, Siamak Haddadi, Prof. Ali Masoudi-Nejad

Journal:

Journal of Basic Microbiology

Year:

2010

Language:

english

File:

PDF, 235 KB

english, 2010

5

WITHDRAWN: Cancer modeling: The holonic agent-based approach

Masoudi-Nejad, Ali, Meshkin, Alireza

Journal:

Seminars in Cancer Biology

Year:

2014

File:

PDF, 31 KB

2014

6

Candidate novel long noncoding RNAs, MicroRNAs and putative drugs for Parkinson's disease using a robust and efficient genome-wide association study

Mortezaei, Zahra, Lanjanian, Hossein, Masoudi-Nejad, Ali

Journal:

Year:

2017

Language:

english

File:

PDF, 1.03 MB

english, 2017

7

A multimodal deep learning-based drug repurposing approach for treatment of COVID-19

Hooshmand, Seyed Aghil, Zarei Ghobadi, Mohadeseh, Hooshmand, Seyyed Emad, Azimzadeh Jamalkandi, Sadegh, Alavi, Seyed Mehdi, Masoudi-Nejad, Ali

Journal:

Molecular Diversity

Year:

2020

File:

PDF, 4.77 MB

2020

8

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

Ali Masoudi-Nejad, Sara Movahedi, Ruy Jáuregui

Journal:

Year:

2011

Language:

english

File:

PDF, 2.02 MB

english, 2011

9

An alternative to radiation hybrid mapping for large-scale genome analysis in barley

Ali Masoudi-Nejad, Shuhei Nasuda, Marie-Therese Bihoreau, Robbie Waugh, Takashi Ryu Endo

Journal:

Molecular Genetics and Genomics

Year:

2005

Language:

english

File:

PDF, 427 KB

english, 2005

10

Reconstruction ofArabidopsis thalianafully integrated small RNA pathway

Sadegh Azimzadeh Jamalkandi, Ali Masoudi-Nejad

Journal:

Functional & Integrative Genomics

Year:

2009

Language:

english

File:

PDF, 423 KB

english, 2009

11

RNAi pathway integration inCaenorhabditis elegansdevelopment

Sadegh Azimzadeh Jamalkandi, Ali Masoudi-Nejad

Journal:

Functional & Integrative Genomics

Year:

2011

Language:

english

File:

PDF, 792 KB

english, 2011

12

Emerging roles of epigenetic mechanisms in Parkinson’s disease

Ehsan Habibi, Ali Masoudi-Nejad, Hamid Mostafavi Abdolmaleky, Stephen J. Haggarty

Journal:

Functional & Integrative Genomics

Year:

2011

Language:

english

File:

PDF, 965 KB

english, 2011

13

Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae

Darabi, Maryam, Masoudi-Nejad, Ali, Nemat-Zadeh, Ghorbanali

Journal:

Molecular Biology Reports

Year:

2012

Language:

english

File:

PDF, 2.17 MB

english, 2012

14

Expression of chalcone synthase influences flavonoid content and frequency of rhizogenesis in microshoots ofJuglans regiaL.

Monireh Cheniany, Hassan Ebrahimzadeh, Ali Masoudi-nejad

Journal:

Plant Cell, Tissue and Organ Culture

Year:

2012

Language:

english

File:

PDF, 489 KB

english, 2012

15

Computational analysis of RNA–protein interaction interfaces via the Voronoi diagram

Sedigheh Mahdavi, Ali Mohades, Ali Salehzadeh Yazdi, Samad Jahandideh, Ali Masoudi-Nejad

Journal:

Journal of Theoretical Biology

Year:

2012

Language:

english

File:

PDF, 1.19 MB

english, 2012

16

Molecular epidemiology of hepatitis C virus among injection drug users in Iran: a slight change in prevalence of HCV genotypes over time

Katayoun Samimi-Rad, Mohsen Nasiri Toosi, Ali Masoudi-nejad, Ali Najafi, Ramin Rahimnia, Fatemeh Asgari, Alireza Namazi Shabestari, Gholamreza Hassanpour, Seyed-Moayed Alavian, Freshteh Asgari

Journal:

Archives of Virology

Year:

2012

Language:

english

File:

PDF, 226 KB

english, 2012

17

Candidate gene prioritization

Masoudi-Nejad, Ali, Meshkin, Alireza, Haji-Eghrari, Behzad, Bidkhori, Gholamreza

Journal:

Molecular Genetics and Genomics

Year:

2012

Language:

english

File:

PDF, 763 KB

english, 2012

18

Modeling and analysis of abnormality detection in biomolecular nano-networks

Ghavami, Siavash, Lahouti, Farshad, Masoudi-Nejad, Ali

Journal:

Nano Communication Networks

Year:

2012

Language:

english

File:

PDF, 878 KB

english, 2012

19

PPIevo: Protein–protein interaction prediction from PSSM based evolutionary information

Zahiri, Javad, Yaghoubi, Omid, Mohammad-Noori, Morteza, Ebrahimpour, Reza, Masoudi-Nejad, Ali

Journal:

Year:

2013

Language:

english

File:

PDF, 517 KB

english, 2013

20

[SpringerBriefs in Systems Biology] Next Generation Sequencing and Sequence Assembly Volume 4 ||

Masoudi-Nejad, Ali, Narimani, Zahra, Hosseinkhan, Nazanin

Year:

2013

Language:

english

File:

PDF, 4.88 MB

english, 2013

21

Molecular cloning, sequencing, and chromosome mapping of a 1A-encoded ω-type prolamin sequence from wheat

Masoudi-Nejad, Ali, Nasuda, Shuhei, Kawabe, Akira, Endo, Takashi R

Journal:

Year:

2002

File:

PDF, 1.08 MB

2002

22

Computational structure analysis of biomacromolecule complexes by interface geometry

Mahdavi, Sedigheh, Salehzadeh-Yazdi, Ali, Mohades, Ali, Masoudi-Nejad, Ali

Journal:

Computational Biology and Chemistry

Year:

2013

Language:

english

File:

PDF, 1.68 MB

english, 2013

23

[SpringerBriefs in Systems Biology] Next Generation Sequencing and Sequence Assembly Volume 4 || Next-Generation Sequencing Methodologies

Masoudi-Nejad, Ali, Narimani, Zahra, Hosseinkhan, Nazanin

Year:

2013

Language:

english

File:

PDF, 1.91 MB

english, 2013

24

[SpringerBriefs in Systems Biology] Next Generation Sequencing and Sequence Assembly Volume 4 || Emergence of Next-Generation Sequencing

Masoudi-Nejad, Ali, Narimani, Zahra, Hosseinkhan, Nazanin

Year:

2013

Language:

english

File:

PDF, 3.01 MB

english, 2013

25

[SpringerBriefs in Systems Biology] Next Generation Sequencing and Sequence Assembly Volume 4 || The Assembly of Sequencing Data

Masoudi-Nejad, Ali, Narimani, Zahra, Hosseinkhan, Nazanin

Year:

2013

Language:

english

File:

PDF, 1.74 MB

english, 2013

26

HomoTarget: A new algorithm for prediction of microRNA targets in Homo sapiens

Ahmadi, Hamed, Ahmadi, Ali, Azimzadeh-Jamalkandi, Sadegh, Shoorehdeli, Mahdi Aliyari, Salehzadeh-Yazdi, Ali, Bidkhori, Gholamreza, Masoudi-Nejad, Ali

Journal:

Year:

2013

Language:

english

File:

PDF, 772 KB

english, 2013

27

Drug-target and disease networks: polypharmacology in the post-genomic era

Masoudi-Nejad, Ali, Mousavian, Zaynab, Bozorgmehr, Joseph H

Journal:

In Silico Pharmacology

Year:

2013

Language:

english

File:

PDF, 201 KB

english, 2013

28

Human RNAi pathway: crosstalk with organelles and cells

Azimzadeh Jamalkandi, Sadegh, Azadian, Esmaeel, Masoudi-Nejad, Ali

Journal:

Functional & Integrative Genomics

Year:

2014

Language:

english

File:

PDF, 832 KB

english, 2014

29

Predictive genomics: A cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data

Wang, Edwin, Zaman, Naif, Mcgee, Shauna, Milanese, Jean-Sébastien, Masoudi-Nejad, Ali, O’Connor-McCourt, Maureen

Journal:

Seminars in Cancer Biology

Year:

2015

Language:

english

File:

PDF, 1.29 MB

english, 2015

30

Normalized Similarity Index: An adjusted index to prioritize article citations

Nassiri, Isar, Masoudi-Nejad, Ali, Jalili, Mahdi, Moeini, Ali

Journal:

Journal of Informetrics

Year:

2013

Language:

english

File:

PDF, 1012 KB

english, 2013

31

Discovering dominant pathways and signal–response relationships in signaling networks through nonparametric approaches

Nassiri, Isar, Masoudi-Nejad, Ali, Jalili, Mahdi, Moeini, Ali

Journal:

Year:

2013

Language:

english

File:

PDF, 1.10 MB

english, 2013

32

[IEEE 2010 IEEE International Conference on BioInformatics and BioEngineering - Philadelphia, PA, USA (2010.05.31-2010.06.3)] 2010 IEEE International Conference on BioInformatics and BioEngineering - Improved Immune Genetic Algorithm for Clustering Protein-Protein Interaction Network

Ravaee, Hamid, Masoudi-Nejad, Ali, Omidi, Saeed, Moeini, Ali

Year:

2010

Language:

english

File:

PDF, 323 KB

english, 2010

33

Drug–target interaction prediction via chemogenomic space: learning-based methods

Mousavian, Zaynab, Masoudi-Nejad, Ali

Journal:

Expert Opinion on Drug Metabolism & Toxicology

Year:

2014

Language:

english

File:

PDF, 920 KB

english, 2014

34

Microarray gene expression analysis of the human airway in patients exposed to sulfur mustard

Najafi, Ali, Masoudi-Nejad, Ali, Imani Fooladi, Abbas Ali, Ghanei, Mostafa, Nourani, Mohamad Reza

Journal:

Journal of Receptor and Signal Transduction Research

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

35

Cancer modeling and network biology: Accelerating toward personalized medicine

Masoudi-Nejad, Ali, Wang, Edwin

Journal:

Seminars in Cancer Biology

Year:

2015

Language:

english

File:

PDF, 217 KB

english, 2015

36

Informative Bayesian Model Selection: a method for identifying interactions in genome-wide data

Aflakparast, Mehran, Masoudi-Nejad, Ali, . Bozorgmehr, Joseph H, Visweswaran, Shyam

Journal:

Molecular BioSystems

Year:

2014

Language:

english

File:

PDF, 1.79 MB

english, 2014

37

LocFuse: Human protein–protein interaction prediction via classifier fusion using protein localization information

Zahiri, Javad, Mohammad-Noori, Morteza, Ebrahimpour, Reza, Saadat, Samaneh, Bozorgmehr, Joseph H., Goldberg, Tatyana, Masoudi-Nejad, Ali

Journal:

Year:

2014

Language:

english

File:

PDF, 1.13 MB

english, 2014

38

[IEEE 2012 23rd International Workshop on Database and Expert Systems Applications (DEXA) - Vienna, Austria (2012.09.3-2012.09.7)] 2012 23rd International Workshop on Database and Expert Systems Applications - Hubs and Non-hubs in Protein-Protein Interaction Networks: A Biophysical Interpretation

Salehzadeh-Yazdi, Ali, Masoudi-Nejad, Ali, Saboury, Ali Akbar, Akbari-Birgani, Shiva

Year:

2012

Language:

english

File:

PDF, 192 KB

english, 2012

39

[SpringerBriefs in Systems Biology] Microscopic Scale of Cancer Systems Biology Volume 13 ||

Masoudi-Nejad, Ali, Bidkhori, Gholamreza, Ashtiani, Saman Hosseini, Najafi, Ali

Year:

2015

Language:

english

File:

PDF, 4.90 MB

english, 2015

40

Alterations in cancer cell metabolism: The Warburg effect and metabolic adaptation

Asgari, Yazdan, Zabihinpour, Zahra, Salehzadeh-Yazdi, Ali, Schreiber, Falk, Masoudi-Nejad, Ali

Journal:

Year:

2015

Language:

english

File:

PDF, 750 KB

english, 2015

41

Erratum to: Bioinformatics study of the 3-hydroxy-3-methylglotaryl-coenzyme A reductase (HMGR) gene in Gramineae

Darabi, Maryam, Izadi-Darbandi, Ali, Masoudi-Nejad, Ali, Naghavi, Mohammad Reza, Nemat-Zadeh, Ghorbanali

Journal:

Molecular Biology Reports

Year:

2015

Language:

english

File:

PDF, 115 KB

english, 2015

42

Controllability in Cancer Metabolic Networks According to Drug Targets as Driver Nodes

Asgari, Yazdan, Salehzadeh-Yazdi, Ali, Schreiber, Falk, Masoudi-Nejad, Ali, Csermely, Peter

Journal:

Year:

2013

Language:

english

File:

PDF, 2.38 MB

english, 2013

43

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

HosseinKhan, Nazanin, Zarrineh, Peyman, Rokni-Zadeh, Hassan, Ashouri, Mohammad Reza, Masoudi-Nejad, Ali

Journal:

Molecular BioSystems

Year:

2015

Language:

english

File:

PDF, 1.43 MB

english, 2015

44

Retraction Note to: Candidate gene prioritization

Masoudi-Nejad, Ali, Meshkin, Alireza, Haji-Eghrari, Behzad, Bidkhori, Gholamreza

Journal:

Molecular Genetics and Genomics

Year:

2015

Language:

english

File:

PDF, 351 KB

english, 2015

45

[IEEE 2008 International Conference on Biomedical Engineering And Informatics (BMEI) - Sanya, China (2008.05.27-2008.05.30)] 2008 International Conference on BioMedical Engineering and Informatics - A New Approach for Touching Cells Segmentation

Nasr-Isfahani, Shirin, Mirsafian, Atefeh, Masoudi-Nejad, Ali

Year:

2008

Language:

english

File:

PDF, 481 KB

english, 2008

46

Drug–target interaction prediction from PSSM based evolutionary information

Mousavian, Zaynab, Khakabimamaghani, Sahand, Kavousi, Kaveh, Masoudi-Nejad, Ali

Journal:

Journal of Pharmacological and Toxicological Methods

Year:

2016

Language:

english

File:

PDF, 1.44 MB

english, 2016

47

Information Theory in Systems Biology: Protein-Protein Interaction and Signaling Networks

Mousavian, Zaynab, Díaz, José, Masoudi-Nejad, Ali

Journal:

Seminars in Cell & Developmental Biology

Year:

2015

Language:

english

File:

PDF, 398 KB

english, 2015

48

Determination of the Best Concentration of Streptozotocin to Create a Diabetic Brain Using Histological Techniques

Dehghan-Shasaltaneh, Marzieh, Naghdi, Nasser, Choopani, Samira, Alizadeh, Leila, Bolouri, Bahram, Masoudi-Nejad, Ali, Riazi, Gholam Hossein

Journal:

Journal of Molecular Neuroscience

Year:

2016

Language:

english

File:

PDF, 1.81 MB

english, 2016

49

Flow of Information in Biological Systems

Masoudi-Nejad, Ali, Zenil, Hector

Journal:

Seminars in Cell & Developmental Biology

Year:

2016

Language:

english

File:

PDF, 115 KB

english, 2016

50

EGENES: Transcriptome-Based Plant Database of Genes with Metabolic Pathway Information and Expressed Sequence Tag Indices in KEGG

Ali Masoudi-Nejad, Susumu Goto, Ruy Jauregui, Masumi Ito, Shuichi Kawashima, Yuki Moriya, Takashi R. Endo and Minoru Kanehisa

Journal:

PLANT PHYSIOLOGY

Year:

2007

Language:

english

File:

PDF, 2.74 MB

english, 2007