Works by Sharifi-Zarchi, Ali

Results: 34

Evaluation of the Ankylosing Spondylitis Transcriptome for Oxidative Phosphorylation Pathway: The Shared Pathway with Neurodegenerative Diseases.

Published in:

2021

By:

Lari, Arezou;
Pourbadie, Hamid Gholami;
Sharifi-Zarchi, Ali;
Aslani, Saeed;
Samimi, Leila Nejatbakhsh;
Jamshidi, Ahmadreza;
Mahmoudi, Mahdi;
Gholami Pourbadie, Hamid;
Nejatbakhsh Samimi, Leila

Publication type:

journal article

Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic.

Published in:

PLoS ONE, 2022, v. 17, n. 5, p. 1, doi. 10.1371/journal.pone.0267847

By:

Yavarian, Jila;
Nejati, Ahmad;
Salimi, Vahid;
Shafiei Jandaghi, Nazanin Zahra;
Sadeghi, Kaveh;
Abedi, Adel;
Sharifi Zarchi, Ali;
Gouya, Mohammad Mehdi;
Mokhtari-Azad, Talat

Publication type:

Article

Pan-cancer analysis of microRNA expression profiles highlights microRNAs enriched in normal body cells as effective suppressors of multiple tumor types: A study based on TCGA database.

Published in:

PLoS ONE, 2022, v. 17, n. 4, p. 1, doi. 10.1371/journal.pone.0267291

By:

Moradi, Sharif;
Kamal, Aryan;
Aboulkheyr Es, Hamidreza;
Farhadi, Farnoosh;
Ebrahimi, Marzieh;
Chitsaz, Hamidreza;
Sharifi-Zarchi, Ali;
Baharvand, Hossein

Publication type:

Article

DNA-RNA Hybrid (R-Loop): From a Unified Picture of the Mammalian Telomere to the Genome-Wide Profile.

Published in:

Cells (2073-4409), 2021, v. 10, n. 6, p. 1556, doi. 10.3390/cells10061556

By:

Rassoulzadegan, Minoo;
Sharifi-Zarchi, Ali;
Kianmehr, Leila

Publication type:

Article

Genome-Wide Distribution of Nascent Transcripts in Sperm DNA, Products of a Late Wave of General Transcription.

Published in:

Cells (2073-4409), 2019, v. 8, n. 10, p. 1196, doi. 10.3390/cells8101196

By:

Kianmehr, Leila;
Khazali, Homayoun;
Rajabi-Maham, Hassan;
Sharifi-Zarchi, Ali;
Cuzin, François;
Rassoulzadegan, Minoo

Publication type:

Article

Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis.

Published in:

BMC Medical Genomics, 2019, v. 12, n. 1, p. 1, doi. 10.1186/s12920-019-0632-2

By:

Karimizadeh, Elham;
Sharifi-Zarchi, Ali;
Nikaein, Hassan;
Salehi, Seyedehsaba;
Salamatian, Bahar;
Elmi, Naser;
Gharibdoost, Farhad;
Mahmoudi, Mahdi

Publication type:

Article

A novel panel of blood-based microRNAs capable of discrimination between benign breast disease and breast cancer at early stages.

Published in:

RNA Biology, 2021, v. 18, p. 747, doi. 10.1080/15476286.2021.1989218

By:

Sadeghi, Hanieh;
Kamal, Aryan;
Ahmadi, Marzieh;
Najafi, Hadi;
Sharifi Zarchi, Ali;
Haddad, Peyman;
Shayestehpour, Bahareh;
Kamkar, Leila;
Salamati, Masoumeh;
Geranpayeh, Loabat;
Lashkari, Marzieh;
Totonchi, Mehdi

Publication type:

Article

Down-Regulation of miR-200c and Up-Regulation of miR-30c Target both Stemness and Metastasis Genes in Breast Cancer.

Published in:

Cell Journal (Yakhteh), 2020, v. 21, n. 4, p. 467, doi. 10.22074/cellj.2020.6406

By:

Rahimi, Mahsa;
Sharifi-Zarchi, Ali;
Zarghami, Nosratollah;
Geranpayeh, Lobat;
Ebrahimi, Marzieh;
Alizadeh, Effat

Publication type:

Article

Downregulation of Extracellular Matrix and Cell Adhesion Molecules in Cumulus Cells of Infertile Polycystic Ovary Syndrome Women with and without Insulin Resistance.

Published in:

Cell Journal (Yakhteh), 2019, v. 21, n. 1, p. 35, doi. 10.22074/cellj.2019.5576

By:

Hassani, Fatemeh;
Oryan, Shahrbanoo;
Eftekhari-Yazdi, Poopak;
Bazrgar, Masood;
Moini, Ashraf;
Nasiri, Nahid;
Sharifi-Zarchi, Ali

Publication type:

Article

Comparative In Vitro Evaluation of Human Dental Pulp and Follicle Stem Cell Commitment.

Published in:

Cell Journal (Yakhteh), 2017, v. 18, n. 4, p. 609

By:

Karamzadeh, Razieh;
Baghaban Eslaminejad, Mohamadreza;
Sharifi-Zarchi, Ali

Publication type:

Article

An integrated analysis to predict micro‐RNAs targeting both stemness and metastasis in breast cancer stem cells.

Published in:

Journal of Cellular & Molecular Medicine, 2019, v. 23, n. 4, p. 2442, doi. 10.1111/jcmm.14090

By:

Rahimi, Mahsa;
Sharifi‐Zarchi, Ali;
Firouzi, Javad;
Azimi, Mahnaz;
Zarghami, Nosratollah;
Alizadeh, Effat;
Ebrahimi, Marzieh

Publication type:

Article

Expression and Function of C1orf132 Long-Noncoding RNA in Breast Cancer Cell Lines and Tissues.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 13, p. 6768, doi. 10.3390/ijms22136768

By:

Shafaroudi, Afsaneh Malekzadeh;
Sharifi-Zarchi, Ali;
Rahmani, Saeid;
Nafissi, Nahid;
Mowla, Seyed Javad;
Lauria, Andrea;
Oliviero, Salvatore;
Matin, Maryam M.

Publication type:

Article

Transcriptomic analysis of laser-capture microdissected tumors reveals RAD51AP1 as a tumor-specific marker associated progression from pancreatic intraepithelial neoplasia to invasive pancreatic cancer.

Published in:

Cancer Cell International, 2025, v. 25, n. 1, p. 1, doi. 10.1186/s12935-025-03810-1

By:

Rezagholizadeh, Fereshteh;
Salimi, Adel;
Sharifi-Zarchi, Ali;
Azmoudeh-Ardalan, Farid;
Mousavizadeh, Kazem;
Tajik, Fatemeh;
Mahshid, Panahi;
Khorramdelazad, Hossein;
Wadji, Masoud Baghai;
Kashanizadeh, Atefeh;
Lotfalizadeh, Alireza;
Javad Mowla, Seyed;
Joghataei, Mohammad Taghi

Publication type:

Article

The assessment of efficient representation of drug features using deep learning for drug repositioning.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-3165-y

By:

Moridi, Mahroo;
Ghadirinia, Marzieh;
Sharifi-Zarchi, Ali;
Zare-Mirakabad, Fatemeh

Publication type:

Article

Dysregulation of ribosome-related genes in ankylosing spondylitis: a systems biology approach and experimental method.

Published in:

2021

By:

Lari, Arezou;
Pourbadie, Hamid Gholami;
Sharifi-Zarchi, Ali;
Akhtari, Maryam;
Samimi, Leila Nejatbakhsh;
Jamshidi, Ahmadreza;
Mahmoudi, Mahdi

Publication type:

journal article

Novel splicing variant and gonadal mosaicism in DYRK1A gene identified by whole-genome sequencing in multiplex autism spectrum disorder families.

Published in:

Neurogenetics, 2024, v. 25, n. 4, p. 377, doi. 10.1007/s10048-024-00768-6

By:

Agha Gholizadeh, Mehdi;
Behjati, Farkhondeh;
Ghasemi Firouzabadi, Saghar;
Heidari, Erfan;
Razmara, Ehsan;
Almadani, Navid;
Sharifi Zarchi, Ali;
Garshasbi, Masoud

Publication type:

Article

FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots.

Published in:

Bioinformatics, 2020, v. 36, n. 12, p. 3662, doi. 10.1093/bioinformatics/btaa175

By:

Naznooshsadat, Etminan;
Elham, Parvinnia;
Ali, Sharifi-Zarchi

Publication type:

Article

Enhanced Waddington landscape model with cell–cell communication can explain molecular mechanisms of self-organization.

Published in:

Bioinformatics, 2019, v. 35, n. 20, p. 4081, doi. 10.1093/bioinformatics/btz201

By:

Fooladi, Hosein;
Moradi, Parsa;
Sharifi-Zarchi, Ali;
Khalaj, Babak Hosein

Publication type:

Article

DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-52937-5

By:

Azarkhalili, Behrooz;
Saberi, Ali;
Chitsaz, Hamidreza;
Sharifi-Zarchi, Ali

Publication type:

Article

Increased robustness of early embryogenesis through collective decision-making by key transcription factors.

Published in:

BMC Systems Biology, 2015, v. 9, n. 1, p. 1, doi. 10.1186/s12918-015-0169-8

By:

Sharifi-Zarchi, Ali;
Totonchi, Mehdi;
Khaloughi, Keynoush;
Karamzadeh, Razieh;
Araúzo-Bravo, Marcos J.;
Baharvand, Hossein;
Tusserkani, Ruzbeh;
Pezeshk, Hamid;
Chitsaz, Hamidreza;
Sadeghi, Mehdi

Publication type:

Article

Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. 1, doi. 10.1038/s41598-019-38798-y

By:

Abdolhosseini, Farzad;
Azarkhalili, Behrooz;
Maazallahi, Abbas;
Kamal, Aryan;
Motahari, Seyed Abolfazl;
Sharifi-Zarchi, Ali;
Chitsaz, Hamidreza

Publication type:

Article

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-4353-7

By:

Sharifi-Zarchi, Ali;
Gerovska, Daniela;
Adachi, Kenjiro;
Totonchi, Mehdi;
Pezeshk, Hamid;
Taft, Ryan J.;
Schöler, Hans R.;
Chitsaz, Hamidreza;
Sadeghi, Mehdi;
Baharvand, Hossein;
Araúzo-Bravo, Marcos J.

Publication type:

Article

ARYANA: Aligning Reads by Yet Another Approach.

Published in:

BMC Bioinformatics, 2014, v. 15, p. 1, doi. 10.1186/1471-2105-15-S9-S12

By:

Gholami, Milad;
Arbabi, Aryan;
Sharifi-Zarchi, Ali;
Chitsaz, Hamidreza;
Sadeghi, Mehdi

Publication type:

Article

Genome-wide DNA methylation profiling in ectopic and eutopic of endometrial tissues.

Published in:

Journal of Assisted Reproduction & Genetics, 2019, v. 36, n. 8, p. 1743, doi. 10.1007/s10815-019-01508-8

By:

Barjaste, Nadia;
Shahhoseini, Maryam;
Afsharian, Parvaneh;
Sharifi-Zarchi, Ali;
Masoudi-Nejad, Ali

Publication type:

Article

Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians.

Published in:

Zoological Letters, 2018, v. 4, n. 1, p. N.PAG, doi. 10.1186/s40851-018-0102-2

By:

An, Yang;
Kawaguchi, Akane;
Zhao, Chen;
Toyoda, Atsushi;
Sharifi-Zarchi, Ali;
Mousavi, Seyed Ahmad;
Bagherzadeh, Reza;
Inoue, Takeshi;
Ogino, Hajime;
Fujiyama, Asao;
Chitsaz, Hamidreza;
Baharvand, Hossein;
Agata, Kiyokazu

Publication type:

Article

An integrative Bayesian network approach to highlight key drivers in systemic lupus erythematosus.

Published in:

Arthritis Research & Therapy, 2020, v. 22, n. 1, p. 1, doi. 10.1186/s13075-020-02239-3

By:

Maleknia, Samaneh;
Salehi, Zahra;
Rezaei Tabar, Vahid;
Sharifi-Zarchi, Ali;
Kavousi, Kaveh

Publication type:

Article

Natural Biased Coin Encoded in the Genome Determines Cell Strategy.

Published in:

PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0103569

By:

Dorri, Faezeh;
Mahini, Hamid;
Sharifi-Zarchi, Ali;
Totonchi, Mehdi;
Tusserkani, Ruzbeh;
Pezeshk, Hamid;
Sadeghi, Mehdi

Publication type:

Article

The metabolic network model of primed/naive human embryonic stem cells underlines the importance of oxidation-reduction potential and tryptophan metabolism in primed pluripotency.

Published in:

Cell & Bioscience, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1186/s13578-019-0334-7

By:

Yousefi, Meisam;
Marashi, Sayed-Amir;
Sharifi-Zarchi, Ali;
Taleahmad, Sara

Publication type:

Article

miR-361-5p as a promising qRT-PCR internal control for tumor and normal breast tissues.

Published in:

PLoS ONE, 2021, v. 16, n. 6, p. 1, doi. 10.1371/journal.pone.0253009

By:

Ghanbari, Sogol;
Salimi, Adel;
Rahmani, Saeid;
Nafissi, Nahid;
Sharifi-Zarchi, Ali;
Mowla, Seyed Javad

Publication type:

Article

Temporal activation of LRH‐1 and RAR‐γ in human pluripotent stem cells induces a functional naïve‐like state.

Published in:

EMBO Reports, 2020, v. 21, n. 10, p. 1, doi. 10.15252/embr.201847533

By:

Taei, Adeleh;
Kiani, Tahereh;
Taghizadeh, Zeinab;
Moradi, Sharif;
Samadian, Azam;
Mollamohammadi, Sepideh;
Sharifi‐Zarchi, Ali;
Guenther, Stefan;
Akhlaghpour, Azimeh;
Asgari Abibeiglou, Behrouz;
Najar‐Asl, Mostafa;
Karamzadeh, Razieh;
Khalooghi, Keynoosh;
Braun, Thomas;
Hassani, Seyedeh‐Nafiseh;
Baharvand, Hossein

Publication type:

Article

Integration of Gastric Cancer RNA‐Seq Datasets Along With PPI Network Suggests That Nonhub Nodes Have the Potential to Become Biomarkers.

Published in:

Cancer Reports, 2025, v. 8, n. 1, p. 1, doi. 10.1002/cnr2.70126

By:

Siavoshi, Akram;
Piran, Mehran;
Sharifi‐Zarchi, Ali;
Ataellahi, Fatemeh

Publication type:

Article

Proteome Analysis of Ground State Pluripotency.

Published in:

Scientific Reports, 2015, p. 17985, doi. 10.1038/srep17985

By:

Taleahmad, Sara;
Mirzaei, Mehdi;
Parker, Lindsay M.;
Hassani, Seyedeh-Nafiseh;
Mollamohammadi, Sepideh;
Sharifi-Zarchi, Ali;
Haynes, Paul A.;
Baharvand, Hossein;
Salekdeh, Ghasem Hosseini

Publication type:

Article

Downregulation of ITM2A Gene Expression in Macrophages of Patients with Ankylosing Spondylitis.

Published in:

International Archives of Allergy & Immunology, 2021, v. 182, n. 11, p. 1113, doi. 10.1159/000516179

By:

Lari, Arezou;
Gholami Pourbadie, Hamid;
Jafari, Mohieddin;
Sharifi-Zarchi, Ali;
Akhtari, Maryam;
Nejatbakhsh Samimi, Leila;
Jamshidi, Ahmadreza;
Mahmoudi, Mahdi

Publication type:

Article

StrongestPath: a Cytoscape application for protein–protein interaction analysis.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04230-4

By:

Mousavian, Zaynab;
Khodabandeh, Mehran;
Sharifi-Zarchi, Ali;
Nadafian, Alireza;
Mahmoudi, Alireza

Publication type:

Article