Ali Sharifi-Zarchi

Affiliations

Department of Computer Engineering, Sharif University of Technology, Tehran, Iran. asharifi@sharif.edu.

ORCID: http://orcid.org/0000-0002-0087-7596

Publications (28)

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

Scientific reports

Avec: Behrooz Azarkhalili , Ali Saberi , Hamidreza Chitsaz , Ali Sharifi-Zarchi

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

BMC musculoskeletal disorders

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

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

Bioinformatics (Oxford, England)

Avec: Hosein Fooladi , Parsa Moradi , Ali Sharifi-Zarchi , Babak Hosein Khalaj

PIAS2-mediated blockade of IFN-β signaling: a basis for sporadic Parkinson disease dementia.

Molecular psychiatry

Avec: Joana Magalhaes , Emilie Tresse , Patrick Ejlerskov , Erling Hu , Yawei Liu , Andrea Marin , Alexia Montalant , Letizia Satriano , Carsten Friis Rundsten , Eva Maria Meier Carlsen , Rasmus Rydbirk , Ali Sharifi-Zarchi , Jesper Bøje Andersen , Susana Aznar , Tomasz Brudek , Konstantin Khodosevich , Marco Prinz , Jean-François Marie Perrier , Manu Sharma , Thomas Gasser , Shohreh Issazadeh-Navikas

Determination of genetic characterization and circulation pattern of Respiratory Syncytial Virus (RSV) in children with a respiratory infection, Tehran, Iran, during 2018-2019.

Virus research

Avec: Forough Tavakoli , Anahita Izadi , Jila Yavarian , Ali Sharifi-Zarchi , Vahid Salimi , Talat Mokhtari-Azad

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

BMC medical genomics

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

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

Cells

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

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

Journal of cellular and molecular medicine

Avec: Mahsa Rahimi , Ali Sharifi-Zarchi , Javad Firouzi , Mahnaz Azimi , Nosratollah Zarghami , Effat Alizadeh , Marzieh Ebrahimi

A novel metabolic disorder in the degradation pathway of endogenous methanol due to a mutation in the gene of alcohol dehydrogenase.

Clinical biochemistry

Avec: Maryam Razzaghy-Azar , Mitra Nourbakhsh , Mehdi Vafadar , Mona Nourbakhsh , Saeed Talebi , Ali Sharifi-Zarchi , Elham Salehi Siavashani , Masoud Garshasbi

Time-resolved Small-RNA Sequencing Identifies MicroRNAs Critical for Formation of Embryonic Stem Cells from the Inner Cell Mass of Mouse Embryos.

Stem cell reviews and reports

Avec: Sharif Moradi , Stefan Guenther , Samira Soori , Ali Sharifi-Zarchi , Carsten Kuenne , Vahid Khoddami , Pouya Tavakol , Susanne Kreutzer , Thomas Braun , Hossein Baharvand

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

Cell & bioscience

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

Expression and Function of

International journal of molecular sciences

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

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

PloS one

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

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

BMC bioinformatics

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

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.

PloS one

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

InterOpt: Improved gene expression quantification in qPCR experiments using weighted aggregation of reference genes.

iScience

Avec: Adel Salimi , Saeid Rahmani , Ali Sharifi-Zarchi

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

Cell journal

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

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

BMC bioinformatics

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

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

Journal of assisted reproduction and genetics

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

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

Scientific reports

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

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

Cell journal

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

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

Arthritis research & therapy

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

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

International archives of allergy and immunology

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

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

Iranian journal of allergy, asthma, and immunology

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

Defining microRNA signatures of hair follicular stem and progenitor cells in healthy and androgenic alopecia patients.

Journal of dermatological science

Avec: Parvaneh Mohammadi , Mohammad Ali Nilforoushzadeh , Khalil Kass Youssef , Ali Sharifi-Zarchi , Sharif Moradi , Pardis Khosravani , Raheleh Aghdami , Payam Taheri , Ghasem Hosseini Salekdeh , Hossein Baharvand , Nasser Aghdami

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

EMBO reports

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

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

Cells

Avec: Minoo Rassoulzadegan , Ali Sharifi-Zarchi , Leila Kianmehr

Revealing the grammar of small RNA secretion using interpretable machine learning.

Cell genomics

Avec: Bahar Zirak , Mohsen Naghipourfar , Ali Saberi , Delaram Pouyabahar , Amirhossein Zarezadeh , Lixi Luo , Lisa Fish , Doowon Huh , Albertas Navickas , Ali Sharifi-Zarchi , Hani Goodarzi

Réseau de co-auteurs

Mahdi Mahmoudi 4 collaborations

Sharif Moradi 4 collaborations

Hossein Baharvand 4 collaborations

Hamidreza Chitsaz 3 collaborations

Arezou Lari 3 collaborations

Hamid Gholami Pourbadie 3 collaborations

Leila Nejatbakhsh Samimi 3 collaborations

Ahmadreza Jamshidi 3 collaborations

Marzieh Ebrahimi 3 collaborations

Saeid Rahmani 3 collaborations

Behrooz Azarkhalili 2 collaborations

Ali Saberi 2 collaborations

Maryam Akhtari 2 collaborations

Leila Kianmehr 2 collaborations

Minoo Rassoulzadegan 2 collaborations

Mahsa Rahimi 2 collaborations

Nosratollah Zarghami 2 collaborations

Effat Alizadeh 2 collaborations

Stefan Guenther 2 collaborations

Thomas Braun 2 collaborations

Nahid Nafissi 2 collaborations

Seyed Javad Mowla 2 collaborations

Adel Salimi 2 collaborations

Aryan Kamal 2 collaborations

Hosein Fooladi 1 collaboration

Parsa Moradi 1 collaboration

Babak Hosein Khalaj 1 collaboration

Joana Magalhaes 1 collaboration

Emilie Tresse 1 collaboration

Patrick Ejlerskov 1 collaboration

Erling Hu 1 collaboration

Yawei Liu 1 collaboration

Andrea Marin 1 collaboration

Alexia Montalant 1 collaboration

Letizia Satriano 1 collaboration

Carsten Friis Rundsten 1 collaboration

Eva Maria Meier Carlsen 1 collaboration

Rasmus Rydbirk 1 collaboration

Jesper Bøje Andersen 1 collaboration

Susana Aznar 1 collaboration

Tomasz Brudek 1 collaboration

Konstantin Khodosevich 1 collaboration

Marco Prinz 1 collaboration

Jean-François Marie Perrier 1 collaboration

Manu Sharma 1 collaboration

Thomas Gasser 1 collaboration

Shohreh Issazadeh-Navikas 1 collaboration

Forough Tavakoli 1 collaboration

Anahita Izadi 1 collaboration

Jila Yavarian 1 collaboration

Vahid Salimi 1 collaboration

Talat Mokhtari-Azad 1 collaboration

Elham Karimizadeh 1 collaboration

Hassan Nikaein 1 collaboration

Seyedehsaba Salehi 1 collaboration

Bahar Salamatian 1 collaboration

Naser Elmi 1 collaboration

Farhad Gharibdoost 1 collaboration

Homayoun Khazali 1 collaboration

Hassan Rajabi-Maham 1 collaboration

François Cuzin 1 collaboration

Javad Firouzi 1 collaboration

Mahnaz Azimi 1 collaboration

Maryam Razzaghy-Azar 1 collaboration

Mitra Nourbakhsh 1 collaboration

Mehdi Vafadar 1 collaboration

Mona Nourbakhsh 1 collaboration

Saeed Talebi 1 collaboration

Elham Salehi Siavashani 1 collaboration

Masoud Garshasbi 1 collaboration

Samira Soori 1 collaboration

Carsten Kuenne 1 collaboration

Vahid Khoddami 1 collaboration

Pouya Tavakol 1 collaboration

Susanne Kreutzer 1 collaboration

Meisam Yousefi 1 collaboration

Sayed-Amir Marashi 1 collaboration

Sara Taleahmad 1 collaboration

Afsaneh Malekzadeh Shafaroudi 1 collaboration

Andrea Lauria 1 collaboration

Salvatore Oliviero 1 collaboration

Maryam M Matin 1 collaboration

Sogol Ghanbari 1 collaboration

Zaynab Mousavian 1 collaboration

Mehran Khodabandeh 1 collaboration

Alireza Nadafian 1 collaboration

Alireza Mahmoudi 1 collaboration

Hamidreza Aboulkheyr Es 1 collaboration

Farnoosh Farhadi 1 collaboration

Lobat Geranpayeh 1 collaboration

Mahroo Moridi 1 collaboration

Marzieh Ghadirinia 1 collaboration

Fatemeh Zare-Mirakabad 1 collaboration

Nadia Barjaste 1 collaboration

Maryam Shahhoseini 1 collaboration

Parvaneh Afsharian 1 collaboration

Ali Masoudi-Nejad 1 collaboration

Farzad Abdolhosseini 1 collaboration

Abbas Maazallahi 1 collaboration

Seyed Abolfazl Motahari 1 collaboration

Fatemeh Hassani 1 collaboration

Shahrbanoo Oryan 1 collaboration

Poopak Eftekhari-Yazdi 1 collaboration

Masood Bazrgar 1 collaboration

Ashraf Moini 1 collaboration

Nahid Nasiri 1 collaboration

Samaneh Maleknia 1 collaboration

Zahra Salehi 1 collaboration

Vahid Rezaei Tabar 1 collaboration

Kaveh Kavousi 1 collaboration

Mohieddin Jafari 1 collaboration

Saeed Aslani 1 collaboration

Parvaneh Mohammadi 1 collaboration

Mohammad Ali Nilforoushzadeh 1 collaboration

Khalil Kass Youssef 1 collaboration

Pardis Khosravani 1 collaboration

Raheleh Aghdami 1 collaboration

Payam Taheri 1 collaboration

Ghasem Hosseini Salekdeh 1 collaboration

Nasser Aghdami 1 collaboration

Adeleh Taei 1 collaboration

Tahereh Kiani 1 collaboration

Zeinab Taghizadeh 1 collaboration

Azam Samadian 1 collaboration

Sepideh Mollamohammadi 1 collaboration

Azimeh Akhlaghpour 1 collaboration

Behrouz Asgari Abibeiglou 1 collaboration

Mostafa Najar-Asl 1 collaboration

Razieh Karamzadeh 1 collaboration

Keynoosh Khalooghi 1 collaboration

Seyedeh-Nafiseh Hassani 1 collaboration

Bahar Zirak 1 collaboration

Mohsen Naghipourfar 1 collaboration

Delaram Pouyabahar 1 collaboration

Amirhossein Zarezadeh 1 collaboration

Lixi Luo 1 collaboration

Lisa Fish 1 collaboration

Doowon Huh 1 collaboration

Albertas Navickas 1 collaboration

Hani Goodarzi 1 collaboration