ARYANA: Aligning Reads by Yet Another Approach. - Milad Gholami; Aryan Arbabi; Ali Sharifi-Zarchi; Hamidreza Chitsaz; Mehdi Sadeghi (BMC Bioinform., 2014)

Increased robustness of early embryogenesis through collective decision-making by key transcription factors. - Ali Sharifi-Zarchi; Mehdi Totonchi; Keynoush Khaloughi; Razieh Karamzadeh; Marcos J. Araúzo-Bravo; Hossein Baharvand; Ruzbeh Tusserkani; Hamid Pezeshk; Hamidreza Chitsaz; Mehdi Sadeghi (BMC Syst. Biol., 2015)

GTED: Graph Traversal Edit Distance. - Ali Ebrahimpour Boroojeny; Akash Shrestha; Ali Sharifi-Zarchi; Suzanne Renick Gallagher; Süleyman Cenk Sahinalp; Hamidreza Chitsaz (RECOMB, 2018)

Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks. - Farzad Abdolhosseini; Behrooz Azarkhalili; Abbas Maazallahi; Aryan Kamal; Seyed Abolfazl Motahari; Ali Sharifi-Zarchi; Hamidreza Chitsaz (CoRR, 2018)

Inferring Molecular Pathology and micro-RNA Transcriptome from mRNA Profiles of Cancer Biopsies through Deep Multi-Task Learning. - Behrooz Azarkhalili; Ali Saberi; Hamidreza Chitsaz; Ali Sharifi-Zarchi (CoRR, 2018)

Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization. - Hosein Fooladi; Parsa Moradi; Ali Sharifi-Zarchi; Babak Hossein Khalaj (Bioinform., 2019)

The assessment of efficient representation of drug features using deep learning for drug repositioning. - Mahroo Moridi; Marzieh Ghadirinia; Ali Sharifi-Zarchi; Fatemeh Zare-Mirakabad (BMC Bioinform., 2019)

FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots. - Etminan Naznooshsadat; Elham Parvinnia; Ali Sharifi-Zarchi (Bioinform., 2020)

Graph Traversal Edit Distance and Extensions. - Ali Ebrahimpour Boroojeny; Akash Shrestha; Ali Sharifi-Zarchi; Suzanne Renick Gallagher; Süleyman Cenk Sahinalp; Hamidreza Chitsaz (J. Comput. Biol., 2020)

PyGTED: Python Application for Computing Graph Traversal Edit Distance. - Ali Ebrahimpour Boroojeny; Akash Shrestha; Ali Sharifi-Zarchi; Suzanne Renick Gallagher; Süleyman Cenk Sahinalp; Hamidreza Chitsaz (J. Comput. Biol., 2020)

StrongestPath: a Cytoscape application for protein-protein interaction analysis. - Zaynab Mousavian; Mehran Khodabandeh; Ali Sharifi-Zarchi; Alireza Nadafian; Alireza Mahmoudi (BMC Bioinform., 2021)

Novel Pipeline for Diagnosing Acute Lymphoblastic Leukemia Sensitive to Related Biomarkers. - Amirhossein Askari-Farsangi; Ali Sharifi-Zarchi; Mohammad Hossein Rohban (CoRR, 2023)

Aryana-bs: context-aware alignment of bisulfite-sequencing reads. - Hassan Nikaein; Ali Sharifi-Zarchi; Afsoon Afzal; Saeedeh Ezzati; Farzane Rasti; Hamidreza Chitsaz; Kunde Ramamoorthy Govindarajan (BMC Bioinform., 2025)