Ali Sharifi-Zarchi

15 papers B 1Journal 14
YearRankTypeTitle / Venue / Authors
2025 J jnl
Aryana-bs: context-aware alignment of bisulfite-sequencing reads.
BMC Bioinform.
Hassan Nikaein, Ali Sharifi-Zarchi, Afsoon Afzal, Saeedeh Ezzati, Farzane Rasti, Hamidreza Chitsaz, Kunde Ramamoorthy Govindarajan
2025 J jnl
Infinity and Beyond: Compositional Alignment in VAR and Diffusion T2I Models.
CoRR
Hossein Shahabadi, Niki Sepasian, Arash Mari Oriyad, Ali Sharifi-Zarchi, Mahdieh Soleymani Baghshah
2025 J jnl
uGMM-NN: Univariate Gaussian Mixture Model Neural Network.
CoRR
Ali Sharifi-Zarchi
2023 J jnl
Novel Pipeline for Diagnosing Acute Lymphoblastic Leukemia Sensitive to Related Biomarkers.
CoRR
Amirhossein Askari-Farsangi, Ali Sharifi-Zarchi, Mohammad Hossein Rohban
2021 J jnl
StrongestPath: a Cytoscape application for protein-protein interaction analysis.
BMC Bioinform.
Zaynab Mousavian, Mehran Khodabandeh, Ali Sharifi-Zarchi, Alireza Nadafian, Alireza Mahmoudi
2020 J jnl
FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots.
Bioinform.
Etminan Naznooshsadat, Elham Parvinnia, Ali Sharifi-Zarchi
2020 J jnl
Graph Traversal Edit Distance and Extensions.
J. Comput. Biol.
Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2020 J jnl
PyGTED: Python Application for Computing Graph Traversal Edit Distance.
J. Comput. Biol.
Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2019 J jnl
Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization.
Bioinform.
Hosein Fooladi, Parsa Moradi, Ali Sharifi-Zarchi, Babak Hossein Khalaj
2019 J jnl
The assessment of efficient representation of drug features using deep learning for drug repositioning.
BMC Bioinform.
Mahroo Moridi, Marzieh Ghadirinia, Ali Sharifi-Zarchi, Fatemeh Zare-Mirakabad
2018 J jnl
Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks.
CoRR
Farzad Abdolhosseini, Behrooz Azarkhalili, Abbas Maazallahi, Aryan Kamal, Seyed Abolfazl Motahari, Ali Sharifi-Zarchi, Hamidreza Chitsaz
2018 B conf
GTED: Graph Traversal Edit Distance.
RECOMB
Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz
2018 J jnl
Inferring Molecular Pathology and micro-RNA Transcriptome from mRNA Profiles of Cancer Biopsies through Deep Multi-Task Learning.
CoRR
Behrooz Azarkhalili, Ali Saberi, Hamidreza Chitsaz, Ali Sharifi-Zarchi
2015 J jnl
Increased robustness of early embryogenesis through collective decision-making by key transcription factors.
BMC Syst. Biol.
Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
2014 J jnl
ARYANA: Aligning Reads by Yet Another Approach.
BMC Bioinform.
Milad Gholami, Aryan Arbabi, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Mehdi Sadeghi