2025
Computer Science Symposium 2025
Genome-Wide Methylation and Cognitive Function: A Random Forest Approach
to Predicting Cognitive Impairment
Hamed Abdollahi, Carolyn Banister, Ana Pocivavsek, Nicholas Riccardi,
Leonardo Bonilha, Julius Fridriksson, Homayoun Valafar
We employed a genome-wide analysis of DNA methylation profiles in conjunction with a
Random Forest machine learning model to identify key methylation signatures predictive of
cognitive disease. Our findings reveal specific CpG loci significantly associated with
cognitive performance, suggesting potential epigenetic biomarkers involved in the molecular
underpinnings of cognitive aging and dementia.
2024
Cancers 2024
Integrating Omics Data and AI for Cancer Diagnosis and Prognosis
Yousaku Ozaki, Phil Broughton, Hamed Abdollahi, Homayoun Valafar,
and Anna V. Blenda
This review paper examines the varying uses of AI for diagnosis and prognosis, analyzing
89 studies that applied AI to multi-omics data, radiomics, pathomics, and clinical data
in cancer research. Eight studies integrated genomics, transcriptomics, epigenomics,
and proteomics. Incorporating AI into cancer diagnosis and prognosis represents a
significant advancement with considerable clinical potential.
NISBRE 2024
Gene Expression Profiles Under the Influence of Kynurenic Acid During Progeny
Hamed Abdollahi, Courtney Wright, Ana Pocivavsek, Homayoun Valafar
Tryptophan metabolism plays a crucial role in sleep disorders and neurodegenerative diseases.
This study examined differentially expressed genes between male and female rats exposed to
elevated kynurenic acid concentration during the fetal period. Among 2,060 significantly
over-expressed genes, 199 exhibited differential expression in females and 216 in males
across various time points.
Int. J. Biological Macromolecules 2024
Polydopamine-Contained Hydrogel Nanocomposites with Combined Antimicrobial and
Antioxidant Properties for Accelerated Wound Healing
Mahin Abdollahi, Sina Andalib, Roghayeh Ghorbani, Davoud Afshar, Mohammad Gholinejad,
Hamed Abdollahi, Ali Akbari, Nasser Nikfarjam
A multifunctional polyacrylamide/PVA-based hydrogel containing synthesized
poly(ionic liquid) and polydopamine-coated polyphenolic nanosheet was developed for wound
dressing. The hydrogel demonstrated high antimicrobial activity (over 95%) against
E. coli, S. aureus, and C. albicans, achieving 100% wound
closure after 14 days compared to 68% for commercial dressing (Tegaderm).
2023
Current Opinion in Structural Biology 2023
Computational Modeling of Multiple Conformational States of Proteins
with Residual Dipolar Coupling Data
Hamed Abdollahi*, James H. Prestegard, Homayoun Valafar
Residual dipolar couplings (RDCs) provide access to amplitudes and directions of motion
in biomolecules, characteristics important to protein function. This report summarizes
how RDCs have been used to confirm internal dynamics, characterize motion types, and
recover atomic-scale structural ensembles — with growing applicability to
AlphaFold-produced structures.
CSCI 2023
TransONet: Automatic Segmentation of Vasculature in Computed Tomographic
Angiograms Using Deep Learning
Alireza Bagheri Rajeoni, Breanna Pederson, Ali Firooz, Hamed Abdollahi,
Andrew K. Smith, Daniel G. Clair, Susan M. Lessner, Homayoun Valafar
A deep learning model was proposed to segment the vascular system in CTA images of patients
undergoing surgery for peripheral arterial disease. The approach achieved average Dice
accuracies of 93.5% and 80.64% in test datasets, highlighting its accuracy and clinical
utility for vascular system analysis.
2021
Computational & Structural Biotechnology Journal
Pilot Study: Initial Investigation Suggests Differences in EMT-Associated
Gene Expression in Breast Tumor Regions
Kylie L. King, Hamed Abdollahi, Zoe Dinkel, Alannah Akins,
Homayoun Valafar, Heather Dunn
This pilot study evaluated gene expression in triple-negative breast cancer (TNBC) samples
from African American and Caucasian patients using statistical methods and machine learning.
Decision tree models achieved 83.33% accuracy, identifying CD29, EGF, SNAI1, and CHD2 as
the most significant differentially expressed genes in relevant tumor regions.
Archives of Virology 2021
Coronavirus: Proteomics Analysis of Chicken Kidney Tissue Infected with
Variant 2 (IS-1494)-like Avian Infectious Bronchitis Virus
Hamed Abdollahi, Mostafa Rezaei-Tavirani, Arash Ghalyanchilangeroudi,
Hossein Maghsoudloo, Masood Hashemzadeh, Hossein Hosseini, Abbas Barin
Proteome changes in kidney tissue of SPF chickens infected with the IS/1494/06 nephrotropic
variant of avian coronavirus were investigated by 2D electrophoresis and MS-MALDI/TOF/TOF.
Topological PPI network analysis revealed 10 key genes at 2 dpi and 9 genes at 7 dpi,
suggesting cellular metabolism alteration and heat shock protein involvement during viral
pathogenesis.
2020
Infection, Genetics and Evolution 2020
Spatial Spread and Emergence of Reassortant H5 Highly Pathogenic Avian
Influenza Viruses in Iran
Hamed Abdollahi, Ali Safar Maken Ali, Isabella Monne,
Adelaide Milani, Alice Fusaro, Bianca Zecchin
Complete genome sequencing of 28 H5Nx viruses circulating in Iran (2016–2018) revealed
the first characterization of HPAI H5N6 clade 2.3.4.4B in Iran, six novel H5N8 genotypes,
and evidence of Iran as a hotspot for virus introduction and dissemination to the
Middle East — underscoring the need for enhanced surveillance in the region.
2017–2018
VirusDisease 2018
Complete Genome Analysis of Iranian IS-1494-Like Avian Infectious Bronchitis Virus
Fatemeh Sadat Mousavi, Arash Ghalyanchilangeroudi, Hossein Hosseini, Bahar Nayeri Fasaei,
Seyed Ali Ghafouri, Hamed Abdollahi, Mohammad Hosein Fallah-Mehrabadi,
Naser Sadri
Full-length genome determination of the Iranian IS-1494-like IBV (Mahed isolate; 27,652 nt)
containing 13 ORFs, including rarely reported ORFs 4b, 4c, and 6b. Phylogenetic analysis
revealed highest sequence homology with Gray and JMK strains, with evidence of
recombination driving the adaptation and evolution of new viral genotypes.
Tropical Animal Health and Production 2017
Clade 2.3.4.4 Avian Influenza A (H5N8) Outbreak in Commercial Poultry
Seyed Ali Ghafouri, Arash GhalyanchiLangeroudi, Hossein Maghsoudloo,
Reza KH Farahani, Hamed Abdollahi, Farshad Tehrani,
Mohammad Hossein Fallah
Detection and genetic characterization of HPAI H5N8 clade 2.3.4.4 (Group B / Gochang-like)
in a commercial layer farm in Tehran province (November 2016), the first such clade detected
in Iran. Highest similarity found with Russian 2016 sequences, highlighting Iran's high risk
of HPAI H5 introduction from East Asia.
For a complete and up-to-date list of publications, please visit my Google Scholar profile.
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