Computational tools for aptamer identification and optimization

D Sun, M Sun, J Zhang, X Lin, Y Zhang, F Lin… - TrAC Trends in …, 2022 - Elsevier
Aptamers are single-stranded DNA or RNA oligonucleotides that can selectively bind to a
specific target. They are generally obtained by SELEX, but the procedure is challenging and …

Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery

K Sato, M Hamada - Briefings in Bioinformatics, 2023 - academic.oup.com
Computational analysis of RNA sequences constitutes a crucial step in the field of RNA
biology. As in other domains of the life sciences, the incorporation of artificial intelligence …

Tuning hyperparameters of machine learning algorithms and deep neural networks using metaheuristics: A bioinformatics study on biomedical and biological cases

S Nematzadeh, F Kiani, M Torkamanian-Afshar… - … biology and chemistry, 2022 - Elsevier
The performance of a model in machine learning problems highly depends on the dataset
and training algorithms. Choosing the right training algorithm can change the tale of a …

PSCSO: Enhanced sand cat swarm optimization inspired by the political system to solve complex problems

F Kiani, FA Anka, F Erenel - Advances in Engineering Software, 2023 - Elsevier
Abstract The Sand Cat Swarm Optimization (SCSO) algorithm is a recently introduced
metaheuristic with balanced behavior in the exploration and exploitation phases. However, it …

Recent advances in micro/nanomaterial-based aptamer selection strategies

DM Kim, MJ Go, J Lee, D Na, SM Yoo - Molecules, 2021 - mdpi.com
Aptamers are artificial nucleic acid ligands that have been employed in various fundamental
studies and applications, such as biological analyses, disease diagnostics, targeted …

High-throughput analysis of the interactions between viral proteins and host cell RNAs

H Lanjanian, S Nematzadeh, S Hosseini… - Computers in biology …, 2021 - Elsevier
RNA-protein interactions of a virus play a major role in the replication of RNA viruses. The
replication and transcription of these viruses take place in the cytoplasm of the host cell; …

Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm

Y Masoudi-Sobhanzadeh, A Masoudi-Nejad - BMC bioinformatics, 2020 - Springer
Background Drug repurposing aims to detect the new therapeutic benefits of the existing
drugs and reduce the spent time and cost of the drug development projects. The synthetic …

In silico design of novel aptamers utilizing a hybrid method of machine learning and genetic algorithm

M Torkamanian-Afshar, S Nematzadeh, M Tabarzad… - Molecular …, 2021 - Springer
Aptamers can be regarded as efficient substitutes for monoclonal antibodies in many
diagnostic and therapeutic applications. Due to the tedious and prohibitive nature of SELEX …

A knowledge-based protein-protein interaction inhibition (KPI) pipeline: an insight from drug repositioning for COVID-19 inhibition

H Lanjanian, S Hosseini, Z Narimani… - Journal of …, 2023 - Taylor & Francis
The inhibition of protein-protein interactions (PPIs) by small molecules is an exciting drug
discovery strategy. Here, we aimed to develop a pipeline to identify candidate small …

NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins

S Nematzadeh, N Aydin, Z Kurt… - Current …, 2024 - ingentaconnect.com
Background: Interactions of RNA and DNA with proteins are crucial for elucidating
intracellular processes in living organisms, diagnosing disorders, designing aptamer drugs …