A novel multi-objective optimization framework using NSGA-II for gene co-expression network inference

Behnam Aghajan

doi:10.1016/j.compbiolchem.2026.108944

2026-02-10

PRE

Behnam Aghajan

Mohammad Reza Ghaemi *

Ali M. Mosammam

Emran Heshmati

Khosrow Khalifeh *

DOI：10.1016/j.compbiolchem.2026.108944

原文链接

原文求助

摘要

En 中文

• 基因共表达网络（GCNs）被广泛用于解析功能基因模块和调控通路，但其可靠性常因转录组数据的噪声而受到影响。 • 我们引入了一种基于非支配排序遗传算法II（NSGA-II）的新型多目标优化框架，用于构建共表达网络。 • 与传统方法（WGCNA和ARACNE）相比，NSGA-II可同时优化关键网络属性，包括稀疏性、模块度、无标度拓扑结构和边可重复性，同时保留生物学真实性。

Keyword:

Gene co-expression networks

NSGA-II

multi-objective optimization

network inference

biological realism

期刊

Computational Biology and Chemistry

IF:

3.1

论文数:

696

被引数:

机构

University of Zanjan

学者数:

286

论文数: 155

被引数: 1.8K

引用论文

Lactic acid promotes PD-1 expression in regulatory T cells in highly glycolytic tumor microenvironments 乳酸促进高糖酵解肿瘤微环境中调节性T细胞的PD-1表达

Cancer Cell

IF0

2022-02-01

OAAI

Shogo Kumagai; Shohei Koyama; Kota Itahashi; Tokiyoshi Tanegashima; Yi-tzu Lin; Yosuke Togashi; Takahiro Kamada; Takuma Irie; Genki Okumura; Hidetoshi Kono; Daisuke Ito; Rika Fujii; Sho Watanabe; Atsuo Sai; Shota Fukuoka; Eri Sugiyama; Go Watanabe; Takuya Owari; Hitomi Nishinakamura; Daisuke Sugiyama; Yuka Maeda; Akihito Kawazoe; Hiroki Yukami; Keigo Chida; Yuuki Ohara; Tatsuya Yoshida; Yuki Shinno; Yuki Takeyasu; Masayuki Shirasawa; Kenta Nakama; Keiju Aokage; Jun Suzuki; Genichiro Ishii; Takeshi Kuwata; Naoya Sakamoto; Masahito Kawazu; Toshihide Ueno; Taisuke Mori; Naoya Yamazaki; Masahiro Tsuboi; Yasushi Yatabe; Takahiro Kinoshita; Toshihiko Doi; Kohei Shitara; Hiroyuki Mano; Hiroyoshi Nishikawa

Network biology:: Understanding the cell's functional organization 网络生物学:: 了解细胞的功能组织

NATURE REVIEWS GENETICS

IF52

2004-02-01

6.5K

PREAI

Barabási, AL; Oltvai, ZN

Identification of Key Candidate Genes and Pathways in Colorectal Cancer by Integrated Bioinformatical Analysis

International Journal of Molecular Sciences

IF0

2017-03-28

OAAI

Yongchen Guo; Yonghua Bao; Ming Ma; Wancai Yang

Alveolar Development and Disease

AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

IF5.3

2015-07-01

OAAI

Whitsett, Jeffrey A.; Weaver, Timothy E.

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

BMC Bioinformatics

IF0

2006-03-20

OAAI

Adam A Margolin; Ilya Nemenman; Katia Basso; Chris Wiggins; Gustavo Stolovitzky; Riccardo Dalla Favera; Andrea Califano

Gene Expression-Based Classification of Non-Small Cell Lung Carcinomas and Survival Prediction

PLoS ONE

IF0

2010-04-22

OAAI

Jun Hou; Joachim Aerts; Bianca den Hamer; Wilfred van IJcken; Michael den Bakker; Peter Riegman; Cor van der Leest; Peter van der Spek; John A. Foekens; Henk C. Hoogsteden; Frank Grosveld; Sjaak Philipsen

minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual Information

BMC Bioinformatics

IF0

2008-10-29

OAAI

Patrick E Meyer; Frédéric Lafitte; Gianluca Bontempi

A Multi-objective Optimization Model for Redundancy Reduction in Convolutional Neural Networks

Neural Processing Letters

IF0

2023-03-16

PREAI

Ali Boufssasse; El houssaine Hssayni; Nour-Eddine Joudar; Mohamed Ettaouil