Latent space search based multimodal optimization with personalized edge-network biomarker for multi-purpose early disease prediction

SPNE: sample-perturbed network entropy for revealing critical states of complex biological systems

(2023) Jiayuan Zhong et al.   BRIEFINGS IN BIOINFORMATICS

Multi-modal optimization to identify personalized biomarkers for disease prediction of individual patients with cancer

(2022) Jing Liang et al.   BRIEFINGS IN BIOINFORMATICS

Graph contextualized attention network for predicting synthetic lethality in human cancers

(2021) Yahui Long et al.   BIOINFORMATICS

Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis

(2021) Wei-Feng Guo et al.   PLoS Computational Biology

Paired Offspring Generation for Constrained Large-Scale Multiobjective Optimization

(2021) Cheng He et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

Single-cell transcriptomics reveal DHX9 in mature B cell as a dynamic network biomarker before lymph node metastasis in CRC

(2021) Huisheng Liu et al.   Molecular Therapy-Oncolytics

Vec2image: an explainable artificial intelligence model for the feature representation and classification of high-dimensional biological data by vector-to-image conversion

(2021) Hui Tang et al.   BRIEFINGS IN BIOINFORMATICS

Deep latent space fusion for adaptive representation of heterogeneous multi-omics data

(2021) Chengming Zhang et al.   BRIEFINGS IN BIOINFORMATICS

An Adaptive Localized Decision Variable Analysis Approach to Large-Scale Multiobjective and Many-Objective Optimization

(2021) Lianbo Ma et al.   IEEE Transactions on Cybernetics

A Review of Population-Based Metaheuristics for Large-Scale Black-Box Global Optimization—Part II

(2021) Mohammad Nabi Omidvar et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

A Review of Population-Based Metaheuristics for Large-Scale Black-Box Global Optimization—Part I

(2021) Mohammad Nabi Omidvar et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

iGMDR: Integrated Pharmacogenetic Resource Guide to Cancer Therapy and Research

(2020) Xiang Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Multimodal Multiobjective Evolutionary Optimization With Dual Clustering in Decision and Objective Spaces

(2020) Qiuzhen Lin et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

A Multipopulation Evolutionary Algorithm for Solving Large-Scale Multimodal Multiobjective Optimization Problems

(2020) Ye Tian et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

Solving Large-Scale Multiobjective Optimization Problems With Sparse Optimal Solutions via Unsupervised Neural Networks

(2020) Ye Tian et al.   IEEE Transactions on Cybernetics

Characterizing the Personalized Microbiota Dynamics for Disease Classification by Individual-Specific Edge-Network Analysis

(2019) Xiangtian Yu et al.   Frontiers in Genetics

A novel network control model for identifying personalized driver genes in cancer

(2019) Wei-Feng Guo et al.   PLoS Computational Biology

DMCM: A Data-adaptive Mutation Clustering Method to Identify Cancer-related Mutation Clusters

(2018) Xinguo Lu et al.   BIOINFORMATICS

Facilitating Anti-Cancer Combinatorial Drug Discovery by Targeting Epistatic Disease Genes

(2018) Yuan Quan et al.   MOLECULES

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Detection for disease tipping points by landscape dynamic network biomarkers

(2018) Xiaoping Liu et al.   National Science Review

PlatEMO: A MATLAB Platform for Evolutionary Multi-Objective Optimization [Educational Forum]

(2017) Ye Tian et al.   IEEE Computational Intelligence Magazine

A Multi-objective Particle Swarm Optimizer Using Ring Topology for Solving Multimodal Multi-objective Problems

(2017) Caitong Yue et al.   IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

A note on using the F-measure for evaluating record linkage algorithms

(2017) David Hand et al.   STATISTICS AND COMPUTING

Quantifying critical states of complex diseases using single-sample dynamic network biomarkers

(2017) Xiaoping Liu et al.   PLoS Computational Biology

RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation

(2016) Robert A. Jones et al.   JOURNAL OF CLINICAL INVESTIGATION

Personalized characterization of diseases using sample-specific networks

(2016) Xiaoping Liu et al.   NUCLEIC ACIDS RESEARCH

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

(2016) Hyunghoon Cho et al.   Cell Systems

Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals

(2015) Tao Zeng et al.   BRIEFINGS IN BIOINFORMATICS

DGIdb 2.0: mining clinically relevant drug–gene interactions

(2015) Alex H. Wagner et al.   NUCLEIC ACIDS RESEARCH

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

Diagnosing phenotypes of single-sample individuals by edge biomarkers

(2015) Wanwei Zhang et al.   Journal of Molecular Cell Biology

EdgeMarker: Identifying differentially correlated molecule pairs as edge-biomarkers

(2014) Wanwei Zhang et al.   JOURNAL OF THEORETICAL BIOLOGY

Edge biomarkers for classification and prediction of phenotypes

(2014) Tao Zeng et al.   Science China-Life Sciences

DCDB 2.0: a major update of the drug combination database

(2014) Y. Liu et al.   Database-The Journal of Biological Databases and Curation

Prediction and early diagnosis of complex diseases by edge-network

(2013) Xiangtian Yu et al.   BIOINFORMATICS

Edgotype: a fundamental link between genotype and phenotype

(2013) Nidhi Sahni et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers

(2012) Luonan Chen et al.   Scientific Reports

Genetic Interactions in Cancer Progression and Treatment

(2011) Alan Ashworth et al.   CELL