Systematic study of the boundary composition in Poisson Boltzmann calculations. - Parimal Kar; Yanjie Wei; Ulrich H. E. Hansmann; Siegfried Höfinger (J. Comput. Chem., 2007)

A New Classification Method for Human Gene Splice Site Prediction. - Dan Wei; Weiwei Zhuang; Qingshan Jiang; Yanjie Wei (HIS, 2012)

DGraph: Algorithms for Shortgun Reads Assembly Using De Bruijn Graph. - Jintao Meng 001; Jianrui Yuan; Jiefeng Cheng; Yanjie Wei; Shengzhong Feng (NPC, 2012)

Small World Asynchronous Parallel Model for Genome Assembly. - Jintao Meng 001; Jianrui Yuan; Jiefeng Cheng; Yanjie Wei; Shengzhong Feng (NPC, 2012)

A novel hierarchical clustering algorithm for gene sequences. - Dan Wei; Qingshan Jiang; Yanjie Wei; Shengrui Wang (BMC Bioinform., 2012)

An Energy Efficient Clustering Scheme for Data Aggregation in Wireless Sensor Networks. - Jintao Meng 001; Jian-Rui Yuan; Shengzhong Feng; Yanjie Wei (J. Comput. Sci. Technol., 2013)

Modeling and analysis of gene regulatory networks with a Bayesian-driven approach. - Shuqiang Wang; Jinxing Hu; Yanyan Shen; Ling Yin 002; Yanjie Wei (ISCIT, 2014)

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores. - Jintao Meng 001; Bingqiang Wang; Yanjie Wei; Shengzhong Feng; Pavan Balaji (BMC Bioinform., 2014)

SWAP-Assembler 2: Scalable Genome Assembler towards Millions of Cores - Practice and Experience. - Jintao Meng 001; Yanjie Wei; Sangmin Seo; Pavan Balaji (CCGRID, 2015)

MPI+Threads: runtime contention and remedies. - Abdelhalim Amer; Huiwei Lu; Yanjie Wei; Pavan Balaji; Satoshi Matsuoka (PPoPP, 2015)

Personalized clinical data screening: Special issue on health informatics. - Miaomiao Zhao; Yunpeng Cai; Jiankui He; Guanyu Wang; Dongqing Wei; Yanjie Wei; Caiwan Zhang; Fengfeng Zhou (Comput. Biol. Medicine, 2015)

SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Extreme Scale. - Jintao Meng 001; Sangmin Seo; Pavan Balaji; Yanjie Wei; Bingqiang Wang; Shengzhong Feng (ICPP, 2016)

A hybrid method for splice site prediction based on Markov model and codon information. - Dan Wei; Yin Peng; Yanjie Wei; Qingshan Jiang; Jinglong Fang (Int. J. Data Min. Bioinform., 2016)

Any-Time Methods for Time-Series Prediction with Missing Observations. - Yanjie Wei; Hongzhi Wang 001; Shengfei Shi; Hong Gao 001; Jianzhong Li 001 (BigData Congress, 2017)

Scalable Assembly for Massive Genomic Graphs. - Jintao Meng 001; Ning Guo; Jianqiu Ge; Yanjie Wei; Pavan Balaji; Bingqiang Wang (CCGrid, 2017)

Bloomfish: A Highly Scalable Distributed K-mer Counting Framework. - Tao Gao; Yanfei Guo; Yanjie Wei; Bingqiang Wang; Yutong Lu; Pietro Cicotti; Pavan Balaji; Michela Taufer (ICPADS, 2017)

K-mer Counting for Genomic Big Data. - Jianqiu Ge; Ning Guo; Jintao Meng 001; Bingqiang Wang; Pavan Balaji; Shengzhong Feng; Jiaxiu Zhou; Yanjie Wei (BigData Congress, 2018)

Ensemble Learning Based Gender Recognition from Physiological Signals. - Huiling Zhang; Ning Guo; Guangyuan Liu; Junhao Hu; Jiaxiu Zhou; Shengzhong Feng; Yanjie Wei (BigData Congress, 2018)

SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. - Kai Xu; Robin Kobus; Yuandong Chan; Ping Gao 005; Xiangxu Meng; Yanjie Wei; Bertil Schmidt; Weiguo Liu (ICPP, 2018)

Lock Contention Management in Multithreaded MPI. - Abdelhalim Amer; Huiwei Lu; Pavan Balaji; Milind Chabbi; Yanjie Wei; Jeff R. Hammond; Satoshi Matsuoka (ACM Trans. Parallel Comput., 2018)

Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. - Zekun Yin; Tianyu Zhang; André Müller; Hui Liu; Yanjie Wei; Bertil Schmidt; Weiguo Liu (HPCC/SmartCity/DSS, 2019)

An Auto Code Generator for Stencil on SW26010. - Xiaomin Zhu; Yunhui Zeng; Yanjie Wei; Shengzhong Feng; Weiguo Liu; Pavan Balaji (HPCC/SmartCity/DSS, 2019)

Efficient Gene Assembly and Identification for Many Genome Samples. - Zhichun Zheng; Ning Guo; Konda Mani Saravanan; Yanjie Wei (ICCC, 2019)

Autoregressive-Model-Based Methods for Online Time Series Prediction with Missing Values: an Experimental Evaluation. - Xi Chen; Hongzhi Wang 001; Yanjie Wei; Jianzhong Li 001; Hong Gao 001 (CoRR, 2019)

A novel machine learning based approach for iPS progenitor cell identification. - Haishan Zhang; Ximing Shao; Yin Peng; Yanning Teng; Konda Mani Saravanan; Huiling Zhang; Hongchang Li; Yanjie Wei (PLoS Comput. Biol., 2019)

Protein Interresidue Contact Prediction Based on Deep Learning and Massive Features from Multi-sequence Alignment. - Huiling Zhang; Hao Wu; Hing-Fung Ting; Yanjie Wei (PDCAT, 2020)

A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro. - Haiping Zhang; Yang Yang; Junxin Li; Min Wang; Konda Mani Saravanan; Jinli Wei; Justin Tze-Yang Ng; Md. Tofazzal Hossain; Maoxuan Liu; Huiling Zhang; Xiaohu Ren; Yi Pan 001; et al. (PLoS Comput. Biol., 2020)

An Infrared Defect Sizing Method Based on Enhanced Phase Images. - Yanjie Wei; Zhilong Su; Shuangshuang Mao; Dongsheng Zhang (Sensors, 2020)

A novel virtual drug screening pipeline with deep-leaning as core component identifies inhibitor of pancreatic alpha-amylase. - Haiping Zhang; Tingting Zhang; Konda Mani Saravanan; Linbu Liao; Hao Wu 003; Haishan Zhang; Huiling Zhang; Yi Pan 001; Xuli Wu; Yanjie Wei (BIBM, 2021)

The Classification System and Biomarkers for Autism Spectrum Disorder: A Machine Learning Approach. - Zhongyang Dai; Haishan Zhang; Feifei Lin; Shengzhong Feng; Yanjie Wei; Jiaxiu Zhou (ISBRA, 2021)

An Efficient Greedy Incremental Sequence Clustering Algorithm. - Zhen Ju; Huiling Zhang; Jingtao Meng; Jingjing Zhang; Xuelei Li; Jianping Fan 002; Yi Pan 001; Weiguo Liu; Yanjie Wei (ISBRA, 2021)

RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. - Zekun Yin; Xiaoming Xu 004; Jinxiao Zhang; Yanjie Wei; Bertil Schmidt; Weiguo Liu (Bioinform., 2021)

RabbitQC: high-speed scalable quality control for sequencing data. - Zekun Yin; Hao Zhang 142; Meiyang Liu; Wen Zhang; Honglei Song; Haidong Lan; Yanjie Wei; Beifang Niu; Bertil Schmidt; Weiguo Liu (Bioinform., 2021)

Evaluation of residue-residue contact prediction methods: From retrospective to prospective. - Huiling Zhang; Zhendong Bei; Wenhui Xi; Min Hao 002; Zhen Ju; Konda Mani Saravanan; Haiping Zhang; Ning Guo; Yanjie Wei (PLoS Comput. Biol., 2021)

RabbitQCPlus: More Efficient Quality Control for Sequencing Data. - Lifeng Yan; Zekun Yin; Hao Zhang 142; Zhan Zhao; Mingkai Wang; André Müller; Robin Kobus; Yanjie Wei; Beifang Niu; Bertil Schmidt; Weiguo Liu (BIBM, 2022)

Simulating Spiking Neural Networks Based on SW26010pro. - Zhichao Wang; Xuelei Li; Jintao Meng 001; Yi Pan 001; Yanjie Wei (ISBRA, 2022)

Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components. - Haiping Zhang; Konda Mani Saravanan; Yang Yang; Yanjie Wei; Yi Pan 001; John Z. H. Zhang (Briefings Bioinform., 2022)

Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term. - Liangzhen Zheng; Jintao Meng 001; Kai Jiang; Haidong Lan; Zechen Wang; Mingzhi Lin; Weifeng Li; Hongwei Guo; Yanjie Wei; Yuguang Mu (Briefings Bioinform., 2022)

RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. - Hao Zhang 142; Qixin Chang; Zekun Yin; Xiaoming Xu 004; Yanjie Wei; Bertil Schmidt; Weiguo Liu (Bioinform., 2022)

Identification of Autism spectrum disorder based on a novel feature selection method and Variational Autoencoder. - Fangyu Zhang; Yanjie Wei; Jin Liu 012; Yanlin Wang 003; Wenhui Xi; Yi Pan 001 (Comput. Biol. Medicine, 2022)

Meta-data Study in Autism Spectrum Disorder Classification Based on Structural MRI. - Ruimin Ma; Yanlin Wang 003; Yanjie Wei; Yi Pan 001 (CoRR, 2022)

nGIA: A novel Greedy Incremental Alignment based algorithm for gene sequence clustering. - Zhen Ju; Huiling Zhang; Jintao Meng 001; Jingjing Zhang; Jianping Fan 002; Yi Pan 001; Weiguo Liu; Xuelei Li; Yanjie Wei (Future Gener. Comput. Syst., 2022)

circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome. - Wenliang Zhang; Yang Liu; Zhuochao Min; Guodong Liang; Jing Mo; Zhen Ju; Binghui Zeng; Wen Guan; Yan Zhang; Jianliang Chen; Qianshen Zhang; Hanguang Li; et al. (Nucleic Acids Res., 2022)

COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale. - Wenliang Zhang; Yan Zhang; Zhuochao Min; Jing Mo; Zhen Ju; Wen Guan; Binghui Zeng; Yang Liu; Jianliang Chen; Qianshen Zhang; Hanguang Li; Chunxia Zeng; et al. (Nucleic Acids Res., 2022)

Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. - Jintao Meng 001; Chen Zhuang; Peng Chen 035; Mohamed Wahib; Bertil Schmidt; Xiao Wang 004; Haidong Lan; Dou Wu; Minwen Deng; Yanjie Wei; Shengzhong Feng (IEEE Trans. Parallel Distributed Syst., 2022)

A Novel Deep Learning Approach Featuring Graph-Based Algorithm for Cell Segmentation and Tracking. - Keliang Zhao; Jovial Niyogisubizo; Linxia Xiao; Yi Pan 001; Dongqing Wei; Didi Rosiyadi; Yanjie Wei (BIBM, 2023)

Complex Time Series Analysis Based on Conditional Random Fields. - Yanjie Wei; Haifeng Guo; Donghua Yang; Mengmeng Li; Bo Zheng; Hongzhi Wang 001 (ICPCSEE (1), 2023)

PCPI: Prediction of circRNA and Protein Interaction Using Machine Learning Method. - Md. Tofazzal Hossain; Md. Selim Reza; Xuelei Li; Yin Peng; Shengzhong Feng; Yanjie Wei (ISBRA, 2023)

Identification and Functional Annotation of circRNAs in Neuroblastoma Based on Bioinformatics. - Jingjing Zhang; Md. Tofazzal Hossain; Zhen Ju; Wenhui Xi; Yanjie Wei (ISBRA, 2023)

Autism Spectrum Disorder Classification in Children based on Structural MRI Features Extracted using Contrastive Variational Autoencoder. - Ruimin Ma; Ruitao Xie; Yanlin Wang 003; Jintao Meng 001; Yanjie Wei; Wenhui Xi; Yi Pan 001 (CoRR, 2023)

Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. - Zhipeng Cai 001; Min Li 007; Pavel Skums; Yanjie Wei (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. - Hao Zhang 142; Honglei Song; Xiaoming Xu 004; Qixin Chang; Mingkai Wang; Yanjie Wei; Zekun Yin; Bertil Schmidt; Weiguo Liu (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function. - Zechen Wang; Liangzhen Zheng; Sheng Wang 001; Mingzhi Lin; Zhihao Wang; Adams Wai-Kin Kong; Yuguang Mu; Yanjie Wei; Weifeng Li (Briefings Bioinform., 2023)

Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. - Haiping Zhang; Konda Mani Saravanan; Yanjie Wei; Yang Jiao; Yang Yang; Yi Pan 001; Xuli Wu; John Z. H. Zhang (J. Chem. Inf. Model., 2023)

Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design. - Hilbert Yuen In Lam; Robbe Pincket; Hao Han; Xing Er Ong; Zechen Wang; Jamie Hinks; Yanjie Wei; Weifeng Li; Liangzhen Zheng; Yuguang Mu (Nat. Mac. Intell., 2023)

JCcirc: circRNA full-length sequence assembly through integrated junction contigs. - Jingjing Zhang; Huiling Zhang; Zhen Ju; Yin Peng; Yi Pan 001; Wenhui Xi; Yanjie Wei (Briefings Bioinform., 2023)

SWsnn: A Novel Simulator for Spiking Neural Networks. - Zhichao Wang; Xuelei Li; Jianping Fan 002; Jintao Meng 001; Zhenli Lin; Yi Pan 001; Yanjie Wei (J. Comput. Biol., 2023)

The Algorithms of Predicting DNA Binding Site with Combined Feature Encoding and Optimum Decision. - Zhendong Liu; Jun Liu; Dongqing Wei; Yanjie Wei; Rongjun Man (BCB, 2024)

Meta-data Study in Autism Spectrum Disorder Classification Based on Structural MRI. - Ruimin Ma; Ying Huang; Yi Pan 001; Yanlin Wang 003; Yanjie Wei (BCB, 2024)

Deep Learning for Autism Spectrum Disorder Identification Based on Children's Facial Images: A Multi-Feature Fusion Perspective. - Wondimagegn Bekele Munto; Mengying Zhou; Yi Pan 001; Yanjie Wei; Wenhui Xi (BCB, 2024)

Missense Mutation Effect Prediction using Categorical Boosting Optimized with Sparrow Search Algorithm. - Huiling Zhang; Jingjing Zhang; Ganzhang Zheng; Xiaochuan Chen; Zaoqing Liang; Haiyan Wang; Yanjie Wei (BCB, 2024)

CCVAN: A Conditional Molecular Generation Model based on conditional VAE and Wasserstein GAN. - Jianqiang Zheng; Ziqi Xu 003; Junwen Huang; Xiaochuan Chen; Yuetong Li; Yanjie Wei; Huiling Zhang (BCB, 2024)

An In-Depth Assessment of Sequence Clustering Software in Bioinformatics. - Zhen Ju; Mingyu Wang; Xuelei Li; Jintao Meng 001; Wenhui Xi; Yanjie Wei (ISBRA (1), 2024)

PmmNDD: Predicting the Pathogenicity of Missense Mutations in Neurodegenerative Diseases via Ensemble Learning. - Xijian Li; Ying Huang; Runxuan Tang; Guangcheng Xiao; Xiaochuan Chen; Ruilin He; Zhaolei Zhang; Jiana Luo; Yanjie Wei; Yijun Mao; Huiling Zhang (ISBRA (3), 2024)

autoGEMM: Pushing the Limits of Irregular Matrix Multiplication on Arm Architectures. - Du Wu; Jintao Meng 001; Wenxi Zhu; Minwen Deng; Xiao Wang 004; Tao Luo 014; Mohamed Wahib; Yanjie Wei (SC, 2024)

A new paradigm for applying deep learning to protein-ligand interaction prediction. - Zechen Wang; Sheng Wang 001; Yangyang Li; Jingjing Guo; Yanjie Wei; Yuguang Mu; Liangzhen Zheng; Weifeng Li (Briefings Bioinform., 2024)

Distributed Heterogeneous Spiking Neural Network Simulator Using Sunway Accelerators. - Xuelei Li; Zhichao Wang; Yi Pan 001; Jintao Meng 001; Shengzhong Feng; Yanjie Wei (Big Data Min. Anal., 2024)

Autism Spectrum Disorder Classification with Interpretability in Children Based on Structural MRI Features Extracted Using Contrastive Variational Autoencoder. - Ruimin Ma; Ruitao Xie; Yanlin Wang 003; Jintao Meng 001; Yanjie Wei; Yunpeng Cai; Wenhui Xi; Yi Pan 001 (Big Data Min. Anal., 2024)

Editorial: Special Section on Challenges and Opportunities in Biomedical Big Data Analysis: From Large Language Models to Clinical Applications. - Yanjie Wei; Huiling Zhang; Zhipeng Cai 001; Fa Zhang 001; Zhaolei Zhang (Big Data Min. Anal., 2024)

Dual-View Pyramid Pooling in Deep Neural Networks for Improved Medical Image Classification and Confidence Calibration. - Xiaoqing Zhang; Qiushi Nie; Zunjie Xiao; Jilu Zhao; Xiao Wu; Pengxin Guo; Runzhi Li; Jin Liu; Yanjie Wei; Yi Pan (CoRR, 2024)

Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modeling. - Zhihao Wang; Fan Zhou; Zechen Wang; Qiuyue Hu; Yong-Qiang Li; Sheng Wang; Yanjie Wei; Liangzhen Zheng; Weifeng Li; Xiangda Peng (J. Chem. Inf. Model., 2024)

SeedHit: A GPU Friendly Pre-Align Filtering Algorithm. - Zhen Ju; Jingjing Zhang; Xuelei Li; Jintao Meng 001; Yanjie Wei (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

ParaCoder: Parallel Code Generation with Large Language Model. - Xiaowen Huang; Xu Zhang; Lvfang Tao; Renjie Mao; Nan Zhou; Wenxi Zhu; Minwen Deng; Jintao Meng 001; Yanjie Wei; Amelie Chi Zhou; Bingqiang Wang; Shengzhong Feng (FCPC@PPOPP, 2025)

NM-SpMM: Accelerating Matrix Multiplication Using N: M Sparsity with GPGPU. - Cong Ma; Du Wu; Zhelang Deng; Jiang Chen; Xiaowen Huang; Jintao Meng 001; Wenxi Zhu; Bingqiang Wang; Amelie Chi Zhou; Peng Chen 035; Minwen Deng; Yanjie Wei; et al. (IPDPS, 2025)

An Efficient Parallel List Ranking Algorithm for Graph Concatenation on BSP Graph System. - Maocheng Cao; Zhelang Deng; Qiucheng Miao; Jintao Meng 001; Yanjie Wei; Jiefeng Cheng (ISBRA (2), 2025)

AlloPED: Leveraging Protein Language Models and Structure Features for Allosteric Site Prediction. - Xiaochuan Chen; Jianqiang Zheng; Zhenni Huang; Ziqi Xu 003; Junye Huang; Yueyi Tan; Yanjie Wei; Huiling Zhang (ISBRA (2), 2025)

Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-Based Cell Segmentation in Microscopy Images. - Jovial Niyogisubizo; Keliang Zhao; Jintao Meng 001; Yi Pan 001; Didi Rosiyadi; Yanjie Wei (J. Comput. Biol., 2025)

A New Benchmark and Algorithm for Clothes-Changing Video Person Re-Identification. - Likai Wang 002; Xiangqun Zhang 003; Ruize Han; Yanjie Wei; Song Wang 002; Wei Feng 005 (IEEE Trans. Inf. Forensics Secur., 2025)

NM-SpMM: Accelerating Matrix Multiplication Using N:M Sparsity with GPGPU. - Cong Ma; Du Wu; Zhelang Deng; Jiang Chen; Xiaowen Huang; Jintao Meng 001; Wenxi Zhu; Bingqiang Wang; Amelie Chi Zhou; Peng Chen 035; Minwen Deng; Yanjie Wei; et al. (CoRR, 2025)

Adaptive Jailbreaking Strategies Based on the Semantic Understanding Capabilities of Large Language Models. - Mingyu Yu; Wei Wang; Yanjie Wei; Sujuan Qin (CoRR, 2025)

From indoor to outdoor: Unsupervised domain adaptive gait recognition. - Likai Wang 002; Wei Feng 005; Ruize Han; Xiangqun Zhang 003; Yanjie Wei; Song Wang 002 (Pattern Recognit., 2026)