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2020 – today
- 2025
[j36]Jovial Niyogisubizo
, Keliang Zhao, Jintao Meng, Yi Pan, Didi Rosiyadi, Yanjie Wei:
Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-Based Cell Segmentation in Microscopy Images. J. Comput. Biol. 32(2): 225-237 (2025)- [j35]Likai Wang, Xiangqun Zhang, Ruize Han, Yanjie Wei, Song Wang, Wei Feng:
A New Benchmark and Algorithm for Clothes-Changing Video Person Re-Identification. IEEE Trans. Inf. Forensics Secur. 20: 1993-2005 (2025) - [c35]Xiaowen Huang, Xu Zhang, Lvfang Tao, Renjie Mao, Nan Zhou, Wenxi Zhu, Minwen Deng, Jintao Meng, Yanjie Wei, Amelie Chi Zhou, Bingqiang Wang, Shengzhong Feng:
ParaCoder: Parallel Code Generation with Large Language Model. FCPC@PPOPP 2025: 1-7 - [i6]Cong Ma, Du Wu, Zhelang Deng, Jiang Chen, Xiaowen Huang, Jintao Meng, Wenxi Zhu, Bingqiang Wang, Amelie Chi Zhou, Peng Chen, Minwen Deng, Yanjie Wei, Shengzhong Feng, Yi Pan:
NM-SpMM: Accelerating Matrix Multiplication Using N:M Sparsity with GPGPU. CoRR abs/2503.01253 (2025) - 2024
- [j34]Zechen Wang, Sheng Wang, Yangyang Li, Jingjing Guo, Yanjie Wei, Yuguang Mu, Liangzhen Zheng, Weifeng Li:
A new paradigm for applying deep learning to protein-ligand interaction prediction. Briefings Bioinform. 25(3) (2024) - [j33]Ruimin Ma, Ruitao Xie, Yanlin Wang, Jintao Meng, Yanjie Wei, Yunpeng Cai, Wenhui Xi, Yi Pan:
Autism Spectrum Disorder Classification with Interpretability in Children Based on Structural MRI Features Extracted Using Contrastive Variational Autoencoder. Big Data Min. Anal. 7(3): 781-793 (2024) - [j32]Yanjie Wei, Huiling Zhang, Zhipeng Cai, Fa Zhang, Zhaolei Zhang:
Editorial: Special Section on Challenges and Opportunities in Biomedical Big Data Analysis: From Large Language Models to Clinical Applications. Big Data Min. Anal. 7(4): 1114-1115 (2024) - [j31]Xuelei Li, Zhichao Wang, Yi Pan, Jintao Meng, Shengzhong Feng, Yanjie Wei:
Distributed Heterogeneous Spiking Neural Network Simulator Using Sunway Accelerators. Big Data Min. Anal. 7(4): 1301-1320 (2024) - [j30]Zhihao Wang, Fan Zhou, Zechen Wang, Qiuyue Hu, Yong-Qiang Li, Sheng Wang, Yanjie Wei, Liangzhen Zheng, Weifeng Li, Xiangda Peng:
Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modeling. J. Chem. Inf. Model. 64(15): 6205-6215 (2024) - [j29]Zhen Ju, Jingjing Zhang, Xuelei Li, Jintao Meng, Yanjie Wei:
SeedHit: A GPU Friendly Pre-Align Filtering Algorithm. IEEE ACM Trans. Comput. Biol. Bioinform. 21(6): 1794-1802 (2024) - [c34]Zhendong Liu, Jun Liu, Dongqing Wei, Yanjie Wei, Rongjun Man:
The Algorithms of Predicting DNA Binding Site with Combined Feature Encoding and Optimum Decision. BCB 2024: 39:1-39:8 - [c33]Wondimagegn Bekele Munto, Mengying Zhou, Yi Pan, Yanjie Wei, Wenhui Xi:
Deep Learning for Autism Spectrum Disorder Identification Based on Children's Facial Images: A Multi-Feature Fusion Perspective. BCB 2024: 74:1 - [c32]Ruimin Ma, Ying Huang, Yi Pan, Yanlin Wang, Yanjie Wei:
Meta-data Study in Autism Spectrum Disorder Classification Based on Structural MRI. BCB 2024: 75:1 - [c31]Jianqiang Zheng, Ziqi Xu, Junwen Huang, Xiaochuan Chen, Yuetong Li, Yanjie Wei, Huiling Zhang:
CCVAN: A Conditional Molecular Generation Model based on conditional VAE and Wasserstein GAN. BCB 2024: 87:1 - [c30]Huiling Zhang, Jingjing Zhang, Ganzhang Zheng, Xiaochuan Chen, Zaoqing Liang, Haiyan Wang, Yanjie Wei:
Missense Mutation Effect Prediction using Categorical Boosting Optimized with Sparrow Search Algorithm. BCB 2024: 98:1 - [c29]Xijian Li, Ying Huang, Runxuan Tang, Guangcheng Xiao, Xiaochuan Chen, Ruilin He, Zhaolei Zhang, Jiana Luo, Yanjie Wei, Yijun Mao, Huiling Zhang:
PmmNDD: Predicting the Pathogenicity of Missense Mutations in Neurodegenerative Diseases via Ensemble Learning. ISBRA (3) 2024: 64-75 - [c28]Zhen Ju, Mingyu Wang, Xuelei Li, Jintao Meng, Wenhui Xi, Yanjie Wei:
An In-Depth Assessment of Sequence Clustering Software in Bioinformatics. ISBRA (1) 2024: 359-370 - [c27]Du Wu, Jintao Meng, Wenxi Zhu, Minwen Deng, Xiao Wang, Tao Luo, Mohamed Wahib, Yanjie Wei:
autoGEMM: Pushing the Limits of Irregular Matrix Multiplication on Arm Architectures. SC 2024: 21 - [i5]Xiaoqing Zhang, Qiushi Nie, Zunjie Xiao, Jilu Zhao, Xiao Wu, Pengxin Guo, Runzhi Li, Jin Liu, Yanjie Wei, Yi Pan:
Dual-View Pyramid Pooling in Deep Neural Networks for Improved Medical Image Classification and Confidence Calibration. CoRR abs/2408.02906 (2024) - 2023
- [j28]Zechen Wang, Liangzhen Zheng, Sheng Wang, Mingzhi Lin, Zhihao Wang, Adams Wai-Kin Kong, Yuguang Mu, Yanjie Wei, Weifeng Li:
A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function. Briefings Bioinform. 24(1) (2023) - [j27]Jingjing Zhang, Huiling Zhang, Zhen Ju, Yin Peng, Yi Pan, Wenhui Xi, Yanjie Wei:
JCcirc: circRNA full-length sequence assembly through integrated junction contigs. Briefings Bioinform. 24(6) (2023) - [j26]Zhichao Wang, Xuelei Li, Jianping Fan, Jintao Meng, Zhenli Lin, Yi Pan, Yanjie Wei:
SWsnn: A Novel Simulator for Spiking Neural Networks. J. Comput. Biol. 30(9): 951-960 (2023) - [j25]Haiping Zhang, Konda Mani Saravanan, Yanjie Wei, Yang Jiao, Yang Yang, Yi Pan, Xuli Wu, John Z. H. Zhang:
Deep Learning-Based Bioactive Therapeutic Peptide Generation and Screening. J. Chem. Inf. Model. 63(3): 835-845 (2023) - [j24]Hilbert Yuen In Lam, Robbe Pincket, Hao Han, Xing Er Ong, Zechen Wang, Jamie Hinks, Yanjie Wei, Weifeng Li, Liangzhen Zheng, Yuguang Mu:
Application of variational graph encoders as an effective generalist algorithm in computer-aided drug design. Nat. Mac. Intell. 5(7): 754-764 (2023) - [j23]Hao Zhang, Honglei Song, Xiaoming Xu, Qixin Chang, Mingkai Wang, Yanjie Wei, Zekun Yin, Bertil Schmidt, Weiguo Liu:
RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. IEEE ACM Trans. Comput. Biol. Bioinform. 20(3): 2341-2348 (2023) - [j22]Zhipeng Cai, Min Li, Pavel Skums, Yanjie Wei:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 20(6): 3329-3331 (2023) - [c26]Keliang Zhao, Jovial Niyogisubizo, Linxia Xiao, Yi Pan, Dongqing Wei, Didi Rosiyadi, Yanjie Wei:
A Novel Deep Learning Approach Featuring Graph-Based Algorithm for Cell Segmentation and Tracking. BIBM 2023: 1752-1757 - [c25]Yanjie Wei, Haifeng Guo, Donghua Yang, Mengmeng Li, Bo Zheng, Hongzhi Wang:
Complex Time Series Analysis Based on Conditional Random Fields. ICPCSEE (1) 2023: 221-232 - [c24]Md. Tofazzal Hossain, Md. Selim Reza, Xuelei Li, Yin Peng, Shengzhong Feng, Yanjie Wei:
PCPI: Prediction of circRNA and Protein Interaction Using Machine Learning Method. ISBRA 2023: 97-106 - [c23]Jingjing Zhang, Md. Tofazzal Hossain, Zhen Ju, Wenhui Xi, Yanjie Wei:
Identification and Functional Annotation of circRNAs in Neuroblastoma Based on Bioinformatics. ISBRA 2023: 351-363 - [i4]Ruimin Ma, Ruitao Xie, Yanlin Wang, Jintao Meng, Yanjie Wei, Wenhui Xi, Yi Pan:
Autism Spectrum Disorder Classification in Children based on Structural MRI Features Extracted using Contrastive Variational Autoencoder. CoRR abs/2307.00976 (2023) - 2022
- [j21]Liangzhen Zheng, Jintao Meng, Kai Jiang, Haidong Lan, Zechen Wang, Mingzhi Lin, Weifeng Li, Hongwei Guo, Yanjie Wei, Yuguang Mu:
Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term. Briefings Bioinform. 23(3) (2022) - [j20]Haiping Zhang, Konda Mani Saravanan, Yang Yang, Yanjie Wei, Yi Pan, John Z. H. Zhang:
Generating and screening de novo compounds against given targets using ultrafast deep learning models as core components. Briefings Bioinform. 23(4) (2022) - [j19]Hao Zhang, Qixin Chang, Zekun Yin, Xiaoming Xu, Yanjie Wei, Bertil Schmidt, Weiguo Liu:
RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. Bioinform. 38(10): 2932-2933 (2022) - [j18]Fangyu Zhang, Yanjie Wei, Jin Liu, Yanlin Wang, Wenhui Xi, Yi Pan:
Identification of Autism spectrum disorder based on a novel feature selection method and Variational Autoencoder. Comput. Biol. Medicine 148: 105854 (2022) - [j17]Zhen Ju, Huiling Zhang, Jintao Meng, Jingjing Zhang, Jianping Fan, Yi Pan, Weiguo Liu, Xuelei Li, Yanjie Wei:
nGIA: A novel Greedy Incremental Alignment based algorithm for gene sequence clustering. Future Gener. Comput. Syst. 136: 221-230 (2022) - [j16]Wenliang Zhang, Yang Liu, Zhuochao Min, Guodong Liang, Jing Mo, Zhen Ju, Binghui Zeng, Wen Guan, Yan Zhang, Jianliang Chen, Qianshen Zhang, Hanguang Li, Chunxia Zeng, Yanjie Wei, Godfrey Chi-Fung Chan:
circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome. Nucleic Acids Res. 50(D1): 83-92 (2022) - [j15]Wenliang Zhang, Yan Zhang, Zhuochao Min, Jing Mo, Zhen Ju, Wen Guan, Binghui Zeng, Yang Liu, Jianliang Chen, Qianshen Zhang, Hanguang Li, Chunxia Zeng, Yanjie Wei, Godfrey Chi-Fung Chan:
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale. Nucleic Acids Res. 50(D1): 747-757 (2022) - [j14]Jintao Meng, Chen Zhuang, Peng Chen, Mohamed Wahib, Bertil Schmidt, Xiao Wang, Haidong Lan, Dou Wu, Minwen Deng, Yanjie Wei, Shengzhong Feng:
Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. IEEE Trans. Parallel Distributed Syst. 33(11): 2885-2899 (2022) - [c22]Lifeng Yan, Zekun Yin, Hao Zhang, Zhan Zhao, Mingkai Wang, André Müller, Robin Kobus, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu:
RabbitQCPlus: More Efficient Quality Control for Sequencing Data. BIBM 2022: 619-626 - [c21]Zhichao Wang, Xuelei Li, Jintao Meng, Yi Pan, Yanjie Wei:
Simulating Spiking Neural Networks Based on SW26010pro. ISBRA 2022: 356-368 - [i3]Fangyu Zhang, Yanjie Wei, Jin Liu, Yanlin Wang, Wenhui Xi, Yi Pan:
Identification of Autism spectrum disorder based on a novel feature selection method and Variational Autoencoder. CoRR abs/2204.03654 (2022) - [i2]Ruimin Ma, Yanlin Wang, Yanjie Wei, Yi Pan:
Meta-data Study in Autism Spectrum Disorder Classification Based on Structural MRI. CoRR abs/2206.05052 (2022) - 2021
- [j13]Zekun Yin, Hao Zhang, Meiyang Liu, Wen Zhang, Honglei Song, Haidong Lan, Yanjie Wei, Beifang Niu, Bertil Schmidt, Weiguo Liu:
RabbitQC: high-speed scalable quality control for sequencing data. Bioinform. 37(4): 573-574 (2021) - [j12]Zekun Yin, Xiaoming Xu, Jinxiao Zhang, Yanjie Wei, Bertil Schmidt, Weiguo Liu:
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. Bioinform. 37(6): 873-875 (2021) - [j11]Huiling Zhang, Zhendong Bei, Wenhui Xi, Min Hao, Zhen Ju, Konda Mani Saravanan, Haiping Zhang, Ning Guo, Yanjie Wei:
Evaluation of residue-residue contact prediction methods: From retrospective to prospective. PLoS Comput. Biol. 17(5) (2021) - [c20]Haiping Zhang, Tingting Zhang, Konda Mani Saravanan, Linbu Liao, Hao Wu, Haishan Zhang, Huiling Zhang, Yi Pan, Xuli Wu, Yanjie Wei:
A novel virtual drug screening pipeline with deep-leaning as core component identifies inhibitor of pancreatic alpha-amylase. BIBM 2021: 104-111 - [c19]Zhongyang Dai, Haishan Zhang, Feifei Lin, Shengzhong Feng, Yanjie Wei, Jiaxiu Zhou:
The Classification System and Biomarkers for Autism Spectrum Disorder: A Machine Learning Approach. ISBRA 2021: 289-299 - [c18]Zhen Ju, Huiling Zhang, Jingtao Meng, Jingjing Zhang, Xuelei Li, Jianping Fan, Yi Pan, Weiguo Liu, Yanjie Wei:
An Efficient Greedy Incremental Sequence Clustering Algorithm. ISBRA 2021: 596-607 - [e1]Yanjie Wei, Min Li, Pavel Skums, Zhipeng Cai:
Bioinformatics Research and Applications - 17th International Symposium, ISBRA 2021, Shenzhen, China, November 26-28, 2021, Proceedings. Lecture Notes in Computer Science 13064, Springer 2021, ISBN 978-3-030-91414-1 [contents] - 2020
- [j10]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, Yin Peng, Yi Shi, Xiaochun Wan, Yingxia Liu, Yanjie Wei:
A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro. PLoS Comput. Biol. 16(12) (2020) - [j9]Yanjie Wei, Zhilong Su, Shuangshuang Mao, Dongsheng Zhang:
An Infrared Defect Sizing Method Based on Enhanced Phase Images. Sensors 20(13): 3626 (2020) - [c17]Huiling Zhang, Hao Wu, Hing-Fung Ting, Yanjie Wei:
Protein Interresidue Contact Prediction Based on Deep Learning and Massive Features from Multi-sequence Alignment. PDCAT 2020: 219-228
2010 – 2019
- 2019
- [j8]Haishan Zhang, Ximing Shao, Yin Peng, Yanning Teng, Konda Mani Saravanan, Huiling Zhang, Hongchang Li, Yanjie Wei:
A novel machine learning based approach for iPS progenitor cell identification. PLoS Comput. Biol. 15(12) (2019) - [c16]Zekun Yin, Tianyu Zhang, André Müller, Hui Liu, Yanjie Wei, Bertil Schmidt, Weiguo Liu:
Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. HPCC/SmartCity/DSS 2019: 168-176 - [c15]Xiaomin Zhu, Yunhui Zeng, Yanjie Wei, Shengzhong Feng, Weiguo Liu, Pavan Balaji:
An Auto Code Generator for Stencil on SW26010. HPCC/SmartCity/DSS 2019: 182-190 - [c14]Zhichun Zheng, Ning Guo, Konda Mani Saravanan, Yanjie Wei:
Efficient Gene Assembly and Identification for Many Genome Samples. ICCC 2019: 1-11 - [i1]Xi Chen, Hongzhi Wang, Yanjie Wei, Jianzhong Li, Hong Gao:
Autoregressive-Model-Based Methods for Online Time Series Prediction with Missing Values: an Experimental Evaluation. CoRR abs/1908.06729 (2019) - 2018
- [j7]Abdelhalim Amer, Huiwei Lu, Pavan Balaji, Milind Chabbi, Yanjie Wei, Jeff R. Hammond, Satoshi Matsuoka:
Lock Contention Management in Multithreaded MPI. ACM Trans. Parallel Comput. 5(3): 12:1-12:21 (2018) - [c13]Jianqiu Ge, Ning Guo, Jintao Meng, Bingqiang Wang, Pavan Balaji, Shengzhong Feng, Jiaxiu Zhou, Yanjie Wei:
K-mer Counting for Genomic Big Data. BigData Congress 2018: 345-351 - [c12]Huiling Zhang, Ning Guo, Guangyuan Liu, Junhao Hu, Jiaxiu Zhou, Shengzhong Feng, Yanjie Wei:
Ensemble Learning Based Gender Recognition from Physiological Signals. BigData Congress 2018: 352-359 - [c11]Kai Xu, Robin Kobus, Yuandong Chan, Ping Gao, Xiangxu Meng, Yanjie Wei, Bertil Schmidt, Weiguo Liu:
SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. ICPP 2018: 39:1-39:10 - 2017
- [c10]Yanjie Wei, Hongzhi Wang, Shengfei Shi, Hong Gao, Jianzhong Li:
Any-Time Methods for Time-Series Prediction with Missing Observations. BigData Congress 2017: 427-430 - [c9]Jintao Meng, Ning Guo, Jianqiu Ge, Yanjie Wei, Pavan Balaji, Bingqiang Wang:
Scalable Assembly for Massive Genomic Graphs. CCGrid 2017: 665-670 - [c8]Tao Gao, Yanfei Guo, Yanjie Wei, Bingqiang Wang, Yutong Lu, Pietro Cicotti, Pavan Balaji, Michela Taufer:
Bloomfish: A Highly Scalable Distributed K-mer Counting Framework. ICPADS 2017: 170-179 - 2016
- [j6]Dan Wei, Yin Peng, Yanjie Wei, Qingshan Jiang, Jinglong Fang:
A hybrid method for splice site prediction based on Markov model and codon information. Int. J. Data Min. Bioinform. 16(4): 345-362 (2016) - [c7]Jintao Meng, Sangmin Seo, Pavan Balaji, Yanjie Wei, Bingqiang Wang, Shengzhong Feng:
SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Extreme Scale. ICPP 2016: 195-204 - 2015
- [j5]Miaomiao Zhao, Yunpeng Cai, Jiankui He, Guanyu Wang, Dongqing Wei, Yanjie Wei, Caiwan Zhang, Fengfeng Zhou:
Personalized clinical data screening: Special issue on health informatics. Comput. Biol. Medicine 61: 161-162 (2015) - [c6]Jintao Meng, Yanjie Wei, Sangmin Seo, Pavan Balaji:
SWAP-Assembler 2: Scalable Genome Assembler towards Millions of Cores - Practice and Experience. CCGRID 2015: 769-772 - [c5]Abdelhalim Amer, Huiwei Lu, Yanjie Wei, Pavan Balaji, Satoshi Matsuoka:
MPI+Threads: runtime contention and remedies. PPoPP 2015: 239-248 - 2014
- [j4]Jintao Meng, Bingqiang Wang, Yanjie Wei, Shengzhong Feng, Pavan Balaji:
SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores. BMC Bioinform. 15(S-9): S2 (2014) - [c4]Shuqiang Wang, Jinxing Hu, Yanyan Shen, Ling Yin, Yanjie Wei:
Modeling and analysis of gene regulatory networks with a Bayesian-driven approach. ISCIT 2014: 289-293 - 2013
- [j3]Jintao Meng, Jian-Rui Yuan, Shengzhong Feng, Yanjie Wei:
An Energy Efficient Clustering Scheme for Data Aggregation in Wireless Sensor Networks. J. Comput. Sci. Technol. 28(3): 564-573 (2013) - 2012
- [j2]Dan Wei, Qingshan Jiang, Yanjie Wei, Shengrui Wang:
A novel hierarchical clustering algorithm for gene sequences. BMC Bioinform. 13: 174 (2012) - [c3]Dan Wei, Weiwei Zhuang, Qingshan Jiang, Yanjie Wei:
A New Classification Method for Human Gene Splice Site Prediction. HIS 2012: 121-130 - [c2]Jintao Meng, Jianrui Yuan, Jiefeng Cheng, Yanjie Wei, Shengzhong Feng:
DGraph: Algorithms for Shortgun Reads Assembly Using De Bruijn Graph. NPC 2012: 14-21 - [c1]Jintao Meng, Jianrui Yuan, Jiefeng Cheng, Yanjie Wei, Shengzhong Feng:
Small World Asynchronous Parallel Model for Genome Assembly. NPC 2012: 145-155
2000 – 2009
- 2007
- [j1]Parimal Kar, Yanjie Wei, Ulrich H. E. Hansmann, Siegfried Höfinger:
Systematic study of the boundary composition in Poisson Boltzmann calculations. J. Comput. Chem. 28(16): 2538-2544 (2007)
Coauthor Index
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