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ResearcherID: HHM-8839-2022

Keywords

Bioinformatics, Adversarial Learning, Natural Language Processing

Countries

China

Biography

I am an assistant professor in Harbin Institute of Technology, Shenzhen, China. My research interests include AI for science, Adversarial Learning, Natural Language Processing.

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Employment (1)

Harbin Institute of Technology Shenzhen: Shenzhen, Guangdong, CN

2021-03-01 to present | Assistant Professor (Department of Computer Science and Technology)
Employment
Source: Self-asserted source
Junjie Chen

Works (36)

High-performance diffusion model for inverse design of high <i>T</i><sub>c</sub> superconductors with effective doping and accurate stoichiometry

InfoMat
2024 | Journal article
DOI: 10.1002/INF2.12519
WOSUID: WOS:001155072900001
Contributors: Zhong, Chengquan; Zhang, Jingzi; Wang, Yuelin; Long, Yanwu; Zhu, Pengzhou; Liu, Jiakai; Hu, Kailong; Chen, Junjie; Lin, Xi
Source: check_circle
Web of Science Researcher Profile Sync

ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction

IEEE Transactions on Neural Networks and Learning Systems
2024 | Journal article
DOI: 10.1109/TNNLS.2024.3419250
Contributors: JiangYi Shao; JunJie Chen; Bin Liu
Source: check_circle
Crossref

iMFP-LG: Identification of Novel Multi-Functional Peptides by Using Protein Language Models and Graph-Based Deep Learning

Genomics, Proteomics & Bioinformatics
2024-11-25 | Journal article
DOI: 10.1093/gpbjnl/qzae084
Contributors: Jiawei Luo; Kejuan Zhao; Junjie Chen; Caihua Yang; Fuchuan Qu; Yumeng Liu; Xiaopeng Jin; Ke Yan; Yang Zhang; Bin Liu
Source: check_circle
Crossref

Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization

Briefings in Bioinformatics
2024-11-22 | Journal article
DOI: 10.1093/bib/bbae715
Contributors: Xianliang Liu; Jiawei Luo; Xinyan Wang; Yang Zhang; Junjie Chen
Source: check_circle
Crossref

Deep Generative Model for Inverse Design of High-Temperature Superconductor Compositions with Predicted <i>T</i> <sub>c</sub> > 77 K

ACS Applied Materials & Interfaces
2023 | Journal article
DOI: 10.1021/ACSAMI.3C00593
WOSUID: WOS:001011465300001
Contributors: Zhong, Chengquan; Zhang, Jingzi; Lu, Xiaoting; Zhang, Ke; Liu, Jiakai; Hu, Kailong; Chen, Junjie; Lin, Xi
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Flexible and Controllable Protein Design by Prefix-tuning Large-Scale Protein Language Models

2023-12-05 | Preprint
DOI: 10.1101/2023.12.03.569747
Contributors: Jiawei Luo; Xianliang Liu; Jiahao Li; Qingcai Chen; Junjie Chen
Source: check_circle
Crossref

Discovery of novel multi-functional peptides by using protein language models and graph-based deep learning

2023-04-17 | Preprint
DOI: 10.1101/2023.04.14.536982
Contributors: Jiawei Luo; Kejuan Zhao; Junjie Chen; Caihua Yang; Fuchuan Qu; Ke Yan; Yang Zhang; Bin Liu
Source: check_circle
Crossref

Split-Transformer Impute (STI): A Transformer Framework for Genotype Imputation

2023-03-06 | Preprint
DOI: 10.1101/2023.03.05.531190
Contributors: Mohammad Erfan Mowlaei; Chong Li; Oveis Jamialahmadi; Raquel Dias; Junjie Chen; Benyamin Jamialahmadi; Timothy Richard Rebbeck; Vincenzo Carnevale; Sudhir Kumar; Xinghua Shi
Source: check_circle
Crossref

CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction

Bioinformatics
2023-03-01 | Journal article
DOI: 10.1093/bioinformatics/btad123
Contributors: Zhourun Wu; Mingyue Guo; Xiaopeng Jin; Junjie Chen; Bin Liu; Pier Luigi Martelli
Source: check_circle
Crossref

iEnhancer-ELM: improve enhancer identification by extracting position-related multiscale contextual information based on enhancer language models

Bioinformatics Advances
2023-01-05 | Journal article
DOI: 10.1093/bioadv/vbad043
Contributors: Jiahao Li; Zhourun Wu; Wenhao Lin; Jiawei Luo; Jun Zhang; Qingcai Chen; Junjie Chen; Guoqiang Yu
Source: check_circle
Crossref

Single Cell Self-Paced Clustering with Transcriptome Sequencing Data

International Journal of Molecular Sciences
2022-03-31 | Journal article
DOI: 10.3390/ijms23073900
Part of ISSN: 1422-0067
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

ProtRe-CN: Protein Remote Homology Detection by Combining Classification Methods and Network Methods via Learning to Rank

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2021 | Journal article
DOI: 10.1109/tcbb.2021.3108168
Part of ISSN: 1545-5963
Part of ISSN: 1557-9964
Part of ISSN: 2374-0043
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

A BERT-Based Generation Model to Transform Medical Texts to SQL Queries for Electronic Medical Records: Model Development and Validation

JMIR Medical Informatics
2021-12-08 | Journal article
DOI: 10.2196/32698
Contributors: Youcheng Pan; Chenghao Wang; Baotian Hu; Yang Xiang; Xiaolong Wang; Qingcai Chen; Junjie Chen; Jingcheng Du
Source: check_circle
Crossref

Gaze-driven Interaction System for Cognitive Ability Assessment

2021 11th International Conference on Intelligent Control and Information Processing (ICICIP)
2021-12-03 | Conference paper
DOI: 10.1109/icicip53388.2021.9642161
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

PAR-GAN: Improving the Generalization of Generative Adversarial Networks Against Membership Inference Attacks

Proceedings of the 27th ACM SIGKDD Conference on Knowledge Discovery &amp; Data Mining
2021-08-14 | Conference paper
DOI: 10.1145/3447548.3467445
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Science
2021-04-02 | Journal article
DOI: 10.1126/science.abf7117
Part of ISSN: 0036-8075
Part of ISSN: 1095-9203
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Statistical and Machine Learning Methods for eQTL Analysis

Methods in Molecular Biology
2020 | Book chapter
DOI: 10.1007/978-1-0716-0026-9_7
Part of ISBN: 9781071600252
Part of ISBN: 9781071600269
Part of ISSN: 1064-3745
Part of ISSN: 1940-6029
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen
grade
Preferred source (of 2)‎

Association of CNVs with methylation variation

npj Genomic Medicine
2020-12 | Journal article
DOI: 10.1038/s41525-020-00145-w
Part of ISSN: 2056-7944
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Differential Privacy Protection Against Membership Inference Attack on Machine Learning for Genomic Data

Biocomputing 2021
2020-11 | Conference paper
DOI: 10.1142/9789811232701_0003
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Population-scale Genomic Data Augmentation Based on Conditional Generative Adversarial Networks

Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics
2020-09-21 | Conference paper
DOI: 10.1145/3388440.3412475
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

A Sparse Convolutional Predictor with Denoising Autoencoders for Phenotype Prediction

Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics
2019-09-04 | Conference paper
DOI: 10.1145/3307339.3342179
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Sparse Convolutional Denoising Autoencoders for Genotype Imputation

Genes
2019-08-28 | Journal article
DOI: 10.3390/genes10090652
Part of ISSN: 2073-4425
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen
grade
Preferred source (of 2)‎

Protein Remote Homology Detection and Fold Recognition Based on Sequence-Order Frequency Matrix

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2019-01-01 | Journal article
DOI: 10.1109/tcbb.2017.2765331
Part of ISSN: 1545-5963
Part of ISSN: 1557-9964
Part of ISSN: 2374-0043
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen
grade
Preferred source (of 2)‎

A comprehensive review and comparison of different computational methods for protein remote homology detection

Briefings in Bioinformatics
2018-03-01 | Journal article
DOI: 10.1093/bib/bbw108
Part of ISSN: 1467-5463
Part of ISSN: 1477-4054
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

SOFM-Top: Protein Remote Homology Detection and Fold Recognition Based on Sequence-Order Frequency Matrix

Intelligent Computing Theories and Application
2017 | Book chapter
DOI: 10.1007/978-3-319-63312-1_41
Part of ISBN: 9783319633114
Part of ISBN: 9783319633121
Part of ISSN: 0302-9743
Part of ISSN: 1611-3349
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen
grade
Preferred source (of 2)‎

Protein remote homology detection based on bidirectional long short-term memory

BMC Bioinformatics
2017-12 | Journal article
DOI: 10.1186/s12859-017-1842-2
Part of ISSN: 1471-2105
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank

Bioinformatics
2017-11-01 | Journal article
DOI: 10.1093/bioinformatics/btx429
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Protein Remote Homology Detection Based on an Ensemble Learning Approach

BioMed Research International
2016 | Journal article
DOI: 10.1155/2016/5813645
Part of ISSN: 2314-6133
Part of ISSN: 2314-6141
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Protein Remote Homology Detection by Combining Pseudo Dimer Composition with an Ensemble Learning Method

Current Proteomics
2016 | Journal article
DOI: 10.2174/157016461302160514002939
WOSUID: WOS:000376947100003
Contributors: Liu, Bin; Chen, Junjie; Wang, Shanyi
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dRHP-PseRA: detecting remote homology proteins using profile-based pseudo protein sequence and rank aggregation

Scientific Reports
2016-09 | Journal article
DOI: 10.1038/srep32333
Part of ISSN: 2045-2322
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

iMiRNA-SSF: Improving the Identification of MicroRNA Precursors by Combining Negative Sets with Different Distributions

Scientific Reports
2016-05 | Journal article
DOI: 10.1038/srep19062
Part of ISSN: 2045-2322
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

miRNA-dis: microRNA precursor identification based on distance structure status pairs

Molecular BioSystems
2015 | Journal article
DOI: 10.1039/c5mb00050e
Part of ISSN: 1742-206X
Part of ISSN: 1742-2051
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Application of learning to rank to protein remote homology detection

Bioinformatics
2015-11-01 | Journal article
DOI: 10.1093/bioinformatics/btv413
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Protein remote homology detection by combining Chou’s distance-pair pseudo amino acid composition and principal component analysis

Molecular Genetics and Genomics
2015-10 | Journal article
DOI: 10.1007/s00438-015-1044-4
Part of ISSN: 1617-4615
Part of ISSN: 1617-4623
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

Nucleic Acids Research
2015-07-01 | Journal article
DOI: 10.1093/nar/gkv458
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Identification of Real MicroRNA Precursors with a Pseudo Structure Status Composition Approach

PLOS ONE
2015-03-30 | Journal article
DOI: 10.1371/journal.pone.0121501
Part of ISSN: 1932-6203
Contributors: Junjie Chen
Source: Self-asserted source
Junjie Chen

Peer review (8 reviews for 3 publications/grants)

Review activity for Bioinformatics advances. (4)
Review activity for Biomedical signal processing and control. (1)
Review activity for IEEE transactions on information forensics and security. (3)
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