scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data.

Zhaolei Zhang

Zhiyi Zou Ying Liu 0027 Yuting Bai Jiawei Luo 0001 Zhaolei Zhang scTrans: Sparse attention powers fast and accurate cell type annotation in single-cell RNA-seq data. 1012904 2025 21 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1012904 db/journals/ploscb/ploscb21.html#ZouLBLZ25 streams/journals/ploscb

Yanjie Wei Huiling Zhang Zhipeng Cai 0001 Fa Zhang 0001 Zhaolei Zhang Editorial: Special Section on Challenges and Opportunities in Biomedical Big Data Analysis: From Large Language Models to Clinical Applications. 1114-1115 2024 7 Big Data Min. Anal. 4 https://doi.org/10.26599/bdma.2024.9020077 db/journals/bigdatama/bigdatama7.html#WeiZCZZ24 streams/journals/bigdatama

Xiaozhe Yi Panpan Jin Zhaolei Zhang Erhuan Zang Yu Tian Xinyi Li Jinxin Liu Yunbo Wang Linchun Shi Identification, isoform classification, ligand binding, and database construction of the protein-tyrosine sulfotransferase family in metazoans. 109208 2024 182 Comput. Biol. Medicine https://doi.org/10.1016/j.compbiomed.2024.109208 https://www.wikidata.org/entity/Q130681747 db/journals/cbm/cbm182.html#YiJZZTLLWS24 streams/journals/cbm

Kevin Zhang Junhao Zhu Dehan Kong Zhaolei Zhang Modeling single cell trajectory using forward-backward stochastic differential equations. 1012015 2024 20 PLoS Comput. Biol. 4 https://doi.org/10.1371/journal.pcbi.1012015 db/journals/ploscb/ploscb20.html#ZhangZKZ24 streams/journals/ploscb

Zhaolei Zhang Yu Liu 0020 Cheng-Xiang Wang 0001 Hengtai Chang Ji Bian Jingfan Zhang Machine Learning Based Clustering and Modeling for 6G UAV-to-Ground Communication Channels. 14113-14126 2024 October 73 IEEE Trans. Veh. Technol. 10 https://doi.org/10.1109/TVT.2024.3403190 db/journals/tvt/tvt73.html#ZhangLWCBZ24 streams/journals/tvt

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. 64-75 2024 ISBRA (3) https://doi.org/10.1007/978-981-97-5087-0_6 conf/isbra/2024-3 db/conf/isbra/isbra2024-3.html#LiHTXCHZLWMZ24 streams/conf/isbra Jingquan Li Yu Liu 0020 Jingfan Zhang Zhaolei Zhang Hengtai Chang Jie Huang 0004 Hardware Implementation of a Novel UAV Multi-Trajectory Dual-Mobility Channel Emulator. 1-6 2024 WCNC https://doi.org/10.1109/WCNC57260.2024.10570680 conf/wcnc/2024 db/conf/wcnc/wcnc2024.html#Li0ZZCH24

Jianguo Chen 0001 Nan Yang Yuhui Pan Hailing Liu Zhaolei Zhang Synchronous Medical Image Augmentation framework for deep learning-based image segmentation. 102161 2023 March 104 Comput. Medical Imaging Graph. https://doi.org/10.1016/j.compmedimag.2022.102161 db/journals/cmig/cmig104.html#ChenYPLZ23

Zhaolei Zhang Yu Liu Jie Huang Jingfan Zhang Jingquan Li Ruisi He Channel Characterization and Modeling for 6G UAV-Assisted Emergency Communications in Complicated Mountainous Scenarios. 4998 2023 23 Sensors 11 https://doi.org/10.3390/s23114998 db/journals/sensors/sensors23.html#ZhangLHZLH23

Jingfan Zhang Yu Liu 0020 Jie Huang 0004 Hengtai Chang Zhaolei Zhang Jingquan Li Channel Modeling and Characteristics Analysis under Different 3D Dynamic Trajectories for UAV-Assisted Emergency Communications. 5372 2023 23 Sensors 12 https://doi.org/10.3390/s23125372 db/journals/sensors/sensors23.html#ZhangLHCZL23

Jianguo Chen 0001 Kenli Li 0001 Zhaolei Zhang Keqin Li 0001 Philip S. Yu A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19. 158:1-158:32 2022 54 ACM Comput. Surv. 8 https://doi.org/10.1145/3465398 https://www.wikidata.org/entity/Q130959847 db/journals/csur/csur54.html#ChenLZLY22

Jianguo Chen 0001 Nan Yang Mimi Zhou Zhaolei Zhang Xulei Yang A configurable deep learning framework for medical image analysis. 7375-7392 2022 34 Neural Comput. Appl. 10 https://doi.org/10.1007/s00521-021-06873-z https://www.wikidata.org/entity/Q114960294 db/journals/nca/nca34.html#ChenYZZY22

Ying Liu 0027 Ruihui Li Jiawei Luo 0001 Zhaolei Zhang Inferring RNA-binding protein target preferences using adversarial domain adaptation. 2022 18 PLoS Comput. Biol. 2 https://doi.org/10.1371/journal.pcbi.1009863 https://www.wikidata.org/entity/Q113308733 db/journals/ploscb/ploscb18.html#LiuLLZ22

Hongli Ma Han Wen Zhiyuan Xue Guojun Li Zhaolei Zhang RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites. 2022 18 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1010293 https://www.wikidata.org/entity/Q113308414 db/journals/ploscb/ploscb18.html#MaWXLZ22

Wei Hao 0002 Donglei Rong Zhaolei Zhang Qiyu Wu 0003 Young-Ji Byon Kefu Yi Jinjun Tang Nengchao Lyu Development of a Safety Prediction Method for Arterial Roads Based on Big-Data Technology and Stacked AutoEncoder-Gated Recurrent Unit. 20110-20122 2022 23 IEEE Trans. Intell. Transp. Syst. 11 https://doi.org/10.1109/TITS.2022.3172480 db/journals/tits/tits23.html#HaoRZWBYTL22

Shuhui Liu Yupei Zhang Xuequn Shang 0001 Zhaolei Zhang ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes. 2021 22 Briefings Bioinform. 6 https://doi.org/10.1093/bib/bbab164 db/journals/bib/bib22.html#LiuZSZ21

Shun Liao Jamie Kiros Jiyang Chen Zhaolei Zhang Ting Chen Improving domain adaptation in de-identification of electronic health records through self-training. 2093-2100 2021 28 J. Am. Medical Informatics Assoc. 10 https://doi.org/10.1093/jamia/ocab128 db/journals/jamia/jamia28.html#LiaoKCZC21

Chen Chen 0061 Jinxin Ma Tao Qi Baojiang Cui Weikong Qi Zhaolei Zhang Peng Sun Firmware code instrumentation technology for internet of things-based services. 941-954 2021 24 World Wide Web 3 https://doi.org/10.1007/s11280-020-00838-3 db/journals/www/www24.html#ChenMQCQZS21

Zhaolei Zhang Jian Xu Guishan Dong Junyan Lin Application and Challenges of Blockchain in Heterogeneous Identity Trust. 163-168 2021 BlockSys https://doi.org/10.1007/978-981-16-7993-3_12 conf/blocksys/2021 db/conf/blocksys/blocksys2021.html#ZhangXDL21 Guishan Dong Yuxiang Chen Yao Hao Jian Bai Zhaolei Zhang Sijie Liao A Unified Trust Service Scheme for Heterogeneous Identity Alliance. 167-173 2020 NaNA https://doi.org/10.1109/NaNA51271.2020.00037 conf/nana/2020 db/conf/nana/nana2020.html#DongCHBZL20

Jianguo Chen 0001 Kenli Li 0001 Zhaolei Zhang Keqin Li 0001 Philip S. Yu A Survey on Applications of Artificial Intelligence in Fighting Against COVID-19. 2020 abs/2007.02202 CoRR https://arxiv.org/abs/2007.02202 db/journals/corr/corr2007.html#abs-2007-02202

Yuxiang Chen Guishan Dong Yao Hao Zhaolei Zhang Haiyang Peng Shui Yu 0001 An Open Identity Authentication Scheme Based on Blockchain. 421-438 2019 ICA3PP (1) https://doi.org/10.1007/978-3-030-38991-8_28 conf/ica3pp/2019-1 db/conf/ica3pp/ica3pp2019-1.html#ChenDHZPY19 Guishan Dong Yuxiang Chen Yao Hao Zhaolei Zhang Peng Zhang Shui Yu 0001 Tiger Tally: Cross-Domain Scheme for Different Authentication Mechanism. 533-549 2019 ICA3PP (1) https://doi.org/10.1007/978-3-030-38991-8_35 conf/ica3pp/2019-1 db/conf/ica3pp/ica3pp2019-1.html#DongCHZZY19

Guishan Dong Yuxiang Chen Zhaolei Zhang Jian Bai Yao Hao 基于区块链的身份管理认证研究 (Research on Identity Management Authentication Based on Blockchain). 52-59 2018 45 计算机科学 11 https://doi.org/10.11896/j.issn.1002-137X.2018.11.006 http://www.jsjkx.com/EN/10.11896/j.issn.1002-137X.2018.11.006 db/journals/jsjkx/jsjkx45.html#DongCZBH18

Hyunmin Lee Zhen Hao Wu Zhaolei Zhang Dimension Reduction on Open Data Using Variational Autoencoder. 1080-1085 2018 ICDM Workshops https://doi.org/10.1109/ICDMW.2018.00156 conf/icdm/2018w db/conf/icdm/icdm2018w.html#LeeWZ18

Ka-Chun Wong Yue Li 0017 Chengbin Peng 0001 Zhaolei Zhang SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles. 17-24 2015 31 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btu604 https://www.wikidata.org/entity/Q38472899 db/journals/bioinformatics/bioinformatics31.html#WongLPZ15

Cheng Liang 0001 Yue Li 0017 Jiawei Luo 0001 Zhaolei Zhang A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. 2348-2355 2015 31 Bioinform. 14 https://doi.org/10.1093/bioinformatics/btv159 https://www.wikidata.org/entity/Q35581027 db/journals/bioinformatics/bioinformatics31.html#LiangLLZ15

Lee Zamparo Zhaolei Zhang Deep Autoencoders for Dimensionality Reduction of High-Content Screening Data. 2015 abs/1501.01348 CoRR http://arxiv.org/abs/1501.01348 db/journals/corr/corr1501.html#ZamparoZ15

Yue Li 0017 Anna Goldenberg Ka-Chun Wong Zhaolei Zhang A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. 621-628 2014 30 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btt599 https://www.wikidata.org/entity/Q30679409 db/journals/bioinformatics/bioinformatics30.html#LiGWZ14

Ka-Chun Wong Zhaolei Zhang SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences. 1112-1119 2014 30 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btt769 https://www.wikidata.org/entity/Q43414036 db/journals/bioinformatics/bioinformatics30.html#WongZ14

Yue Li 0017 Cheng Liang 0001 Ka-Chun Wong Jiawei Luo 0001 Zhaolei Zhang Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. 2627-2635 2014 30 Bioinform. 18 https://doi.org/10.1093/bioinformatics/btu373 https://www.wikidata.org/entity/Q47763320 db/journals/bioinformatics/bioinformatics30.html#LiLWLZ14

Yue Li 0017 Minggao Liang Zhaolei Zhang Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia. 2014 10 PLoS Comput. Biol. 10 https://doi.org/10.1371/journal.pcbi.1003908 https://www.wikidata.org/entity/Q34393824 db/journals/ploscb/ploscb10.html#LiLZ14

Ka-Chun Wong Chun-Ho Wu Ricky K. P. Mok Chengbin Peng 0001 Zhaolei Zhang Evolutionary multimodal optimization using the principle of locality. 138-170 2012 194 Inf. Sci. https://doi.org/10.1016/j.ins.2011.12.016 https://www.wikidata.org/entity/Q56865406 db/journals/isci/isci194.html#WongWMPZ12

Ke Jin Jingjing Li Frederick S. Vizeacoumar Zhijian Li Renqiang Min Lee Zamparo Franco J. Vizeacoumar Alessandro Datti Brenda J. Andrews Charles Boone Zhaolei Zhang PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae. 687-694 2012 40 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkr827 https://www.wikidata.org/entity/Q38500319 db/journals/nar/nar40.html#JinLVLMZVDABZ12

Dong Dong Xiaojian Shao Zhaolei Zhang Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective. 147-152 2011 27 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btq637 https://www.wikidata.org/entity/Q48171847 db/journals/bioinformatics/bioinformatics27.html#DongSZ11

Dong Dong Xiaojian Shao Naiyang Deng Zhaolei Zhang Gene expression variations are predictive for stochastic noise. 403-413 2011 39 Nucleic Acids Res. 2 https://doi.org/10.1093/nar/gkq844 https://www.wikidata.org/entity/Q41857422 db/journals/nar/nar39.html#DongSDZ11

Andrei L. Turinsky Brian Turner Rosanne C. Borja James A. Gleeson Michael Heath Shuye Pu Thomas Switzer Dong Dong Yunchen Gong Tuan On Xuejian Xiong Andrew Emili Jack Greenblatt John Parkinson Zhaolei Zhang Shoshana J. Wodak DAnCER: Disease-Annotated Chromatin Epigenetics Resource. 889-894 2011 39 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkq857 https://www.wikidata.org/entity/Q24609602 db/journals/nar/nar39.html#TurinskyTBGHPSDGOXEGPZW11

Jian Ren 0002 Zexian Liu Xinjiao Gao Changjiang Jin Mingliang Ye Hanfa Zou Longping Wen Zhaolei Zhang Yu Xue 0001 Xuebiao Yao MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore. 155-160 2010 38 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkp784 https://www.wikidata.org/entity/Q33506945 db/journals/nar/nar38.html#RenLGJYZWZXY10

Jingjing Li Yu Liu 0093 TaeHyung Kim Renqiang Min Zhaolei Zhang Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility. 2010 6 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1000910 https://www.wikidata.org/entity/Q33701750 db/journals/ploscb/ploscb6.html#LiLKMZ10

Martin Renqiang Min Laurens van der Maaten Zineng Yuan Anthony J. Bonner Zhaolei Zhang Deep Supervised t-Distributed Embedding. 791-798 2010 ICML https://icml.cc/Conferences/2010/papers/149.pdf conf/icml/2010 db/conf/icml/icml2010.html#MinMYBZ10

Jingjing Li Martin Renqiang Min Anthony J. Bonner Zhaolei Zhang A Probabilistic Framework to Improve microRNA Target Prediction by Incorporating Proteomics Data. 955-972 2009 7 J. Bioinform. Comput. Biol. 6 https://doi.org/10.1142/S021972000900445X https://www.wikidata.org/entity/Q33518814 db/journals/jbcb/jbcb7.html#LiMBZ09

Renqiang Min Anthony J. Bonner Jingjing Li Zhaolei Zhang Learned Random-Walk Kernels and Empirical-Map Kernels for Protein Sequence Classification. 457-474 2009 16 J. Comput. Biol. 3 https://doi.org/10.1089/cmb.2008.0031 https://www.wikidata.org/entity/Q44604029 db/journals/jcb/jcb16.html#MinBLZ09

Xingyi Guo Zhaolei Zhang Mark B. Gerstein Deyou Zheng Small RNAs Originated from Pseudogenes: cis- or trans-Acting? 2009 5 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1000449 https://www.wikidata.org/entity/Q28752303 db/journals/ploscb/ploscb5.html#GuoZGZ09

Martin Renqiang Min David A. Stanley Zineng Yuan Anthony J. Bonner Zhaolei Zhang A Deep Non-linear Feature Mapping for Large-Margin kNN Classification. 357-366 2009 ICDM https://doi.org/10.1109/ICDM.2009.27 https://doi.ieeecomputersociety.org/10.1109/ICDM.2009.27 conf/icdm/2009 db/conf/icdm/icdm2009.html#MinSYBZ09 Martin Renqiang Min Rui Kuang Anthony J. Bonner Zhaolei Zhang Learning Random-Walk Kernels for Protein Remote Homology Identification and Motif Discovery. 133-144 2009 SDM https://doi.org/10.1137/1.9781611972795.12 conf/sdm/2009 db/conf/sdm/sdm2009.html#MinKBZ09

Martin Renqiang Min David A. Stanley Zineng Yuan Anthony J. Bonner Zhaolei Zhang Large-Margin kNN Classification Using a Deep Encoder Network http://arxiv.org/abs/0906.1814 2009 CoRR abs/0906.1814 db/journals/corr/corr0906.html#abs-0906-1814

Sumedha Gunewardena Zhaolei Zhang A hybrid model for robust detection of transcription factor binding sites. 484-491 2008 24 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btm629 https://www.wikidata.org/entity/Q48075527 db/journals/bioinformatics/bioinformatics24.html#GunewardenaZ08

Ivan Borozan Limin Chen Bryan Paeper Jenny E. Heathcote Aled M. Edwards Michael G. Katze Zhaolei Zhang Ian D. McGilvray MAID : An effect size based model for microarray data integration across laboratories and platforms. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-305 https://www.wikidata.org/entity/Q30482830 db/journals/bmcbi/bmcbi9.html#BorozanCPHEKZM08

John E. Karro Yangpan Yan Deyou Zheng Zhaolei Zhang Nicholas Carriero Philip Cayting Paul M. Harrison Mark Gerstein Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. 55-60 2007 35 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkl851 https://www.wikidata.org/entity/Q24675776 db/journals/nar/nar35.html#KarroYZZCCHG07

Martin Renqiang Min Anthony J. Bonner Zhaolei Zhang Modifying kernels using label information improves SVM classification performance. 13-18 2007 ICMLA https://doi.org/10.1109/ICMLA.2007.84 https://doi.ieeecomputersociety.org/10.1109/ICMLA.2007.84 conf/icmla/2007 db/conf/icmla/icmla2007.html#MinBZ07

Zhaolei Zhang Nicholas Carriero Deyou Zheng John E. Karro Paul M. Harrison Mark Gerstein PseudoPipe: an automated pseudogene identification pipeline. 1437-1439 2006 22 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btl116 https://www.wikidata.org/entity/Q47215043 db/journals/bioinformatics/bioinformatics22.html#ZhangCZKHG06

Sumedha Gunewardena Peter Jeavons 0001 Zhaolei Zhang Enhancing the Prediction of Transcription Factor Binding Sites by Incorporating Structural Properties and Nucleotide Covariations. 929-945 2006 13 J. Comput. Biol. 4 https://doi.org/10.1089/cmb.2006.13.929 https://www.wikidata.org/entity/Q51940281 db/journals/jcb/jcb13.html#GunewardenaJZ06

Sumedha Gunewardena Zhaolei Zhang Accounting for Structural Properties and Nucleotide Co-variations in the Quantitative Prediction of Binding Affinities of Protein-DNA Interactions. 379-390 2006 conf/psb/2006 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb06/gunewardena.pdf db/conf/psb/psb2006.html#GunewardenaZ06 Brenda J. Andrews Jian Bai Yuting Bai Ji Bian Anthony J. Bonner Charles Boone Rosanne C. Borja Ivan Borozan Young-Ji Byon Zhipeng Cai 0001 Nicholas Carriero Philip Cayting Hengtai Chang Chen Chen 0061 Jianguo Chen 0001 Jiyang Chen Limin Chen Ting Chen Xiaochuan Chen Yuxiang Chen Baojiang Cui Alessandro Datti Naiyang Deng Dong Dong Guishan Dong Aled M. Edwards Andrew Emili Xinjiao Gao Mark GersteinMark B. Gerstein James A. Gleeson Anna Goldenberg Yunchen Gong Jack Greenblatt Sumedha Gunewardena Xingyi Guo Wei Hao 0002 Yao Hao Paul M. Harrison Ruilin He Ruisi He Michael Heath Jenny E. Heathcote Jie Huang Jie Huang 0004 Ying Huang Peter Jeavons 0001 Changjiang Jin Ke Jin Panpan Jin John E. Karro Michael G. Katze TaeHyung Kim Jamie Kiros Dehan Kong Rui Kuang Hyunmin Lee Guojun Li Jingjing Li Jingquan Li Kenli Li 0001 Keqin Li 0001 Ruihui Li Xijian Li Xinyi Li Yue Li 0017 Zhijian Li Cheng Liang 0001 Minggao Liang Shun Liao Sijie Liao Junyan Lin Hailing Liu Jinxin Liu Shuhui Liu Ying Liu 0027 Yu Liu Yu Liu 0020 Yu Liu 0093 Zexian Liu Jiana Luo Jiawei Luo 0001 Nengchao Lyu Hongli Ma Jinxin Ma Laurens van der Maaten Yijun Mao Ian D. McGilvray Martin Renqiang MinRenqiang Min Ricky K. P. Mok Tuan On Bryan Paeper Yuhui Pan John Parkinson Chengbin Peng 0001 Haiyang Peng Shuye Pu Tao Qi Weikong Qi Jian Ren 0002 Donglei Rong Xuequn Shang 0001 Xiaojian Shao Linchun Shi David A. Stanley Peng Sun Thomas Switzer Jinjun Tang Runxuan Tang Yu Tian Andrei L. Turinsky Brian Turner Franco J. Vizeacoumar Frederick S. Vizeacoumar Cheng-Xiang Wang 0001 Yunbo Wang Yanjie Wei Han Wen Longping Wen Shoshana J. Wodak Ka-Chun Wong Chun-Ho Wu Qiyu Wu 0003 Zhen Hao Wu Guangcheng Xiao Xuejian Xiong Jian Xu Yu Xue 0001 Zhiyuan Xue Yangpan Yan Nan Yang Xulei Yang Xuebiao Yao Mingliang Ye Kefu Yi Xiaozhe Yi Philip S. Yu Shui Yu 0001 Zineng Yuan Lee Zamparo Erhuan Zang Fa Zhang 0001 Huiling Zhang Jingfan Zhang Kevin Zhang Peng Zhang Yupei Zhang Deyou Zheng Mimi Zhou Junhao Zhu Hanfa Zou Zhiyi Zou