publications

2024

  1. arXiv
    DYNA: Disease-Specific Language Model for Variant Pathogenicity
    Zhan, Huixin, and Zhang, Zijun
    arXiv preprint arXiv:2406.00164 2024
    HTML Code
  2. medRxiv
    Training-free Design of Deep Networks as Ensembles of Clinical Experts
    Wu, Tinghui, Chen, Wuyang, and Zhang, Zijun
    medRxiv 2024
    HTML PDF Code
  3. arXiv
    Efficient and Scalable Fine-Tune of Language Models for Genome Understanding
    Zhan, Huixin, Wu, Ying Nian, and Zhang, Zijun
    arXiv preprint arXiv:2402.08075 2024
    HTML Code

2023

  1. NeurIPS
    Parameter-Efficient Fine-Tune on Open Pre-trained Transformers for Genomic Sequence
    Zhan, Huixin, and Zhang, Zijun Frank
    In NeurIPS 2023 Generative AI and Biology (GenBio) Workshop 2023
    HTML
  2. NeurIPS
    Automated distillation of genomic equations governing single cell gene expression
    Honig, Edouardo, Ruf-Zamojski, Frederique, Sealfon, Stuart, Wu, Ying Nian, and Zhang, Zijun Frank
    In NeurIPS 2023 AI for Science Workshop 2023
    HTML
  3. MLCB
    ProPath: Disease-Specific Protein Language Model for Variant Pathogenicity
    Zhan, Huixin, and Zhang, Zijun
    arXiv preprint arXiv:2311.03429 2023
    HTML
  4. Circulation
    Abnormal Dynamic Remodeling of the 12-Lead Electrocardiogram is a Risk Marker for Sudden Cardiac Death
    Pham, Hoang Nhat, Holmstrom, Lauri, Chugh, Harpriya, Uy-Evanado, Audrey, Nakamura, Kotoka, Zhang, Zijun, Fortmann, Stephen P, Salvucci, Angelo, Jui, Jonathan, Reinier, Kyndaron, and others,
    Circulation 2023
  5. bioRxiv
    Widespread impact of natural genetic variations in CRISPR/Cas9 outcomes
    Li, Victoria R, Tadych, Alicja, Wong, Aaron K, and Zhang, Zijun
    bioRxiv 2023
    HTML Code
  6. arXiv
    Reusability report: Prostate cancer stratification with diverse biologically-informed neural architectures
    Pedersen, Christian, Tesileanu, Tiberiu, Wu, Tinghui, Golkar, Siavash, Cranmer, Miles, Zhang, Zijun, and Ho, Shirley
    arXiv preprint arXiv:2309.16645 2023
    HTML Code
  7. Nat. Comput. Sci.
    Interpretable neural architecture search and transfer learning for understanding CRISPR/Cas9 off-target enzymatic reactions
    Zhang, Zijun, Lamson, Adam R, Shelley, Michael, and Troyanskaya, Olga
    Nature Computational Science 2023
    HTML Code
  8. CR Methods
    Atlas of primary cell-type-specific sequence models of gene expression and variant effects
    Sokolova, Ksenia, Theesfeld, Chandra L, Wong, Aaron K, Zhang, Zijun, Dolinski, Kara, and Troyanskaya, Olga G
    Cell Reports Methods 2023
    PDF
  9. Review
    Artificial Intelligence in Ventricular Arrhythmias and Sudden Death
    Holmström, Lauri, Zhang, Frank Zijun, Ouyang, David, Dey, Damini, Slomka, Piotr J, and Chugh, Sumeet S
    Arrhythmia & Electrophysiology Review 2023
    HTML
  10. Bioinformatics
    Explainable Multilayer Graph Neural Network for Cancer Gene Prediction
    Chatzianastasis, Michail, Vazirgiannis, Michalis, and Zhang, Zijun
    Bioinformatics 2023
    HTML Code
  11. CR Methods
    Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease
    Zhang, Zijun, Sauerwald, Natalie, Cappuccio, Antonio, Ramos, Irene, Nair, Venugopalan D, Nudelman, German, Zaslavsky, Elena, Ge, Yongchao, Gaitas, Angelo, Ren, Hui, and others,
    Cell Reports Methods 2023
    HTML Code

2022

  1. Cell Syst
    Pre-infection antiviral innate immunity contributes to sex differences in SARS-CoV-2 infection
    Sauerwald, Natalie, Zhang, Zijun, Ramos, Irene, Nair, Venugopalan D, Schanoski, Alessandra Soares, Ge, Yongchao, Mao, Weiguang, Alshammary, Hala, Gonzalez-Reiche, Ana S, Guchte, Adriana, and others,
    Cell Systems 2022
    HTML Code

2021

  1. Nat. Mach. Intell.
    An automated framework for efficiently designing deep convolutional neural networks in genomics
    Zhang, Zijun, Park, Christopher Y, Theesfeld, Chandra L, and Troyanskaya, Olga G
    Nature Machine Intelligence 2021
    HTML Code
  2. MLCB
    AMBIENT: accelerated convolutional neural network architecture search for regulatory genomics
    Zhang, Zijun, Cofer, Evan M, and Troyanskaya, Olga G
    bioRxiv 2021
    HTML Code
  3. Bioinformatics
    CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes
    Li, Victoria R, Zhang, Zijun, and Troyanskaya, Olga G
    Bioinformatics 2021
    HTML Code

2020

  1. Development
    Cleft lip and cleft palate in Esrp1 knockout mice is associated with alterations in epithelial-mesenchymal crosstalk
    Lee, SungKyoung, Sears, Matthew J, Zhang, Zijun, Li, Hong, Salhab, Imad, Krebs, Philippe, Xing, Yi, Nah, Hyun-Duck, Williams, Trevor, and Carstens, Russ P
    Development 2020
    HTML

2019

  1. Nat. Methods
    Deep-learning augmented RNA-seq analysis of transcript splicing
    Zhang, Zijun, Pan, Zhicheng, Ying, Yi, Xie, Zhijie, Adhikari, Samir, Phillips, John, Carstens, Russ P, Black, Douglas L, Wu, Yingnian, and Xing, Yi
    Nature methods 2019
    HTML Code
  2. arXiv
    Neural architecture search for joint optimization of predictive power and biological knowledge
    Zhang, Zijun, Zhou, Linqi, Gou, Liangke, and Wu, Ying Nian
    arXiv preprint arXiv:1909.00337 2019
    HTML

2018

  1. AJHG
    The expanding landscape of alternative splicing variation in human populations
    Park, Eddie, Pan, Zhicheng, Zhang, Zijun, Lin, Lan, and Xing, Yi
    The American Journal of Human Genetics 2018
    HTML
  2. Genome Biol.
    A panoramic view of RNA modifications: exploring new frontiers
    Zhang, Zijun, Park, Eddie, Lin, Lan, and Xing, Yi
    2018
    HTML

2017

  1. Bioinformatics
    DEF: an automated dead-end filling approach based on quasi-endosymbiosis
    Liu, Lili, Zhang, Zijun, Sheng, Taotao, and Chen, Ming
    Bioinformatics 2017
    HTML Code
  2. NAR
    CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome
    Zhang, Zijun, and Xing, Yi
    Nucleic Acids Research 2017
    HTML Code

2013

  1. PLOS
    PSI: a comprehensive and integrative approach for accurate plant subcellular localization prediction
    Liu, Lili, Zhang, Zijun, Mei, Qian, and Chen, Ming
    PLoS One 2013
    HTML Code
  2. JIB
    An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice
    Liu, Lili, Mei, Qian, Yu, Zhenning, Sun, Tianhao, Zhang, Zijun, and Chen, Ming
    Journal of integrative bioinformatics 2013
    HTML Code