- 2025 -

[1]. Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis, Genome Biology, Advance Access, 2025. (iSTBench）

[2]. Weakly-supervised peptide-TCR binding prediction facilitates neoantigen identification, Cell System, Advance Access. 2025.（TCRBagger）

[3]. Benchmarking single-cell multi-modal data integrations, Nature Methods. Advance Access, 2025. (SCMMI_Benchmark)

[4]. Causal disentanglement for single-cell representations and controllable counterfactual generation, Nature Communications. Advance Access, 2025.(CausCell)

[5]. PrimeNet: rational design of Prime editing pegRNAs by deep learning, Briefings in Bioinformatics. Advance Access, 2025. (PrimeNet)

[6]. SpaLinker identifies phenotype-associated spatial tumor microenvironment features by integrating bulk and spatial sequencing data, Cell Genomics. Advances Access, 2025.(SpaLinker)

- 2024 -

[1]. Discovering CRISPR-Cas system with self-processing pre-crRNA capability by foundation models, Nature Communications. Advance Access, 2024.(CHOOSER)

[2]. PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization, Nucleic Acids Research. Advance Access, 2024.(PerturBase)

[3]. Genomics-guided Representation Learning for Pathologic Pan-cancer Tumor Microenvironment Subtype Prediction, MICCAI. Advance Access, 2024.(PathoTME）

[4]. Toward subtask decomposition-based learning and benchmarking for genetic perturbation outcome prediction and beyond, Nature Computational Science. Advance Access, 2024. (STAMP)

[5]. Unified cross-modality integration and analysis of T-cell receptors and T-cell transcriptomes by low-resource-aware representation learning, Cell Genomics. Advance Access, 2024. (UniTCR )

[6]. Inter3D: Capture of TAD reorganization endows variant patterns of gene transcription, Genomics Proteomics & Bioinformatics. Advance Access, 2024. （Inter3D) 

[7]. Multi-slice Spatial Transcriptome Domain Analysis with SpaDo, Genome Biology. Advance Access, 2024. （SpaDo)

- 2023 -

[1]. Personalized tumor combination therapy optimization using the single-cell transcriptome, Genome Medicine. Advance Access, 2023. （comboSC)

[2].Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints, Nature Communications. Advance Access, 2023. （CRISOT)

[3].Pan-Peptide Meta Learning for T-Cell Receptor-Antigen Binding Recognition, Nature Machine Intelligence. Advance Access, 2023. (PanPep)

- 2022-

[1].Systematic exploration of optimized base-editing gRNA design and pleiotropic effects with BExplorer, Genomics Proteomics & Bioinformatics. Advance Access, 2022. (BExplorer)

[2]. Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy, Science China-Life Sciences, Advance Access, 2022  (scPrivacy)

[3]. DrSim: Similarity learning for transcriptional phenotypic drug discovery, Genomics Proteomics & Bioinformatics. Advance Access, 2022. (DrSim)

[4]. X-MOL: large-scale pre-training for molecular understanding and diverse molecular analysis, Science Bulletin, Advance Access, 2022. (X-MOL)

[5]. A deep generative model for multi-view profiling of single cell RNA-seq and ATAC-seq data, Genome Biology, Advance Access, 2022.(scMVP)

- 2021 -

[1]. DeepReac+: Deep active learning for quantatitative modeling of organic chemical reactions, Chemical Science, Advance Access, 2021.(DeepReac+)

[2]. iCREISEE: an integrative  analysis of CRISPR screen by reducing false positive hits, Briefings in Bioinformatics, Advance Access, 2021.(iCRISEE)

[3]. PRODeepSyn: integrating protein-protein interaction network with omics data to predict anticancer synergistic drug combinations, Briefings in Bioinformatics, Advance Access, 2021. (PRODeepSyn)

[4]. The tumor therapy landscape of synthetic lethality, Nature Communications, Advance Access, 2021. (SLKG)

 

[5]. Integrating multiple references for single cell assignment, Nucleic Acids Research, Advance Access, 2021.(mtSC)

- 2020 -

 

[1]. Learning for single cell assignment, Science Advances, Advance Access, 2020. (scLearn)

[2]. Benchmarking and integrating CRISPR off-target detection and prediction, Nucleic Acids Research, Advance Access, 2020. (iGWOS)

[3]. Shaoqi Chen et al, Qi Liu#, FL-QSAR: a federated learning based QSAR prototype for collaborative drug discovery, Bioinformatics, Advance Access, 2020.(FL-QSAR)

[4]. Zhiting Wei et al, Qi Liu#, iDMer: an integrative and Mechanism-driven response system for identifying compound interventions for sudden virus break, Briefings in Bioinformatics, Advance Access, 2020.(iDMer)

[5]. ASNEO, Identificaiton of Personalized Alternative Splicing Based NEOantigens with RNA-seq,  Aging, Advance Access, 2020.  (ASNEO)

- 2019 -

[1]. pTuneos: prioritizing Tumor neoantigens from next-generation sequencing data, Genome Medicine, Advance Access, 2019. (pTuneos)
 

[2]. The landscape of tumor fusion neoantigens: a pan-cancer analysis, iScience, Advance Access, 2019. (neoFusion)

[3]. MetaMed: Linking microbiota functions with medicine therapeutics, mSystems, Advance Access, 2019. (MetaMed)

[4].  Model based Understanding of SIngle Cell CRISPR screening, Nature Communications, 2019. (MUSIC)

- 2018 -

[1]. DeepCRISPR: optimized CRISPR guide RNA design by deep learning, Genome Biology 2018. (DeepCRISPR)

[2]. C3: Concensus Cancer Driver Gene Caller, GPB 2018. (C3 )

- 2016 -

[1]. Deciphering relationshp between microhomology and in-frame mutation occurence in human CRISPR-based gene knockout, Molecular Therapy-Nucleic Acids, 2016. (CAGE)

[2]. MetaTopics: an integration tool to analyze microbial community profile by topic model, BMC Genomics, 2016. ( MetaTopics )