Qiao Liu

发表

Quantifying functional impact of non-coding variants with multi-task Bayesian neural network

Tao Jiang, Chencheng Xu, Qiao Liu, 2019, Bioinform..

DeepHistone: a deep learning approach to predicting histone modifications

R. Jiang, Rui Jiang, Qiao Liu, 2018, BMC Genomics.

Small Molecule Modulation of Microbiome Ecosystem: A Systems Pharmacology Perspective

Lei Xie, Qiao Liu, Bohyun Lee, 2020, bioRxiv.

Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG

Wing Hong Wong, Qiao Liu, Zhana Duren, 2022, Genome Biology.

Incorporating Gene Expression in Genome-wide Prediction of Chromatin Accessibility via Deep Learning

Wing Hong Wong, Xuegong Zhang, R. Jiang, 2019, bioRxiv.

Deep generative modeling and clustering of single cell Hi-C data

Wei Zhang, Rui Jiang, Qiao Liu, 2022, bioRxiv.

Small molecule modulation of microbiota: a systems pharmacology perspective

Qiao Liu, Linfu Xie, Bohyun Lee, 2022, BMC Bioinformatics.

A context-aware deconfounding autoencoder for robust prediction of personalized clinical drug response from cell-line compound screening

Qiao Liu, Linfu Xie, You Wu, 2022, Nature Machine Intelligence.

Deep learning prediction of chemical-induced dose-dependent and context-specific multiplex phenotype responses and its application to personalized alzheimer’s disease drug repurposing

Lei Xie, Qiao Liu, Yue Qiu, 2022, PLoS Comput. Biol..

HiChIPdb: a comprehensive database of HiChIP regulatory interactions

Wing Hong Wong, Rui Jiang, Qiao Liu, 2022, Nucleic Acids Res..

Robust Prediction of Personalized In Vivo Response to Unseen Drugs From In Vitro Screens Using a Novel Context-Aware Deconfounding Autoencoder

Lei Xie, Qiao Liu, Di He, 2021 .

Robust Prediction of Patient-Specific Clinical Response to Unseen Drugs From in vitro Screens Using Context-aware Deconfounding Autoencoder

Lei Xie, Qiao Liu, Di He, 2021, bioRxiv.

VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease

Qiao Liu, Lei Xie, Hanghang Tong, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions

Xuegong Zhang, R. Jiang, Chunquan Li, 2021, Nucleic Acids Res..

Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature

Qiao Liu, Lei Xie, Di He, 2019, PLoS Comput. Biol..

DeepHistone: a deep learning approach to predicting histone modifications

R. Jiang, Qiao Liu, Mengmeng Wu, 2018, BMC Genom..

Chromatin accessibility prediction via a hybrid deep convolutional neural network

Qiao Liu, Fei Xia, Rui Jiang, 2017, Bioinform..

Multimodal single cell data integration challenge: results and lessons learned

Daniel B. Burkhardt, Malte D. Luecken, Smita Krishnaswamy, 2022, bioRxiv.

Simultaneous deep generative modelling and clustering of single-cell genomic data

Qiao Liu, Rui Jiang, Wing Hung Wong, 2020, Nature Machine Intelligence.

EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information

Rui Jiang, Hongfei Cui, Shengquan Chen, 2019, Quantitative Biology.

DualGCN: a dual graph convolutional network model to predict cancer drug response

Xuegong Zhang, Rui Jiang, Qiao Liu, 2022, BMC Bioinformatics.

Predictive Modeling of Multiplex Chemical Phenomics for Novel Cells and Patients: Applied to Personalized Alzheimer’s Disease Drug Repurposing

Lei Xie, Qiao Liu, Yue Qiu, 2021, bioRxiv.

DeepCDR: a hybrid graph convolutional network for predicting cancer drug response

R. Jiang, Qiao Liu, Mu Zhou, 2020, bioRxiv.

TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations

Lei Xie, Qiao Liu, Lei Xie, 2020, bioRxiv.

A sequence-based method to predict the impact of regulatory variants using random forest

Qiao Liu, Rui Jiang, Mingxin Gan, 2017, BMC Systems Biology.

Graph Convolutional Networks for Multi-modality Medical Imaging: Methods, Architectures, and Clinical Applications

Dimitris N. Metaxas, Qiao Liu, Mu Zhou, 2022, 2202.08916.

DeepCAGE: Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility

Xuegong Zhang, W. Wong, R. Jiang, 2022, Genom. Proteom. Bioinform..

Density estimation using deep generative neural networks

Wing Hong Wong, R. Jiang, Qiao Liu, 2021, Proceedings of the National Academy of Sciences of the United States of America.

Feature-Enhanced Graph Networks for Genetic Mutational Prediction Using Histopathological Images in Colon Cancer

Shaoting Zhang, Mu Zhou, Qiao Liu, 2020, MICCAI.

hicGAN infers super resolution Hi-C data with generative adversarial networks

Hairong Lv, Rui Jiang, Qiao Liu, 2019, Bioinform..

Roundtrip: A Deep Generative Neural Density Estimator

W. Wong, R. Jiang, Qiao Liu, 2020, ArXiv.

Applications of transformer-based language models in bioinformatics: a survey

Qiao Liu, Rui Fan, Wanwen Zeng, 2023, Bioinformatics advances.

DeepCDR: a hybrid graph convolutional network for predicting cancer drug response

Rui Jiang, Mu Zhou, Zhiqiang Hu, 2020, bioRxiv.

DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction

R. Jiang, Qiao Liu, Rui Fan, 2022, bioRxiv.

Multi-scale predictive modeling discovers Ibudilast as a polypharmacological agent to improve hippocampal-dependent spatial learning and memory and mitigate plaque and tangle pathology in a transgenic rat model of Alzheimer’s disease

P. Serrano, Lei Xie, Qiao Liu, 2021, bioRxiv.

Reinforced Molecular Optimization with Neighborhood-Controlled Grammars pdf

Minlie Huang, Tao Jiang, Qiao Liu, 2020, NeurIPS.

EpiGePT : a Pretrained Transformer model for epigenomics 1

Wing Hong Wong, Rui Jiang, Qiao Liu, 2023 .

Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring

Wing Hong Wong, D. Aberle, Wenyuan Li, 2023, Proceedings of the National Academy of Sciences of the United States of America.

scGraph: a graph neural network-based approach to automatically identify cell types

Xuegong Zhang, Rui Jiang, Qiao Liu, 2022, Bioinform..

Hierarchical multi-omics data integration and modeling predict cell-specific chemical proteomics and drug responses

Qiao Liu, Linfu Xie, You Wu, 2023, Cell reports methods.

DeepHistone: a deep learning approach to predicting histone modifications

Hairong Lv, Rui Jiang, Qijin Yin, 2018, BMC Genomics.

EpiGePT: a Pretrained Transformer model for epigenomics

Wing Hong Wong, Rui Jiang, Qiao Liu, 2023, bioRxiv.

Identifying Context-specific Network Features for CRISPR-Cas9 Targeting Efficiency Using Accurate and Interpretable Deep Neural Network

Di He, Lei Xie, Qiao Liu, 2018, bioRxiv.

Datasets: density estimation using deep generative neural network

W. Wong, Qiao Liu, Jiaze Xu, 2020 .