Qiao Liu

All Publications

• Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring. Proceedings of the National Academy of Sciences of the United States of America Li, S., Zeng, W., Ni, X., Liu, Q., Li, W., Stackpole, M. L., Zhou, Y., Gower, A., Krysan, K., Ahuja, P., Lu, D. S., Raman, S. S., Hsu, W., Aberle, D. R., Magyar, C. E., French, S. W., Han, S. B., Garon, E. B., Agopian, V. G., Wong, W. H., Dubinett, S. M., Zhou, X. J. 2023; 120 (28): e2305236120

  Abstract

  Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. Despite the great promise, the sensitive and accurate quantification of tissue-derived cfDNA remains challenging to existing methods due to the limited characterization of tissue methylation and the reliance on unsupervised methods. To fully exploit the clinical potential of tissue-derived cfDNA, here we present one of the largest comprehensive and high-resolution methylation atlas based on 521 noncancer tissue samples spanning 29 major types of human tissues. We systematically identified fragment-level tissue-specific methylation patterns and extensively validated them in orthogonal datasets. Based on the rich tissue methylation atlas, we develop the first supervised tissue deconvolution approach, a deep-learning-powered model, cfSort, for sensitive and accurate tissue deconvolution in cfDNA. On the benchmarking data, cfSort showed superior sensitivity and accuracy compared to the existing methods. We further demonstrated the clinical utilities of cfSort with two potential applications: aiding disease diagnosis and monitoring treatment side effects. The tissue-derived cfDNA fraction estimated from cfSort reflected the clinical outcomes of the patients. In summary, the tissue methylation atlas and cfSort enhanced the performance of tissue deconvolution in cfDNA, thus facilitating cfDNA-based disease detection and longitudinal treatment monitoring.

  View details for DOI 10.1073/pnas.2305236120

  View details for PubMedID 37399400

• Deep generative modeling and clustering of single cell Hi-C data. Briefings in bioinformatics Liu, Q., Zeng, W., Zhang, W., Wang, S., Chen, H., Jiang, R., Zhou, M., Zhang, S. 2022

  Abstract

  Deciphering 3D genome conformation is important for understanding gene regulation and cellular function at a spatial level. The recent advances of single cell Hi-C technologies have enabled the profiling of the 3D architecture of DNA within individual cell, which allows us to study the cell-to-cell variability of 3D chromatin organization. Computational approaches are in urgent need to comprehensively analyze the sparse and heterogeneous single cell Hi-C data. Here, we proposed scDEC-Hi-C, a new framework for single cell Hi-C analysis with deep generative neural networks. scDEC-Hi-C outperforms existing methods in terms of single cell Hi-C data clustering and imputation. Moreover, the generative power of scDEC-Hi-C could help unveil the differences of chromatin architecture across cell types. We expect that scDEC-Hi-C could shed light on deepening our understanding of the complex mechanism underlying the formation of chromatin contacts.

  View details for DOI 10.1093/bib/bbac494

  View details for PubMedID 36458445

• HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic acids research Zeng, W., Liu, Q., Yin, Q., Jiang, R., Wong, W. H. 2022

  Abstract

  Elucidating the role of 3D architecture of DNA in gene regulation is crucial for understanding cell differentiation, tissue homeostasis and disease development. Among various chromatin conformation capture methods, HiChIP has received increasing attention for its significant improvement over other methods in profiling of regulatory (e.g. H3K27ac) and structural (e.g. cohesin) interactions. To facilitate the studies of 3D regulatory interactions, we developed a HiChIP interactions database, HiChIPdb (http://health.tsinghua.edu.cn/hichipdb/). The current version of HiChIPdb contains 262M annotated HiChIP interactions from 200 high-throughput HiChIP samples across 108 cell types. The functionalities of HiChIPdb include: (i) standardized categorization of HiChIP interactions in a hierarchical structure based on organ, tissue and cell line and (ii) comprehensive annotations of HiChIP interactions with regulatory genes and GWAS Catalog SNPs. To the best of our knowledge, HiChIPdb is the first comprehensive database that utilizes a unified pipeline to map the functional interactions across diverse cell types and tissues in different resolutions. We believe this database has the potential to advance cutting-edge research in regulatory mechanisms in development and disease by removing the barrier in data aggregation, preprocessing, and analysis.

  View details for DOI 10.1093/nar/gkac859

  View details for PubMedID 36215037

• DeepCAGE: Incorporating transcription factors in genome-wide prediction of chromatin accessibility. Genomics, proteomics & bioinformatics Liu, Q., Hua, K., Zhang, X., Wong, W. H., Jiang, R. 2022

  Abstract

  Although computational approaches have been complementing high-throughput biological experiments for the identification of functional regions in the human genome, it remains a great challenge to systematically decipher interactions between transcription factors and regulatory elements to achieve interpretable annotations of chromatin accessibility across diverse cellular contexts. To solve this problem, we propose DeepCAGE, a deep learning framework that integrates sequence information and binding status of transcription factors, for the accurate prediction of chromatin accessible regions at a genome-wide scale in a variety of cell types. DeepCAGE takes advantage of a densely connected deep convolutional neural network architecture to automatically learn sequence signatures of known chromatin accessible regions and then incorporates such features with expression levels and binding activities of human core transcription factors to predict novel chromatin accessible regions. In a series of systematic comparisons with existing methods, DeepCAGE exhibits superior performance in not only the classification but also the regression of chromatin accessibility signals. In a detailed analysis of transcription factor activities, DeepCAGE successfully extracts novel binding motifs and measures the contribution of a transcription factor to the regulation with respect to a specific locus in a certain cell type. When applied to whole-genome sequencing data analysis, our method successfully prioritizes putative deleterious variants underlying a human complex trait and thus provides insights into the understanding of disease-associated genetic variants. DeepCAGE can be downloaded from https://github.com/kimmo1019/DeepCAGE.

  View details for DOI 10.1016/j.gpb.2021.08.015

  View details for PubMedID 35293310

• OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions. Nucleic acids research Chen, S., Liu, Q., Cui, X., Feng, Z., Li, C., Wang, X., Zhang, X., Wang, Y., Jiang, R. 2021; 49 (W1): W483-W490

  Abstract

  Chromatin accessibility, as a powerful marker of active DNA regulatory elements, provides valuable information for understanding regulatory mechanisms. The revolution in high-throughput methods has accumulated massive chromatin accessibility profiles in public repositories. Nevertheless, utilization of these data is hampered by cumbersome collection, time-consuming processing, and manual chromatin accessibility (openness) annotation of genomic regions. To fill this gap, we developed OpenAnnotate (http://health.tsinghua.edu.cn/openannotate/) as the first web server for efficiently annotating openness of massive genomic regions across various biosample types, tissues, and biological systems. In addition to the annotation resource from 2729 comprehensive profiles of 614 biosample types of human and mouse, OpenAnnotate provides user-friendly functionalities, ultra-efficient calculation, real-time browsing, intuitive visualization, and elaborate application notebooks. We show its unique advantages compared to existing databases and toolkits by effectively revealing cell type-specificity, identifying regulatory elements and 3D chromatin contacts, deciphering gene functional relationships, inferring functions of transcription factors, and unprecedentedly promoting single-cell data analyses. We anticipate OpenAnnotate will provide a promising avenue for researchers to construct a more holistic perspective to understand regulatory mechanisms.

  View details for DOI 10.1093/nar/gkab337

  View details for PubMedID 33999180

  View details for PubMedCentralID PMC8262705

• Simultaneous deep generative modeling and clustering of single cell genomic data. Nature machine intelligence Liu, Q., Chen, S., Jiang, R., Wong, W. H. 2021; 3 (6): 536-544

  Abstract

  Recent advances in single-cell technologies, including single-cell ATAC-seq (scATAC-seq), have enabled large-scale profiling of the chromatin accessibility landscape at the single cell level. However, the characteristics of scATAC-seq data, including high sparsity and high dimensionality, have greatly complicated the computational analysis. Here, we proposed scDEC, a computational tool for single cell ATAC-seq analysis with deep generative neural networks. scDEC is built on a pair of generative adversarial networks (GANs), and is capable of learning the latent representation and inferring the cell labels, simultaneously. In a series of experiments, scDEC demonstrates superior performance over other tools in scATAC-seq analysis across multiple datasets and experimental settings. In downstream applications, we demonstrated that the generative power of scDEC helps to infer the trajectory and intermediate state of cells during differentiation and the latent features learned by scDEC can potentially reveal both biological cell types and within-cell-type variations. We also showed that it is possible to extend scDEC for the integrative analysis of multi-modal single cell data.

  View details for DOI 10.1038/s42256-021-00333-y

  View details for PubMedID 34179690

  View details for PubMedCentralID PMC8223760

• Simultaneous deep generative modelling and clustering of single-cell genomic data NATURE MACHINE INTELLIGENCE Liu, Q., Chen, S., Jiang, R., Wong, W. 2021

  View details for DOI 10.1038/s42256-021-00333-y

  View details for Web of Science ID 000649431300002

• Density estimation using deep generative neural networks. Proceedings of the National Academy of Sciences of the United States of America Liu, Q., Xu, J., Jiang, R., Wong, W. H. 2021; 118 (15)

  Abstract

  Density estimation is one of the fundamental problems in both statistics and machine learning. In this study, we propose Roundtrip, a computational framework for general-purpose density estimation based on deep generative neural networks. Roundtrip retains the generative power of deep generative models, such as generative adversarial networks (GANs) while it also provides estimates of density values, thus supporting both data generation and density estimation. Unlike previous neural density estimators that put stringent conditions on the transformation from the latent space to the data space, Roundtrip enables the use of much more general mappings where target density is modeled by learning a manifold induced from a base density (e.g., Gaussian distribution). Roundtrip provides a statistical framework for GAN models where an explicit evaluation of density values is feasible. In numerical experiments, Roundtrip exceeds state-of-the-art performance in a diverse range of density estimation tasks.

  View details for DOI 10.1073/pnas.2101344118

  View details for PubMedID 33833061

• DeepCDR: a hybrid graph convolutional network for predicting cancer drug response Liu, Q., Hu, Z., Jiang, R., Zhou, M. OXFORD UNIV PRESS. 2020: I911-I918

  Abstract

  Accurate prediction of cancer drug response (CDR) is challenging due to the uncertainty of drug efficacy and heterogeneity of cancer patients. Strong evidences have implicated the high dependence of CDR on tumor genomic and transcriptomic profiles of individual patients. Precise identification of CDR is crucial in both guiding anti-cancer drug design and understanding cancer biology.In this study, we present DeepCDR which integrates multi-omics profiles of cancer cells and explores intrinsic chemical structures of drugs for predicting CDR. Specifically, DeepCDR is a hybrid graph convolutional network consisting of a uniform graph convolutional network and multiple subnetworks. Unlike prior studies modeling hand-crafted features of drugs, DeepCDR automatically learns the latent representation of topological structures among atoms and bonds of drugs. Extensive experiments showed that DeepCDR outperformed state-of-the-art methods in both classification and regression settings under various data settings. We also evaluated the contribution of different types of omics profiles for assessing drug response. Furthermore, we provided an exploratory strategy for identifying potential cancer-associated genes concerning specific cancer types. Our results highlighted the predictive power of DeepCDR and its potential translational value in guiding disease-specific drug design.DeepCDR is freely available at https://github.com/kimmo1019/DeepCDR.Supplementary data are available at Bioinformatics online.

  View details for DOI 10.1093/bioinformatics/btaa822

  View details for Web of Science ID 000606794900041

  View details for PubMedID 33381841

• hicGAN infers super resolution Hi-C data with generative adversarial networks Liu, Q., Lv, H., Jiang, R. OXFORD UNIV PRESS. 2019: I99-I107

  Abstract

  Hi-C is a genome-wide technology for investigating 3D chromatin conformation by measuring physical contacts between pairs of genomic regions. The resolution of Hi-C data directly impacts the effectiveness and accuracy of downstream analysis such as identifying topologically associating domains (TADs) and meaningful chromatin loops. High resolution Hi-C data are valuable resources which implicate the relationship between 3D genome conformation and function, especially linking distal regulatory elements to their target genes. However, high resolution Hi-C data across various tissues and cell types are not always available due to the high sequencing cost. It is therefore indispensable to develop computational approaches for enhancing the resolution of Hi-C data.We proposed hicGAN, an open-sourced framework, for inferring high resolution Hi-C data from low resolution Hi-C data with generative adversarial networks (GANs). To the best of our knowledge, this is the first study to apply GANs to 3D genome analysis. We demonstrate that hicGAN effectively enhances the resolution of low resolution Hi-C data by generating matrices that are highly consistent with the original high resolution Hi-C matrices. A typical scenario of usage for our approach is to enhance low resolution Hi-C data in new cell types, especially where the high resolution Hi-C data are not available. Our study not only presents a novel approach for enhancing Hi-C data resolution, but also provides fascinating insights into disclosing complex mechanism underlying the formation of chromatin contacts.We release hicGAN as an open-sourced software at https://github.com/kimmo1019/hicGAN.Supplementary data are available at Bioinformatics online.

  View details for DOI 10.1093/bioinformatics/btz317

  View details for Web of Science ID 000477703600012

  View details for PubMedID 31510693

  View details for PubMedCentralID PMC6612845

• Chromatin accessibility prediction via a hybrid deep convolutional neural network BIOINFORMATICS Liu, Q., Xia, F., Yin, Q., Jiang, R. 2018; 34 (5): 732–38

  Abstract

  A majority of known genetic variants associated with human-inherited diseases lie in non-coding regions that lack adequate interpretation, making it indispensable to systematically discover functional sites at the whole genome level and precisely decipher their implications in a comprehensive manner. Although computational approaches have been complementing high-throughput biological experiments towards the annotation of the human genome, it still remains a big challenge to accurately annotate regulatory elements in the context of a specific cell type via automatic learning of the DNA sequence code from large-scale sequencing data. Indeed, the development of an accurate and interpretable model to learn the DNA sequence signature and further enable the identification of causative genetic variants has become essential in both genomic and genetic studies.We proposed Deopen, a hybrid framework mainly based on a deep convolutional neural network, to automatically learn the regulatory code of DNA sequences and predict chromatin accessibility. In a series of comparison with existing methods, we show the superior performance of our model in not only the classification of accessible regions against background sequences sampled at random, but also the regression of DNase-seq signals. Besides, we further visualize the convolutional kernels and show the match of identified sequence signatures and known motifs. We finally demonstrate the sensitivity of our model in finding causative noncoding variants in the analysis of a breast cancer dataset. We expect to see wide applications of Deopen with either public or in-house chromatin accessibility data in the annotation of the human genome and the identification of non-coding variants associated with diseases.Deopen is freely available at https://github.com/kimmo1019/Deopen.ruijiang@tsinghua.edu.cn.Supplementary data are available at Bioinformatics online.

  View details for PubMedID 29069282

• Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG. Genome biology Duren, Z., Chang, F., Naqing, F., Xin, J., Liu, Q., Wong, W. H. 2022; 23 (1): 114

  Abstract

  Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory potential, for single cell multiome data. This concept is further used for the construction of subpopulation-specific cis-regulatory networks. The capability of inferring useful regulatory network is demonstrated by the two-fold increment on network inference accuracy compared to the Pearson correlation-based method and the 27-fold enrichment of GWAS variants for inflammatory bowel disease in the cis-regulatory elements. The R package scREG provides comprehensive functions for single cell multiome data analysis.

  View details for DOI 10.1186/s13059-022-02682-2

  View details for PubMedID 35578363

• DualGCN: a dual graph convolutional network model to predict cancer drug response. BMC bioinformatics Ma, T., Liu, Q., Li, H., Zhou, M., Jiang, R., Zhang, X. 2022; 23 (Suppl 4): 129

  Abstract

  BACKGROUND: Drug resistance is a critical obstacle in cancer therapy. Discovering cancer drug response is important to improve anti-cancer drug treatment and guide anti-cancer drug design. Abundant genomic and drug response resources of cancer cell lines provide unprecedented opportunities for such study. However, cancer cell lines cannot fully reflect heterogeneous tumor microenvironments. Transferring knowledge studied from in vitro cell lines to single-cell and clinical data will be a promising direction to better understand drug resistance. Most current studies include single nucleotide variants (SNV) as features and focus on improving predictive ability of cancer drug response on cell lines. However, obtaining accurate SNVs from clinical tumor samples and single-cell data is not reliable. This makes it difficult to generalize such SNV-based models to clinical tumor data or single-cell level studies in the future.RESULTS: We present a new method, DualGCN, a unified Dual Graph Convolutional Network model to predict cancer drug response. DualGCN encodes both chemical structures of drugs and omics data of biological samples using graph convolutional networks. Then the two embeddings are fed into a multilayer perceptron to predict drug response. DualGCN incorporates prior knowledge on cancer-related genes and protein-protein interactions, and outperforms most state-of-the-art methods while avoiding using large-scale SNV data.CONCLUSIONS: The proposed method outperforms most state-of-the-art methods in predicting cancer drug response without the use of large-scale SNV data. These favorable results indicate its potential to be extended to clinical and single-cell tumor samples and advancements in precision medicine.

  View details for DOI 10.1186/s12859-022-04664-4

  View details for PubMedID 35428192

• scGraph: a graph neural network-based approach to automatically identify cell types. Bioinformatics (Oxford, England) Yin, Q., Liu, Q., Fu, Z., Zeng, W., Zhang, B., Zhang, X., Jiang, R., Lv, H. 2022

  Abstract

  MOTIVATION: Single cell technologies play a crucial role in revolutionizing biological research over the past decade, which strengthens our understanding in cell differentiation, development, and regulation from a single-cell level perspective. Single-cell RNA sequencing (scRNA-seq) is one of the most common single cell technologies, which enables probing transcriptional states in thousands of cells in one experiment. Identification of cell types from scRNA-seq measurements is a fundamental and crucial question to answer. Most previous studies directly take gene expression as input while ignoring the comprehensive gene-gene interactions.RESULTS: We propose scGraph, an automatic cell identification algorithm leveraging gene interaction relationships to enhance the performance of the cell type identification. ScGraph is based on a graph neural network to aggregate the information of interacting genes. In a series of experiments, we demonstrate that scGraph is accurate and outperforms eight comparison methods in the task of cell type identification. Moreover, scGraph automatically learns the gene interaction relationships from biological data and the pathway enrichment analysis shows consistent findings with previous analysis, providing insights on the analysis of regulatory mechanism.AVAILABILITY: scGraph is freely available at https://github.com/QijinYin/scGraph and https://figshare.com/articles/software/scGraph/17157743.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  View details for DOI 10.1093/bioinformatics/btac199

  View details for PubMedID 35394015

• DeepHistone: a deep learning approach to predicting histone modifications Yin, Q., Wu, M., Liu, Q., Lv, H., Jiang, R. BMC. 2019: 193

  Abstract

  Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage. However, high-throughput experimental techniques such as ChIP-seq are usually expensive and time-consuming, prohibiting the establishment of a histone modification landscape for hundreds of cell types across dozens of histone markers. These disadvantages have been appealing for computational methods to complement experimental approaches towards large-scale analysis of histone modifications.We proposed a deep learning framework to integrate sequence information and chromatin accessibility data for the accurate prediction of modification sites specific to different histone markers. Our method, named DeepHistone, outperformed several baseline methods in a series of comprehensive validation experiments, not only within an epigenome but also across epigenomes. Besides, sequence signatures automatically extracted by our method was consistent with known transcription factor binding sites, thereby giving insights into regulatory signatures of histone modifications. As an application, our method was shown to be able to distinguish functional single nucleotide polymorphisms from their nearby genetic variants, thereby having the potential to be used for exploring functional implications of putative disease-associated genetic variants.DeepHistone demonstrated the possibility of using a deep learning framework to integrate DNA sequence and experimental data for predicting epigenomic signals. With the state-of-the-art performance, DeepHistone was expected to shed light on a variety of epigenomic studies. DeepHistone is freely available in https://github.com/QijinYin/DeepHistone .

  View details for DOI 10.1186/s12864-019-5489-4

  View details for Web of Science ID 000464120900013

  View details for PubMedID 30967126

  View details for PubMedCentralID PMC6456942

• A sequence-based method to predict the impact of regulatory variants using random forest BMC SYSTEMS BIOLOGY Liu, Q., Gan, M., Jiang, R. 2017; 11: 7

  Abstract

  Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their hosting regulatory elements, it remains a great challenge to characterize the risk of a genetic variant within the implicated genome sequence. Therefore, it is essential to develop an effective computational model that is not only capable of predicting the potential risk of a genetic variant but also valid in interpreting how the function of the genome is affected with the occurrence of the variant.We developed a method named kmerForest that used a random forest classifier with k-mer counts to predict accessible chromatin regions purely based on DNA sequences. We demonstrated that our method outperforms existing methods in distinguishing known accessible chromatin regions from random genomic sequences. Furthermore, the performance of our method can further be improved with the incorporation of sequence conservation features. Based on this model, we assessed importance of the k-mer features by a series of permutation experiments, and we characterized the risk of a single nucleotide polymorphism (SNP) on the function of the genome using the difference between the importance of the k-mer features affected by the occurrence of the SNP. We conducted a series of experiments and showed that our model can well discriminate between pathogenic and normal SNPs. Particularly, our model correctly prioritized SNPs that are proved to be enriched for the binding sites of FOXA1 in breast cancer cell lines from previous studies.We presented a novel method to interpret functional genetic variants purely base on DNA sequences. The proposed k-mer based score offers an effective means of measuring the impact of SNPs on the function of the genome, and thus shedding light on the identification of genetic risk factors underlying complex traits and diseases.

  View details for DOI 10.1186/s12918-017-0389-1

  View details for Web of Science ID 000404915800002

  View details for PubMedID 28361702

  View details for PubMedCentralID PMC5374684