A. Ma

发表

Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning

Dongjun Chung, J. Otero, Juexin Wang, 2021, bioRxiv.

Microglia coordinate cellular interactions during spinal cord repair in mice

Faith H. Brennan, Qi Guo, D. McTigue, 2022, Nature Communications.

Androgen conspires with the CD8+ T cell exhaustion program and contributes to sex bias in cancer

Lei Zhou, Dongjun Chung, L. Fong, 2022, Science Immunology.

QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data

Bingqiang Liu, Qin Ma, Sha Cao, 2019, Bioinform..

Clustering and classification methods for single-cell RNA-sequencing data

Quan Zou, Anjun Ma, Ren Qi, 2020, Briefings Bioinform..

Prediction of protein-protein interactions based on elastic net and deep forest

Bin Yu, Cheng Chen, Bingqiang Liu, 2020, bioRxiv.

A Review of Matched-pairs Feature Selection Methods for Gene Expression Data Analysis

Sen Liang, Qin Ma, Yan Wang, 2018, Computational and structural biotechnology journal.

An explainable graph neural framework to identify cancer-associated intratumoral microbial communities

Qin Ma, Bingqiang Liu, Dong Xu, 2023, bioRxiv.

Computational methods and challenges in analyzing intratumoral microbiome data.

Anjun Ma, Bingqiang Liu, Zhaoqian Liu, 2023, Trends in microbiology.

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

Dong Xu, Qin Ma, Yuexu Jiang, 2020, Nature Communications.

Inductive inference of gene regulatory network using supervised and semi-supervised graph neural networks

Trupti Joshi, Dong Xu, Qin Ma, 2020, bioRxiv.

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health.

Philip D. Blood, Ellen M. Quardokus, Matthew A. Wyczalkowski, 2022, Nature aging.

SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting

Cheng Chen, Qin Ma, Bin Yu, 2020, Bioinform..

DeepMal: Accurate prediction of protein malonylation sites by deep neural networks

Bin Yu, Shan Li, Minghui Wang, 2020 .

Single-Cell Techniques and Deep Learning in Predicting Drug Response.

Dong Xu, Qin Ma, Anjun Ma, 2020, Trends in pharmacological sciences.

Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data

Dongjun Chung, Anjun Ma, Bingqiang Liu, 2021, bioRxiv.

Network analyses in microbiome based on high-throughput multi-omics data

Qin Ma, Anjun Ma, Ewy Mathé, 2020, Briefings Bioinform..

Spatial omics representation and functional tissue module inference using graph Fourier transform

Garry P. Nolan, S. Rodig, D. Barouch, 2023, bioRxiv.

SUSD2 suppresses CD8+ T cell antitumor immunity by targeting IL-2 receptor signaling

D. Carbone, Haitao Wen, Weipeng Gong, 2022, Nature Immunology.

Deep learning analysis of single‐cell data in empowering clinical implementation

Juexin Wang, Dong Xu, A. Ma, 2022, Clinical and translational medicine.

Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data

Yan Wang, Qin Ma, Anjun Ma, 2021, Briefings Bioinform..

Integrative Methods and Practical Challenges for Single-Cell Multi-omics.

Qin Ma, Adam McDermaid, Anjun Ma, 2020, Trends in biotechnology.

MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data

Yan Wang, Nan Sheng, Shuangquan Zhang, 2022, Bioinform..

The use of single-cell multi-omics in immuno-oncology

Anjun Ma, Gang Xin, Qin Ma, 2022, Nature Communications.

Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique

Xiaoying Wang, Bin Yu, Bingqiang Liu, 2018, Bioinform..

It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data

Jing Zhao, Juan Xie, Qin Ma, 2019, Briefings Bioinform..

RESEPT: tissue architecture inference and visualization from spatially resolved transcriptomics

Dong Xu, Dongjun Chung, Juexin Wang, 2021, bioRxiv.

TREATMENT WITH SOLUBLE CD24 ATTENUATES COVID-19-ASSOCIATED SYSTEMIC IMMUNOPATHOLOGY

Dongjun Chung, C. Bolyard, Qin Ma, 2021, Journal of Hematology & Oncology.

Single-cell biological network inference using a heterogeneous graph transformer

Juexin Wang, Duolin Wang, Anjun Ma, 2023, Nature Communications.

Deep transfer learning of cancer drug responses by integrating bulk and single-cell RNA-seq data

Qi-En Wang, Qin Ma, Anjun Ma, 2022, Nature Communications.

Deep Transfer Learning of Drug Responses by Integrating Bulk and Single-cell RNA-seq data

Lang Li, Qin Ma, Anjun Ma, 2021, bioRxiv.

Repression of ferroptotic cell death by mitochondrial calcium signaling

R. Xie, Haitao Wen, Xiaolin Cheng, 2023, Research square.

IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq

Faith H. Brennan, P. Popovich, Qin Ma, 2020, Nucleic Acids Res..

Biological network inference from single-cell multi-omics data using heterogeneous graph transformer

Lingtao Su, Juexin Wang, Zihai Li, 2021, bioRxiv.

Explainable Deep Hypergraph Learning Modeling the Peptide Secondary Structure Prediction

Q. Zou, Qin Ma, Leyi Wei, 2023, Advanced science.

scGMAI: a Gaussian mixture model for clustering single-cell RNA-Seq data based on deep autoencoder.

Xiaolin Wang, Bin Yu, Chen Chen, 2020, Briefings in bioinformatics.

Elucidation of Biological Networks across Complex Diseases Using Single-Cell Omics.

Lang Li, E. Mathé, Qin Ma, 2020, Trends in genetics : TIG.

A Central Edge Selection Based Overlapping Community Detection Algorithm for the Detection of Overlapping Structures in Protein–Protein Interaction Networks

Lan Huang, Bingqiang Liu, Qin Ma, 2018, Molecules.

OP-CBIO181031 2395..2402

Qin Ma, Bin Yu, Bingqiang Liu, 2019 .

QUBIC2: A novel biclustering algorithm for large-scale bulk RNA-sequencing and single-cell RNA-sequencing data analysis

Chi Zhang, Juan Xie, Bingqiang Liu, 2018, bioRxiv.

DESSO-DB: A web database for sequence and shape motif analyses and identification

Qin Ma, Anjun Ma, Cankun Wang, 2022, Computational and structural biotechnology journal.

Assessing deep learning algorithms in cis-regulatory motif finding based on genomic sequencing data

Yan Wang, Dong Xu, Qin Ma, 2020, bioRxiv.

QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.

Juan Xie, Qin Ma, Chi Zhang, 2020, Bioinformatics.

RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis

Q. Ma, Xin Chen, Chao Liu, 2018, bioRxiv.

Computational elucidation of regulatory network responding to acid stress in Lactococcus lactis MG1363

Q. Ma, Xin Chen, Huansheng Cao, 2018 .

MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer

Bingqiang Liu, Dong Xu, Xiaoying Wang, 2023, bioRxiv.

scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data

Juexin Wang, Dong Xu, Hao Cheng, 2022, Bioinform..

A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset

M. McCarter, M. Churchman, G. Riedlinger, 2023, bioRxiv.

Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single-cell transcriptomic analysis

Cankun Wang, Xuefeng Liu, A. Ma, 2023, bioRxiv.

Identification of HPV oncogene and host cell differentiation associated cellular heterogeneity in cervical cancer via single‐cell transcriptomic analysis

Cankun Wang, Xuefeng Liu, A. Ma, 2023, Journal of medical virology.

Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data

Qi Guo, Qin Ma, Cankun Wang, 2023, bioRxiv.

Inference of disease-associated microbial biomarkers based on metagenomic and 1 metatranscriptomic data 2 3

Jing Zhao, Zhaoqian Liu, A. Ma, 2022 .

ssREAD: A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease

Cankun Wang, A. Ma, Megan McNutt, 2023, bioRxiv.

SpaGFT is a graph Fourier transform for tissue module identification from spatially resolved transcriptomics

Yuzhou Chang, Bingqiang Liu, Zihai Li, 2022 .

Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework

Yan Wang, Bingqiang Liu, Qin Ma, 2019, Nucleic acids research.

DNNAce: Prediction of prokaryote lysine acetylation sites through deep neural networks with multi-information fusion

Cheng Chen, Bingqiang Liu, Anjun Ma, 2020 .

Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique

Q. Ma, Bin Yu, Bingqiang Liu, 2018, Bioinform..

Treatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology

Anqi Li, Yuzhou Chang, Zequn Sun, 2022, Journal of Hematology & Oncology.

TREATMENT WITH SOLUBLE CD24 ATTENUATES COVID-19-ASSOCIATED SYSTEMIC IMMUNOPATHOLOGY

Dongjun Chung, Mohammad Yusuf, C. Bolyard, 2021, medRxiv.

Computational elucidation of regulatory network 1 responding to acid stress in Lactococcus lactis MG1363

Q. Ma, Xin Chen, Huansheng Cao, 2018 .

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

Dong Xu, H. Fu, Juexin Wang, 2021, Nature Communications.

A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD)

Cankun Wang, A. Ma, Megan McNutt, 2024, Nature communications.

A Single-cell and Spatial RNA-seq Database for Alzheimer’s Disease (ssREAD)

Cankun Wang, A. Ma, Megan McNutt, 2023, bioRxiv.

A Weighted Two-stage Sequence Alignment Framework to Identify DNA Motifs from ChIP-exo Data

Qin Ma, A. Fennell, Cankun Wang, 2023, bioRxiv.

GraphPred: An approach to predict multiple DNA motifs from ATAC-seq data using graph neural network and coexisting probability

Yan Wang, Anjun Ma, Nan Sheng, 2022, bioRxiv.

Graph Fourier transform for spatial omics representation and analyses of complex organs

D. Barouch, Yuzhou Chang, Bingqiang Liu, 2024, Research square.

An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.

R. Hoyd, Bingqiang Liu, Zhaoqian Liu, 2024, Advanced science.

Autoencoder to Identify Sex-Specific Sub-phenotypes in Alzheimer’s Disease Progression Using Longitudinal Electronic Health Records

Cankun Wang, A. Ma, Yu Huang, 2024, medRxiv.