Selected Publications

* These authors contributed equally to the paper as first authors
$ To whom correspondence should be addressed

2020

Elucidation of Biological Networks Across Complex Diseases Using Single-Cell Omics.
Yang Li, Anjun Ma, Ewy A. Mathe, Bingqiang Liu, Lang Li, Qin Ma$
Trends in Genetics
[In press]


scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses.
Juexin Wang*, Anjun Ma*, Yuzhou Chang, Jianting Gong, Yuexu Jiang, Hongjun Fu, Cankun Wang, Ren Qi, Qin Ma$, Dong Xu$
bioRxiv
[Abstract] [Full paper]


IRIS3: Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq.
Anjun Ma*, Cankun Wang*, Yuzhou Chang, Faith H. Brennan, Adam McDermaid, Bingqiang Liu, Chi Zhang, Phillip G. Popovich, Qin Ma$
Nucleic Acids Research
[Abstract] [Full paper]


Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients.
Xing Shi*, Zhancheng Gao*, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang$, Jun Yu$
Genomics, Proteomics & Bioinformatics
[Abstract] [Full paper]


Integrative Methods and Practical Challenges for Single-cell Multi-omics.
Anjun Ma, Adam McDermaid, Jennifer Xu, Yuzhou Chang, Qin Ma$
Trends in Biotechnology
[Abstract] [Full paper]


Network analyses in microbiome based on high-throughput multi-omics data.
Zhaoqian Liu, Anjun Ma, Ewy Mathe, Marlena Merling, Qin Ma$, Bingqiang Liu$
Briefings in Bioinformatics
[Abstract] [Full paper]


2019

Prediction of Regulatory Motifs from Human ChIP-Sequencing Data using a Deep Learning Framework.
Jinyu Yang, Anjun Ma, Adam D. Hoppe, Cankun Wang, Yang Li, Chi Zhang, Yan Wang, Bingqiang Liu$, Qin Ma$
Nucleic Acids Research
[Abstract] [Full paper]


LTMG: A novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data.
Changlin Wan, Wennan Chang, Yu Zhang, Fenil Shah, Xiaoyu Lu, Yong Zang, Anru Zhang, Sha Cao, Melissa Fishel, Qin Ma$, Chi Zhang$
Nucleic Acids Research
[Abstract] [Full paper]


SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting.
Bin Yu$, Wenying Qiu, Cheng Chen, Anjun Ma, Jing Jiang, Hongyan Zhou, Qin Ma$
Bioinformatics
[Abstract] [Full paper]


IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.
Brandon Monier*, Adam McDermaid*, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma$
PLoS Computational Biology
[Abstract] [Full paper]


QUBIC2: A novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.
Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang$, Qin Ma$
Bioinformatics
[Abstract] [Full paper]


Protein-protein interaction sites prediction by ensembling random forests with synthetic minority oversampling technique.
Xiaoying Wang*, Bin Yu$*, Anjun Ma, Cheng Chen, Bingqiang Liu, Qin Ma$
Bioinformatics
[Abstract] [Full paper]


MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.
Anjun Ma*, Minxuan Sun*, Adam McDermaid, Bingqiang Liu$, Qin Ma$
Bioinformatics
[Abstract] [Full paper]


Clustering and Classification Methods for Single-cell RNA-sequencing Data.
Ren Qi, Anjun Ma, Qin Ma, Quan Zou$
Briefings in Bioinformatics
[Abstract] [Full paper]


Gene Regulatory Networks for Lignin Biosynthesis in Switchgrass (Panicum virgatum).
Xiaolan Rao, Xin Chen, Hui Shen, Qin Ma, Guifen Li, Yuhong Tang, Maria Pena, William York, Taylor Frazier, Scott Lenaghan, Xirong Xiao, Fang Chen and Richard A. Dixon$
Plant Biotechnology Journal
[Abstract] [Full paper]


2018

Interpretation of differential gene expression results of RNA-Seq data: review and integration.
Adam McDermaid*, Brandon Monier*, Jing Zhao, Bingqiang Liu, Qin Ma$
Briefings in Bioinformatics
[Abstract] [Full paper]


It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.
Juan Xie, Anjun Ma, Anne Fennell, Qin Ma$, Jing Zhao$
Briefings in Bioinformatics
[Abstract] [Full paper]


LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property.
Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang, Ying Li$
Briefings in Bioinformatics
[Abstract] [Full paper]


2017

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.
Sheng-Yong Niu*, Jinyu Yang*, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma$
Briefings in Bioinformatics
[Abstract] [Full paper]


DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.
Jinyu Yang, Xin Chen, Adam McDermaid, Qin Ma$
Bioinformatics
[Abstract] [Full paper]


QUBIC: a Bioconductor package for qualitative biclustering analysis of gene co-expression data.
Yu Zhang*, Juan Xie*, Jinyu Yang, Anne Fennell, Qin Ma$
Bioinformatics
[Abstract] [Full paper]


DOOR: A prokaryote operon database for gene organization and function discovery.
Huansheng Cao*, Qin Ma*, Xin Chen, Ying Xu$
Briefings in Bioinformatics
[Abstract] [Full paper]


An algorithmic perspective of de-novo cis-regulatory motif finding based on ChIP-seq data.
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma$
Briefings in Bioinformatics
[Abstract] [Full paper]


Systems-Level Understanding of the Impact of Ethanol-Induced Stresses and Adaptation in E. coli.
Huansheng Cao*, Wei Du*, Yuedong Yang, Yu Shang, Gaoyang Li, Yaoqi Zhou, Qin Ma$, Ying Xu$
Scientific Reports
[Abstract] [Full paper]


2016

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.
Bingqiang Liu, Chuan Zhou, Guojun Li, Hanyuan Zhang, Erliang Zeng, Qin Ma$
Scientific Reports
[Abstract] [Full paper]


An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.
Bingqiang Liu, Hanyuan Zhang, Chuan Zhou, Guojun Li, Anne Fennell, Guanghui Wang, Yu Kang, Qi Liu, Qin Ma$
BMC Genomics
[Abstract] [Full paper]


The understanding of circular RNAs as special triggers in carcinogenesis.
Zhuoyuan Xin, Qin Ma, Shuangchun Ren, Guoqing Wang$, Fan Li$
Briefings in Functional Genomics
[Abstract] [Full paper]


2015

Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.
Wen-Chi Chou*, Qin Ma*, Shihui Yang, Sha Cao, Dawn M. Klingeman, Steven D. Brown, Ying Xu$
Nucleic Acids Research
[Abstract] [Full paper]


2014

DMINDA: An integrated web server for DNA motif identification and analysis.
Qin Ma*, Hanyuan Zhang*, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu$
Nucleic Acids Research
[Abstract] [Full paper]


DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Xizeng Mao*, Qin Ma, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu$
Nucleic Acids Research
[Abstract] [Full paper]


Comprehensive Characterization of the Genomic Alterations in Human Gastric Cancer.
Juan Cui, Yanbin Yin, Qin Ma, Guoqing Wang, Victor Olman, Yu Zhang, Wen-Chi Chou, Celine S. Hong, Chi Zhang, Sha Cao, Xizeng Mao, Ying Li, Steve Qin, Shaying Zhao, Jing Jiang, Phil Hastings, Fan Li, Ying Xu$
International journal of cancer
[Abstract] [Full paper]


2013

A phylogenetic model for understanding the effect of gene duplication on cancer progressing.
Qin Ma, Jaxk Reeves, David A. Liberles, Lili Yu, Zheng Chang, Jing Zhao, Juan Cui, Ying Xu$, Liang Liu$
Nucleic Acids Research
[Abstract] [Full paper]


Computational Analyses of Transcriptomic Data Reveal the Dynamic Organization of the E. coli Chromosome under Different Conditions.
Qin Ma*, Yanbin Yin, Mark A. Shell, Han Zhang, Guojun Li, Ying Xu$
Nucleic Acids Research
[Abstract] [Full paper]


An integrated toolkit for accurate prediction and analysis of cis regulatory elements at a genome scale.
Qin Ma*, Bingqiang Liu*, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu$
Bioinformatics
[Abstract] [Full paper]


2012

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis.
Shan Wang*, Yanbin Yin*, Qin Ma, Xiaojia Tang, Kan Bao, Dongyun Hao, Ying Xu$
BMC Plant Biology
[Abstract] [Full paper]


2011

Integration of Sequence-Similarity and Functional Association Information Can Overcome Intrinsic Problems in Orthology Mapping across Bacterial Genomes.
Guojun Li, Qin Ma, Xizeng Mao, Yanbin Yin, Xiaoran Zhu, Ying Xu$
Nucleic Acids Research
[Abstract] [Full paper]


A new framework for identifying cis-regulatory motifs in prokaryotes.
Guojun Li, Bingqiang Liu, Qin Ma, Ying Xu$
Nucleic Acids Research
[Abstract] [Full paper]


2009

QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data.
Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, Ying Xu$
Nucleic Acids Research
[Abstract] [Full paper]