Q. Ma

发表

Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective

Ying Xu, Qin Ma, Chao Liu, 2014, Science China Life Sciences.

Root system influence on high dimensional leaf phenotypes over the grapevine growing season

Allison J. Miller, Laura L. Klein, D. Chitwood, 2020, bioRxiv.

Identifying anti-cancer drug response related genes using an integrative analysis of transcriptomic and genomic variations with cell line-based drug perturbations

Wei Zhang, Yi Sun, Qi Liu, 2016, Oncotarget.

RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis

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

Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes

Ying Xu, Guojun Li, Qin Ma, 2011, Nucleic acids research.

Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum

Wen-Chi Chou, Qin Ma, Sha Cao, 2015, Nucleic acids research.

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses

Bingqiang Liu, Erliang Zeng, Guojun Li, 2016, Scientific Reports.

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes

Bingqiang Liu, Guojun Li, Qin Ma, 2016, BMC Genomics.

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

Yaoqi Zhou, Yuedong Yang, Ying Xu, 2017, Scientific Reports.

OP-BIBJ170088 1..8

Ying Xu, Q. Ma, Xin Chen, 2017 .

A new framework for identifying cis-regulatory motifs in prokaryotes

Ying Xu, Bingqiang Liu, Guojun Li, 2010, Nucleic acids research.

QServer: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters

Ying Xu, Guojun Li, Fengfeng Zhou, 2012, PloS one.

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 .

DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses

Xin Chen, Qin Ma, Adam McDermaid, 2017, Bioinform..

Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard

Allison J. Miller, Laura L. Klein, D. Chitwood, 2018, bioRxiv.

MetaMed: Linking Microbiota Functions with Medicine Therapeutics

Wei Jia, Q. Ma, K. Ning, 2019, mSystems.

OP-CBIO130411 2261..2268

Ying Xu, Yanbin Yin, Guojun Li, 2013 .

A phylogenetic model for understanding the effect of gene duplication on cancer progression

Jing Zhao, J. Reeves, D. Liberles, 2013, Nucleic acids research.

A fine-scale map of genome-wide recombination in divergent Escherichia coli population.

Songnian Hu, Jun Yu, Jingfa Xiao, 2020, Briefings in bioinformatics.

Deciphering relationship between microhomology and in-frame mutation occurrence in human CRISPR-based gene knockout.

Guohui Chuai, Jifang Yan, Chi Zhou, 2016, Molecular therapy. Nucleic acids.

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.

LTMG (Left truncated mixture Gaussian) based modeling of transcriptional regulatory heterogeneities in single cell RNA-seq data – a perspective from the kinetics of mRNA metabolism

Q. Ma, Xin Chen, M. Fishel, 2018, bioRxiv.

Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities

Q. Ma, H. Bücking, S. Subramanian, 2019, Front. Microbiol..

New Insights into Clostridia Through Comparative Analyses of Their 40 Genomes

Ying Xu, Yanbin Yin, Q. Ma, 2014, BioEnergy Research.

An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data

Yang Li, Bingqiang Liu, Qin Ma, 2017, Briefings Bioinform..

GmZPR3d Interacts with GmHD-ZIP III Proteins and Regulates Soybean Root and Nodule Vascular Development

Juan Xie, Q. Ma, V. Hindié, 2019, International journal of molecular sciences.

Mining genes involved in the stratification of Paris Polyphyllaseeds using high-throughput embryo Transcriptome sequencing

Songnian Hu, Q. Ma, Bing Zhang, 2013, BMC Genomics.

Gene-centric intra- and inter-clade recombination in a context of Esche-richia coli subpopulations

Songnian Hu, Jun Yu, Jiayan Wu, 2018, bioRxiv.

A tandem duplication within the fibrillin 1 gene is associated with the mouse tight skin mutation.

S. Jimenez, J. Moskow, Q. Ma, 1996, Genome research.

Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard

Allison J. Miller, Laura L. Klein, D. Chitwood, 2018, bioRxiv.

OP-NARE131048 654..659

Ying Xu, Fenglou Mao, Q. Ma, 2013 .

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

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

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.

A link density clustering algorithm based on automatically selecting density peaks for overlapping community detection

Qin Ma, Lan Huang, Wei Pang, 2016 .

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..

Systematic Prediction of Regulatory Motifs from Human ChIP-Sequencing Data Based on a Deep Learning Framework

Qin Ma, Bingqiang Liu, Jinyu Yang, 2018, bioRxiv.

Analysis of the murine All-1 gene reveals conserved domains with human ALL-1 and identifies a motif shared with DNA methyltransferases.

C. Croce, H. Alder, T. Nakamura, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

Jing Zhao, Yu Kang, Qin Ma, 2017, Briefings Bioinform..

IRIS-DGE: An integrated RNA-seq data analysis and interpretation system for differential gene expression

Qin Ma, Jing Zhao, Anne Fennell, 2018, bioRxiv.

GeneQC: A quality control tool for gene expression estimation based on RNA-sequencing reads mapping

Qin Ma, Juan Xie, Xin Chen, 2018, bioRxiv.

QUBIC: a bioconductor package for qualitative biclustering analysis of gene co‐expression data

Yu Zhang, Chi Zhang, Juan Xie, 2016, Bioinform..

Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris)

Q. Ma, M. Nepal, A. Varenhorst, 2018, Biochemical Genetics.

LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property

Yanchun Liang, Wei Du, Qin Ma, 2018, Briefings Bioinform..

Physical properties of DNA may direct the binding of nucleoid-associated proteins along the E. coli genome.

Ying Xu, Guoqing Liu, Q. Ma, 2018, Mathematical biosciences.

Link community detection based on line graphs with a novel link similarity measure

Yan Wang, Qin Ma, Lan Huang, 2016 .

Mining genes involved in the stratification of Paris Polyphylla seeds using high-throughput embryo Transcriptome sequencing

Songnian Hu, Q. Ma, Bing Zhang, 2013, BMC Genomics.

The understanding of circular RNAs as special triggers in carcinogenesis.

Q. Ma, Guoqing Wang, Zhuoyuan Xin, 2016, Briefings in functional genomics.

Gene regulatory networks associated with lateral root and nodule development in soybean

Erliang Zeng, Q. Ma, S. Smita, 2019, bioRxiv.

Deciphering relationship between microhomology and in-frame mutation occurrence in human CRISPR-based gene knockout

Qin Ma, Chenyu Zhu, Guohui Chuai, 2016, Molecular therapy. Nucleic acids.

Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions

Ying Xu, Guojun Li, Qin Ma, 2013, Nucleic acids research.

Interpretation of differential gene expression results of RNA-seq data: review and integration

Jing Zhao, Bingqiang Liu, Qin Ma, 2018, Briefings Bioinform..

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

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

DOOR: a prokaryotic operon database for genome analyses and functional inference

Ying Xu, Qin Ma, Xin Chen, 2019, Briefings Bioinform..

DOOR 2.0: presenting operons and their functions through dynamic and integrated views

Xin Chen, Ying Xu, Jincai Yang, 2013, Nucleic Acids Res..

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

Ying Xu, Guojun Li, Qin Ma, 2009, Nucleic acids research.

De novo transcriptomic analysis and development of EST-SSR markers in the Siberian tiger (Panthera tigris altaica)

Q. Ma, Yuehui Ma, Jianzhang Ma, 2016, Molecular Genetics and Genomics.

Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective

Fei Ji, Ying Xu, Q. Ma, 2014, Science China Life Sciences.

Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency

Qin Ma, Ying Xu, Ying Xu, 2013, Genom. Proteom. Bioinform..

Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies

Xiangrong Liu, Qin Ma, Jichang Wu, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Changes of isoflavones during processing of soy protein isolates

Q. Ma, P. Krishnan, Chunyang Wang, 1998 .

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.

Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients

Yu Kang, Qin Ma, Xing Shi, 2019, Genom. Proteom. Bioinform..

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

Qin Ma, Yanbin Yin, Yanbin Yin, 2012, BMC Plant Biology.

Gene-centric intra- and inter-clade recombination in a context of Esche-richia coli subpopulations

Songnian Hu, Jun Yu, Jiayan Wu, 2017, bioRxiv.

Differential gene expression in non-transgenic and transgenic “M.26” apple overexpressing a peach CBF gene during the transition from eco-dormancy to bud break

Q. Ma, T. Artlip, M. Wisniewski, 2019, Horticulture Research.

Nitrogen remobilization and conservation, and underlying senescence‐associated gene expression in the perennial switchgrass Panicum virgatum

Qin Ma, Michael Udvardi, Patrick X Zhao, 2016, The New phytologist.

DMINDA: an integrated web server for DNA motif identification and analyses

Xin Chen, Ying Xu, Chuan Zhou, 2014, Nucleic Acids Res..

Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard

Allison J. Miller, Laura L. Klein, D. Chitwood, 2018, bioRxiv.

Revisiting operons: an analysis of the landscape of transcriptional units in E. coli

Xin Chen, Ying Xu, Bingqiang Liu, 2015, BMC Bioinformatics.

ViDGER: An R package for integrative interpretation of differential gene expression results of RNA-seq data

Qin Ma, Jing Zhao, Brandon Monier, 2018, bioRxiv.

A probabilistic model-based bi-clustering method for single-cell transcriptomic data analysis

Xin Chen, Qin Ma, Chi Zhang, 2017, bioRxiv.

Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum)

R. Dixon, Hui Shen, S. Lenaghan, 2018, Plant biotechnology journal.

Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum)

R. Dixon, Hui Shen, S. Lenaghan, 2018, Plant biotechnology journal.

Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data

Qin Ma, Richard A. Dixon, Chi Zhang, 2016, BioEnergy Research.

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

Juan Xie, Q. Ma, G. Cramer, 2019, BMC Plant Biology.

Differential gene expression in non-transgenic and transgenic “M.26” apple overexpressing a peach CBF gene during the transition from eco-dormancy to bud break

Q. Ma, T. Artlip, M. Wisniewski, 2019, Horticulture Research.

SeqTU: A Web Server for Identification of Bacterial Transcription Units

Ying Xu, Wen-Chi Chou, Xin Chen, 2017, Scientific Reports.

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes

Qi Liu, Guojun Li, Guanghui Wang, 2016, BMC Genomics.

An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale

Ying Xu, Chuan Zhou, Bingqiang Liu, 2013, Bioinform..

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes

Jun Yu, Jingfa Xiao, T. Jiang, 2017, BMC Genomics.

QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.

Qin Ma, Anne Fennell, Yu Zhang, 2016, Bioinformatics.

Rootstock effects on scion phenotypes in a ‘Chambourcin’ experimental vineyard

Allison J. Miller, Laura L. Klein, D. Chitwood, 2018, Horticulture Research.

Nitrogen remobilization and conservation, and underlying senescence‐associated gene expression in the perennial switchgrass Panicum virgatum

Jun Li, Ying Xu, Yuhong Tang, 2016, The New phytologist.

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

Juan Xie, Q. Ma, G. Cramer, 2019, BMC Plant Biology.

Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris)

Q. Ma, M. Nepal, A. Varenhorst, 2018, Biochemical Genetics.

Is circRNAs biogenesis an accident in pre-mRNA alternative splicing ?

Q. Ma, Guoqing Wang, Zhuoyuan Xin, 2016 .

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

Jing Zhao, Qin Ma, Yu Kang, 2018, Briefings Bioinform..

Gene-centric intra-and inter-clade recombination in a context of Esche-3 richia coli subpopulations 4

Songnian Hu, Jun Yu, Jiayan Wu, 2018 .

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

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

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

Yanbin Yin, Q. Ma, Xiaojia Tang, 2012, BMC Plant Biology.

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

Yu Zhang, Yanchun Liang, Ying Li, 2017, BMC Bioinformatics.

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

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

MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network

Jing Zhao, Yu Zhang, Burair Alsaihati, 2018, Quantitative Biology.