Qin Ma

Publication Activity (10 Years)

Years Active: 2009-2024
Publications (10 Years): 43

Top Topics

Protein Interaction

Unlabeled Samples

Top Venues

Briefings Bioinform.

Nucleic Acids Res.

Publications

Yang Li, Anjun Ma, Yizhong Wang, Qi Guo, Cankun Wang, Hongjun Fu, Bingqiang Liu, Qin Ma
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. Briefings Bioinform. 25 (5) (2024)
Yang Li, Yizhong Wang, Cankun Wang, Anjun Ma, Qin Ma, Bingqiang Liu
A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data. Patterns 5 (3) (2024)
Yitian Fang, Yi Jiang, Leyi Wei, Qin Ma, Zhixiang Ren, Qianmu Yuan, Dong-Qing Wei
DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model. Bioinform. 39 (12) (2023)
Zhaoqian Liu, Qi Wang, Anjun Ma, Shaohong Feng, Dongjun Chung, Jing Zhao, Qin Ma, Bingqiang Liu
Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data. Comput. Biol. Medicine 165 (2023)
Juan Xie, Hyeongseon Jeon, Gang Xin, Qin Ma, Dongjun Chung
LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity. PLoS Comput. Biol. 19 (7) (2023)
Ying Li, Hang Sun, Wensi Fang, Qin Ma, Siyu Han, Rui Wang-Sattler, Wei Du, Qiong Yu
SURE: Screening unlabeled samples for reliable negative samples based on reinforcement learning. Inf. Sci. 629 (2023)
Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma, Yan Wang
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data. Briefings Bioinform. 23 (1) (2022)
Haocheng Gu, Hao Cheng, Anjun Ma, Yang Li, Juexin Wang, Dong Xu, Qin Ma
scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data. Bioinform. 38 (23) (2022)
Lei Jiang, Yuexu Jiang, Cankun Wang, Clement Essien, Juexin Wang, Anjun Ma, Qin Ma, Dong Xu
Machine learning development environment for single-cell sequencing data analyses. BIBM (2022)
Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu
The functional determinants in the organization of bacterial genomes. Briefings Bioinform. 22 (3) (2021)
Dan Shao, Lan Huang, Yan Wang, Kai He, Xueteng Cui, Yao Wang, Qin Ma, Juan Cui
DeepSec: a deep learning framework for secreted protein discovery in human body fluids. Bioinform. 38 (1) (2021)
Ying Li, Qi Zhang, Zhaoqian Liu, Cankun Wang, Siyu Han, Qin Ma, Wei Du
Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations. Briefings Bioinform. 22 (4) (2021)
Yuzhou Chang, Carter Allen, Changlin Wan, Dongjun Chung, Chi Zhang, Zihai Li, Qin Ma
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis. Bioinform. 37 (18) (2021)
Dan Shao, Lan Huang, Yan Wang, Xueteng Cui, Yufei Li, Yao Wang, Qin Ma, Wei Du, Juan Cui
HBFP: a new repository for human body fluid proteome. Database J. Biol. Databases Curation 2021 (2021)
Zhaoqian Liu, Anjun Ma, Ewy A. Mathé, Marlena Merling, Qin Ma, Bingqiang Liu
Network analyses in microbiome based on high-throughput multi-omics data. Briefings Bioinform. 22 (2) (2021)
Bin Yu, Wenying Qiu, Cheng Chen, Anjun Ma, Jing Jiang, Hongyan Zhou, Qin Ma
SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting. Bioinform. 36 (4) (2020)
Ren Qi, Anjun Ma, Qin Ma, Quan Zou
Clustering and classification methods for single-cell RNA-sequencing data. Briefings Bioinform. 21 (4) (2020)
Bin Yu, Cheng Chen, Hongyan Zhou, Bingqiang Liu, Qin Ma
GTB-PPI: Predict Protein-protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting. Genom. Proteom. Bioinform. 18 (5) (2020)
Anjun Ma, Cankun Wang, Yuzhou Chang, Faith H. Brennan, Adam McDermaid, Bingqiang Liu, Chi Zhang, Phillip G. Popovich, Qin Ma
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Cheng Chen, Qingmei Zhang, Bin Yu, Zhaomin Yu, Patrick J. Lawrence, Qin Ma, Yan Zhang
Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier. Comput. Biol. Medicine 123 (2020)
Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang, Qin Ma
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data. Bioinform. 36 (4) (2020)
Minghui Wang, Xiaowen Cui, Bin Yu, Cheng Chen, Qin Ma, Hongyan Zhou
SulSite-GTB: identification of protein S-sulfenylation sites by fusing multiple feature information and gradient tree boosting. Neural Comput. Appl. 32 (17) (2020)
Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang, Ying Li
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. Briefings Bioinform. 20 (6) (2019)
Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao, Chi Zhang
M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data. BMC Bioinform. (24) (2019)
Anjun Ma, Minxuan Sun, Adam McDermaid, Bingqiang Liu, Qin Ma
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. Bioinform. 35 (21) (2019)
Huansheng Cao, Qin Ma, Xin Chen, Ying Xu
DOOR: a prokaryotic operon database for genome analyses and functional inference. Briefings Bioinform. 20 (4) (2019)
Xiaoying Wang, Bin Yu, Anjun Ma, Cheng Chen, Bingqiang Liu, Qin Ma
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique. Bioinform. 35 (14) (2019)
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. PLoS Comput. Biol. 15 (2) (2019)
Hongyan Zhou, Cheng Chen, Minghui Wang, Qin Ma, Bin Yu
Predicting Golgi-Resident Protein Types Using Conditional Covariance Minimization With XGBoost Based on Multiple Features Fusion. IEEE Access 7 (2019)
Xing Shi, Zhancheng Gao, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang, Jun Yu
Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients. Genom. Proteom. Bioinform. 17 (6) (2019)
Adam McDermaid, Brandon Monier, Jing Zhao, Bingqiang Liu, Qin Ma
Interpretation of differential gene expression results of RNA-seq data: review and integration. Briefings Bioinform. 20 (6) (2019)
Bingqiang Liu, Ling Han, Xiangrong Liu, Jichang Wu, Qin Ma
Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (4) (2019)
Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data. Briefings Bioinform. 20 (4) (2019)
Anjun Ma, Minxuan Sun, Adam McDermaid, Bingqiang Liu, Qin Ma
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome. Bioinform. 35 (24) (2019)
Gaoyang Li, Jinyu Yang, Chunguo Wu, Qin Ma
Maximal Margin Distribution Support Vector Regression with coupled Constraints-based Convex Optimization. CoRR (2019)
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data. Briefings Bioinform. 19 (5) (2018)
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes. Briefings Bioinform. 19 (6) (2018)
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes. Briefings Bioinform. 19 (2) (2018)
Yu Zhang, Sha Cao, Jing Zhao, Burair Alsaihati, Qin Ma, Chi Zhang
MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network. Quant. Biol. 6 (1) (2018)
Jinyu Yang, Xin Chen, Adam McDermaid, Qin Ma
DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses. Bioinform. 33 (16) (2017)
Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang, Qin Ma
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation. BMC Bioinform. 18 (1) (2017)
Yu Zhang, Juan Xie, Jinyu Yang, Anne Fennell, Chi Zhang, Qin Ma
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data. Bioinform. 33 (3) (2017)
Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang, Ying Xu
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. BMC Bioinform. 16 (2015)
Xizeng Mao, Qin Ma, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu
DOOR 2.0: presenting operons and their functions through dynamic and integrated views. Nucleic Acids Res. 42 (Database-Issue) (2014)
Qin Ma, Hanyuan Zhang, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu
DMINDA: an integrated web server for DNA motif identification and analyses. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Qin Ma, Ying Xu
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency. Genom. Proteom. Bioinform. 11 (1) (2013)
Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu
regulatory motifs at a genome scale. Bioinform. 29 (18) (2013)
Qin Ma, Jian-Liang Wu, Xiao Yu
Planar graphs without 5-cycles or without 6-cycles. Discret. Math. 309 (10) (2009)