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ORCIDQin Ma 0003
Person information
- affiliation: Ohio State University, Columbus, OH, USA
- affiliation (2015-2018): South Dakota State University, Brookings, SD, USA
- affiliation (2011 - 2015): University of Georgia, Athens, GA, USA
- affiliation (PhD 2010): Shandong University, Department of Mathematics, China
Other persons with the same name
- Qin Ma — disambiguation page
- Qin Ma 0001 — China Agricultural University, College of Information and Electrical Engineering, Beijing, China
- Qin Ma 0002
![[0000-0001-8520-8190]](http://222.178.203.72:19005/whst/63/=cakoznqf//img/orcid-mark.12x12.png "0000-0001-8520-8190")
— University of Luxembourg - Qin Ma 0004 — Mississippi State University, Department of Forestry, Starkville, MS, USA (and 1 more)
- Qin Ma 0005 — State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Qin Ma 0006 — Hebei University, Hebei, Baoding, China
- Qin Ma 0007 — Huazhong University of Science and Technology, Wuhan, China
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2020 – today
- 2025
[j50]Ying Li, Yu Liang, Qianqian Li, Hongmin Sun, Wei Du, Yi Jiang, Qin Ma:
Cross-loop contrast of heterogeneous graphs for interdisciplinary journal recommendation. Expert Syst. Appl. 265: 125949 (2025)- 2024
- [j49]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) - [j48]Juan Xie, Kyeong Joo Jung, Carter Allen, Yuzhou Chang, Subhadeep Paul, Zihai Li, Qin Ma, Dongjun Chung:
Analysis of community connectivity in spatial transcriptomics data. Frontiers Appl. Math. Stat. 10 (2024) - [j47]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): 100927 (2024) - 2023
- [j46]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) - [j45]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: 107458 (2023) - [j44]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: 299-312 (2023) - [j43]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) - 2022
- [j42]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) - [j41]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): 5322-5325 (2022) - [c2]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: 3824-3826 - [c1]Yuetian Luo, Qin Ma, Chi Zhang, Anru R. Zhang:
Provable Second-Order Riemannian Gauss-Newton Method for Low-Rank Tensor Estimation ‖. ICASSP 2022: 9057-9061 - 2021
- [j40]Feifei Cui, Quan Zou, Qin Ma, Leyi Wei, Jijun Tang, Dariusz Mrozek:
IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis. IEEE Access 9: 33110-33119 (2021) - [j39]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): 1639-1655 (2021) - [j38]Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu:
The functional determinants in the organization of bacterial genomes. Briefings Bioinform. 22(3) (2021) - [j37]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) - [j36]Qi Wang, Zhaoqian Liu, Bo Yan, Wen-Chi Chou, Laurence Ettwiller, Qin Ma, Bingqiang Liu:
A novel computational framework for genome-scale alternative transcription units prediction. Briefings Bioinform. 22(6) (2021) - [j35]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) - [j34]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): 3045-3047 (2021) - [j33]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): 228-235 (2021) - 2020
- [j32]Ren Qi, Anjun Ma, Qin Ma, Quan Zou:
Clustering and classification methods for single-cell RNA-sequencing data. Briefings Bioinform. 21(4): 1196-1208 (2020) - [j31]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): 1074-1081 (2020) - [j30]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): 1143-1149 (2020) - [j29]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: 103899 (2020) - [j28]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): 582-592 (2020) - [j27]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): W275-W286 (2020) - [j26]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): 13843-13862 (2020)
2010 – 2019
- 2019
- [j25]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: 144154-144164 (2019) - [j24]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): 1449-1464 (2019) - [j23]Huansheng Cao, Qin Ma, Xin Chen, Ying Xu:
DOOR: a prokaryotic operon database for genome analyses and functional inference. Briefings Bioinform. 20(4): 1568-1577 (2019) - [j22]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): 2009-2027 (2019) - [j21]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): 2044-2054 (2019) - [j20]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): 2395-2402 (2019) - [j19]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): 4474-4477 (2019) - [j18]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): 5397 (2019) - [j17]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. 20-S(24): 672 (2019) - [j16]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): 590-602 (2019) - [j15]Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma:
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis. PLoS Comput. Biol. 15(2) (2019) - [j14]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): 1211-1218 (2019) - [i1]Gaoyang Li, Jinyu Yang, Chunguo Wu, Qin Ma:
Maximal Margin Distribution Support Vector Regression with coupled Constraints-based Convex Optimization. CoRR abs/1905.01620 (2019) - 2018
- [j13]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): 360 (2018) - [j12]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): 1069-1081 (2018) - [j11]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): 1415-1429 (2018) - [j10]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): 40-55 (2018) - 2017
- [j9]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): 450-452 (2017) - [j8]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): 2586-2588 (2017) - [j7]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): 51:1-51:11 (2017) - 2015
- [j6]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: 356:1-356:9 (2015) - 2014
- [j5]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): 654-659 (2014) - [j4]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): 12-19 (2014) - 2013
- [j3]Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu:
An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale. Bioinform. 29(18): 2261-2268 (2013) - [j2]Qin Ma, Ying Xu:
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency. Genom. Proteom. Bioinform. 11(1): 66-71 (2013)
2000 – 2009
- 2009
- [j1]Qin Ma, Jian-Liang Wu, Xiao Yu:
Planar graphs without 5-cycles or without 6-cycles. Discret. Math. 309(10): 2998-3005 (2009)
Coauthor Index
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