Qin Ma

58 papers Misc 1Journal 56Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Foundation Model for Spatial Proteomics.
CoRR
Muhammad Shaban, Yuzhou Chang, Huaying Qiu, Yao Yu Yeo, Andrew H. Song, Guillaume Jaume, Yuchen Wang, Luca L. Weishaupt, Tong Ding, Anurag Vaidya, Abdallah Lamane, Daniel Shao, Mohammed Zidane, Yunhao Bai, Paige McCallum, Shuli Luo, Wenrui Wu, Yang Wang, Precious Cramer, Chi Ngai Chan, Pierre Stéphan, Johanna Schaffenrath, Jia Le Lee, Hendrik A. Michel, Caiwei Tian, Cristina Almagro-Pérez, Sophia J. Wagner, Sharifa Sahai, Ming Y. Lu, Richard J. Chen, Andrew Zhang, Mark Edward M. Gonzales, Ahmad Makky, Jia-Ying Joey Lee, Hao Cheng, Nourhan El Ahmar, Sayed Matar, Maximilian Haist, Darci Phillips, Yuqi Tan, Garry P. Nolan, W. Richard Burack, Jacob D. Estes, Jonathan T. C. Liu, Toni K. Choueiri, Neeraj Agarwal, Marc Barry, Scott J. Rodig, Long Phi Le, Georg Gerber, Christian M. Schürch, Fabian J. Theis, Youn H. Kim, Joe Yeong, Sabina Signoretti, Brooke E. Howitt, Lit-Hsin Loo, Qin Ma, Sizun Jiang, Faisal Mahmood
2025 J jnl
Cross-loop contrast of heterogeneous graphs for interdisciplinary journal recommendation.
Expert Syst. Appl.
Ying Li, Yu Liang, Qianqian Li, Hongmin Sun, Wei Du, Yi Jiang, Qin Ma
2025 J jnl
Relation equivariant graph neural networks to explore the mosaic-like tissue architecture of kidney diseases on spatially resolved transcriptomics.
Bioinform.
Mauminah Raina, Hao Cheng, Ricardo Melo Ferreira, Treyden Stansfield, Chandrima Modak, Ying-Hua Cheng, Hari Naga Sai Kiran Suryadevara, Dong Xu, Michael T. Eadon, Qin Ma, Juexin Wang
2025 J jnl
scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data.
Bioinform.
Jinpu Li, Mauminah Raina, Yiqing Wang, Chunhui Xu, Li Su, Qi Guo, Ricardo Melo Ferreira, Michael T. Eadon, Qin Ma, Juexin Wang, Dong Xu
2024 J jnl
A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.
Patterns
Yang Li, Yizhong Wang, Cankun Wang, Anjun Ma, Qin Ma, Bingqiang Liu
2024 J jnl
Analysis of community connectivity in spatial transcriptomics data.
Frontiers Appl. Math. Stat.
Juan Xie, Kyeong Joo Jung, Carter Allen, Yuzhou Chang, Subhadeep Paul, Zihai Li, Qin Ma, Dongjun Chung
2024 J jnl
CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.
Briefings Bioinform.
Yizhong Wang, Yang Li, Cankun Wang, Chan-Wang Jerry Lio, Qin Ma, Bingqiang Liu
2024 J jnl
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data.
Briefings Bioinform.
Yang Li, Anjun Ma, Yizhong Wang, Qi Guo, Cankun Wang, Hongjun Fu, Bingqiang Liu, Qin Ma
2023 J jnl
DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model.
Bioinform.
Yitian Fang, Yi Jiang, Leyi Wei, Qin Ma, Zhixiang Ren, Qianmu Yuan, Dong-Qing Wei
2023 J jnl
Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data.
Comput. Biol. Medicine
Zhaoqian Liu, Qi Wang, Anjun Ma, Shaohong Feng, Dongjun Chung, Jing Zhao, Qin Ma, Bingqiang Liu
2023 J jnl
LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity.
PLoS Comput. Biol.
Juan Xie, Hyeongseon Jeon, Gang Xin, Qin Ma, Dongjun Chung
2023 J jnl
SURE: Screening unlabeled samples for reliable negative samples based on reinforcement learning.
Inf. Sci.
Ying Li, Hang Sun, Wensi Fang, Qin Ma, Siyu Han, Rui Wang-Sattler, Wei Du, Qiong Yu
2022 J jnl
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.
Briefings Bioinform.
Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma, Yan Wang
2022 — conf
Machine learning development environment for single-cell sequencing data analyses.
BIBM
Lei Jiang, Yuexu Jiang, Cankun Wang, Clement Essien, Juexin Wang, Anjun Ma, Qin Ma, Dong Xu
2022 Misc conf
Provable Second-Order Riemannian Gauss-Newton Method for Low-Rank Tensor Estimation
ICASSP
Yuetian Luo, Qin Ma, Chi Zhang, Anru R. Zhang
2022 J jnl
scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data.
Bioinform.
Haocheng Gu, Hao Cheng, Anjun Ma, Yang Li, Juexin Wang, Dong Xu, Qin Ma
2021 J jnl
A fine-scale map of genome-wide recombination in divergent
Briefings Bioinform.
Yu Kang, Lina Yuan, Xing Shi, Yanan Chu, Zilong He, Xinmiao Jia, Qiang Lin, Qin Ma, Jian Wang, Jingfa Xiao, Songnian Hu, Zhancheng Gao, Fei Chen, Jun Yu
2021 J jnl
A novel computational framework for genome-scale alternative transcription units prediction.
Briefings Bioinform.
Qi Wang, Zhaoqian Liu, Bo Yan, Wen-Chi Chou, Laurence Ettwiller, Qin Ma, Bingqiang Liu
2021 J jnl
Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations.
Briefings Bioinform.
Ying Li, Qi Zhang, Zhaoqian Liu, Cankun Wang, Siyu Han, Qin Ma, Wei Du
2021 J jnl
DeepSec: a deep learning framework for secreted protein discovery in human body fluids.
Bioinform.
Dan Shao, Lan Huang, Yan Wang, Kai He, Xueteng Cui, Yao Wang, Qin Ma, Juan Cui
2021 J jnl
HBFP: a new repository for human body fluid proteome.
Database J. Biol. Databases Curation
Dan Shao, Lan Huang, Yan Wang, Xueteng Cui, Yufei Li, Yao Wang, Qin Ma, Wei Du, Juan Cui
2021 J jnl
IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis.
IEEE Access
Feifei Cui, Quan Zou, Qin Ma, Leyi Wei, Jijun Tang, Dariusz Mrozek
2021 J jnl
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis.
Bioinform.
Yuzhou Chang, Carter Allen, Changlin Wan, Dongjun Chung, Chi Zhang, Zihai Li, Qin Ma
2021 J jnl
Network analyses in microbiome based on high-throughput multi-omics data.
Briefings Bioinform.
Zhaoqian Liu, Anjun Ma, Ewy A. Mathé, Marlena Merling, Qin Ma, Bingqiang Liu
2021 J jnl
The functional determinants in the organization of bacterial genomes.
Briefings Bioinform.
Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu
2020 J jnl
Clustering and classification methods for single-cell RNA-sequencing data.
Briefings Bioinform.
Ren Qi, Anjun Ma, Qin Ma, Quan Zou
2020 J jnl
GTB-PPI: Predict Protein-protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting.
Genom. Proteom. Bioinform.
Bin Yu, Cheng Chen, Hongyan Zhou, Bingqiang Liu, Qin Ma
2020 J jnl
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.
Nucleic Acids Res.
Anjun Ma, Cankun Wang, Yuzhou Chang, Faith H. Brennan, Adam McDermaid, Bingqiang Liu, Chi Zhang, Phillip G. Popovich, Qin Ma
2020 J jnl
Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier.
Comput. Biol. Medicine
Cheng Chen, Qingmei Zhang, Bin Yu, Zhaomin Yu, Patrick J. Lawrence, Qin Ma, Yan Zhang
2020 J jnl
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.
Bioinform.
Juan Xie, Anjun Ma, Yu Zhang, Bingqiang Liu, Sha Cao, Cankun Wang, Jennifer Xu, Chi Zhang, Qin Ma
2020 J jnl
SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting.
Bioinform.
Bin Yu, Wenying Qiu, Cheng Chen, Anjun Ma, Jing Jiang, Hongyan Zhou, Qin Ma
2020 J jnl
SulSite-GTB: identification of protein S-sulfenylation sites by fusing multiple feature information and gradient tree boosting.
Neural Comput. Appl.
Minghui Wang, Xiaowen Cui, Bin Yu, Cheng Chen, Qin Ma, Hongyan Zhou
2019 J jnl
Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.
IEEE ACM Trans. Comput. Biol. Bioinform.
Bingqiang Liu, Ling Han, Xiangrong Liu, Jichang Wu, Qin Ma
2019 J jnl
DOOR: a prokaryotic operon database for genome analyses and functional inference.
Briefings Bioinform.
Huansheng Cao, Qin Ma, Xin Chen, Ying Xu
2019 J jnl
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.
PLoS Comput. Biol.
Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison J. Miller, Anne Fennell, Qin Ma
2019 J jnl
Interpretation of differential gene expression results of RNA-seq data: review and integration.
Briefings Bioinform.
Adam McDermaid, Brandon Monier, Jing Zhao, Bingqiang Liu, Qin Ma
2019 J jnl
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.
Briefings Bioinform.
Juan Xie, Anjun Ma, Anne Fennell, Qin Ma, Jing Zhao
2019 J jnl
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property.
Briefings Bioinform.
Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang, Ying Li
2019 J jnl
M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data.
BMC Bioinform.
Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao, Chi Zhang
2019 J jnl
Maximal Margin Distribution Support Vector Regression with coupled Constraints-based Convex Optimization.
CoRR
Gaoyang Li, Jinyu Yang, Chunguo Wu, Qin Ma
2019 J jnl
Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients.
Genom. Proteom. Bioinform.
Xing Shi, Zhancheng Gao, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang, Jun Yu
2019 J jnl
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.
Bioinform.
Anjun Ma, Minxuan Sun, Adam McDermaid, Bingqiang Liu, Qin Ma
2019 J jnl
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.
Bioinform.
Anjun Ma, Minxuan Sun, Adam McDermaid, Bingqiang Liu, Qin Ma
2019 J jnl
Predicting Golgi-Resident Protein Types Using Conditional Covariance Minimization With XGBoost Based on Multiple Features Fusion.
IEEE Access
Hongyan Zhou, Cheng Chen, Minghui Wang, Qin Ma, Bin Yu
2019 J jnl
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique.
Bioinform.
Xiaoying Wang, Bin Yu, Anjun Ma, Cheng Chen, Bingqiang Liu, Qin Ma
2018 J jnl
An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data.
Briefings Bioinform.
Bingqiang Liu, Jinyu Yang, Yang Li, Adam McDermaid, Qin Ma
2018 J jnl
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.
Briefings Bioinform.
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
2018 J jnl
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.
Briefings Bioinform.
Sheng-Yong Niu, Jinyu Yang, Adam McDermaid, Jing Zhao, Yu Kang, Qin Ma
2018 J jnl
MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network.
Quant. Biol.
Yu Zhang, Sha Cao, Jing Zhao, Burair Alsaihati, Qin Ma, Chi Zhang
2017 J jnl
DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.
Bioinform.
Jinyu Yang, Xin Chen, Adam McDermaid, Qin Ma
2017 J jnl
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.
Bioinform.
Yu Zhang, Juan Xie, Jinyu Yang, Anne Fennell, Chi Zhang, Qin Ma
2017 J jnl
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.
BMC Bioinform.
Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang, Qin Ma
2015 J jnl
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.
BMC Bioinform.
Xizeng Mao, Qin Ma, Bingqiang Liu, Xin Chen, Hanyuan Zhang, Ying Xu
2014 J jnl
DMINDA: an integrated web server for DNA motif identification and analyses.
Nucleic Acids Res.
Qin Ma, Hanyuan Zhang, Xizeng Mao, Chuan Zhou, Bingqiang Liu, Xin Chen, Ying Xu
2014 J jnl
DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Nucleic Acids Res.
Xizeng Mao, Qin Ma, Chuan Zhou, Xin Chen, Hanyuan Zhang, Jincai Yang, Fenglou Mao, Wei Lai, Ying Xu
2013 J jnl
An integrated toolkit for accurate prediction and analysis of
Bioinform.
Qin Ma, Bingqiang Liu, Chuan Zhou, Yanbin Yin, Guojun Li, Ying Xu
2013 J jnl
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency.
Genom. Proteom. Bioinform.
Qin Ma, Ying Xu
2009 J jnl
Planar graphs without 5-cycles or without 6-cycles.
Discret. Math.
Qin Ma, Jian-Liang Wu, Xiao Yu