Qin Ma
Orcid: 0000-0002-3264-8392Affiliations:
- Ohio State University, Columbus, OH, USA
- South Dakota State University, Brookings, SD, USA (2015-2018)
- University of Georgia, Athens, GA, USA (2011 - 2015)
- Shandong University, Department of Mathematics, China (PhD 2010)
According to our database1,
Qin Ma
authored at least 49 papers
between 2009 and 2024.
Collaborative distances:
Collaborative distances:
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Bibliography
2024
A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.
Patterns, March, 2024
Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data.
Briefings Bioinform., 2024
2023
DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model.
Bioinform., December, 2023
Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data.
Comput. Biol. Medicine, October, 2023
SURE: Screening unlabeled samples for reliable negative samples based on reinforcement learning.
Inf. Sci., June, 2023
LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity.
PLoS Comput. Biol., 2023
2022
scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data.
Bioinform., November, 2022
Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.
Briefings Bioinform., 2022
Provable Second-Order Riemannian Gauss-Newton Method for Low-Rank Tensor Estimation <sup>‖</sup>.
Proceedings of the IEEE International Conference on Acoustics, 2022
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022
2021
DeepSec: a deep learning framework for secreted protein discovery in human body fluids.
Bioinform., 2021
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis.
Bioinform., 2021
Database J. Biol. Databases Curation, 2021
A novel computational framework for genome-scale alternative transcription units prediction.
Briefings Bioinform., 2021
Briefings Bioinform., 2021
Briefings Bioinform., 2021
Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations.
Briefings Bioinform., 2021
IEEE Access Special Section Editorial: Feature Representation and Learning Methods With Applications in Large-Scale Biological Sequence Analysis.
IEEE Access, 2021
2020
SulSite-GTB: identification of protein S-sulfenylation sites by fusing multiple feature information and gradient tree boosting.
Neural Comput. Appl., 2020
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.
Nucleic Acids Res., 2020
GTB-PPI: Predict Protein-protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting.
Genom. Proteom. Bioinform., 2020
Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier.
Comput. Biol. Medicine, 2020
SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting.
Bioinform., 2020
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data.
Bioinform., 2020
Briefings Bioinform., 2020
2019
Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.
PLoS Comput. Biol., 2019
Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients.
Genom. Proteom. Bioinform., 2019
Maximal Margin Distribution Support Vector Regression with coupled Constraints-based Convex Optimization.
CoRR, 2019
M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data.
BMC Bioinform., 2019
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique.
Bioinform., 2019
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.
Bioinform., 2019
It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.
Briefings Bioinform., 2019
Interpretation of differential gene expression results of RNA-seq data: review and integration.
Briefings Bioinform., 2019
LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property.
Briefings Bioinform., 2019
Briefings Bioinform., 2019
Predicting Golgi-Resident Protein Types Using Conditional Covariance Minimization With XGBoost Based on Multiple Features Fusion.
IEEE Access, 2019
2018
MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network.
Quant. Biol., 2018
Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.
Briefings Bioinform., 2018
An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data.
Briefings Bioinform., 2018
2017
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.
BMC Bioinform., 2017
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.
Bioinform., 2017
DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.
Bioinform., 2017
2015
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli.
BMC Bioinform., 2015
2014
DOOR 2.0: presenting operons and their functions through dynamic and integrated views.
Nucleic Acids Res., 2014
Nucleic Acids Res., 2014
2013
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency.
Genom. Proteom. Bioinform., 2013
An integrated toolkit for accurate prediction and analysis of <i>cis-</i>regulatory motifs at a genome scale.
Bioinform., 2013
2009