Qin Ma

Orcid: 0000-0002-3264-8392

Affiliations:
  • 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 47 papers between 2009 and 2024.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Dataset
Other 

Links

Online presence:

On csauthors.net:

Bibliography

2024
A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.
Patterns, March, 2024

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

Machine learning development environment for single-cell sequencing data analyses.
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

HBFP: a new repository for human body fluid proteome.
Database J. Biol. Databases Curation, 2021

A novel computational framework for genome-scale alternative transcription units prediction.
Briefings Bioinform., 2021

Network analyses in microbiome based on high-throughput multi-omics data.
Briefings Bioinform., 2021

The functional determinants in the organization of bacterial genomes.
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

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

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

DMINDA: an integrated web server for DNA motif identification and analyses.
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
Planar graphs without 5-cycles or without 6-cycles.
Discret. Math., 2009


  Loading...