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List of works by Qin Ma

A Central Edge Selection Based Overlapping Community Detection Algorithm for the Detection of Overlapping Structures in Protein⁻Protein Interaction Networks

scientific article

A link density clustering algorithm based on automatically selecting density peaks for overlapping community detection

A new framework for identifying cis-regulatory motifs in prokaryotes.

scientific article

A phylogenetic model for understanding the effect of gene duplication on cancer progression

scientific article published on 25 December 2013

A platform for the biomedical application of large language models

scientific article published on 22 January 2025

A probabilistic model-based bi-clustering method for single-cell transcriptomic data analysis

A shared disease-associated oligodendrocyte signature among multiple CNS pathologies

scientific article published in 2022

An Insight into Species from Same Descendent Aspect and the Application into Clostridia

An algorithmic perspective of de novo cis-regulatory motif finding based on ChIP-seq data.

scientific article

An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale

scientific article published on 10 July 2013

An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes

scientific article

Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum

scientific article

Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.

scientific article published on 15 March 2016

Bibliometric Screening of Helicobacter Pylori Pathogenic Genes Through Pathway Enrichment and Operon Analysis

scientific article published on November 2016

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

scientific article

Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass

scientific article

Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress.

scientific article published on 12 September 2013

Comprehensive characterization of the genomic alterations in human gastric cancer.

scientific article published on 3 December 2014

Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies

scientific article published on 15 March 2018

Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions

scientific article

DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses.

scientific article published on 13 April 2017

DMINDA: an integrated web server for DNA motif identification and analyses

scientific article

DOOR 2.0: presenting operons and their functions through dynamic and integrated views.

scientific article

Deciphering relationship between microhomology and in-frame mutation occurrence in human CRISPR-based gene knockout

scientific article published on 14 June 2016

Durability of Booster mRNA Vaccine against SARS-CoV-2 BA.2.12.1, BA.4, and BA.5 Subvariants

scientific article published in 2022

Elucidation of operon structures across closely related bacterial genomes

scientific article

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes

scientific article

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

scientific article

GmZPR3d Interacts with GmHD-ZIP III Proteins and Regulates Soybean Root and Nodule Vascular Development

article

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

article

Identifying anti-cancer drug response related genes using an integrative analysis of transcriptomic and genomic variations with cell line-based drug perturbations

scientific article published on 25 January 2016

Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.

scientific article published on 29 September 2011

Interpretation of differential gene expression results of RNA-seq data: review and integration

article

LTMG (Left truncated mixture Gaussian) based modeling of transcriptional regulatory heterogeneities in single cell RNA-seq data – a perspective from the kinetics of mRNA metabolism

scholarly article published 29 September 2018

Link community detection based on line graphs with a novel link similarity measure

LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property

article

Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season

scientific article published on 30 December 2021

Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum.

scientific article published on 3 March 2016

QServer: A Biclustering Server for Prediction and Assessment of Co-Expressed Gene Clusters ⬇️

scientific article published on March 5, 2012

QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data

scientific article

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

scientific article

RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis.

scientific article published on 30 May 2018

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

scientific article

Revisiting operons: an analysis of the landscape of transcriptional units in E. coli

scientific article

Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard

scientific article published on 01 May 2019

SGL-SVM: A novel method for tumor classification via support vector machine with sparse group Lasso

scientific article published on 28 November 2019

Scalable Data Mining Algorithms in Computational Biology and Biomedicine

scientific article published on 28 February 2017

SeqTU: A Web Server for Identification of Bacterial Transcription Units

scientific article published on 7 March 2017

Systems-level understanding of ethanol-induced stresses and adaptation in E. coli

scientific article published on 16 March 2017

The understanding of circular RNAs as special triggers in carcinogenesis

scientific article published on 13 February 2016

Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective

scientific article published on 18 September 2014

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