List of works - Bairong Shen

A novel mutation in CD40 and its functional characterization.

scientific article

A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies

scientific article

A systems biology perspective on rational design of peptide vaccine against virus infections

scientific article

Altered Expression Levels of MicroRNA-132 and Nurr1 in Peripheral Blood of Parkinson's Disease: Potential Disease Biomarkers

scientific article published on 01 April 2019

Amino acid contact energy networks impact protein structure and evolution.

scientific article

Amino acid network for prediction of catalytic residues in enzymes: a comparison survey.

scientific article

An integrated text mining framework for metabolic interaction network reconstruction

scientific article published on 21 March 2016

Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model.

scientific article published on 21 May 2018

Biomedical data integration, modeling, and simulation in the era of big data and translational medicine

scientific article

Biomedical informatics and computational biology for high-throughput data analysis

scientific article published on 12 February 2014

Biomedical text mining and its applications in cancer research

scientific article

CD93 orchestrates the tumor microenvironment and predicts the molecular subtype and therapy response of bladder cancer

scientific article published in 2022

Characterization of CA XIII, a novel member of the carbonic anhydrase isozyme family

scientific journal article

Comparison of Prognostic MicroRNA Biomarkers in Blood and Tissues for Gastric Cancer

scientific article

Computational Analysis of the Binding Specificities of PH Domains

scientific article published on 31 December 2015

Computational advances in cancer informatics (a).

scientific article published on 13 October 2014

Computational analysis of microRNA function in heart development.

scientific article published on 17 August 2010

Data-driven translational prostate cancer research: from biomarker discovery to clinical decision

scientific article published on 07 March 2020

Deciphering oncogenic drivers: from single genes to integrated pathways

scientific article

Diagnosis value of the serum amyloid A test in neonatal sepsis: a meta-analysis.

scientific article

Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data

scientific article

Effects of time point measurement on the reconstruction of gene regulatory networks

scientific article published on 04 August 2010

Evaluation and comparison of multiple aligners for next-generation sequencing data analysis

scientific article

Genome wide analysis of pathogenic SH2 domain mutations

scientific article

Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data

scientific article

Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer

scientific article

Identification of microRNA as sepsis biomarker based on miRNAs regulatory network analysis

scientific article

Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer.

scientific article

Identification of the genes regulated by Wnt-4, a critical signal for commitment of the ovary.

scientific article published on 30 January 2015

Identifying novel glioma associated pathways based on systems biology level meta-analysis

scientific article

Identifying novel prostate cancer associated pathways based on integrative microarray data analysis

scientific article

InCoB2013 introduces Systems Biology as a major conference theme

scientific article published on 4 November 2013

Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression

scientific article

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach

scientific article

Investigation of the acetylation mechanism by GCN5 histone acetyltransferase

scientific article

Key regulators in prostate cancer identified by co-expression module analysis

scientific article

LIMS and Clinical Data Management

scientific article

Loss of CHGA Protein as a Potential Biomarker for Colon Cancer Diagnosis: A Study on Biomarker Discovery by Machine Learning and Confirmation by Immunohistochemistry in Colorectal Cancer Tissue Microarrays

scientific article published on 27 May 2022

MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery

scientific article published on 17 September 2018

Molecular dynamic simulation to explore the molecular basis of Btk-PH domain interaction with Ins(1,3,4,5)P4.

scientific article

Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data

scientific article

Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection

scientific article published on 13 August 2021

Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets

scientific article

Network vulnerability-based and knowledge-guided identification of microRNA biomarkers indicating platinum resistance in high-grade serous ovarian cancer

scientific article published on 29 October 2019

New genes drive the evolution of gene interaction networks in the human and mouse genomes

scientific article

Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues

scientific article published on 27 August 2018

Novel Biomarker MicroRNAs for Subtyping of Acute Coronary Syndrome: A Bioinformatics Approach.

scientific article published on December 2016

Origination of new immunological functions in the costimulatory molecule B7-H3: the role of exon duplication in evolution of the immune system

scientific article (publication date: 2011)

PON-Sol: prediction of effects of amino acid substitutions on protein solubility.

scientific article

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

scientific article

Post genome-wide association studies functional characterization of prostate cancer risk loci

scientific article

Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer

scientific article published on August 2015

RankViaContact: ranking and visualization of amino acid contacts

scientific article published on 01 November 2003

Residue interaction network analysis of Dronpa and a DNA clamp.

scientific article

SVR_CAF: an integrated score function for detecting native protein structures among decoys.

scientific article

Screening key microRNAs for castration-resistant prostate cancer based on miRNA/mRNA functional synergistic network

scientific article published on 31 October 2015

Segmentation of neuronal structures using SARSA (λ)-based boundary amendment with reinforced gradient-descent curve shape fitting

scientific article

Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea.

scientific article published on 25 October 2017

Structure-based prediction of the effects of a missense variant on protein stability.

scientific article published on 12 October 2012

Systematic investigation of global coordination among mRNA and protein in cellular society

scientific article

The International Natural Product Sciences Taskforce (INPST) and the power of Twitter networking exemplified through #INPST hashtag analysis

scientific article published in January 2023

The construction of an amino acid network for understanding protein structure and function.

scientific article

The landscape of emerging ceRNA crosstalks in colorectal cancer: Systems biological perspectives and translational applications

scientific article published on 01 August 2020

The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?

scientific article

The topology and dynamics of protein complexes: insights from intra- molecular network theory.

scientific article published on March 2013

Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations

scientific article published on 01 August 2019

Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era.

scientific article published on 15 July 2013

Translational biomedical informatics and computational systems medicine.

scientific article

Translational biomedical informatics in the cloud: present and future

scientific article

Two functional microRNA-126s repress a novel target gene p21-activated kinase 1 to regulate vascular integrity in zebrafish

scientific article published on 09 December 2010

Virtual screening and biological evaluation of novel small molecular inhibitors against protein arginine methyltransferase 1 (PRMT1).

scientific article

Wnt4, a pleiotropic signal for controlling cell polarity, basement membrane integrity, and antimüllerian hormone expression during oocyte maturation in the female follicle.

scientific article published on 26 December 2013

List of works by Bairong Shen

A novel mutation in CD40 and its functional characterization.

A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies

A systems biology perspective on rational design of peptide vaccine against virus infections

Altered Expression Levels of MicroRNA-132 and Nurr1 in Peripheral Blood of Parkinson's Disease: Potential Disease Biomarkers

Amino acid contact energy networks impact protein structure and evolution.

Amino acid network for prediction of catalytic residues in enzymes: a comparison survey.

An integrated text mining framework for metabolic interaction network reconstruction

Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model.

Biomedical data integration, modeling, and simulation in the era of big data and translational medicine

Biomedical informatics and computational biology for high-throughput data analysis

Biomedical text mining and its applications in cancer research

CD93 orchestrates the tumor microenvironment and predicts the molecular subtype and therapy response of bladder cancer

Characterization of CA XIII, a novel member of the carbonic anhydrase isozyme family

Comparison of Prognostic MicroRNA Biomarkers in Blood and Tissues for Gastric Cancer

Computational Analysis of the Binding Specificities of PH Domains

Computational advances in cancer informatics (a).

Computational analysis of microRNA function in heart development.

Data-driven translational prostate cancer research: from biomarker discovery to clinical decision

Deciphering oncogenic drivers: from single genes to integrated pathways

Diagnosis value of the serum amyloid A test in neonatal sepsis: a meta-analysis.

Discovery and characterization of long intergenic non-coding RNAs (lincRNA) module biomarkers in prostate cancer: an integrative analysis of RNA-Seq data

Effects of time point measurement on the reconstruction of gene regulatory networks

Evaluation and comparison of multiple aligners for next-generation sequencing data analysis

Genome wide analysis of pathogenic SH2 domain mutations

Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data

Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer

Identification of microRNA as sepsis biomarker based on miRNAs regulatory network analysis

Identification of novel microRNA regulatory pathways associated with heterogeneous prostate cancer.

Identification of the genes regulated by Wnt-4, a critical signal for commitment of the ovary.

Identifying novel glioma associated pathways based on systems biology level meta-analysis

Identifying novel prostate cancer associated pathways based on integrative microarray data analysis

InCoB2013 introduces Systems Biology as a major conference theme

Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression

Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach

Investigation of the acetylation mechanism by GCN5 histone acetyltransferase

Key regulators in prostate cancer identified by co-expression module analysis

LIMS and Clinical Data Management

Loss of CHGA Protein as a Potential Biomarker for Colon Cancer Diagnosis: A Study on Biomarker Discovery by Machine Learning and Confirmation by Immunohistochemistry in Colorectal Cancer Tissue Microarrays

MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery

Molecular dynamic simulation to explore the molecular basis of Btk-PH domain interaction with Ins(1,3,4,5)P4.

Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data

Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection

Network modelling reveals the mechanism underlying colitis-associated colon cancer and identifies novel combinatorial anti-cancer targets

Network vulnerability-based and knowledge-guided identification of microRNA biomarkers indicating platinum resistance in high-grade serous ovarian cancer

New genes drive the evolution of gene interaction networks in the human and mouse genomes

Node-Weighted Amino Acid Network Strategy for Characterization and Identification of Protein Functional Residues

Novel Biomarker MicroRNAs for Subtyping of Acute Coronary Syndrome: A Bioinformatics Approach.

Origination of new immunological functions in the costimulatory molecule B7-H3: the role of exon duplication in evolution of the immune system

PON-Sol: prediction of effects of amino acid substitutions on protein solubility.

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

Post genome-wide association studies functional characterization of prostate cancer risk loci

Protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer

RankViaContact: ranking and visualization of amino acid contacts

Residue interaction network analysis of Dronpa and a DNA clamp.

SVR_CAF: an integrated score function for detecting native protein structures among decoys.

Screening key microRNAs for castration-resistant prostate cancer based on miRNA/mRNA functional synergistic network

Segmentation of neuronal structures using SARSA (λ)-based boundary amendment with reinforced gradient-descent curve shape fitting

Small RNAome sequencing delineates the small RNA landscape of pluripotent adult stem cells in the planarian Schmidtea mediterranea.

Structure-based prediction of the effects of a missense variant on protein stability.

Systematic investigation of global coordination among mRNA and protein in cellular society

The International Natural Product Sciences Taskforce (INPST) and the power of Twitter networking exemplified through #INPST hashtag analysis

The construction of an amino acid network for understanding protein structure and function.

The landscape of emerging ceRNA crosstalks in colorectal cancer: Systems biological perspectives and translational applications

The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?

The topology and dynamics of protein complexes: insights from intra- molecular network theory.

Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations

Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next-generation sequencing era.

Translational biomedical informatics and computational systems medicine.

Translational biomedical informatics in the cloud: present and future

Two functional microRNA-126s repress a novel target gene p21-activated kinase 1 to regulate vascular integrity in zebrafish

Virtual screening and biological evaluation of novel small molecular inhibitors against protein arginine methyltransferase 1 (PRMT1).

Wnt4, a pleiotropic signal for controlling cell polarity, basement membrane integrity, and antimüllerian hormone expression during oocyte maturation in the female follicle.