List of works - Hui Lu

16S rDNA Gene Sequencing Analysis in Functional Dyspepsia Treated With Fecal Microbiota Transplantation.

scientific article published in March 2017

A Herpes Simplex Virus Thymidine Kinase-Induced Mouse Model of Hepatocellular Carcinoma Associated with Up-Regulated Immune-Inflammatory-Related Signals

article

A Novel Joint Gene Set Analysis Framework Improves Identification of Enriched Pathways in Cross Disease Transcriptomic Analysis

article

A Single-Molecule Perspective on the Role of Solvent Hydrogen Bonds in Protein Folding and Chemical Reactions

scientific article published on 01 December 2008

A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.

scientific article published on 24 January 2014

A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology.

scientific article

A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains.

scientific article

Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome

scientific article

An improved machine learning protocol for the identification of correct Sequest search results

scientific article

Application of statistical potentials to protein structure refinement from low resolution ab initio models

scientific article published on 01 December 2003

Assessment of tumor mutation burden calculation from gene panel sequencing data

article

Boosting the prediction and understanding of DNA-binding domains from sequence

scientific article

Calcium induced regulation of skeletal troponin--computational insights from molecular dynamics simulations

scientific article

CellSim: a novel software to calculate cell similarity and identify their co-regulation networks

scientific article published on 04 March 2019

Classification of Benign and Malignant Thyroid Nodules Using a Combined Clinical Information and Gene Expression Signatures.

scientific article

Co-expression among constituents of a motif in the protein-protein interaction network

scientific article

Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications

scientific article

Contour length and refolding rate of a small protein controlled by engineered disulfide bonds.

scientific article published on 6 October 2006

Correlation between gene expression profiles and protein-protein interactions within and across genomes.

scientific article published on 29 March 2005

Correlations Between Phenotypes and Biological Process Ontologies in Monogenic Human Diseases

scientific article published on 28 October 2020

Efficient free-energy-profile reconstruction using adaptive stochastic perturbation protocols ⬇️

scientific article published on November 21, 2011

Genome-wide Functional Annotation of Dual-Specificity Protein- and Lipid-Binding Modules that Regulate Protein Interactions ⬇️

scientific article published on March 22, 2012

Genomic analysis of a spinal muscular atrophy (SMA) discordant family identifies a novel mutation in TLL2, an activator of growth differentiation factor 8 (myostatin): a case report

scientific article published on 30 December 2019

High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI)

scientific article

Identification of cancer-related genes and motifs in the human gene regulatory network

scientific article published on August 2015

Identification of human circadian genes based on time course gene expression profiles by using a deep learning method.

scientific article published on 11 December 2017

Intrinsically disordered protein-specific force field CHARMM36IDPSFF

scientific article published on 01 July 2018

Kernel-based machine learning protocol for predicting DNA-binding proteins

scientific article

Knowledge-based three-body potential for transcription factor binding site prediction.

scientific article published on February 2016

MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins.

scientific article published on 25 August 2007

Mechanical signaling on the single protein level studied using steered molecular dynamics.

scientific article published on 11 August 2009

Mechanical unfolding intermediates in titin modules.

scientific article

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations.

scientific article

Meta-analysis of sex differences in gene expression in schizophrenia

scientific article published on 11 January 2016

Multi-omics facilitated variable selection in Cox-regression model for cancer prognosis prediction

scientific article published on 13 June 2017

Network-based prediction and knowledge mining of disease genes.

scientific article published on 29 May 2015

On the improvement of free-energy calculation from steered molecular dynamics simulations using adaptive stochastic perturbation protocols.

scientific article

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

scientific article

Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions.

scientific article published on 7 February 2007

Reverse engineering of the giant muscle protein titin

scientific article published in Nature

Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability.

scholarly article

Stabilization provided by neighboring strands is critical for the mechanical stability of proteins.

scientific article published on 3 July 2008

Steered molecular dynamics simulations of force-induced protein domain unfolding

scientific article published on 01 June 1999

TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

scientific article

Template-based protein structure modeling using the RaptorX web server.

scientific article

The molecular basis of ceramide-1-phosphate recognition by C2 domains.

scientific article published on 31 December 2012

Three Electronic State Model of the Primary Phototransformation of Bacteriorhodopsin ⬇️

scientific article published on October 1, 1998

Transcription Factors Contribute to Differential Expression in Cellular Pathways in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma

scientific article published on 23 July 2018

Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation

scientific article

VCF-Server: A web-based visualization tool for high-throughput variant data mining and management

scientific article published on 24 May 2019

Visual presentation as a welcome alternative to textual presentation of gene annotation information.

scientific article published on January 2010

List of works by Hui Lu

16S rDNA Gene Sequencing Analysis in Functional Dyspepsia Treated With Fecal Microbiota Transplantation.

A Herpes Simplex Virus Thymidine Kinase-Induced Mouse Model of Hepatocellular Carcinoma Associated with Up-Regulated Immune-Inflammatory-Related Signals

A Novel Joint Gene Set Analysis Framework Improves Identification of Enriched Pathways in Cross Disease Transcriptomic Analysis

A Single-Molecule Perspective on the Role of Solvent Hydrogen Bonds in Protein Folding and Chemical Reactions

A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.

A new method to measure the semantic similarity from query phenotypic abnormalities to diseases based on the human phenotype ontology.

A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains.

Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome

An improved machine learning protocol for the identification of correct Sequest search results

Application of statistical potentials to protein structure refinement from low resolution ab initio models

Assessment of tumor mutation burden calculation from gene panel sequencing data

Boosting the prediction and understanding of DNA-binding domains from sequence

Calcium induced regulation of skeletal troponin--computational insights from molecular dynamics simulations

CellSim: a novel software to calculate cell similarity and identify their co-regulation networks

Classification of Benign and Malignant Thyroid Nodules Using a Combined Clinical Information and Gene Expression Signatures.

Co-expression among constituents of a motif in the protein-protein interaction network

Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications

Contour length and refolding rate of a small protein controlled by engineered disulfide bonds.

Correlation between gene expression profiles and protein-protein interactions within and across genomes.

Correlations Between Phenotypes and Biological Process Ontologies in Monogenic Human Diseases

Efficient free-energy-profile reconstruction using adaptive stochastic perturbation protocols ⬇️

Genome-wide Functional Annotation of Dual-Specificity Protein- and Lipid-Binding Modules that Regulate Protein Interactions ⬇️

Genomic analysis of a spinal muscular atrophy (SMA) discordant family identifies a novel mutation in TLL2, an activator of growth differentiation factor 8 (myostatin): a case report

High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI)

Identification of cancer-related genes and motifs in the human gene regulatory network

Identification of human circadian genes based on time course gene expression profiles by using a deep learning method.

Intrinsically disordered protein-specific force field CHARMM36IDPSFF

Kernel-based machine learning protocol for predicting DNA-binding proteins

Knowledge-based three-body potential for transcription factor binding site prediction.

MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins.

Mechanical signaling on the single protein level studied using steered molecular dynamics.

Mechanical unfolding intermediates in titin modules.

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations.

Meta-analysis of sex differences in gene expression in schizophrenia

Multi-omics facilitated variable selection in Cox-regression model for cancer prognosis prediction

Network-based prediction and knowledge mining of disease genes.

On the improvement of free-energy calculation from steered molecular dynamics simulations using adaptive stochastic perturbation protocols.

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions.

Reverse engineering of the giant muscle protein titin

Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability.

Stabilization provided by neighboring strands is critical for the mechanical stability of proteins.

Steered molecular dynamics simulations of force-induced protein domain unfolding

TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.

Template-based protein structure modeling using the RaptorX web server.

The molecular basis of ceramide-1-phosphate recognition by C2 domains.

Three Electronic State Model of the Primary Phototransformation of Bacteriorhodopsin ⬇️

Transcription Factors Contribute to Differential Expression in Cellular Pathways in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma

Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation

VCF-Server: A web-based visualization tool for high-throughput variant data mining and management

Visual presentation as a welcome alternative to textual presentation of gene annotation information.