List of works - Jinyan Li

'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces

scientific article published on 29 January 2009

50/50 Expressional Odds of Retention Signifies the Distinction between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana.

scientific article published on 9 October 2017

A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.

scientific article

A bioinformatics potpourri.

scientific article published on 19 January 2018

A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts

scientific article published on 14 December 2006

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.

scientific article published in August 2013

Adaptive Swarm Balancing Algorithms for rare-event prediction in imbalanced healthcare data.

scientific article

Adaptive swarm cluster-based dynamic multi-objective synthetic minority oversampling technique algorithm for tackling binary imbalanced datasets in biomedical data classification.

scientific article

An isomiR expression panel based novel breast cancer classification approach using improved mutual information

Antibody-specified B-cell epitope prediction in line with the principle of context-awareness

scientific article published in November 2011

Binding affinity prediction for protein-ligand complexes based on β contacts and B factor

scientific article published on 5 November 2013

Bird Flu Outbreak Prediction via Satellite Tracking

Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes.

scientific article published on 24 August 2017

Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling

scientific article published in March 2002

Clustering orthologous proteins across phylogenetically distant species

scientific article published in May 2008

Co-Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots

scientific article published on 16 December 2015

Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

scientific article published on 16 June 2015

Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships

scientific article

DDI-PULearn: a positive-unlabeled learning method for large-scale prediction of drug-drug interactions

scientific article published on 24 December 2019

DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences

scientific article published on 29 July 2004

DeEPs: A New Instance-Based Lazy Discovery and Classification System

article by Jinyan Li et al published February 2004 in Machine Learning

Delineation of the frequency and boundary of chromosomal copy number variations in paediatric neuroblastoma.

scientific article published on 22 January 2018

Detection of outlier residues for improving interface prediction in protein heterocomplexes.

scientific article

Discovery of significant rules for classifying cancer diagnosis data

scientific article

Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs

scientific article published in February 2011

DomSVR: domain boundary prediction with support vector regression from sequence information alone

scientific article

Elitist Binary Wolf Search Algorithm for Heuristic Feature Selection in High-Dimensional Bioinformatics Datasets.

scientific article published on 28 June 2017

Exploring Consensus RNA Substructural Patterns using Subgraph Mining.

scientific article published on 26 December 2016

Grouping miRNAs of similar functions via weighted information content of gene ontology.

scientific article

Guest Editors' Introduction: Data Mining in Bioinformatics

Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression

scientific article published on 19 July 2021

High-speed and high-ratio referential genome compression

scientific article published on 23 June 2017

Hot spot prediction in protein-protein interactions by an ensemble system

scientific article published on 31 December 2018

Hybrid outcome prediction model for severe traumatic brain injury.

scientific article

Hypotension Risk Prediction via Sequential Contrast Patterns of ICU Blood Pressure.

scientific article

Identification of WD40 repeats by secondary structure-aided profile-profile alignment

scientific article

Identification of lung cancer miRNA-miRNA co-regulation networks through a progressive data refining approach.

scientific article

Identification of pre-microRNAs by characterizing their sequence order evolution information and secondary structure graphs

Imbalance learning for the prediction of N-Methylation sites in mRNAs

Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets

scientific article published on 9 December 2015

Influenza A HA's conserved epitopes and broadly neutralizing antibodies: a prediction method

scientific article

Insights into bacterial genome composition through variable target GC content profiling

scientific article published in January 2010

Integrating water exclusion theory into β contacts to predict binding free energy changes and binding hot spots

scientific article

Introduction to Selected Papers from GIW2018

scientific article published on 01 December 2018

Laplacian normalization and random walk on heterogeneous networks for disease-gene prioritization.

scientific article published on 7 February 2015

Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways

scientific article

Mining for the antibody-antigen interacting associations that predict the B cell epitopes

scientific article

Mining statistically-solid k-mers for accurate NGS error correction

Modeling protein interacting groups by quasi-bicliques: complexity, algorithm, and application

scientific article published in April 2010

ONP-Miner: One-off Negative Sequential Pattern Mining

scientific article published in 2022

Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces

scientific article published on 27 December 2019

Positive-unlabeled learning for the prediction of conformational B-cell epitopes.

scientific article published on 9 December 2015

Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

scholarly article by Yi Zheng et al published 31 December 2018 in BMC Bioinformatics

Prediction of 8-state protein secondary structures by a novel deep learning architecture

scholarly article by Buzhong Zhang published in August 2018

Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers

scientific article

Propensity vectors of low-ASA residue pairs in the distinction of protein interactions

scientific article published in February 2010

Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective

scientific article

Protein binding hot spots prediction from sequence only by a new ensemble learning method.

scientific article published in August 2017

Recognition of CRISPR/Cas9 off-target sites through ensemble learning of uneven mismatch distributions

scientific article published on 01 September 2018

Rule discovery and distance separation to detect reliable miRNA biomarkers for the diagnosis of lung squamous cell carcinoma

scientific article

SOHPRED: a new bioinformatics tool for the characterization and prediction of human S-sulfenylation sites

scientific article published on July 2016

Septic shock prediction for ICU patients via coupled HMM walking on sequential contrast patterns

scientific article published on 20 December 2016

Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information ⬇️

scientific article published on July 28, 2010

Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients.

scientific article published in January 2003

Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences

scientific article

Strong compound-risk factors: efficient discovery through emerging patterns and contrast sets

scientific article published in September 2007

Structural and functional analysis of multi-interface domains.

scientific article

Tertiary structure-based prediction of conformational B-cell epitopes through B factors

scientific article published on June 2014

The long noncoding RNA MALAT1 promotes tumor-driven angiogenesis by up-regulating pro-angiogenic gene expression

scientific article published on 02 February 2016

The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35

scientific article published on 05 November 2019

Twelve C2H2 zinc-finger genes on human chromosome 19 can be each translated into the same type of protein after frameshifts

scientific article published on January 2004

Use of extreme patient samples for outcome prediction from gene expression data.

scientific article

Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes.

scientific article published on 12 February 2016

Using sequential patterns as features for classification models to make accurate predictions on ICU events

scientific article published in August 2015

WITHDRAWN: Improving classification of protein binders for virtual drug screening by novel swarm-based feature selection techniques

retracted scientific article published on 30 September 2016

Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state

scientific article published in December 2012

dbMPIKT: a database of kinetic and thermodynamic mutant protein interactions

scientific article published on 27 November 2018

k-Partite cliques of protein interactions: A novel subgraph topology for functional coherence analysis on PPI networks

scientific article published on 19 September 2013

predCar-site: Carbonylation sites prediction in proteins using support vector machine with resolving data imbalanced issue.

scientific article

List of works by Jinyan Li

'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces

50/50 Expressional Odds of Retention Signifies the Distinction between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana.

A Sequence-Based Dynamic Ensemble Learning System for Protein Ligand-Binding Site Prediction.

A bioinformatics potpourri.

A pHMM-ANN based discriminative approach to promoter identification in prokaryote genomic contexts

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.

Adaptive Swarm Balancing Algorithms for rare-event prediction in imbalanced healthcare data.

Adaptive swarm cluster-based dynamic multi-objective synthetic minority oversampling technique algorithm for tackling binary imbalanced datasets in biomedical data classification.

An isomiR expression panel based novel breast cancer classification approach using improved mutual information

Antibody-specified B-cell epitope prediction in line with the principle of context-awareness

Binding affinity prediction for protein-ligand complexes based on β contacts and B factor

Bird Flu Outbreak Prediction via Satellite Tracking

Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes.

Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling

Clustering orthologous proteins across phylogenetically distant species

Co-Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots

Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships

DDI-PULearn: a positive-unlabeled learning method for large-scale prediction of drug-drug interactions

DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences

DeEPs: A New Instance-Based Lazy Discovery and Classification System

Delineation of the frequency and boundary of chromosomal copy number variations in paediatric neuroblastoma.

Detection of outlier residues for improving interface prediction in protein heterocomplexes.

Discovery of significant rules for classifying cancer diagnosis data

Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs

DomSVR: domain boundary prediction with support vector regression from sequence information alone

Elitist Binary Wolf Search Algorithm for Heuristic Feature Selection in High-Dimensional Bioinformatics Datasets.

Exploring Consensus RNA Substructural Patterns using Subgraph Mining.

Grouping miRNAs of similar functions via weighted information content of gene ontology.

Guest Editors' Introduction: Data Mining in Bioinformatics

Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression

High-speed and high-ratio referential genome compression

Hot spot prediction in protein-protein interactions by an ensemble system

Hybrid outcome prediction model for severe traumatic brain injury.

Hypotension Risk Prediction via Sequential Contrast Patterns of ICU Blood Pressure.

Identification of WD40 repeats by secondary structure-aided profile-profile alignment

Identification of lung cancer miRNA-miRNA co-regulation networks through a progressive data refining approach.

Identification of pre-microRNAs by characterizing their sequence order evolution information and secondary structure graphs

Imbalance learning for the prediction of N-Methylation sites in mRNAs

Inference of gene interaction networks using conserved subsequential patterns from multiple time course gene expression datasets

Influenza A HA's conserved epitopes and broadly neutralizing antibodies: a prediction method

Insights into bacterial genome composition through variable target GC content profiling

Integrating water exclusion theory into β contacts to predict binding free energy changes and binding hot spots

Introduction to Selected Papers from GIW2018

Laplacian normalization and random walk on heterogeneous networks for disease-gene prioritization.

Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways

Mining for the antibody-antigen interacting associations that predict the B cell epitopes

Mining statistically-solid k-mers for accurate NGS error correction

Modeling protein interacting groups by quasi-bicliques: complexity, algorithm, and application

ONP-Miner: One-off Negative Sequential Pattern Mining

Old drug repositioning and new drug discovery through similarity learning from drug-target joint feature spaces

Positive-unlabeled learning for the prediction of conformational B-cell epitopes.

Predicting adverse drug reactions of combined medication from heterogeneous pharmacologic databases

Prediction of 8-state protein secondary structures by a novel deep learning architecture

Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers

Propensity vectors of low-ASA residue pairs in the distinction of protein interactions

Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective

Protein binding hot spots prediction from sequence only by a new ensemble learning method.

Recognition of CRISPR/Cas9 off-target sites through ensemble learning of uneven mismatch distributions

Rule discovery and distance separation to detect reliable miRNA biomarkers for the diagnosis of lung squamous cell carcinoma

SOHPRED: a new bioinformatics tool for the characterization and prediction of human S-sulfenylation sites

Septic shock prediction for ICU patients via coupled HMM walking on sequential contrast patterns

Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information ⬇️

Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients.

Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences

Strong compound-risk factors: efficient discovery through emerging patterns and contrast sets

Structural and functional analysis of multi-interface domains.

Tertiary structure-based prediction of conformational B-cell epitopes through B factors

The long noncoding RNA MALAT1 promotes tumor-driven angiogenesis by up-regulating pro-angiogenic gene expression

The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35

Twelve C2H2 zinc-finger genes on human chromosome 19 can be each translated into the same type of protein after frameshifts

Use of extreme patient samples for outcome prediction from gene expression data.

Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes.

Using sequential patterns as features for classification models to make accurate predictions on ICU events

WITHDRAWN: Improving classification of protein binders for virtual drug screening by novel swarm-based feature selection techniques

Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state

dbMPIKT: a database of kinetic and thermodynamic mutant protein interactions

k-Partite cliques of protein interactions: A novel subgraph topology for functional coherence analysis on PPI networks

predCar-site: Carbonylation sites prediction in proteins using support vector machine with resolving data imbalanced issue.