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List of works by Limsoon Wong

A consensus linkage map of oil palm and a major QTL for stem height

scientific article

A database of annotated promoters of genes associated with common respiratory and related diseases

scientific article published on March 2012

A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression.

scientific article published on January 2012

A probabilistic graph-theoretic approach to integrate multiple predictions for the protein-protein subnetwork prediction challenge

scientific article published in March 2009

A quantum leap in the reproducibility, precision, and sensitivity of gene expression profile analysis even when sample size is extremely small

scientific article published on 26 May 2015

A semi-automated methodology for finding lipid-related GO terms.

scientific article

A short introduction to some recent progress in phylogenetic network reconstruction, genome mapping, gene expression analysis, molecular dynamic simulation, and other problems in bioinformatics ⬇️

scientific article published on 01 August 2012

Accomplishments and challenges in literature data mining for biology

scientific article

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

scientific article published in August 2013

Advanced bioinformatics methods for practical applications in proteomics

scientific article published on 01 January 2019

Advancing Clinical Proteomics via Analysis Based on Biological Complexes: A Tale of Five Paradigms

scientific article published on 25 July 2016

An approach to identifying drug resistance associated mutations in bacterial strains

scientific article

An empirical comparison of several recent epistatic interaction detection methods

scientific article published on 7 September 2011

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

scientific article published in November 2011

Author Correction: Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm

scientific article published in Scientific Reports

B-cell epitope prediction through a graph model

scientific article

Brief overview of bioinformatics activities in Singapore

scientific article published on 25 September 2009

Burial Level Change Defines a High Energetic Relevance for Protein Binding Interfaces.

scientific article published in March 2015

CAMBer: an approach to support comparative analysis of multiple bacterial strains

scientific article

CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains

scientific article published on 8 October 2011

CMPF: class-switching minimized pathfinding in metabolic networks

scientific article

Class-paired Fuzzy SubNETs: A paired variant of the rank-based network analysis family for feature selection based on protein complexes.

scientific article published on 8 April 2017

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

scientific article published in March 2002

Comparative Transcriptomics Unravel Biochemical Specialization of Leaf Tissues of Stevia for Diterpenoid Production.

scientific article published on 5 October 2015

Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets

scientific article

Comparative network-based recovery analysis and proteomic profiling of neurological changes in valproic acid-treated mice.

scientific article published on 17 April 2013

Complex discovery from weighted PPI networks.

scientific article published on 12 May 2009

Computational proteomics: designing a comprehensive analytical strategy.

scientific article published on 18 July 2013

Conservation of water molecules in protein binding interfaces ⬇️

scientific article published on January 1, 2012

Consistency, comprehensiveness, and compatibility of pathway databases ⬇️

scientific article published on September 7, 2010

Contemporary network proteomics and its requirements

scientific article

Correction to “Comparative Network-Based RecoveryAnalysis and Proteomic Profiling of Neurological Changes in ValproicAcid-Treated Mice”.

scientific article published on 4 September 2013

Coupling Graphs, Efficient Algorithms and B-Cell Epitope Prediction

scientific article published on January 2014

DA 1.0: parameter estimation of biological pathways using data assimilation approach

scientific article

DBAC: a simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts.

scientific article

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

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

Dealing with Confounders in Omics Analysis

scientific article published on 20 February 2018

Decomposing PPI networks for complex discovery.

scientific article published on 14 October 2011

Design principles for clinical network-based proteomics.

scientific article published on 27 May 2016

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

scientific article

Determination of a molecular signature of acute T-cell-mediated renal allograft rejection using quantitative real-time RT-PCR of 45 genes on a low density array.

scientific article

Discovery of protein complexes with core-attachment structures from Tandem Affinity Purification (TAP) data.

scientific article

Discovery of significant rules for classifying cancer diagnosis data

scientific article

Discovery of small protein complexes from PPI networks with size-specific supervised weighting

scientific article

Disruption of protein complexes.

scientific article published on 27 March 2013

Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm

scientific article

Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures

scientific article published on 13 April 2006

Editorial - Bioinformatics development at the BGRS\SB conference series: 10th anniversary

scientific article published on 20 March 2017

Effective Response Metric: a novel tool to predict relapse in childhood acute lymphoblastic leukaemia using time-series gene expression profiling

scientific article published on 01 June 2018

Efficient mining of haplotype patterns for linkage disequilibrium mapping

scientific article published in December 2010

Embracing noise to improve cross-batch prediction accuracy

scientific article

Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies.

scientific article

Epidemic reemergence in adaptive complex networks.

scientific article

Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.

scientific article published on 28 October 2013

Evaluating feature-selection stability in next-generation proteomics

scientific article

Evaluating temporal factors in combined interventions of workforce shift and school closure for mitigating the spread of influenza

scientific article

Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions

scientific article published on 21 April 2006

FIMM, a database of functional molecular immunology

scientific article published on January 2000

FIMM, a database of functional molecular immunology: update 2002

scientific article

FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium ⬇️

scientific article

Finding consistent disease subnetworks across microarray datasets

scientific article

Finding consistent disease subnetworks using PFSNet.

scientific article published on 28 November 2013

From the static interactome to dynamic protein complexes: Three challenges

scientific article published on 7 January 2015

GFS: fuzzy preprocessing for effective gene expression analysis.

scientific article

GWAMAR: genome-wide assessment of mutations associated with drug resistance in bacteria

scientific article

Gaps in text-based knowledge discovery for biology.

scientific article published in September 2002

Genome-wide analysis of regions similar to promoters of histone genes

scientific article

Guest Editorial for the International Conference on Genome Informatics (GIW 2013).

scientific article

Hi-Jack: a novel computational framework for pathway-based inference of host-pathogen interactions

scientific article published on 9 March 2015

High-speed and high-ratio referential genome compression

scientific article published on 23 June 2017

How advancement in biological network analysis methods empowers proteomics ⬇️

scientific article published on January 19, 2012

Identification of cell cycle-regulated genes in fission yeast

scientific article

Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns.

scientific article published on May 2002

Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language

scientific article published on 01 January 2018

Improved statistical model checking methods for pathway analysis

scientific article

Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer.

scientific article

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens

scientific article

Integrating Networks and Proteomics: Moving Forward.

scientific article published on 13 June 2016

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

scientific article

International Conference on Genome Informatics (GIW 2013) in Singapore: Introduction to the systems biology contributions

scientific article

Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity ⬇️

scientific article published on September 6, 2012

Introduction to Selected Papers from GIW2018

scientific article published on 01 December 2018

Introduction--some new results and tools for protein function prediction, RNA target site prediction, genotype calling, environmental genomics, and more

scientific article published on 01 December 2011

JBCB, the first decade

scientific article

John Wooley and JBCB.

scientific article published on 9 June 2015

Kleisli: a new tool for data integration in biology

scientific article

LipidGO: database for lipid-related GO terms and applications

scientific article published on December 2013

Low cytosine triphosphate synthase 2 expression renders resistance to 5-fluorouracil in colorectal cancer.

scientific article

MIRACH: efficient model checker for quantitative biological pathway models ⬇️

scientific article published on January 5, 2011

MapReduce for accurate error correction of next-generation sequencing data

scientific article

Methods for protein complex prediction and their contributions towards understanding the organisation, function and dynamics of complexes.

scientific article published on 23 April 2015

NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information

scientific article published on 16 September 2020

NetProt: Complex-based Feature Selection.

scientific article

Network-based pipeline for analyzing MS data: an application toward liver cancer

scientific article

Networks in proteomics analysis of cancer ⬇️

scientific article published on 05 March 2013

New results in biological sequence analysis, complex gene–disease association, qPCR calculation, and biological text mining.

scientific article published in October 2010

Next generation sequencing unravels the biosynthetic ability of spearmint (Mentha spicata) peltate glandular trichomes through comparative transcriptomics.

scientific article

On representation and querying incomplete information in databases with bags

Optimal gene expression analysis by microarrays

scientific article

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.

scientific article

Overcoming drug resistance by co-targeting

PLncDB: plant long non-coding RNA database ⬇️

scientific article published on March 7, 2013

Pharmacodynamic effects of seliciclib, an orally administered cell cycle modulator, in undifferentiated nasopharyngeal cancer

scientific article published in February 2009

Prediction of problematic complexes from PPI networks: sparse, embedded, and small complexes.

scientific article published in August 2015

Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces.

scientific article

Protein complex prediction based on k-connected subgraphs in protein interaction network.

scientific article

Protein complex prediction by date hub removal

scientific article published on 23 March 2018

Protein complex-based analysis is resistant to the obfuscating consequences of batch effects --- a case study in clinical proteomics.

scientific article published on 14 March 2017

Proteomic investigation of intra-tumor heterogeneity using network-based contextualization - A case study on prostate cancer

scientific article published on 16 July 2019

Proteomics Signature Profiling (PSP): A Novel Contextualization Approach for Cancer Proteomics ⬇️

scientific article published on February 9, 2012

Quantitative proteomics signature profiling based on network contextualization

scientific article

Random forests on Hadoop for genome-wide association studies of multivariate neuroimaging phenotypes

scientific article

Relational expressive power of constraint query languages

scientific article published in January 1998

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

scientific article

SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data

scientific article published on 19 March 2018

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

scientific article published in January 2003

Sirius PSB: a generic system for analysis of biological sequences.

scientific article published in December 2009

Spectra-first feature analysis in clinical proteomics - A case study in renal cancer

scientific article published on October 2016

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

scientific article

Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions

scientific article

Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding?

scientific article published on 22 July 2011

Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding

scientific article published on 22 October 2013

Structural and functional analysis of multi-interface domains.

scientific article

Supervised maximum-likelihood weighting of composite protein networks for complex prediction.

scientific article

TICA: Transcriptional Interaction and Coregulation Analyzer

scientific article published on 01 October 2018

Temporal factors in school closure policy for mitigating the spread of influenza

scientific article published on 17 February 2011

The floral transcriptome of ylang ylang (Cananga odorata var. fruticosa) uncovers biosynthetic pathways for volatile organic compounds and a multifunctional and novel sesquiterpene synthase

scientific article published on 8 May 2015

The role of miRNAs in complex formation and control.

scientific article published on 16 December 2011

Transcriptome Analysis Reveals Neuroprotective aspects of Human Reactive Astrocytes induced by Interleukin 1β.

scientific article published on 25 October 2017

Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm.

scientific article

Turning straw into gold: building robustness into gene signature inference

scientific article published in January 2019

Two scenarios for overcoming drug resistance by co-targeting

scientific article published in January 2015

Understanding missing proteins: a functional perspective.

scientific article published on 17 November 2017

Using data fusion for scoring reliability of protein-protein interactions.

scientific article

Using indirect protein interactions for the prediction of Gene Ontology functions

scientific article

Using indirect protein-protein interactions for protein complex prediction.

scientific article published in June 2008

Valproic acid mediates miR-124 to down-regulate a novel protein target, GNAI1.

scientific article published on 27 October 2015

Why Batch Effects Matter in Omics Data, and How to Avoid Them.

scientific article

Why breast cancer signatures are no better than random signatures explained

scientific article published in November 2018

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

eCAMBer: efficient support for large-scale comparative analysis of multiple bacterial strains.

scientific article

eCEO: an efficient Cloud Epistasis cOmputing model in genome-wide association study

scientific article published on 2 March 2011

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