List of works by Kevin Y Yip

A common set of distinct features that characterize noncoding RNAs across multiple species

scientific article

A comprehensive web tool for toehold switch design.

scientific article published on 10 April 2018

A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps.

scientific article published on June 2016

A semi-supervised approach to projected clustering with applications to microarray data.

scientific article

A web services choreography scenario for interoperating bioinformatics applications

scientific article

ACT: aggregation and correlation toolbox for analyses of genome tracks.

scientific article

Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming

scientific article published in Nature Communications

Accurate reconstruction of viral genomes in human cells from short reads using iterative refinement

scientific article published on 06 June 2022

An integrative ENCODE resource for cancer genomics

scientific article published on 29 July 2020

Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations

scientific article

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

scientific article published on 23 December 2014

Biosphere: the interoperation of web services in microarray cluster analysis.

scientific article published on January 2004

CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs.

scientific article published on 7 December 2004

Comparative analysis of single-cell parallel sequencing approaches in oocyte application

scientific article published on 06 December 2018

Comparative analysis of the transcriptome across distant species

scientific article

Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C666-1.

scientific article published on 2 August 2013

Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data

scientific article

Development of Grid-like Applications for Public Health Using Web 2.0 Mashup Techniques

scientific article (publication date: 2008)

EBV-encoded miRNAs target ATM-mediated response in nasopharyngeal carcinoma

scientific article published on 12 December 2017

ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications

scientific article published on 24 January 2014

Establishment and characterization of new tumor xenografts and cancer cell lines from EBV-positive nasopharyngeal carcinoma

scientific article published in Nature Communications

Exome and genome sequencing of nasopharynx cancer identifies NF-κB pathway activating mutations

scientific article

Genome maps across 26 human populations reveal population-specific patterns of structural variation

scientific article published on 04 March 2019

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

scientific article

HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0

scientific article (publication date: October 2008)

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

scientific article published on 19 January 2021

Identification of Genes Associated With Hirschsprung Disease, Based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development

scientific article published on 12 September 2018

Identifying projected clusters from gene expression profiles.

scientific article published in October 2004

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

scientific article

Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

scientific article published on 15 December 2016

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

scientific article

Interactome-transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes

scientific article published on 18 October 2016

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

scientific article published on 19 June 2020

LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics

scientific article (publication date: 9 May 2007)

Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis

scientific article published on 01 September 2018

New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation

scientific article published on 19 February 2019

OMBlast: alignment tool for optical mapping using a seed-and-extend approach

scientific article

OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps

scientific article published on 01 July 2019

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps.

scientific article published in December 2017

OMTools: a software package for visualizing and processing optical mapping data

scientific article

On mining micro-array data by Order-Preserving Submatrix.

scientific article

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines

scientific article

Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'

scientific article published on 01 August 2019

START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries.

scientific article published on 22 September 2017

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing

scientific article published on 20 March 2019

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

scientific article published on 29 July 2020

Sustained antidiabetic effects of a berberine-containing Chinese herbal medicine through regulation of hepatic gene expression.

scientific article published on 6 March 2012

The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module

scientific article

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

scientific article

VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants

scientific article

Whole-genome analysis of noncoding genetic variations identifies multi-scale regulatory element perturbations associated with Hirschsprung disease

scientific article published on 18 September 2020

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation.

scientific article

Yin Yang 1-mediated epigenetic silencing of tumour-suppressive microRNAs activates nuclear factor-κB in hepatocellular carcinoma.

scientific article published on 21 January 2016

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