List of works - Joshua Ho

A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data

scientific article published on 01 March 2018

A genetic ensemble approach for gene-gene interaction identification

scientific article

A model selection approach to discover age-dependent gene expression patterns using quantile regression models.

scientific article

A voting approach to identify a small number of highly predictive genes using multiple classifiers

scientific article

Aberrant Expression of Circulating MicroRNA Leads to the Dysregulation of Alpha-Synuclein and Other Pathogenic Genes in Parkinson's Disease

scientific article published on 23 August 2021

An Embryonic and Induced Pluripotent Stem Cell Model for Ovarian Granulosa Cell Development and Steroidogenesis.

scientific article published in January 2017

An antibody-based leukocyte-capture microarray for the diagnosis of systemic lupus erythematosus.

scientific article published on 13 March 2013

An innovative approach for testing bioinformatics programs using metamorphic testing

scientific article

Application of Metamorphic Testing to Supervised Classifiers

scientific article

Application of a systems approach to study developmental gene regulation

scientific article

Big data: the elements of good questions, open data, and powerful software

scientific article published on 25 January 2019

Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.

scientific article published on 17 December 2015

Biologically active constituents of the secretome of human W8B2+ cardiac stem cells.

scientific article

C3: An R package for cross-species compendium-based cell-type identification

scientific article published on 09 October 2018

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

scientific article

CardiacProfileR: an R package for extraction and visualisation of heart rate profiles from wearable fitness trackers

scientific article published on 21 January 2019

ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

scientific article

Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology

scientific article published on 07 July 2020

Cisplatin prevents breast cancer metastasis through blocking early EMT and retards cancer growth together with paclitaxel

scientific article published on 01 January 2021

Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco

scientific article published on 30 December 2019

Crim1 regulates integrin signaling in murine lens development.

scientific article

Customising an antibody leukocyte capture microarray for systemic lupus erythematosus: beyond biomarker discovery.

scientific article published on 02 December 2009

Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding.

scientific article published on 13 June 2019

Decoding the complex genetic causes of heart diseases using systems biology

scientific article

Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.

scientific article published on 19 January 2018

Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus

scientific article published on 24 March 2019

Effect of machine learning re-sampling techniques for imbalanced datasets in 18F-FDG PET-based radiomics model on prognostication performance in cohorts of head and neck cancer patients

scientific article published on 06 April 2020

Enhanced cardiac repair by telomerase reverse transcriptase over-expression in human cardiac mesenchymal stromal cells

scientific article published on 22 July 2019

Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud

scientific article published on 24 December 2016

Gene-gene interaction filtering with ensemble of filters

scientific article

Hactive: a smartphone application for heart rate profiling

scientific article published on 14 July 2020

Host and microbiome multi-omics integration: applications and methodologies

scientific article published on 09 January 2019

How to test bioinformatics software?

scientific article published on 13 August 2015

Identification of active signaling pathways by integrating gene expression and protein interaction data

article

Identification of clinically actionable variants from genome sequencing of families with congenital heart disease

scientific article published on 08 October 2018

Identification of satellite cells from anole lizard skeletal muscle and demonstration of expanded musculoskeletal potential

scientific article published on 25 December 2017

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

scientific article published on 6 October 2017

Impact of sequencing depth in ChIP-seq experiments.

scientific article

Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells.

scientific article published on 14 February 2017

Intercalated discs: multiple proteins perform multiple functions in non-failing and failing human hearts.

scientific article published on 22 January 2009

Light-focusing human micro-lenses generated from pluripotent stem cells model lens development and drug-induced cataract in vitro

scientific article published on 7 December 2017

Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci.

scientific article

MQuad enables clonal substructure discovery using single cell mitochondrial variants

scientific article published on 08 March 2022

Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities

scientific article published on 25 April 2022

Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity

scientific article published on 23 June 2016

Maternal obesity heritably perturbs offspring metabolism for three generations without serial programming.

scientific article

Modelling, inference and big data in biophysics.

scientific article published on 30 July 2017

NAD Deficiency, Congenital Malformations, and Niacin Supplementation.

scientific article published in August 2017

Network modelling of gene regulation

scientific article

PBrowse: a web-based platform for real-time collaborative exploration of genomic data.

scientific article

Scalability and Validation of Big Data Bioinformatics Software

scientific article published on 20 July 2017

Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.

scientific article

Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

article

Targeted next-generation sequencing identifies pathogenic variants in familial congenital heart disease

scientific article published on December 2014

Testing and Validating Machine Learning Classifiers by Metamorphic Testing

scientific article

The method to quantify cell elasticity based on the precise measurement of pressure inducing cell deformation in microfluidic channels

scientific article published on 23 January 2021

Ultrafast clustering of single-cell flow cytometry data using FlowGrid

scientific article published on 05 April 2019

Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie

scientific article published on 8 December 2014

Verification of phylogenetic inference programs using metamorphic testing.

scientific article published in December 2011

XGSA: A statistical method for cross-species gene set analysis

scientific article published on September 2016

hiHMM: Bayesian non-parametric joint inference of chromatin state maps

scientific article published on 27 February 2015

iSyTE 2.0: a database for expression-based gene discovery in the eye.

scientific article published on 19 September 2017

iSyTE: integrated Systems Tool for Eye gene discovery.

scientific article published on 21 March 2012

List of works by Joshua Ho

A Screening Approach to Identify Clinically Actionable Variants Causing Congenital Heart Disease in Exome Data

A genetic ensemble approach for gene-gene interaction identification

A model selection approach to discover age-dependent gene expression patterns using quantile regression models.

A voting approach to identify a small number of highly predictive genes using multiple classifiers

Aberrant Expression of Circulating MicroRNA Leads to the Dysregulation of Alpha-Synuclein and Other Pathogenic Genes in Parkinson's Disease

An Embryonic and Induced Pluripotent Stem Cell Model for Ovarian Granulosa Cell Development and Steroidogenesis.

An antibody-based leukocyte-capture microarray for the diagnosis of systemic lupus erythematosus.

An innovative approach for testing bioinformatics programs using metamorphic testing

Application of Metamorphic Testing to Supervised Classifiers

Application of a systems approach to study developmental gene regulation

Big data: the elements of good questions, open data, and powerful software

Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.

Biologically active constituents of the secretome of human W8B2+ cardiac stem cells.

C3: An R package for cross-species compendium-based cell-type identification

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data

CardiacProfileR: an R package for extraction and visualisation of heart rate profiles from wearable fitness trackers

ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.

Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology

Cisplatin prevents breast cancer metastasis through blocking early EMT and retards cancer growth together with paclitaxel

Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco

Crim1 regulates integrin signaling in murine lens development.

Customising an antibody leukocyte capture microarray for systemic lupus erythematosus: beyond biomarker discovery.

Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding.

Decoding the complex genetic causes of heart diseases using systems biology

Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest.

Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus

Effect of machine learning re-sampling techniques for imbalanced datasets in 18F-FDG PET-based radiomics model on prognostication performance in cohorts of head and neck cancer patients

Enhanced cardiac repair by telomerase reverse transcriptase over-expression in human cardiac mesenchymal stromal cells

Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud

Gene-gene interaction filtering with ensemble of filters

Hactive: a smartphone application for heart rate profiling

Host and microbiome multi-omics integration: applications and methodologies

How to test bioinformatics software?

Identification of active signaling pathways by integrating gene expression and protein interaction data

Identification of clinically actionable variants from genome sequencing of families with congenital heart disease

Identification of satellite cells from anole lizard skeletal muscle and demonstration of expanded musculoskeletal potential

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

Impact of sequencing depth in ChIP-seq experiments.

Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells.

Intercalated discs: multiple proteins perform multiple functions in non-failing and failing human hearts.

Light-focusing human micro-lenses generated from pluripotent stem cells model lens development and drug-induced cataract in vitro

Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci.

MQuad enables clonal substructure discovery using single cell mitochondrial variants

Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities

Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity

Maternal obesity heritably perturbs offspring metabolism for three generations without serial programming.

Modelling, inference and big data in biophysics.

NAD Deficiency, Congenital Malformations, and Niacin Supplementation.

Network modelling of gene regulation

PBrowse: a web-based platform for real-time collaborative exploration of genomic data.

Scalability and Validation of Big Data Bioinformatics Software

Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.

Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

Targeted next-generation sequencing identifies pathogenic variants in familial congenital heart disease

Testing and Validating Machine Learning Classifiers by Metamorphic Testing

The method to quantify cell elasticity based on the precise measurement of pressure inducing cell deformation in microfluidic channels

Ultrafast clustering of single-cell flow cytometry data using FlowGrid

Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie

Verification of phylogenetic inference programs using metamorphic testing.

XGSA: A statistical method for cross-species gene set analysis

hiHMM: Bayesian non-parametric joint inference of chromatin state maps

iSyTE 2.0: a database for expression-based gene discovery in the eye.

iSyTE: integrated Systems Tool for Eye gene discovery.