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

Genome Biology, 2017-03, Vol.18 (1), p.59-59, Article 59

2017

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

Epigenetics & chromatin, 2019-06, Vol.12 (1), p.36-36, Article 36

2019

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

eLife, 2019-03, Vol.8

2019

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Testing and validating machine learning classifiers by metamorphic testing

The Journal of systems and software, 2011-04, Vol.84 (4), p.544-558

2011

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Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

Genome Biology, 2020-07, Vol.21 (1), p.1-167, Article 167

2020

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

Nucleic acids research, 2018-01, Vol.46 (D1), p.D875

2018

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DCATS: differential composition analysis for flexible single-cell experimental designs

Genome Biology, 2023-06, Vol.24 (1), p.151-151, Article 151

2023

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Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Familial Congenital Heart Disease

Journal of the American College of Cardiology, 2014-12, Vol.64 (23), p.2498-2506

2014

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The implications of Arctic sea ice decline on shipping

Marine policy, 2010-05, Vol.34 (3), p.713-715

Ho, Joshua

2010

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An innovative approach for testing bioinformatics programs using metamorphic testing

BMC bioinformatics, 2009-01, Vol.10 (1), p.24-24, Article 24

2009

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Generalized and scalable trajectory inference in single-cell omics data with VIA

Nature communications, 2021-09, Vol.12 (1), p.5528-5528, Article 5528

2021

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

BMC genomics, 2011-02, Vol.12 (1), p.134-134, Article 134

2011

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MQuad enables clonal substructure discovery using single cell mitochondrial variants

Nature communications, 2022-03, Vol.13 (1), p.1205-1205, Article 1205

2022

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Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori

Nature communications, 2023-04, Vol.14 (1), p.2196-2196, Article 2196

2023

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Host and microbiome multi-omics integration: applications and methodologies

Biophysical reviews, 2019-02, Vol.11 (1), p.55-65

2019

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FlowGrid enables fast clustering of very large single-cell RNA-seq data

Bioinformatics, 2021-12, Vol.38 (1), p.282-283

2021

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PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells

Bioinformatics, 2020-05, Vol.36 (9), p.2778-2786

2020

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Automatic flow delay through passive wax valves for paper-based analytical devices

Lab on a chip, 2021-10, Vol.21 (21), p.4166-4176

2021

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Impact of sequencing depth in ChIP-seq experiments

Nucleic acids research, 2014-05, Vol.42 (9), p.e74

2014

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Computed tomography-based deep-learning prediction of neoadjuvant chemoradiotherapy treatment response in esophageal squamous cell carcinoma

Radiotherapy and oncology, 2021-01, Vol.154, p.6-13

2021

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An edge-device-compatible algorithm for valvular heart diseases screening using phonocardiogram signals with a lightweight convolutional neural network and self-supervised learning

Computer methods and programs in biomedicine, 2024-01, Vol.243, p.107906-107906, Article 107906

2024

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Assessment of Intratumoral and Peritumoral Computed Tomography Radiomics for Predicting Pathological Complete Response to Neoadjuvant Chemoradiation in Patients With Esophageal Squamous Cell Carcinoma

JAMA network open, 2020-09, Vol.3 (9), p.e2015927

2020

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Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer

BMC microbiology, 2020-04, Vol.20 (Suppl 1), p.83-13, Article 83

2020

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

BMC genomics, 2018-01, Vol.19 (Suppl 1), p.929-929, Article 929

2018

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

BMC bioinformatics, 2014, Vol.15 Suppl 16 (Suppl 16), p.S15-S15, Article S15

2014

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

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

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

Testing and validating machine learning classifiers by metamorphic testing

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

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

DCATS: differential composition analysis for flexible single-cell experimental designs

Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Familial Congenital Heart Disease

The implications of Arctic sea ice decline on shipping

An innovative approach for testing bioinformatics programs using metamorphic testing

Generalized and scalable trajectory inference in single-cell omics data with VIA

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

MQuad enables clonal substructure discovery using single cell mitochondrial variants

Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori

Host and microbiome multi-omics integration: applications and methodologies

FlowGrid enables fast clustering of very large single-cell RNA-seq data

PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells

Automatic flow delay through passive wax valves for paper-based analytical devices

Impact of sequencing depth in ChIP-seq experiments

Computed tomography-based deep-learning prediction of neoadjuvant chemoradiotherapy treatment response in esophageal squamous cell carcinoma

An edge-device-compatible algorithm for valvular heart diseases screening using phonocardiogram signals with a lightweight convolutional neural network and self-supervised learning

Assessment of Intratumoral and Peritumoral Computed Tomography Radiomics for Predicting Pathological Complete Response to Neoadjuvant Chemoradiation in Patients With Esophageal Squamous Cell Carcinoma

Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer

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

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

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