Works matching AU Ho, Joshua W. K.

Results: 56

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

Published in:

Bioinformatics, 2017, v. 33, n. 13, p. 1916, doi. 10.1093/bioinformatics/btx092

By:

Pengyi Yang;
Oldfield, Andrew;
Taiyun Kim;
Yang, Andrian;
Jean Yee Hwa Yang;
Ho, Joshua W. K.

Publication type:

Article

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

Published in:

Bioinformatics, 2016, v. 32, n. 17, p. i620, doi. 10.1093/bioinformatics/btw428

By:

Djordjevic, Djordje;
Kusumi, Kenro;
Ho, Joshua W. K.

Publication type:

Article

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

Published in:

Bioinformatics, 2015, v. 31, n. 13, p. 2066, doi. 10.1093/bioinformatics/btv117

By:

Kyung-Ah Sohn;
Ho, Joshua W. K.;
Djordjevic, Djordje;
Hyun-hwan Jeong;
Park, Peter J.;
Ju Han Kim

Publication type:

Article

SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides.

Published in:

Bioinformatics, 2006, v. 22, n. 17, p. 2162

By:

Joshua W. K. Ho;
Cameron E. Adams;
Jie Bin Lew;
Timothy J. Matthews;
Chiu Chin Ng;
Arash Shahabi-Sirjani;
Leng Hong Tan;
Yu Zhao;
Simon Easteal;
Susan R Wilson;
Lars S Jermiin

Publication type:

Article

Dynamic changes in antibiotic resistance genes and gut microbiota after Helicobacter pylori eradication therapies.

Published in:

Helicobacter, 2022, v. 27, n. 2, p. 1, doi. 10.1111/hel.12871

By:

Wang, Lingling;
Yao, Haobin;
Tong, Teresa;
Lau, KamShing;
Leung, Suet Yi;
Ho, Joshua W. K.;
Leung, Wai K.

Publication type:

Article

Ultrafast clustering of single-cell flow cytometry data using FlowGrid.

Published in:

BMC Systems Biology, 2019, v. 13, p. N.PAG, doi. 10.1186/s12918-019-0690-2

By:

Ye, Xiaoxin;
Ho, Joshua W. K.

Publication type:

Article

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

Published in:

BMC Systems Biology, 2018, v. 12, n. 9, p. N.PAG, doi. 10.1186/s12918-018-0655-x

By:

Kabir, Md Humayun;
Patrick, Ralph;
Ho, Joshua W. K.;
O'Connor, Michael D.

Publication type:

Article

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

Published in:

BMC Genomics, 2011, v. 12, n. 1, p. 134, doi. 10.1186/1471-2164-12-134

By:

Ho, Joshua W. K.;
Bishop, Eric;
Karchenko, Peter V.;
Nègre, Nicolas;
White, Kevin P.;
Park, Peter J.

Publication type:

Article

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

Published in:

BMC Genomics, 2009, v. 10, p. 1, doi. 10.1186/1471-2164-10-S3-S16

By:

Ho, Joshua W. K.;
Stefani, Maurizio;
Remedios, Cristobal G. dos;
Charleston, Michael A.

Publication type:

Article

Developing a named entity framework for thyroid cancer staging and risk level classification using large language models.

Published in:

NPJ Digital Medicine, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s41746-025-01528-y

By:

Fung, Matrix M. H.;
Tang, Eric H. M.;
Wu, Tingting;
Luk, Yan;
Au, Ivan C. H.;
Liu, Xiaodong;
Lee, Victor H. F.;
Wong, Chun Ka;
Wei, Zhili;
Cheng, Wing Yiu;
Tai, Isaac C. Y.;
Ho, Joshua W. K.;
Wong, Jason W. H.;
Lang, Brian H. H.;
Leung, Kathy S. M.;
Wong, Zoie S. Y.;
Wu, Joseph T.;
Wong, Carlos K. H.

Publication type:

Article

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

Published in:

JAMA Network Open, 2020, v. 3, n. 9, p. e2015927, doi. 10.1001/jamanetworkopen.2020.15927

By:

Hu, Yihuai;
Xie, Chenyi;
Yang, Hong;
Ho, Joshua W. K.;
Wen, Jing;
Han, Lujun;
Chiu, Keith W. H.;
Fu, Jianhua;
Vardhanabhuti, Varut

Publication type:

Article

Machine learning application for the prediction of SARS-CoV-2 infection using blood tests and chest radiograph.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-93719-2

By:

Du, Richard;
Tsougenis, Efstratios D.;
Ho, Joshua W. K.;
Chan, Joyce K. Y.;
Chiu, Keith W. H.;
Fang, Benjamin X. H.;
Ng, Ming Yen;
Leung, Siu-Ting;
Lo, Christine S. Y.;
Wong, Ho-Yuen F.;
Lam, Hiu-Yin S.;
Chiu, Long-Fung J.;
So, Tiffany Y;
Wong, Ka Tak;
Wong, Yiu Chung I.;
Yu, Kevin;
Yeung, Yiu-Cheong;
Chik, Thomas;
Pang, Joanna W. K.;
Wai, Abraham Ka-chung

Publication type:

Article

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

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-29874-5

By:

Thean, Dawn G. L.;
Chu, Hoi Yee;
Fong, John H. C.;
Chan, Becky K. C.;
Zhou, Peng;
Kwok, Cynthia C. S.;
Chan, Yee Man;
Mak, Silvia Y. L.;
Choi, Gigi C. G.;
Ho, Joshua W. K.;
Zheng, Zongli;
Wong, Alan S. L.

Publication type:

Article

MQuad enables clonal substructure discovery using single cell mitochondrial variants.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28845-0

By:

Kwok, Aaron Wing Cheung;
Qiao, Chen;
Huang, Rongting;
Sham, Mai-Har;
Ho, Joshua W. K.;
Huang, Yuanhua

Publication type:

Article

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

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25773-3

By:

Stassen, Shobana V.;
Yip, Gwinky G. K.;
Wong, Kenneth K. Y.;
Ho, Joshua W. K.;
Tsia, Kevin K.

Publication type:

Article

Efficient Differentiation of Steroidogenic and Germ-Like Cells from Epigenetically-Related iPSCs Derived from Ovarian Granulosa Cells.

Published in:

PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0119275

By:

Anchan, Raymond;
Gerami-Naini, Behzad;
Lindsey, Jennifer S.;
Ho, Joshua W. K.;
Kiezun, Adam;
Lipskind, Shane;
Ng, Nicholas;
LiCausi, Joseph A.;
Kim, Chloe S.;
Brezina, Paul;
Tuschl, Thomas;
Maas, Richard;
Kearns, William G.;
Williams, Zev

Publication type:

Article

How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?

Published in:

PLoS ONE, 2014, v. 9, n. 11, p. 1, doi. 10.1371/journal.pone.0111661

By:

Djordjevic, Djordje;
Yang, Andrian;
Zadoorian, Armella;
Rungrugeecharoen, Kevin;
Ho, Joshua W. K.

Publication type:

Article

An Antibody-Based Leukocyte-Capture Microarray for the Diagnosis of Systemic Lupus Erythematosus.

Published in:

PLoS ONE, 2013, v. 8, n. 3, p. 1, doi. 10.1371/journal.pone.0058199

By:

Lin, Ming-Wei;
Ho, Joshua W. K.;
Harrison, Leonard C.;
dos Remedios, Cristobal G.;
Adelstein, Stephen

Publication type:

Article

An Evolutionarily Conserved Enhancer Regulates Bmp4 Expression in Developing Incisor and Limb Bud.

Published in:

PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0038568

By:

Jumlongras, Dolrudee;
Lachke, Salil A.;
O'Connell, Daniel J.;
Aboukhalil, Anton;
Xiao Li;
Sung E. Choe;
Joshua W. K. Ho;
Turbe-Doan, Annick;
Robertson, Erin A.;
Olsen, Bjorn R.;
Bulyk, Martha L.;
Amendt, Brad A.;
Maas, Richard L.

Publication type:

Article

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

Published in:

BMC Genomics, 2019, v. 20, p. 1, doi. 10.1186/s12864-019-6341-6

By:

Yang, Andrian;
Kishore, Abhinav;
Phipps, Benjamin;
Ho, Joshua W. K.

Publication type:

Article

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

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37975-y

By:

Wang, Lingling;
Yao, Haobin;
Morgan, Daniel C.;
Lau, Kam Shing;
Leung, Suet Yi;
Ho, Joshua W. K.;
Leung, Wai K.

Publication type:

Article

A Wnt-Bmp Feedback Circuit Controls Intertissue Signaling Dynamics in Tooth Organogenesis.

Published in:

Science Signaling, 2012, v. 5, n. 206, p. 1, doi. 10.1126/scisignal.2002414

By:

O'Connell, Daniel J.;
Ho, Joshua W. K.;
Mammoto, Tadanori;
Turbe-Doan, Annick;
O'Connell, Joyce T.;
Haseley, Psalm S.;
Koo, Samuel;
Kamiya, Nobuhiro;
Ingber, Donald E.;
Park, Peter J.;
Maas, Richard L.

Publication type:

Article

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

Published in:

Epigenetics & Chromatin, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13072-019-0273-x

By:

Szczesnik, Tomasz;
Ho, Joshua W. K.;
Sherwood, Richard

Publication type:

Article

PD-L1 regulates inflammatory programs of macrophages from human pluripotent stem cells.

Published in:

Life Science Alliance, 2024, v. 7, n. 2, p. 1, doi. 10.26508/lsa.202302461

By:

Handi Cao;
Yang Xiang;
Shihui Zhang;
Yiming Chao;
Jilong Guo;
Aurich, Theo;
Ho, Joshua W. K.;
Yuanhua Huang;
Pentao Liu;
Ryohichi Sugimura

Publication type:

Article

MetaQuad: shared informative variants discovery in metagenomic samples.

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae030

By:

Xu, Sheng;
Morgan, Daniel C;
Qian, Gordon;
Huang, Yuanhua;
Ho, Joshua W K

Publication type:

Article

scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae011

By:

Meng, Qiuchen;
Wei, Lei;
Ma, Kun;
Shi, Ming;
Lin, Xinyi;
Ho, Joshua W K;
Li, Yinqing;
Zhang, Xuegong

Publication type:

Article

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

Published in:

Proteomics - Clinical Applications, 2010, v. 4, n. 6/7, p. 679

By:

Ho, Joshua W. K.;
Lin, Ming-Wei;
Adelstein, Stephen;
dos Remedios, Cristobal G.

Publication type:

Article

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

Published in:

Proteomics - Clinical Applications, 2010, v. 4, n. 2, p. 179

By:

Ho, Joshua W. K.;
Lin, Ming-Wei;
Adelstein, Stephen;
dos Remedios, Cristobal G.

Publication type:

Article

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

Published in:

BMC Microbiology, 2020, v. 20, n. 1, p. 1, doi. 10.1186/s12866-020-01762-2

By:

Wang, Qing;
Ye, Jianzhong;
Fang, Daiqiong;
Lv, Longxian;
Wu, Wenrui;
Shi, Ding;
Li, Yating;
Yang, Liya;
Bian, Xiaoyuan;
Wu, Jingjing;
Jiang, Xianwan;
Wang, Kaicen;
Wang, Qiangqiang;
Hodson, Mark P.;
Thibaut, Loïc M.;
Ho, Joshua W. K.;
Giannoulatou, Eleni;
Li, Lanjuan

Publication type:

Article

Deep Learning for Clinical Image Analyses in Oral Squamous Cell Carcinoma: A Review.

Published in:

2021

By:

Chu, Chui Shan;
Lee, Nikki P.;
Ho, Joshua W. K.;
Choi, Siu-Wai;
Thomson, Peter J.

Publication type:

journal article

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 11, p. e62, doi. 10.1093/nar/gkad307

By:

Sun, Yuliangzi;
Shim, Woo Jun;
Shen, Sophie;
Sinniah, Enakshi;
Pham, Duy;
Su, Zezhuo;
Mizikovsky, Dalia;
White, Melanie D;
Ho, Joshua W K;
Nguyen, Quan;
Bodén, Mikael;
Palpant, Nathan J

Publication type:

Article

Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 20, p. e123, doi. 10.1093/nar/gkz718

By:

Humphreys, David T;
Fossat, Nicolas;
Demuth, Madeleine;
Tam, Patrick P L;
Ho, Joshua W K

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2018, v. 46, n. D1, p. D875, doi. 10.1093/nar/gkx837

By:

Kakrana, Atul;
Yang, Andrian;
Anand, Deepti;
Djordjevic, Djordje;
Ramachandruni, Deepti;
Singh, Abhyudai;
Huang, Hongzhan;
Ho, Joshua W K;
Lachke, Salil A

Publication type:

Article

Incidence of Emergency Department Visits for Sexual Abuse Among Youth in Hong Kong Before and During the COVID-19 Pandemic.

Published in:

JAMA Network Open, 2022, v. 5, n. 10, p. e2236278, doi. 10.1001/jamanetworkopen.2022.36278

By:

Wong, Janet Yuen Ha;
Luk, Luke Y. F.;
Yip, Tsz Fung;
Lee, Teddy Tai Loy;
Wai, Abraham Ka Chung;
Ho, Joshua W. K.

Publication type:

Article

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

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-47022-w

By:

Le, Thi Yen Loan;
Pickett, Hilda A.;
Yang, Andrian;
Ho, Joshua W. K.;
Thavapalachandran, Sujitha;
Igoor, Sindhu;
Yang, Sile F.;
Farraha, Melad;
Voges, Holly K.;
Hudson, James E.;
dos Remedios, Cristobal G.;
Bryan, Tracy M.;
Kizana, Eddy;
Chong, James J. H.

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2014, v. 15, n. Suppl 16, p. 1, doi. 10.1186/1471-2105-15-S16-S15

By:

Giannoulatou, Eleni;
Shin-Ho Park;
Humphreys, David T.;
Ho, Joshua W. K.

Publication type:

Article

Gene-gene interaction filtering with ensemble of filters.

Published in:

BMC Bioinformatics, 2011, v. 12, n. Suppl 1, p. 1, doi. 10.1186/1471-2105-12-S1-S10

By:

Pengyi Yang;
Ho, Joshua W. K.;
Yee Hwa Yang;
Zhou, Bing B.

Publication type:

Article

A genetic ensemble approach for gene-gene interaction identification.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 524, doi. 10.1186/1471-2105-11-524

By:

Pengyi Yang;
Ho, Joshua W. K.;
Zomaya, Albert Y.;
Zhou, Bing B.

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S1-S19

By:

Hassan, Md Rafiul;
Hossain, M. Maruf;
Bailey, James;
Macintyre, Geoff;
Ho, Joshua W. K.;
Ramamohanarao, Kotagiri

Publication type:

Article

An innovative approach for testing bioinformatics programs using metamorphic testing.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-24

By:

Tsong Yueh Chen;
Ho, Joshua W. K.;
Huai Liu;
Xiaoyuan Xie

Publication type:

Article

Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels.

Published in:

Bioinformatics, 2025, v. 41, n. 1, p. 1, doi. 10.1093/bioinformatics/btae727

By:

Yin, Danqing;
Cao, Yue;
Chen, Junyi;
Mak, Candice L Y;
Yu, Ken H O;
Zhang, Jiaxuan;
Li, Jia;
Lin, Yingxin;
Ho, Joshua W K;
Yang, Jean Y H

Publication type:

Article

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

Published in:

Bioinformatics, 2022, v. 38, n. 1, p. 282, doi. 10.1093/bioinformatics/btab521

By:

Fang, Xiunan;
Ho, Joshua W K

Publication type:

Article

dv-trio: a family-based variant calling pipeline using DeepVariant.

Published in:

Bioinformatics, 2020, v. 36, n. 11, p. 3549, doi. 10.1093/bioinformatics/btaa116

By:

Ip, Eddie K K;
Hadinata, Clinton;
Ho, Joshua W K;
Giannoulatou, Eleni

Publication type:

Article

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

Published in:

Bioinformatics, 2020, v. 36, n. 9, p. 2778, doi. 10.1093/bioinformatics/btaa042

By:

Stassen, Shobana V;
Siu, Dickson M D;
Lee, Kelvin C M;
Ho, Joshua W K;
So, Hayden K H;
Tsia, Kevin K

Publication type:

Article

Vulture: cloud-enabled scalable mining of microbial reads in public scRNA-seq data.

Published in:

GigaScience, 2024, v. 13, n. 1, p. 1, doi. 10.1093/gigascience/giad117

By:

Chen, Junyi;
Yin, Danqing;
Wong, Harris Y H;
Duan, Xin;
Yu, Ken H O;
Ho, Joshua W K

Publication type:

Article

StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases.

Published in:

Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03347-y

By:

Stassen, Shobana V.;
Kobashi, Minato;
Lam, Edmund Y.;
Huang, Yuanhua;
Ho, Joshua W. K.;
Tsia, Kevin K.

Publication type:

Article

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

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1188-0

By:

Lin, Peijie;
Troup, Michael;
Ho, Joshua W. K.

Publication type:

Article

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

Published in:

BMC Genomics, 2018, v. 19, p. 153, doi. 10.1186/s12864-017-4340-z

By:

Wang, Xin;
Lin, Peijie;
Ho, Joshua W. K.

Publication type:

Article

Introduction to the Special Issue on GIW/ABACBS 2019.

Published in:

Journal of Bioinformatics & Computational Biology, 2020, v. 18, n. 01, p. N.PAG, doi. 10.1142/S0219720020020011

By:

Ho, Joshua W. K.

Publication type:

Article

VERIFICATION OF PHYLOGENETIC INFERENCE PROGRAMS USING METAMORPHIC TESTING.

Published in:

Journal of Bioinformatics & Computational Biology, 2011, v. 9, n. 6, p. 729, doi. 10.1142/S021972001100563X

By:

SADI, MD. SHAIK;
KUO, FEI-CHING;
HO, JOSHUA W. K.;
CHARLESTON, MICHAEL A.;
CHEN, T. Y.

Publication type:

Article