People

Dr Joshua W. K. Ho

Associate Professor, HKU

Lead Scientist, D24H


BSc (Hon 1, University Medal), Biochemistry and Computer Science, The University of Sydney
PhD, Bioinformatics, The University of Sydney

Dr Ken Yu

Biomedical Big Data Specialist


BSc, Biotechnology, University of California, Davis
MSc, Bioinformatics and Computational Biology, George Mason University
PhD, Anatomical and Cellular Pathology, The Chinese University of Hong Kong

Dr Haobin Yao

Postdoctoral Fellow


PhD, Computer Science, The University of Hong Kong

Dr Sharon Xue

Postdoctoral Fellow


BSc, Biotechnology, Hebei University of Economics & Business, China
MSc, Microbiology, Huazhong Agricultural University
PhD, Molecular Biology, The University of Hong Kong

Dr Junyi Chen

Postdoctoral Fellow


PhD, Computer Science, City University of Hong Kong

Dr Daniel Morgan

Postdoctoral Fellow


BSc, Microbiology & Molecular Biology, Miami University
MSc, Bioinformatics, The Ohio State University
PhD, Network & Systems Biology, Stockholm University
Research Fellow, Network Medicine, Harvard Medical School & Brigham and Women's Hospital

Zezhuo Su

Postdoctoral Fellow


BSc, Biotechnology, Hunan University of Technology
MSc, Molecular and Cell Biology, Sun Yat-Sen University
PhD, Cancer single cell biology, Univeristy of Hong Kong

Xiunan Fang

PhD Student


BSc (Hon 1), Electrical Engineering and Information Technology, Harbin Institute of Technology & The University of Sydney
MSc, Information Engineering, Chinese University of Hong Kong

Gordon Qian

PhD Student


BSc (First Class Honours), Molecular Cell Biology and Bioinformatics, University of New South Wales

Ian Lee

PhD Student


BSc, Biology, University of Portsmouth
MSc, Bioinformatics & System Biology, University of Manchester

Xinyi Lin

PhD Student


BS, Biological Science and Statistics, Sun Yat-sen University
MS, Biostatistics, Columbia University

Weizhong Zheng

PhD Student


BSc, Biological Science, Sun Yat-sen University

Sheng Xu

PhD Student


BSc, Biological Science, Tsinghua University

Shichao Ma

PhD Student


BSc (First Class Honours), Computer Science, King's College London
MSc, Computer Science, The University of Hong Kong

Chui Shan Chu

PhD Student


BSc, Chemistry, The University of Sydney
MMedSc, Clinical Physics, The University of Hong Kong

Aaron Kwok

MPhil Student


BBiomedSc, Biomedical Sciences, The University of Hong Kong

Henry Yee

MRes[Med] Student


MBBS, The University of Hong Kong (2018-)

Edmond Yip

Project Specialist


BEng, Mechanical Engineering, The University of Hong Kong

Luke Luk

AI Specialist


BSc, Mathematics and Information Engineering, The Chinese University of Hong Kong

Kevin Lau

Research Assistant


BSc, Physics, The Chinese University of Hong Kong
MPhil, Physics, The Chinese University of Hong Kong

Angela Yin

Research Assistant


BBiomed, Biomedicine, The University of Melbourne
Master of IT, Software Engineering, The University of Sydney

Victoria Yeo

Research Assistant


MBBS, The University of Hng Kong (2019-)

Mun Kay Ho

Research Assistant


BBiomedSc, The University of Hong Kong (2019-)

Nikkie Stables

Research Assistant


BSocSc, Psychology & Counseling, The University of Hng Kong

Lijie Zhong

System Analyst


BEng,Computer Science, Shandong University
MSc,Computer Science, Hong Kong Baptist University


Alumni

Dr Eleni Giannoulatou (senior postdoc 2013-2015 at VCCRI; Now Division Head at VCCRI)
Dr Paul Lin (postdoc 2016-2017 at VCCRI; Now technical manager at the Independent Hospital Pricing Authority, Australia)
Dr Djordje Djordjevic (PhD student 2014-2017 at UNSW; Now Computational Biologist at Novo Nordisk, Denmark)
Dr Xin Wang (PhD student 2014-2018 at UNSW; Now postdoc at Northwestern University, USA)
Dr Tomasz Szczesnik (PhD student 2014-2018 at UNSW; Now postdoc at ETH Zurich, Switzerland)
Dr Andrian Yang (PhD student 2015-2018 at UNSW; Now postdoc at EMBL-EBI, Cambridge, UK)

Research Projects

The Ho Laboratory focuses on the use of bioinformatics and systems biology approaches to tackle longstanding problems in basic and translational medicine. A range of specific research projects can be developed within the broad theme of scalable big data analytics for healthcare translation. Here are some major research themes. Multiple projects are available under each theme.:

  • Scalable single cell data analytics. Single-cell RNA sequencing (scRNA-Seq) enables researchers to study heterogeneity among tens of thousands of individual cells and define cell types from a transcriptomic perspective. However, fast and reliable analysis of these large and noisy data requires new statistical and computational considerations. In this project we will develop scalable bioinformatics methods to analyze a range of scRNA-seq data to answer important biological questions.

  • Microbiome functional systems biology through metagenomic and multi-omic data analysis. Our laboratory is developing computational and statistical tools that can efficiently process large metagenomic data, and integrate them with other omics or deep phenotyping data. Our goal is to understand how the microbiome found in a specific location of the body, e.g., the gut, can affect a person's health.

  • Analytics of mass-spectrometry-based untargeted proteomics, metabolomics and lipidomics. Being able to discover an unbiased collection of proteins, metabolites and lipids in any biological sample is critical in our ability to discover how cellular functions are regulated at the molecular level. The analysis of these data posed many challenges. Our laboratory is working toward developing analytical pipelines to facilitate integrative analysis of these data.

  • Medical artificial intelligence, mobile health and wearable devices. Being able to track the changes of a person's physiological parameters in real time is now increasingly feasible due to the wide availability of consumer-grade smartphones and wearable devices (e.g., fitbit, AppleWatch, etc). Our group is developing new big data machine-learning algorithms to extract, de-noise, analyze and correlate physical activity data and heart rate dynamics. Our long-term goal is to establish new non-invasive screening tools to monitor a person's health status.

Recruitment

For postdoc/students/RA who wants to join this laboratory: All projects require proficiency in at least one programming/scripting language (R, Perl, Python, Java, C++, C). Familiarity with the Unix operating system is desirable but not required. Individual projects can be tailored to fit each student's personal interest and skill set. Most projects involve close interactions with local and international collaborators. This is a highly interdisciplinary laboratory. We welcome prospective group members from diverse background, such as medicine, biology, physics, computer science, mathematics, statistics, and engineering. Expression of interest, along with your CV, can be sent to Dr. Ho.

We also have various positions available via the Laboratory of Data Discovery for Health (D24H).

Publication

Google Scholar     PubMed     Publons

Edited journal special issue

  1. Ho JWK, Giannoulatou E, Special Issue on Big Data for Biophysical Reviews (Volume 11, Issue 1, February 2019)
  2. Ho JWK, Sohn K-A, Song J, Akutsu T, Ranganathan S, Li J, Special Issue in BMC Genomics (Volume 20, Supplement 10, December 2019) for Proceedings of the Joint International GIW & ABACBS-2019 Conference: genomics
  3. Ho JWK, Sohn K-A, Song J, Akutsu T, Ranganathan S, Li J, Special Issue in BMC Medical Genomics (Volume 12, Supplement 9, December 2019) for  Proceedings of the Joint International GIW & ABACBS-2019 Conference: medical genomics
  4. Ho JWK, Sohn K-A, Song J, Akutsu T, Ranganathan S, Li J, Special Issue in BMC Medical Genomics (Volume 13, Supplement 3, February 2020) for  Proceedings of the Joint International GIW & ABACBS-2019 Conference: medical genomics
  5. Ho JWK, Sohn K-A, Song J, Akutsu T, Ranganathan S, Li J, Special Issue in BMC Bioinformatics (Volume 20, Supplement 23, December 2019) for  Proceedings of the Joint International GIW & ABACBS-2019 Conference: bioinformatics
  6. Ho JWK, Sohn K-A, Song J, Akutsu T, Ranganathan S, Li J, Special Issue in BMC Bioinformatics (Volume 21, Supplement 3, April 2020) for  Proceedings of the Joint International GIW & ABACBS-2019 Conference: bioinformatics (part 2)
  7. Ho JWK, Sohn K-A, Song J, Akutsu T, Ranganathan S, Li J, Special Issue in BMC Microbiology (Volume 20, Supplement 1, April 2020) for  Proceedings of the Joint International GIW & ABACBS-2019 Conference: microbiology
  8. Ho JWK, Special Issue in Journal of Bioinformatics and Computational Biology (Volume 10, Issue 1, February 2020) for  GIW/ABACBS 2019

[* Co-first authors, ^ Co-corresponding authors]

Pre-print manusripts

  1. Zheng W, Fong JHC, Wan YK, Chu AHY, Huang Y, Wong ASL, Ho JWK (2022) Multi-task learning uncovers robust translation cis-regulatory features. bioRxiv: link
  2. Lin X, Chau C, Huang Y^, Ho JWK^ (2022) DCATS: differential composition analysis for complex single-cell experimental designs. bioRxiv: link
  3. Yang A*, Yao Y*, Fang X*, Li J, Xia Y, Kwok CSM, Lo MCK, Siu DMD, Tsia KK, Ho JWK (2020) starmapVR: immersive visualisation of single cell spatial omic data. bioRxiv: link
  4. Yang A, Yao Y, Li J,Ho JWK (2018) starmap: Immersive visualisation of single cell data using smartphone-enabled virtual reality. bioRxiv: link

Book chapters

  1. Ye X, Ho JWK (2019) Expression Clustering. Encyclopedia of Bioinformatics and Computational Biology, Vol 2, Elsevier, 388-395
  2. Giannoulatou E, Kamali AH, Yang A, Chen TY, Ho JWK (2016) Quality assurance in genome-scale bioinformatics analyses. In Computational Biology & Bioinformatics: Gene Regulation (Ed. Wong KC), CRC Press, 259-278
  3. Wang X, McCormick HM, Djordjevic D, Giannoulatou E, Suter CM, Ho JWK (2016) Epigenomic analysis of chromatin organization and DNA methylation. In Computational Biology & Bioinformatics: Gene Regulation (Ed. Wong KC), CRC Press, 181-211
  4. O'Connell DJ, Ho JWK, Maas RL (2013) Systems biology of early tooth development. In Stem cells in craniofacial development, regeneration and repair (Eds. Huang GT-J and Thesleff I), Wiley, 179-202
  5. Ho JWK, Alekseyenko AA, Kuroda MI, Park PJ (2011) Genome-wide mapping of protein-DNA interactions by ChIP-seq. In Tag-based Approaches for Next Generation Sequencing: Merging two High-throughput Technologies (Eds. Kahl, Harbers), Wiley, 139-152
  6. Mohamed AN, Lal S, Ho JWK, Brown A, Lui R, Nguyen L, Yong ASC, Su Y, Braet F, Dyer W,Junius F, Cumming RG, Freedman SB, Kritharides L, dos Remedios CG (2010) How to interrogate the cellular immune system inpatients with ischemic heart disease. In Myocardial Ischemia: Causes, Symptoms and Treatment (Eds. Vukovic D, Kiyan V), NovaPublishers
  7. Jermiin LS, Ho JWK, Lau KW, Jayaswal V (2009) SeqVis: A tool for detecting compositional heterogeneity among aligned nucleotide sequences. In Bioinformatics for DNA sequence analysis (Ed. Posada D),Humana Press, Totowa, NJ. 65-91

Original research papers / review papers

  1. Yang A*, Alakarage D*, Cuny H, Ip EKK, Almog M, Lu J, Das D, Enriquez A, Szot JO, Humphreys DT, Blue GM, Ho JWK, Winlaw DS, Dunwoodie SL^, Giannoulatou E^ (2022) Congenital Heart Disease Gene: a Curated Database for Congenital Heart Disease Genes. Circulation: Genomic and Precision Medicine (online ahead of print: 10.1161/CIRCGEN.121.003539)
  2. Kwok AWC, Qiao C, Huang R, Sham MH, Ho JWK^, Huang ^ (2022) MQuad enables clonal substrcuture discovery using single cell mitochondrial variants. Nature Communications, 13, 1205 BioRxiv version: link
  3. Thean DGL*, Chu HY*, Fong JHC, Chan BKC, Zhou P, Kwok CCS, Chan YM, Mak SYL, Choi GCG Ho JWK, Zheng Z, Wong ASL (2022) Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities. Nature Communications, 13, 2219
  4. dos Remedios C, Cranfield C, Whelan D, Cox C, Shearwin K, Ho J, Allen T, Shibuya R, Hibino E, Hayashi K, Li A (2022) A special issue of the Australian society for Biophysics. Biophysical Reviews, 14, 1-2
  5. Fang X, Ho JWK (2022) FlowGrid enables fast clustering of very large single-cell RNA-seq data. Bioinformatics, 38(1), 282-283
  6. Wang L, Yao H, Tong T, Lau KS, Leung SY, Ho JWK, Leung WK (2022) Dynamic changes in antibiotic resistance genes and gut microbiota after Helicobacter Pylori eradication therapies. Helicobacter, 27, e12871
  7. Zhou L*, Yu KHO*, Wong TL*, Zhang Z, Chan CH, Loon JHC, Che N, Yu HJ, Tan KV, Tong M, Ngan ES, Ho JWK^, Ma SKY^ (2021) Lineage tracing and single-cell analysis reveal proliferative Prom1+ tumour-propagating cells and their dynamic cellular transition during liver cancer progression. Gut, (in press)
  8. Meng H, Chen C, Zhu Y, Li Z, Ye F, Ho JWK, Chen H (2021) Automatic flow delay through passive wax valves for paper-based analytical devices . Lab on a Chip, 21, 4166-4176
  9. Chu CS, Lee NP, Ho JWK, Choi SW, Thomson PJ (2021) Deep Learning for Clinical Image Analyses in Oral Squamous Cell Carcinoma. JAMA Otolaryngol Head Neck Surg, 147(10): 893-900
  10. Cai M., Chai S., Xiong T., Wei J., Mao W., Zhu Y., Li X., Wei W., Dai X., Yang B., Liu W., Shu B., Wang M., Lu T., Cai Y., Zheng Z., Mei Z., Zhou Y., Yang J., Zhao J., Shen L, Ho JWK, Chen J, Xiong N (2021) Aberrant Expression of Circulating MicroRNA Leads to the Dysregulation of Alpha-Synuclein and Other Pathogenic Genes in Parkinson’s Disease. Frontiers in Cells and Developental Biology, 9, fcell.2021.695007
  11. Stassen SV, Yip GGK, Wong KKY, Ho JWK, Tsia KK (2021) Generalized and scalable trajectory inference in single-cell omics data with VIA. Nature Communications, 12, 5538 Biorxiv version: link
  12. Ayer A, Fazakerley DJ, Suarna C, Maghzal GJ, Sheipouri D, Lee KJ, Bradley MC, Fernandez-del-Rio L, Tumanov S, Kong SMY, van der Venn JN, Yang A, Ho JWK, Glarke SG, James DE, Dawes IW, Vance DE, Clarke CF, Jacobs RL, Stocker R (2021) Genetic screening reveals phospholipid metabolism as a key regulator of the biosynthesis of the redox-active lipid coenzyme Q . Redox Biology, 46, 102127
  13. Du R, Tsougenis D, Ho JWK, Chan JKY, Chiu KWH, Fang BXH, Ng MY, Leung ST, Lo CSY, Wong HYF, Lam HYS, Chiu LFJ, So TY, Wong KT, Wong YCI, Yu K, Yeung YC, Chik T, Pang JWK, Wai AKC, Kuo MD, Lam TPW, Khong PL, Cheung NT, Vardhanabhuti V (2021) Machine learning application for the prediction of SARS-CoV-2 infection using blood tests and chest radiograph. Scientific Reports, 11, 14250
  14. Xie CY*, Hu YH,* Ho JWK, Han LJ, Yang H, Wen J, Lam KO, Wong IYH, Law SYK, Chiu KWH, Fu JH^, Vardhanabhuti V^ (2021) Using Genomics Feature Selection Method in Radiomics Pipeline Improves Prognostication Performance in Locally Advanced Esophageal Squamous Cell Carcinoma — A Pilot Study. Cancers, 13(9), 2145
  15. Chen Z, Yip TF, Zhu Y, Ho JWK^, Chen H^ (2021) The method to quantify cell elasticity based on the precise measurement of pressure inducing cell deformation in microfluidic channels. MethodsX, 8, 101247
  16. Chen C, Zhu Y, Ho JWK, Chen H (2021) The method to dynamically screen and print single cells using microfluidics with pneumatic microvalves. MethodsX, 8, 101190
  17. Wang H*, Guo S*, Kim SJ, Shao F, Ho JWK, Wong KU, Miao Z, Hao D, Zhao M, Xu J, Zeng J, Wong KH, Di L, Wong AHH, Xu X, Deng CX (2021) Cisplatin prevents breast cancer metastasis through blocking early EMT and retards cancer growth together with paclitaxel. Theranostics, 11(5), 2442-2459
  18. Hu Y, Xie C, Yang H, Ho JWK, Wen J, Han L, Lam KO, Wong IYH, Law SYK, Chiu KWH, Vardhanabhuti V, Fu J (2021) Computed tomography-based deep-learning prediction of neoadjuvant chemoradiotherapy treatment response in esophageal squamous cell carcinoma. Radiotherapy and Oncology, 154, 6-13
  19. Szczesnik T, Chu L, Ho JWK, Sherwood R (2020) A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding. Cell Systems, 11(3), 315-327. Biorxiv version: link
  20. Hu Y, Xie C, Yang H, Ho JWK, Wen J, Han L, Chiu KWH, Fu J, Vardhanabhuti V (2020) 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, 3(9), e2015927
  21. Ho JWK (2020) Biophysical Review's `meet the editors series'—a profile of Joshua W. K. Ho. Biophysical Reviews, 12, 745-748 SharedIt link
  22. Goldberg A, Ho JWK (2020) Hactive: a smartphone application for heart rate profiling. Biophysical Reviews, 12, 777–779 SharedIt link
  23. Qian G, Ho JWK (2020) Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology. Biophysical Reviews, 12, 851–863 SharedIt link
  24. Patrick R*, Humphreys DT*, Janbandhu V, Oshlack A, Ho JWK, Harvey RP^, Lo KK^ (2020) Sierra: discovery of differential transcrpt usage from polyA-captured single-cell RNA-seq data. Genome Biology, 21, 167 bioRxiv: link
  25. Yu KHO, Fang X, Yao H, Ng B, Leung TK, Wang LL, Lin CH, Chan A, Leung WK, Leung SY, Ho JWK (2020) Evaluation of experimental protocols for shotgun whole-genome metagenomic discovery of antibiotic resistance genes IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi: 10.1109/TCBB.2020.3004063 (advanced online access)
  26. Ip EKK, Hadinata C, Ho JWK, Giannoulatou E (2020) dv-trio: a family-based variant calling pipeline using DeepVariant. Bioinformatics, 36(11), 3549-3551
  27. Wang Q, Ye J, Fang D, Lv L, Wu W, Shi D, Li Y, Yang L, Bian X, Wu J, Jiang X, Wang K, Wang W, Hodson MP, Thibaut LM, Ho JWK, Giannoulatou E^, Li L^ (2020) 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, 20, 83
  28. Xie C, Du R, Ho JWK, Pang HH, Chiu KWH, Lee EYP, Varhanabhuti V (2020) 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. European Journal of Nuclear Medicine and Molecular Imaging (in press). SharedIt link
  29. Stassen SV, Siu DMD, Lee KCM, Ho JWK, So HKH, Tsia K (2020) PARC: ultrafast and accurate clustering of phenotypic data of millions of single cels. Bioinformatics, 6(9), 2778-2786. bioRxiv: link
  30. Tam PPL, Ho JWK (2020) Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes. Development, 147, dev179788
  31. Yang A, Kishore A, Phipps B, Ho JWK (2019) Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco. BMC Genomics, 20, 927
  32. Wang Q, Kotoula V, Hsu P-C, Papadopoulou K, Ho JWK, Fountzilas G, Giannoulatou E (2019) Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data. BMC Medical Genomics, 12, 181
  33. Yang A*, Tang JYS*, Troup M, Ho JWK (2019) Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads. F1000Research, 8, 1587
  34. Humphreys DT, Fossat N, Demuth M, Tam PPL, Ho JWK (2019) Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing. Nucleic Acids Research, 47(20), e123
  35. Le TYL, Pickett HA, Yang A, Ho JWK, Thavapalachandran S, Igoor S, Yang SF, Farraha M, Voges HK, Hudson JE, dos Remedios CG, Bryan TM, Kizana E, Chong JJH (2019) Enhanced cardiac repair by telomerase reverse transcriptase over-expression in human cardiac mesenchymal stromal cells. Scientific Reports, 9, 10579
  36. Szczesnik T, Ho JWK, Sherwood R (2019) Dam mutants provide improved sensitivity and spatial resolution for profling transcription factor binding. Epigenetics & Chromatin, 12, 36
  37. Ho JWK, Scadding M (2019) Classroom Activities for Teaching Artificial Intelligence to Primary School Students. In Proceedings of International Conference on Computational Thinking Education 2019, 157-159
  38. van Eyk CL, Samaraweera SE, Scott A, Webber DL, Harvey DP, Mecinger O, O'Keefe LV, Cropley JE, Young P, Ho J, Suter C, Richards RI (2019) ‘Non-self’ Mutation: Double-stranded RNA elicits antiviral pathogenic response in a Drosophila model of expanded CAG repeat neurodegenerative diseases. Human Molecular Genetics, 28(18), 3000-3012
  39. Ye X, Ho JWK (2019) Ultrafast clustering of single-cell flow cytometry data using FlowGrid. BMC Systems Biology, 13(Suppl 2), 35. bioRxiv link
  40. Farbehi N*, Patrick R*, Dorison A, Xaymardan M, Janbandhu V, Wystub-Lis K, Ho JWK, Nordon RE^, Harvey RP^ (2019) Single-cell expression profiling reveals dynamic flux of cardiac stromal vascular and immune cells in health and injury. eLife, 8, e43882
  41. Djordjevic D, Tang JYS, Chen YX, Kwan SLS, Ling RWK, Qian G, Woo CYY, Ellis SJ, Ho JWK (2019) Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus. Computational Biology and Chemistry, 80, 152-158. bioRxiv link
  42. Alankarage D, Ip E, Szot JO, Munro J, Blue GM, Harrison K, Cuny H, Enriquez A, Troup M, Humphreys DT, Wilson M, Harvey RP, Sholler GF, Graham RM, Ho JWK, Kirk EP, Pachter N, Chapman G, Winlaw DS, Giannoulatou E, Dunwoodie SL (2019) Identification of clinically actionable variants from genome sequencing of families with congenital heart disease. Genetics in Medicine, 21, 1111-1120
  43. Ho JWK, Giannoulatou E (2019) Big data: the elements of good questions, open data, and powerful software. Biophysical Reviews, 11, 1-3.
  44. Djordjevic D, Cawood BK, Rispin SK, Shah A, Yim LHH, Ho JWK (2019) CardiacProfileR: An R package for extraction and visualisation of heart rate profiles from wearable fitness trackers. Biophysical Reviews, 11, 119-121. BioRxiv: link
  45. Wang Q, Wang K, Wu W, Giannoulatou E, Ho JWK, Li L (2019) Host and microbiome multi-omics integration: applications and methodologies. Biophysical Reviews, 11, 55-65
  46. Kabir MH, Patrick R, Ho JWK^, O'Connor MD^ (2018) Identification of active signaling pathways by intergrating gene expression and protein interaction data. BMC Systems Biology, 12(Suppl 9), 120
  47. Kabir MH, Djordjevic D, O'Connor MD, Ho JWK (2018) C3: An R package for cross-species compendium-based cell-type identification. Computational Biology and Chemistry, 77, 187-192. Preprint available at bioRxiv: link
  48. Szot JO, Cuny H, Blue GM, Humphreys DT, Ip E, Harrison K, Sholler GF, Giannoulatou E, Leo P, Duncan EL, Sparrow DB, Ho JWK, Graham RM, Pachter N, Chapman G, Winlaw DS, Dunwoodie SL (2018) A screening approach to identify clinically actionable variants causing congenital heart disease in exome data. Circulation: Genomics and Precision Medicine, 11, e001978.
  49. Nie S*, Wang X*, Sivakumaran P*, Chong MMW, Liu X, Karnezis T, Bandara N, Takov K, Nowell CJ, Wilcox S, Shambrook M, Hill AF, Harris NC, Newcomb AE, Strappe P, Shayan R, Hernandez D, Clarke J, Hanssen E, Davidson SM, Dusting GJ, Pebay A, Ho JWK, Williamson N, Lim SY (2018) Human W8B2+ cardiac stem cells: Biologically active constituents of the secretome. Scientific Reports, 8, 1579
  50. Palade J*, Djordjevic D*, Hutchins ED, George RM, Cornelius JA, Rawls A, Ho JWK, Kusumi K^, Wilson-Rawls J^ (2018) Identification of satellite cells from anole lizard skeletal muscle and demonstration of expanded musculoskeletal potential. Developmental Biology, 433(2), 344-356
  51. Murphy P, Kabir HM, Srivastava T, Mason ME, Dewi CU, Lim S, Yang A, Djordjevic D, Killingsworth M, Ho JWK, Harman DG, O'Connor MD (2018) Light-focusing human micro-lenses generated from pluripotent stem cells model lens development and drug-induced cataract in vitro. Development, 145, dev155838
  52. Kakrana A*, Yang A*, Anand D, Djordjevic D, Ramachandruni D, Singh A, Huang H, Ho JWK^, Lachke SA^ (2018) iSyTE 2.0: a database for expression-based gene discovery in the eye. Nucleic Acids Research, 46(D1), D875-D885
  53. Eaton SA, Aiken AJ, Young PE, Ho JWK, Cropley JE, Suter CM (2018) Maternal obesity heritably perturbs offspring metabolism for three generations without serial programming. International Journal of Obesity, 42, 911-914
  54. Lipskind S, Lindsey JS, Gerami-Naini B, Eaton JL, O'Connell D, Kiezun A, Ho JWK, Ng N, Parasar P, Ng M, Nickerson M, Demirci U, Maas R, Anchan RM (2018) An embryonic and induced pluripotent stem cell model for ovarian granulosa cell development and steroidogenesis. Reproductive Sciences, 25(5), 712-726
  55. Wang X, Lin P, Ho JWK (2018) Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using Random Forest. BMC Genomics, 19(Suppl 1), 929
  56. Rizzetto S, Eltahla AA, Lin P, Bull R, Lloyd A, Ho JWK, Venturi V, Luciani F (2017) Impact of sequencing depth and read length on single cell RNA sequencing data: Lessons from T cells. Scientific Reports, 7, 12781
  57. Ho JWK, Grant GH (2017) Modelling, inference and big data in biophysics. Biophysical Reviews, 9(4), 297-298
  58. Shi H, Enriquez A, Rapadas M, Martin EMMA, Wang R, Moreau J, Lim CK, Szot JO, Ip E, Hughes J, Sugimoto K, Humphreys D, McInerney-Leo AM, Leo PJ, Maghzal GJ, Halliday J, Smith J, Colley A, Mark PR, Collins F, Sillence DO, Winlaw DS, Ho JWK, Guillemin GJ, Brown MA, Kikuchi K, Thomas PQ, Stocker R, Giannoulatou E, Chapman G, Duncan EL, Sparrow DB, Dunwoodie SL (2017) NAD Deficiency, Congenital Malformations and Niacin Supplementation. New England Journal of Medicine, 377, 544-552
  59. Yang A, Troup M, Ho JWK (2017) Scalability and validation of big data bioinformatics software. Computational and Structural Biotechnology Journal, 15, 379-386
  60. Lin P, Troup M, Ho JWK (2017) CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data. Genome Biology, 18, 59
  61. Tang JYS, Yang A, Chen TY, Ho JWK (2017) Harnessing multiple source test cases in metamorphic testing: A case study in bioinformatics. In Proceedings of the IEEE/ACM 2nd International Workshop on Metamorphic Testing, 10-13
  62. Yang P, Oldfield A, Kim T, Yang A, Yang JYH, Ho JWK (2017) Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells. Bioinformatics, 33(13), 1916-1920
  63. Szot PS, Yang A, Wang X, Parsania C, Röhm W, Wong KH, Ho JWK (2017) PBrowse: A web-based platform for real-time collaborative exploration of genomic data. Nucleic Acids Research, 45 (9): e67
  64. Yang A, Troup M, Lin P, Ho JWK (2017) Falco: A quick and flexible single-cell RNA-seq processing framework on the cloud. Bioinformatics, 33(5), 767-769
  65. Djordjevic D, Kusumi K, Ho JWK (2016) XGSA: A statistical method for cross-species gene set analysis. Bioinformatics, 32(17), i620-i628
  66. Cropley JE, Eaton SA, Aiken A, Young PE, Giannoulatou E, Ho JWK, Buckland ME, Keam SP, Hutvagner, Humphreys DT, Langley KG, Henstridge DC, Martin DIK, Febbraio MA, Suter CM (2016) Male-lineage transmission of an acquired metabolic phenotype induced by grand-paternal obesity. Molecular Metabolism, 5(8), 699-708
  67. Troup M, Yang A, Kamali AH, Giannoulatou E, Chen TY, Ho JWK (2016) A cloud-based framework for applying metamorphic testing to a bioinformatics pipeline. In Proceedings of the IEEE/ACM 1st International Workshop on Metamorphic Testing, 33-36
  68. Zhang Y, Fan J, Ho JWK, Hu T, Kneeland SC, Fan X, Xi Q, Sellarole MA, de Vries WN, Lu W, Lachke SA, Lang RA, John SWM, Maas RL (2016) Crim regulates integrin signaling in murine lens development. Development, 143(2), 356-366
  69. Al-Zyoud WA, Hynson RMG, Grnuelas LA, Coster ACF, Duff AP, Baker MAB, Stewart AG, Giannoulatou E, Ho JWK, Gaus K, Liu D, Lee LK, Boecking T (2016) Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site. Nucleic Acids Research, 44(3), 1411-1420
  70. Kamali AH, Giannoulatou E, Chen TY, Charleston MA, McEwan AL, Ho JWK (2015) How to test bioinformatics software? Biophysical Reviews 7(3), 343-352
  71. Sohn KA*, Ho JWK*, Djordjevic D, Jeong HH, Park PJ, Kim JH (2015) hiHMM: Bayesian non-parametric joint inference of chromatin state maps. Bioinformatics 31(13), 2066-2074
  72. Anchan R, Gerami-Naini B, Lindsey JS, Ho JWK, Kiezun A, Lipskind S, Ng N, LiCausi JA, Kim CS, Brezina P, Tuschl T, Maas RL, Kearns WG, Williams Z (2015)Efficient differentiation of steroidogenic and germ-like cells from epigenetically-related iPSCs derived from ovarian granulosa cells. PLoS One, 10(3),e0119275
  73. Djordjevic D, Deshpande V, Szczesnik T, Yang A, Humphreys DT, Giannoulatou E, Ho JWK (2015) Decoding the complex genetic causes of heart diseases using systems biology. Biophysical Reviews 7, 141-159
  74. Blue GM, Kirk EP, Giannoulatou E, Dunwoodie SL, Ho JWK, Hilton DCK, White SM, Sholler GF, Harvey RP, Winlaw DS (2014) Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Familial Congenital Heart Disease. Journal of American College of Cardiology, 64(23):2498-2506 [Editorial comment by JACC]
  75. Djordjevic D, Yang A, Zadoorian A, Rungrugeecharoen K, Ho JWK (2014) How difficult is inference of mammalian causal gene regulatory networks? PLoS One, 9(11), e111661 [Recommended by F1000Prime]
  76. Giannoulatou E, Park SH, Humphreys DT, Ho JWK (2014) Verification and validation of bioinformatics software without a gold standard: A case study of BWA and Bowtie. BMC Bioinformatics, 15(Suppl 16), S15
  77. Ho JWK*, Jung YL*, Liu T*, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SCJ, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SA, Chen QB, Chen RAJ , Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SCR, Liu XS, Lieb JD, AhringerJ, Karpen GH, Park PJ (2014) Comparative analysis of metazoan chromatin organization. Nature, 512(7515), 449-52 [News and Views by Nature]
  78. Jung Y, Luquette L, Ho JWK, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein C, Karpen G, Kuroda M, Park PJ (2014)Impact of sequencing depth in ChIP-seq experiments. Nucleic Acids Research, 42(9), e74
  79. Zhang B*, Day DS*, Ho JW, Song L, Cao J, Christodoulou D, Seidman JG, Crawford GE, Park PJ, Pu WT (2013)A dynamic H3K27ac signature identifies VEGF-stimulated endothelial enhancers and requires EP300 activity. Genome Research, 23(6), 917-927
  80. Lin MW*, Ho JWK*, Harrison LC, dos Remedios CG, Adelstein S. (2013) An antibody leukocyte capture microarrayin the diagnosis of Systemic Lupus Erythematosus. PLoS One, 8(3), e58199
  81. Chen L, Chen Z, Baker K, Halvorsen EM, da Cunha AP, Flak MB, Gerber G, Huang Y-H, Hosomi S, Arthur JC, Dery KJ, Nagaishi T, Beauchemin N, Holmes KV, Ho JWK, Shively JE,Jobin C, Onderdonk AB, Bry L, Weiner HL, Higgins DE, Blumberg RS. (2012) The Short isoform of the CEACAM1 receptor inintestinal T cells regulates mucosal immunity and homeostasis via Tfh cell induction. Immunity, 37, 930-946
  82. Ho JWK (2012) Application of a systems approach to studydevelopmental gene regulation. Biophysical Reviews, 4(3), 245-253
  83. Jumlongras D*, Lachke SA*, O'Connell DJ, Aboukhalil A, Li X, Choe SE, Ho JWK, Turbe-Doan A, Robertson EA, Olsen BR, Bulyk ML, Amendt BA, Maas RL. (2012) An evolutionarily conserved enhancerregulates Bmp4 expression in developing incisor and limb bud. PLoS One, 7(6), e38568
  84. Alekseyenko AA*, Ho JWK*, Peng S*, Gelbart M, Tolstorukov M, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB,Elgin SCR, Karpen GH, Pirrotta V, Kuroda MI, Park PJ (2012) Sequence-specific targeting ofdosage compensation in Drosophila favors an active chromatin context. PLoS Genetics, 8, e1002646
  85. Lachke SA*, Ho JWK*, Kryukov GV*, O'Connell DJ, Aboukhalil A, Bulyk M, Park PJ, Maas RL (2012) iSyTE: integrated systems tool for eyegene discovery. Investigative Ophthalmology & Visual Sciences, 53, 1617-1627
  86. O'Connell DJ*, Ho JWK*, Mammoto T, Turbe-Doan A, O'Connell JT, Haseley PS, Koo S, Kamiya N, Ingber DE, Park PJ, Maas RL (2012) A Wnt-Bmp feedback circuit controls intertissuesignaling dynamics in tooth organogenesis. Science Signaling, 5, ra4 [Featured on the cover of this issue ofthe journal]
  87. Sadi MS, Kuo FC, Ho JWK, Charleston MA, Chen TY (2011) Verification of phylogenetic inference programsusing metamorphic testing. Journal of Bioinformatics and Computational Biology, 6, 729-747
  88. Zacharek SJ, Fillmore CM, Gludish D, Zamponi R, Chou A, Ho JWK, Gazit R, Bock C, Jager N, Smith ZD, Lee J-H, Lau A, Kim T, Roach RR, Rossi DJ, Meissner A,Gimelbrant AA, Park PJ, Kim CF (2011) Lungstem cell self-renewal relies on Bmi1-dependent control of expression at imprinted loci. Cell Stem Cell, 9, 272-281
  89. Ho JWK, Bishop E, Kharchenko PV, Negre N, White K, Park PJ (2011) ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis. BMC Genomics, 12, 134 [labeled as "Highly accessed" by BMC Bioinformatics]
  90. Ho JWK, Charleston MA (2011) Network modeling of gene regulation. Biophysical Reviews, 3, 1-13
  91. Xie X, Ho JWK , Murphy C, Kaiser G, Xu B, Chen TY (2011) Testing and Validating Machine Learning Classifiers by Metamorphic Testing. Journal of Systems and Software, 84, 544-558
  92. Yang P*, Ho JWK*, Yang YH, Zhou BB (2011) Gene-gene interaction filtering withensemble of filters. BMC Bioinformatics, 12, S10
  93. Yang P, Ho JWK, Zomaya AY, Zhou BB (2010) A genetic ensemble approach for gene-gene interactionidentification. BMC Bioinformatics, 11, 524 [labeled as "Highly accessed" by BMC Bioinformatics]
  94. dos Remedios CG, Estigoy C, Cameron D, Ho JWK, Herbert B, Padula M, Pickford R, Guilhaus M, Odeberg J, Ponten F (2010) Proteomics of Human Cardiac Intercalated Disc: A more Complex Multi-Functional Structure than was Previously Thought. Biophysical Journal 98: 755a-756a
  95. Kong SW*, Hu YW*, Ho JWK, Ikeda S, Polster S, John R, Hall JL, Bisping E, Pieske B, dos Remedios CG, Pu WT (2010)Heart Failure Associated Changesin RNA Splicing of Sarcomere Genes. Circulation Cardiovasular Genetics, 3, 138-146
  96. Ho JWK*, Lin MW*, Braet F, Su YY, Adelstein S, dos Remedios CG (2010) Customising an antibodyleukocyte capture microarray for Systemic Lupus Erythematosus: Beyond biomarker discovery. Proteomics Clinical Applications, 4, 179-189 [Featured on the cover of this issue of the journal]
  97. Ho JWK, Stefani M, dos Remedios CG, Charleston MA (2009) A model selection approach to discoverage-dependent gene expression patterns using quantile regression models. BMC Genomics, 10, S16
  98. Xie X, Ho J Murphy C, Kaiser G, Xu B, Chen TY (2009) Application of Metamorphic Testing to Supervised Classifiers. In Proceedings of The 9th International Conference on Quality Software [Winner of the best paper award]
  99. Mohamed A, Koundinya R, Junius F, Dyer W, Yong A, Ho J, Kritharides L, Freedman B, dos Remedios C (2009) CD antibodymicroarrays as an objective tool to differentiate between inflammatory conditions of coronary arteries. In Heart, Lung and Circulation, 18S, S110
  100. Estigoy CB, Ponten F, Odeberg J, Herbert B, Guilhaus M, Charleston M, Ho JWK, Cameron D, dos RemediosCG (2009) IntercalatedDiscs: Multiple proteins perform multiple functions in non-failing and failing human hearts. Biophysical Reviews, 1, 43-49
  101. Chen TY, Ho JWK, Liu H, Xie X (2009) An innovative approach for testing bioinformatics programsusing metamorphic testing. BMC Bioinformatics, 10, 24 [labeled as "Highly accessed" by BMC Bioinformatics]
  102. Hassan MR, Hossain MM, Bailey J, Macintyre G, Ho JWK, Kotagiri R (2009) A voting approach to identify a small number of highly predictivegenes using multiple classifiers. BMC Bioinformatics, 10, S19
  103. Ho JWK, Koundinya R, Caetano TS, dos Remedios CG, Charleston MA (2008) Inferring differential leukocyteactivity from antibody microarrays using a latent variable model. Genome Informatics, 21, 126-137
  104. Ho JWK, Stefani M, dos Remedios CG, Charleston MA (2008) Differential variability analysis of gene expression and its application to human diseases, Bioinformatics, 24, i390-i398
  105. Ho JWK, Charleston MA (2007) Modeling the Evolution of GeneRegulatory Networks. In Proceedings of The Eighth International Conference on Systems Biology (ICSB 2007), Long Beach, USA
  106. Ho JWK, Morrissey B, Downard KM (2007) A ComputerAlgorithm for the Identification of Protein Interaction from the Spectra of Masses (PRISM). Journal of American Society of Mass Spectrometry, 18, 563-566
  107. Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS(2006) SeqVis: Visualization ofcompositional heterogeneity in large alignments of nucleotides. Bioinformatics, 22(17), 2162-2163
  108. Ho JWK, Manwaring T, Hong SH, Roehm U, Fung DCY, Xu K, Kraska T, Hart D (2006) PathBank: Web-based Querying and Visualization of an IntegratedBiological Pathway Database. In Banissi E, Sarfraz M, Huang ML, Wu Q (Eds) Computer Graphics, Imaging and Visualization - Techniquesand Application (Proceedings of CGIV2006), IEEE Computer Society,84-89
  109. Ho J, Lukov L, Chawla S (2005) Sequential Pattern Mining with Constraints on Large Protein Databases. InChakrabarti S, Sudarshan S, Radha Krishnan P (Eds) Proceedings of the 12th International Conference on Management of Data (COMAD2005b), 89-100
  110. Ho J, Hong SH (2005) Drawing Clustered Graph in Three Dimensions. In Haely P, Nikolov NS (Eds) Proceedings of the 13th International Symposium of Graph Drawing (GD2005). Lecture Notes in Computer Science, Springer, 492-502
  111. Ahmed A, Dwyer T, Foster M, Fu X, Ho J, Hong SH, Koschutzki D, Murray C, Nikolov N, Taib R, Tarassov A, Xu K, (2005) GEOMI:GEOmetry for Maximum Insight. In Haely P, Nikolov NS (Eds) Proceedings of the 13th International Symposium of Graph Drawing(GD2005). Lecture Notes in Computer Science, Springer, 468-479

Software

  • CIDR is an R package thay implements an ultrafast and accurate dimensionality reduction and clustering algorithm for single-cell RNA-seq data. The method is described in this Genome Biology paper.
  • Falco is flexible big data framework for fast processing of single-cell RNA-seq data on the cloud. The method is described in this Bioinformatics paper.
  • PBrowse is web-based platform for real-time collaborative exploration and sharing of genomic data. A test server can be found here. The method is described in this Nucleic Acids Research paper.
  • PAD is a web-based bioinformatics tool for analysing transcription factor (TF) co-binding at gene-proximal or distal regulatory elements in mouse embryonic stem cells. A test server can be found here. The method is described in this Bioinformatics paper.
  • XGSA is an R package that implements our statistical method for cross-species gene set analysis. A full description of the method can be found in this Bioinformatics paper.
  • ENCODE-X Cross-species chromatin data browser is an online portal for ENCODE and modENCODE chromatin datasets. A full description of the data can be found in our Nature paper.
  • hiHMM is a new Bayesian non-parametric method to jointly infer chromatin state maps in multiple genomes (different cell types, developmental stages, even multiple species) using genome-wide histone modification data.
  • ToothCODE is an online portal of embryonic mouse tooth development data generated by the tooth regeneration team of SysCODE.
  • iSyTE is an integrated systems tool for eye gene discovery.
  • SeqVis is a stand-alone, platform-independent Java application developed with the aim to facilitate analysis and 3D visualization of compositional heterogeneity in species-rich alignments of nucleotide sequences. A software website can be found here and here
  • SeqVis 2.0 is a web-based version of SeqVis. The demo can be found here: https://vccri.github.io/SeqVis/
  • DVA is a R script that performs differential variability analysis. A full description of this method can be found in this Bioinformatics paper.
  • C3 is an R package for cross-species compendium-based cell-type identification.
  • GEOracle is an R/shiny package for identifying and analysing perturbation experiments in NCBI GEO. Source code can be found in GitHub.
  • Scavenger a phyton tool to recover false negative unmapped reads.
  • Ularcirc is an R package for visualisation and analysis of circular RNA.
  • CardiacProfileR is an R package for extraction and visualisation of heart rate profiles from wearable fitness trackers.
  • starmapVis is a web-based visualisation tool that enables immersive visualisation of spatial single cell omic data. starmap can be accessed from a desktop, laptop or a mobile device from the following link: https://github.com/holab-hku/starmapVis.
  • FlowGrid is an ultrafast clustering algorithm for single-cell flow cytometry data. It implements a novel grid-based DBSCAN clustering algorithm.
  • DCATS is an R package for differential composition analysis of complex single cell experimental designs.
  • MQuad is a tool that detects mitochondrial mutations that are informative for clonal substructure inference. It uses a binomial mixture model to assess the heteroplasmy of mtDNA variants among background noise.

Data sets

  • Antibody microarray of patients with Systemic Lupus Erythematosus (GEO)
  • Histone modification and gene expression in dosage compensation of Drosophila melanogaster (GEO)
  • Developmental timecourse of mouse ocular lens and whole embryo control (GEO)
  • Gene expression during embryonic mouse molar tooth development (GEO)

Contact

Dr. Joshua W. K. Ho
Associate Professor
School of Biomedical Sciences, Li Ka Shing Faculty of Medicine
Rm 4-44, Laboratory Block, 21 Sassoon Road
Hong Kong SAR, China

Email: jwkho@hku.hk