Select Publications


Ho JWK, 2010, Principles and Applications of Bioinformatics for Systems Medicine, University of Sydney

Book Chapters

Wang X; McCormick HM; Djordjevic D; Giannoulatou E; Suter CM; Ho JWK, 2016, 'Epigenomic Analysis of Chromatin Organization and DNA Methylation', in Wong KC (ed.), COMPUTATIONAL BIOLOGY AND BIOINFORMATICS: GENE REGULATION GENE RNA PROTEIN EPIGENETICS, CRC PRESS-TAYLOR & FRANCIS GROUP, pp. 181 - 211,

Giannoulatou E; Kamali AH; Yang A; Chen TY; Ho JWK, 2016, 'Quality Assurance in Genome-Scale Bioinformatics Analyses', in Wong KC (ed.), COMPUTATIONAL BIOLOGY AND BIOINFORMATICS: GENE REGULATION GENE RNA PROTEIN EPIGENETICS, CRC PRESS-TAYLOR & FRANCIS GROUP, pp. 259 - 278,

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 in patients with ischemic heart disease', in Myocardial Ischemia: Causes, Symptoms and Treatment, pp. 195 - 216

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, Humana Press, pp. 65 - 91,

Ho J; Hong SH, 2006, 'Drawing clustered graphs in three dimensions', in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pp. 492 - 502,

Journal articles

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, vol. 9, pp. 10579,

Szczesnik T; Ho JWK; Sherwood R, 2019, 'Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding', Epigenetics and Chromatin, vol. 12,

Eyk CLV; 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, vol. 28, pp. 3000 - 3012,

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, vol. 80, pp. 152 - 158,

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, vol. 8,

Ho JWK; Giannoulatou E, 2019, 'Big data: the elements of good questions, open data, and powerful software', Biophysical Reviews, vol. 11, pp. 1 - 3,

Djordjevic D; Cawood BK; Rispin SK; Shah A; Yim LHH; Hayward CS; Ho JWK, 2019, 'CardiacProfileR: an R package for extraction and visualisation of heart rate profiles from wearable fitness trackers', Biophysical Reviews, vol. 11, pp. 119 - 121,

Wang Q; Wang K; Wu W; Giannoulatou E; Ho JWK; Li L, 2019, 'Host and microbiome multi-omics integration: applications and methodologies', Biophysical Reviews, vol. 11, pp. 55 - 65,

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, vol. 21, pp. 1111 - 1120,

Kabir MH; Patrick R; Ho JWK; O'Connor MD, 2018, 'Identification of active signaling pathways by integrating gene expression and protein interaction data', BMC Systems Biology, vol. 12,

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, vol. 77, pp. 187 - 192,

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, vol. 42, pp. 911 - 914,

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, vol. 25, pp. 712 - 726,

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. Genomic and precision medicine, vol. 11, pp. e001978,

Wang X; Lin P; Ho JWK, 2018, 'Discovery of cell-type specific DNA motif grammar in cis-regulatory elements using random Forest', BMC Genomics, vol. 19,

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; Hernández D; Clarke J; Hanssen E; Davidson SM; Dusting GJ; Pébay A; Ho JWK; Williamson N; Lim SY, 2018, 'Biologically active constituents of the secretome of human W8B2+ cardiac stem cells', Scientific Reports, vol. 8,

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, vol. 46, pp. D875 - D885,

Murphy P; Kabir MH; Srivastava T; Mason ME; Dewi CU; Lim S; Yang A; Djordjevic D; Killingsworth MC; 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 (Cambridge), vol. 145,

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, vol. 433, pp. 344 - 356,

Rizzetto S; Eltahla AA; Lin P; Bull R; Lloyd AR; Ho JWK; Venturi V; Luciani F, 2017, 'Impact of sequencing depth and read length on single cell RNA sequencing data of T cells', Scientific Reports, vol. 7,

Ho JWK; Grant GH, 2017, 'Modelling, inference and big data in biophysics', Biophysical Reviews, vol. 9, pp. 297 - 298,

Shi H; Enriquez A; Rapadas M; Martin EMMA; Wang R; Moreau J; Lim CK; Szot JO; Ip E; Hughes JN; Sugimoto K; Humphreys DT; 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, vol. 377, pp. 544 - 552,

Szot PS; Yang A; Wang X; Parsania C; Röhm U; Wong KH; Ho JWK, 2017, 'PBrowse: A web-based platform for real-time collaborative exploration of genomic data', Nucleic Acids Research, vol. 45, pp. e67,

Yang A; Troup M; Ho JWK, 2017, 'Scalability and Validation of Big Data Bioinformatics Software', Computational and Structural Biotechnology Journal, vol. 15, pp. 379 - 386,

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, vol. 33, pp. 1916 - 1920,

Yang A; Troup M; Lin P; Ho JWK, 2017, 'Falco: A quick and flexible single-cell RNA-seq processing framework on the cloud', Bioinformatics, vol. 33, pp. 767 - 769,

Lin P; Troup M; Ho JWK, 2017, 'CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data', Genome Biology, vol. 18,

Cropley JE; Eaton SA; Aiken A; Young PE; Giannoulatou E; Ho JWK; Buckland ME; Keam SP; Hutvagner G; 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, vol. 5, pp. 699 - 708,

Al-Zyoud WA; Hynson RMG; Ganuelas LA; Coster ACF; Duff AP; Baker MAB; Stewart AG; Giannoulatou E; Ho JWK; Gaus K; Liu D; Lee LK; Böcking 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, vol. 44, pp. 1411 - 1420,

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, 'Crim1 regulates integrin signaling in murine lens development', Development (Cambridge), vol. 143, pp. 356 - 366,

Kamali AH; Giannoulatou E; Chen TY; Charleston MA; McEwan AL; Ho JWK, 2015, 'How to test bioinformatics software?', Biophysical Reviews, vol. 7, pp. 343 - 352,

Sohn K-A; Ho JWK; Djordjevic D; Jeong H-H; Park PJ; Kim JH, 2015, 'hiHMM: Bayesian non-parametric joint inference of chromatin state maps', Bioinformatics, vol. 31, pp. btv117 - btv117,

Anchan R; Gerami-Naini B; Lindsey JS; Ho JW; 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, vol. 10, pp. e0119275 - e0119275,

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, vol. 7, pp. 141 - 159,

Jung YL; Luquette LJ; Ho JWK; Ferrari F; Tolstorukov M; Minoda A; Issner R; Epstein CB; Karpen GH; Kuroda MI; others , 2014, 'Impact of sequencing depth in ChIP-seq experiments', Nucleic acids research, vol. 42, pp. e74 - e74,

Giannoulatou E; Park S-H; Humphreys DT; Ho JWK, 2014, 'Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie', BMC bioinformatics, vol. 15, pp. S15 - S15,

Alekseyenko AA; Ho JWK; Peng S; Gelbart M; Tolstorukov MY; Plachetka A; Kharchenko PV; Jung YL; Gorchakov AA; Larschan E; others , 2014, 'Correction: Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context', PLoS genetics, vol. 10,

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 the American College of Cardiology, vol. 64, pp. 2498 - 2506,

Djordjevic D; Yang A; Zadoorian A; Rungrugeecharoen K; Ho JWK, 2014, 'How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?', PLoS ONE, vol. 9, pp. e111661 - e111661,

Zhang B; Day DS; Ho J; Song L; Seidman JG; Crawford GE; Park PJ; Pu WT, 2014, 'VEGF changes chromatin landscape in endothelial cell', ANGIOGENESIS, vol. 17, pp. 957 - 957,

Ho JWK; Jung YL; Liu T; Alver BH; Lee S; Ikegami K; Sohn K-A; Minoda A; Tolstorukov MY; Appert A; others , 2014, 'Comparative analysis of metazoan chromatin organization', Nature, vol. 512, pp. 449 - 452,

Lin M-W; Ho JWK; Harrison LC; dos Remedios CG; Adelstein S, 2013, 'An antibody-based leukocyte-capture microarray for the diagnosis of systemic lupus erythematosus', PloS one, vol. 8, pp. e58199 - e58199,

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 VEGFA-stimulated endothelial enhancers and requires EP300 activity', Genome research, vol. 23, pp. 917 - 927,

O Connell DJ; Ho JWK; Maas RL, 2013, 'Systems biology of early tooth development', Stem Cells in Craniofacial Development and Regeneration, pp. 179 - 202,

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