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Pre-print manusripts

  1. Ye X, Ho JWK (2018) Ultrafast clustering of single-cell flow cytometry data using FlowGrid. bioRxiv: link
  2. Yang A*, Tang JYS*, Troup M, Ho JWK (2018) Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads. bioRxiv: link
  3. Yang A, Yao Y, Li J,Ho JWK (2018) starmap: Immersive visualisation of single cell data using smartphone-enabled virtual reality. bioRxiv: link
  4. Djordjevic D, Cawood BK, Rispin SK, Yim LHH, Ho JWK (2018) CardiacProfileR: An R package for extraction and visualisation of heart rate profiles from wearable fitness trackers. bioRxiv: link
  5. Humphreys DT, Fossat N, Tam PPL, Ho JWK (2018) Ularcirc: Visualisation and enhanced analysis of circular RNAs via back and canonical forward splicing. bioRxiv: link
  6. Kabir MH, Djordjevic D, O'Connor MD, Ho JWK (2018) C3: An R package for cross-species compendium-based cell-type identification. bioRxiv: link
  7. Djordjevic D, Chen YX, Kwan SLS, Ling RWK, Qian G, Woo CYY, Ellis SJ, Ho JWK (2017) GEOracle: Mining perturbation experiments using free text metadata in Gene Expression Omnibus. bioRxiv: link

Book chapters

  1. Ye X, Ho JWK (2018) Expression Clustering. Encyclopedia of Bioinformatics and Computational Biology, Elsevier (in press)
  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

[* Co-first authors]

  1. 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.
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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 (2017) An embryonic and induced pluripotent stem cell model for ovarian granulosa cell development and steroidogenesis. Reproductive Sciences (in press)
  9. 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
  10. Ho JWK, Grant GH (2017) Modelling, inference and big data in biophysics. Biophysical Reviews, 9(4), 297-298
  11. 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
  12. Yang A, Troup M, Ho JWK (2017) Scalability and validation of big data bioinformatics software. Computational and Structural Biotechnology Journal, 15, 379-386
  13. Lin P, Troup M, Ho JWK (2017) CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data. Genome Biology, 18, 59
  14. 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
  15. 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
  16. 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
  17. 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
  18. Djordjevic D, Kusumi K, Ho JWK (2016) XGSA: A statistical method for cross-species gene set analysis. Bioinformatics, 32(17), i620-i628
  19. 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
  20. 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
  21. 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
  22. 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
  23. Kamali AH, Giannoulatou E, Chen TY, Charleston MA, McEwan AL, Ho JWK (2015) How to test bioinformatics software? Biophysical Reviews 7(3), 343-352
  24. 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
  25. 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
  26. 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
  27. 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]
  28. 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]
  29. 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
  30. 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 Anshul, 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]
  31. 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
  32. 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
  33. 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
  34. 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
  35. Ho JWK (2012) Application of a systems approach to studydevelopmental gene regulation. Biophysical Reviews, 4(3), 245-253
  36. 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
  37. 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
  38. 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
  39. 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]
  40. 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
  41. 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
  42. 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]
  43. Ho JWK, Charleston MA (2011) Network modeling of gene regulation. Biophysical Reviews, 3, 1-13
  44. 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
  45. Yang P*, Ho JWK*, Yang YH, Zhou BB (2011) Gene-gene interaction filtering withensemble of filters. BMC Bioinformatics, 12, S10
  46. 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]
  47. 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
  48. 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
  49. 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]
  50. 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
  51. 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]
  52. 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
  53. 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
  54. 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]
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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