• Data scientist, computational biologist
  • Toronto, ON

About

I am currently Head of Data Science, Genomics at BioSymetrics.

I completed my PhD in the Department of Molecular Genetics at the University of Toronto (co-supervised by Ben Blencowe and Quaid Morris). My research was focused on developing computational and machine learning methods to study the transcriptome using high-throughput sequencing datasets. Some of my PhD projects can be found in here.

Prior to starting my PhD, I was a research intern with the Microsoft Biology Initiative group at Microsoft Research.

Interests

Education

Selected Publications

Full publication list available on Google Scholar

  1. Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity
    Ha, K.C.H., Sterne-Weiler, T., Morris, Q., Weatheritt, R.J., Blencowe, B.J. (2021). Nat Commun. 12:335.
  2. Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9–Cas12a platform
    Gonatopoulos-Pournatzis, T., Aregger, M., Brown, K.R., Farhangmehr, S., Braunschweig, U., Ward, H.N., Ha, K.C.H., Weiss, A., Billmann, M., Durbic, T., Myers, C.L., Blencowe, B.J., Moffat, J. (2020). Nat Biotechnol. 38:638-648.
  3. Efficient and accurate quantitative profiling of alternative splicing patterns of any complexity on a laptop
    Sterne-Weiler, T., Weather, R. J., Best, A., Ha, K.C.H., Blencowe, B.J. (2018). Mol Cell. 72:P187-200.E6.
  4. QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
    Ha, K.C.H., Blencowe, B.J., Morris, Q. (2018). Genome Biol. 19:45.
  5. An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms
    Tapial, J., Ha, K.C.H.*, Sterne-Weiler, T.*, Gohr, A.*, Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayon, T., Manzanares, M., Ponomarenko, J., Blencowe, B.J., Irimia, M. (2017). Genome Res. 27:1759–1768.
  6. RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection
    Cook, K.B., Vembu, S., Ha, K.C.H., Zheng, H., Laverty, K.U., Hughes, T.R., Ray, D., Morris, Q.D. (2017). Methods. 126:18-28.
  7. MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs
    Rodrigues, D.C., Kim, D.-S., Yang, G., Zaslavsky, K., Ha, K.C.H., Mok, R.S.F., Ross, P.J., Zhao, M., Piekna, A., Wei, W., Blencowe, B.J., Morris, Q., Ellis, J. (2016). Cell Rep. 17:720–734.
  8. Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines
    Ha, K.C.H., Lalonde, E., Li, L., Cavallone, L., Natrajan, R., Lambros, M.B., Mitsopoulos, C., Hakas, J., Kozarewa, I., Fenwick, K., Lord, C.J., Ashworth, A., Vincent-Salomon, A., Basik, M., Reis-Filho, J.S., Majewski, J., Foulkes, W.D. (2011). BMC Med. Genomics. 4:75.
  9. RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression
    Lalonde, E., Ha, K.C.H., Wang, Z., Bemmo, A., Kleinman, C.L., Kwan, T., Pastinen, T., Majewski, J. (2011). Genome Res. 21:545–54.
  10. Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation
    Ha, K.C.H., Coulombe-Huntington, J., Majewski, J. (2009). BMC Genomics. 10:519.
  11. Germ-line DNA copy number variation frequencies in a large North American population
    Zogopoulos, G., Ha, K.C.H., Naqib, F., Moore, S., Kim, H., Montpetit, A., Robidoux, F., Laflamme, P., Cotterchio, M., Greenwood, C., Scherer, S.W., Zanke, B., Hudson, T.J., Bader, G.D., Gallinger, S. (2007). Hum. Genet. 122:345–353.