Justin Cha


Justin Cha is a PhD student in the Computational Biology Program. He received his bachelor's degree in Biomedical Engineering at the Georgia Institute of Technology before working as an Associate Computational Biologist in the Getz Lab at the Broad Institute. For the Pugh lab, he works on software development and high-throughput computing (HTC) for the analysis of sequencing data.


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# Research Interests

I have a general interest in genomics bioinformatics and software development, and I am currently working on a tool to identify and categorize DNA-protein binding sites based on occupancy patterns.

Experience

September 2018 – July 2021
Broad Institute of Harvard and MIT – Cambridge, MA

Associate Computational Biologist II

At the Broad Institute, I am a member of the Getz Lab, one of the world’s leading labs for cancer genomics. I have worked on several exciting projects pushing at the forefront of the field. One was an analysis of genomic progression in head and neck squamous cell carcinoma (HNSCC). For this project, I made use of a novel set of computational methods to reconstruct the trajectory of genomic events from exome sequencing data. This allowed us to see which mutations and other variants tend to occur early on in the progression of cancer, which will be useful in treatment development and prognosis.

Publications

2024
Molecular basis of global promoter sensing and nucleosome capture by the SWR1 chromatin remodeler.

Louder, R. K., Park, G., Ye, Z., Cha, J. S., Gardner, A. M., Lei, Q., Ranjan, A., Hollmuller, E., Stengel, F., Pugh, B. F., Wu, C., Cell, 2024

Developmental mosaicism underlying EGFR-mutant lung cancer presenting with multiple primary tumors.

Burr, R., Leshchiner, I., Costantino, C. L., Blohmer, M., Sundaresan, T., Cha, J., Seeger, K., Guay, S., Danysh, B. P., Gore, I., Jacobs, R. A., Slowik, K., Utro, F., Rhrissorrakrai, K., Levovitz, C., Barth, J. L., Dubash, T., Chirn, B., Parida, L., Sequist, L. V., Lennerz, J. K., Mino-Kenudson, M., Maheswaran, S., Naxerova, K., Getz, G., Haber, D. A., Nature Cancer, 2024

2023
Pirtobrutinib targets BTK C481S in ibrutinib-resistant CLL but second-site BTK mutations lead to resistance.

Naeem, A., Utro, F., Wang, Q., Cha, J., Vihinen, M., Martindale, S., Zhou, Y., Ren, Y., Tyekucheva, S., Kim, A. S., Fernandes, S. M., Saksena, G., Rhrissorrakrai, K., Levovitz, C., Danysh, B. P., Slowik, K., Jacobs, R. A., Davids, M. S., Lederer, J. A., Zain, R., Smith, C. I. E., Leshchiner, I., Parida, L., Getz, G., Brown, J. R., Blood Advances, 2023

Genetic events associated with venetoclax resistance in CLL identified by whole exome sequencing of patient samples.

Khalsa, J. K.*, Cha, J.*, Utro, F.*, Naeem, A.*, Murali, I.*, Kuang, Y., Vasquez, K., Li, L., Tyekucheva, S., Fernandes, S. M., Veronese, L., Guieze, R., Sasi, B. K., Wang, Z., Machado, J. H., Bai, H., Alasfour, M., Rhrissorrakrai, K., Levovitz, C., Danysh, B. P., Slowik, K., Jacobs, R. A., Davids, M. S., Paweletz, C. P., Leshchiner, I., Parida, L., Getz, G., Brown, J. R., Blood, 2023

Inferring early genetic progression in cancers with unobtainable premalignant disease.

Leshchiner, I.*, Mroz, E. A.*, Cha, J.*, Rosebrock, D., Spiro, O., Bonilla-Velez, J., Faquin, W. C., Lefranc-Torres, A., Lin, D. T., Michaud, W. A., Getz, G., Rocco, J. W., Nature Cancer, 2023

2020
Genomic profiling of smoldering multiple myeloma identifies patients at a high risk of disease progression.

Bustoros, M., Sklavenitis-Pistofidis, R., Park, J., Redd, R., Zhitomirsky, B., Dunford, A. J., Salem, K., Tai, Y. T., Anand, S., Mouhieddine, T. H., Chavda, S. J., Boehner, C., Elagina, L., Neuse, C. J., Cha, J., Rahmat, M., Taylor-Weiner, A., Van Allen, E., Kumar, S., Kastritis, E., Leshchiner, I., Morgan, E. A., Laubach, J., Casneuf, T., Richardson, P., Munshi, N. C., Anderson, K. C., Trippa, L., Aguet, F., Stewart, C., Dimopoulos, M. A., Yong, K., Bergsagel, P. L., Manier, S., Getz, G., Ghobrial, I. M., Journal of Clinical Oncology, 2020

Skills



Programming Languages
  • Python
  • Julia
  • JavaScript
  • SQL
  • Rust
  • Matlab


    • Quantitative
  • Data analysis
  • Statistics
  • Genomics


    • Communication
  • Technical presentation/writing
  • Data visualization
  • Teaching

    • Tutorials

    Python

    Data model
    Iterators and generators
    Decorators