Dr Jake Bradford

2024

• Schmitz, C., Bradford, J., Salomone, R. & Perrin, D. (2024). Fast and scalable off-target assessment for CRISPR guide RNAs using partial matches. Proceedings of the 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1649–1654. Institute of Electrical and Electronics Engineers Inc.. https://eprints.qut.edu.au/256544
• Rafi, A. M., Nogina, D., Penzar, D., Lee, D., Lee, D., Kim, N., Kim, S., Kim, D., Shin, Y., Kwak, I. Y., Meshcheryakov, G., Lando, A., Zinkevich, A., Kim, B. C., Lee, J., Kang, T., Vaishnav, E. D., Yadollahpour, P., AiWei, Y., JingZhe, W., JiaXing, C., Schmitz, C., Salomone, R., Perrin, D., Bradford, J., Kumar S, P., Gupta, K., Palaniappan, A., Malousi, A., Kyriakidis, K., Kardamiliotis, K., Emrich, S., Babjac, A., Queen, O., Lu, Z., Madsen, J., Kavaliauskaite, G., Møller, A., Soylemez, O., Schubach, M., Dash, P. M., Röner, S., Li, Y., Brors, B., Feuerbach, L., Körner, C., Abad, N., Wan, C., Barton, C., Greaves, P., Alsaggaf, I., Huang, K. L., Chen, J. Y., Wu, C. H., Chen, S. H., Shih, E. S. C., Wang, H. K., Huang, C. H., Chen, T. M., Takatsu, M., Hiratsuka, Y., Davuluri, R. V., Liu, H., Ji, Y., Surana, P., Sathian, R., Dutta, P., Zhou, Z., Wen, J., Dixit, G., Ding, K., Yang, Y., Chen, K., Ding, M., Guan, Y., Tinti, M., Jones, D. T., Chen, X., Koo, P., Narayanan, A., Prakash, A., Labelson, E., Yu, Y., Ghotra, R., Qiu, W., Zhang, W., Tu, X., Nguyen, T., Tran, D., Trapotsi, M. A., Svensson, F., Bornelöv, S., Kim, S., Albrecht, J., Regev, A., Gong, W., Kulakovskiy, I. V., Meyer, P., de Boer, C. G. & other (2024). A community effort to optimize sequence-based deep learning models of gene regulation. Nature Biotechnology. https://eprints.qut.edu.au/256545

2023

• Tinoco, A. I., Mitchison-Field, L. M. Y., Bradford, J., Renicke, C., Perrin, D., Bay, L. K., Pringle, J. R. & Cleves, P. A. (2023). Role of the bicarbonate transporter SLC4 gamma in stony-coral skeleton formation and evolution. Proceedings of the National Academy of Sciences of the United States of America, Article e2216144120, 120(24). https://eprints.qut.edu.au/241779
• Lovell, D., Martens, W., Bradford, J., Bradley, A., Crowe, A., McKague, M. & Perrin, D. (2023). Comparison of independent, participant-led, high-resolution studies of pitch-matching in post-lingual single-sided cochlear implant recipients. Journal of the Acoustical Society of America, 154(4 Supplement). https://eprints.qut.edu.au/246146

2022

• Bradford, J., Chappell, T. & Perrin, D. (2022). Rapid Whole-Genome Identification of High Quality CRISPR Guide RNAs with the Crackling Method. CRISPR Journal, 5(3), 410–421. https://eprints.qut.edu.au/234989

2020

• Cleves, P. A., Tinoco, A. I., Bradford, J., Perrin, D., Bay, L. K. & Pringle, J. R. (2020). Reduced thermal tolerance in a coral carrying CRISPR-induced mutations in the gene for a heat-shock transcription factor. Proceedings of the National Academy of Sciences of the United States of America, 117(46), 28899–28905. https://eprints.qut.edu.au/207993

2019

• Bradford, J. & Perrin, D. (2019). Improving CRISPR guide design with consensus approaches. BMC Genomics, Article 931, 20. https://eprints.qut.edu.au/208020
• Bradford, J. & Perrin, D. (2019). A benchmark of computational CRISPR-Cas9 guide design methods. PLoS Computational Biology, Article e1007274, 15(8). https://eprints.qut.edu.au/208021