Newell, R. J. P., Pienaar, R., Balderson, B., Piper, M., Essebier, A., & Bodén, M., 2021. ChIP-R: Assembling reproducible sets of ChIP-seq and ATAC-seq peaks from multiple replicates, Genomics, 113(4), pp.1855-1866
Foley, G., Mora, A., Ross, C. M., Bottoms, S., Sützl, L., Lamprecht, M. L., Zaugg, J., Essebier, A., Balderson, B., Newell, R. J. P., Thomson, R. E. S., Kobe, B., Barnard, R. T., Guddat, L., Schenk, G., Carsten, J., Gumulya, Y., Rost, B., Haltrich, D., … Bodén, M., 2022. Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP) (p. 2019.12.30.891457). bioRxiv. https://doi.org/10.1101/2019.12.30.891457
Wang, Y., Ni, G., Tian, W., Yang, L., Hosegood, I., Newell, R. J. P., Woodcroft, B. J., Yang, B., Hu, S., Guo, J., 2022. Detection of SARS-CoV-2 Variants of Concern with Tiling Amplicon Sequencing from Wastewater. ACS ES&T Water. https://doi.org/10.1021/acsestwater.2c00083
Publications to be completed
Newell, R. J. P., McMaster, E. S., Bodén, M., Tyson, G. W., & Woodcroft, B. J., 2022. Rosella: A novel unsupervised machine learning approach for the reconstruction of metagenome-assembled genomes.
Newell, R. J. P., McMaster, E. S., Craig, P., McIlroy, S. J., Bodén, M., Tyson, G. W., & Woodcroft, B. J., 2022. Lorikeet: Strain resolved metagenome analysis using local reassembly based variant calling.
Newell, R. J. P., Sullivan, M. J., Zaugg, J., Sternes, P., Hugenholtz, P., Tyson, G. W., & Woodcroft, B. J., 2022. Aviary: A scalable and comprehensive hybrid assembly & MAG recovery pipeline