James M. Ferguson
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https://scholar.google.com.au/citations?user=PZe3hvQAAAAJ&hl=en
2022
Gamaarachchi, H., H. Samarakoon, S. P. Jenner, J. M. Ferguson, T. G. Amos, J. M. Hammond, H. Saadat, M. A. Smith, S. Parameswaran and I. W. Deveson (2022). "Fast nanopore sequencing data analysis with SLOW5." Nature Biotechnology.
paper | github
2021
Ferguson, J. M., H. Gamaarachchi, T. Nguyen, A. Gollon, S. Tong, C. Aquilina-Reid, R. Bowen-James and I. W. Deveson (2021). "InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses." Bioinformatics.
Du, Q., G. C. Smith, P. L. Luu, J. M. Ferguson, N. J. Armstrong, C. E. Caldon, E. M. Campbell, S. S. Nair, E. Zotenko, C. M. Gould, M. Buckley, K.-M. Chia, N. Portman, E. Lim, D. Kaczorowski, C.-L. Chan, K. Barton, I. W. Deveson, M. A. Smith, J. E. Powell, K. Skvortsova, C. Stirzaker, J. Achinger-Kawecka and S. J. Clark (2021). "DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity." Cell Reports 36(12).
paper
Edwards, R. J., M. A. Field, J. M. Ferguson, O. Dudchenko, J. Keilwagen, B. D. Rosen, G. S. Johnson, E. S. Rice, D. Hillier, J. M. Hammond, S. G. Towarnicki, A. Omer, R. Khan, K. Skvortsova, O. Bogdanovic, R. A. Zammit, E. L. Aiden, W. C. Warren and J. W. O. Ballard (2021). "Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome." BMC Genomics 22(1): 188.
2020
Smith, M. A., T. Ersavas, J. M. Ferguson, H. Liu, M. C. Lucas, O. Begik, L. Bojarski, K. Barton and E. M. Novoa (2020). "Molecular barcoding of native RNAs using nanopore sequencing and deep learning." Genome Res 30(9): 1345-1353.
Bull, R. A., T. N. Adikari, J. M. Ferguson, J. M. Hammond, I. Stevanovski, A. G. Beukers, Z. Naing, M. Yeang, A. Verich, H. Gamaarachchi, K. W. Kim, F. Luciani, S. Stelzer-Braid, J. S. Eden, W. D. Rawlinson, S. J. van Hal and I. W. Deveson (2020). "Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis." Nat Commun 11(1): 6272.
Samarakoon, H., S. Punchihewa, A. Senanayake, J. M. Hammond, I. Stevanovski, J. M. Ferguson, R. Ragel, H. Gamaarachchi and I. W. Deveson (2020). "Genopo: a nanopore sequencing analysis toolkit for portable Android devices." Commun Biol 3(1): 538.
paper | github | app store
2019
Singh, M., G. Al-Eryani, S. Carswell, J. M. Ferguson, J. Blackburn, K. Barton, D. Roden, F. Luciani, T. Giang Phan, S. Junankar, K. Jackson, C. C. Goodnow, M. A. Smith and A. Swarbrick (2019). "High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes." Nat Commun 10(1): 3120.
Ferguson, J. M. and M. A. Smith (2019). "SquiggleKit: a toolkit for manipulating nanopore signal data." Bioinformatics 35(24): 5372-5373.