Toggle nav
Gene editing Tissue clearing Digital health Misc
Reprints are available upon request.
2019
S Choobdar et al. (2019). "Assessment of network module identification across complex diseases ", Nature Methods 16:843-852. Misc
A Nazib, C Fookes, D Perrin (2019). "Towards Extreme-Resolution Image Registration with Deep Learning ", Proceedings of the 16th International Symposium on Biomedical Imaging (ISBI 2019), IEEE. Tissue clearing
A Nazib, C Fookes, D Perrin (2019). "Dense Deformation Network for High Resolution Tissue Cleared Image Registration ", arXiv 1906.06180. Tissue clearing
J Bradford, D Perrin (2019). "A benchmark of computational CRISPR-Cas9 guide design methods ", PLOS Computational Biology 15(8):e1007274.Gene editing
S Roomkham, M Hittle, J Cheung, D Lovell, E Mignot, D Perrin (2019). "Sleep monitoring with the Apple Watch: comparison to a clinically validated actigraph ", F1000Research 8:754. Digital health
B Zhou et al. (2019). "Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2 ", Nucleic Acids Research 47:3846-3861. Gene editing
B Zhou et al. (2019). "Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562 ", Genome Research 29:1-13. Gene editing
2018
JB Stephansen et al. (2018). "Neural network analysis of sleep stages enables efficient diagnosis of narcolepsy ", Nature Communications 9(1):5229. Digital health
T Chappell, S Geva, JM Hogan, F Huygens, IU Rathnayake, S Rudd, W Kelly, D Perrin (2018). "Rapid analysis of metagenomic data using signature-based clustering ", BMC Bioinformatics 19(Supp 20):509. Misc
A Nazib, C Fookes, D Perrin (2018). "A comparative analysis of registration tools: traditional vs deep learning approach on high resolution tissue cleared data ", arXiv 1810.08315. Tissue clearing
J Bradford, D Perrin (2018). "A benchmark of computational CRISPR-Cas9 guide design methods ", BioRxiv, 498782. Gene editing
S Roomkham, M Hittle, D Lovell, D Perrin (2018). "Can we use the Apple Watch to measure sleep reliably? ", Journal of Sleep Research 27:e153_12766. Digital health
Y Niwa et al. (2018). "Muscarinic acetylcholine receptors Chrm1 and Chrm3 are essential for REM sleep ", Cell Reports 24:2231-2247. Gene editing Tissue clearing
A Nazib, J Galloway, C Fookes, D Perrin (2018). "Performance of Registration Tools on High-Resolution 3D Brain Images ", Proceedings of the 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pp. 566-569. Tissue clearing
S Roomkham, D Lovell, J Cheung, D Perrin (2018). "Promises and challenges in the use of consumer-grade devices for sleep monitoring ", IEEE Reviews in Biomedical Engineering 11:53-67. Digital health
D Perrin, G Zuccon (2018). "Recursive module extraction using Louvain and PageRank ", F1000Research 7:1286. Misc
B Zhou, SS Ho, LC Leung, TR Ward, M Ho, MJ Plastini, SC Vermilyea, ME Emborg, TG Golos, P Mourrain, D Perrin, KJ Parker, AE Urban (2018). "Haplotype-phased Callithrix jacchus embryonic stem cell line for genome editing using CRISPR/Cas9 ", bioRxiv 373886. Gene editing
B Zhou, SS Ho, SU Greer, N Spies, JM Bell, X Zhang, X Zhu, JG Arthur, S Byeon, R Pattni, I Saha, G Song, HP Ji, D Perrin, WH Wong, A Abyzov, AE Urban (2018). "Haplotype-resolved and integrated genome analysis of ENCODE cell line HepG2 ", bioRxiv 378497. Gene editing
S Choobdar, ME Ahsen, J Crawford, M Tomasoni, D Lamparter, J Lin, B Hescott, X Hu, J Mercer, T Natoli, R Narayan, The DREAM Module Identification Challenge Consortium, A Subramanian, G Stolovitzky, Z Kutalik, K Lage, DK Slonim, J Saez-Rodriguez, LJ Cowen, S Bergmann, D Marbach (2018). "Open community challenge reveals molecular network modules with key roles in diseases ", bioRxiv 265553. Misc
B Zhou, SS Ho, SU Greer, X Zhu, JM Bell, JG Arthur, N Spies, X Zhang, S Byeon, R Pattni, N Ben-Efraim, MS Haney, RR Haraksingh, HP Ji, G Song, D Perrin, WH Wong, A Abyzov, AE Urban (2018). "Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562 ", bioRxiv 192344. Gene editing
2017
LS Lo, J Galloway, B Ploderer, D Perrin (2017). "Armbeta: towards accessible wearable technology to quantify upper limb movement and activities ", Proceedings of the 29th Australian Conference on Computer-Human Interaction (OzCHI), pp. 356-360. Digital health
B Zhou, SS Ho, X Zhu, X Zhang, N Spies, S Byeon, JG Arthur, R Pattni, N Ben-Efraim, MS Haney, RR Haraksingh, G Song, D Perrin, WH Wong, A Abyzov, AE Urban (2017). "Comprehensive, Integrated, and Phased Whole-Genome Analysis of the Primary ENCODE Cell Line K562 ", bioRxiv 192344. Gene editing
T Chappell, S Geva, JM Hogan, F Huygens, W Kelly, D Perrin (2017). "Signature-based clustering for analysis of the wound microbiome ", Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 339-346. Misc
JB Stephansen, A Ambati, EB Leary, HE Moore, O Carrillo, L Lin, B Hogl, A Stefani, SC Hong, TW Kim, F Pizza, G Plazzi, S Vandi, E Antelmi, D Perrin, ST Kuna, PK Schweitzer, C Kushida, PE Peppard, P Jennum, HBD Sorensen, E Mignot (2017). "The use of neural networks in the analysis of sleep stages and the diagnosis of narcolepsy ", arXiv:1710.02094. Digital health
2016
F Tatsuki, GA Sunagawa, S Shi, EA Susaki, H Yukinaga, D Perrin, K Sumiyama, M Ukai-Tadenuma, H Fujishima, R Ohno, D Tone, KL Ode, K Matsumoto, HR Ueda (2016). "Involvement of Ca2+-dependent hyperpolarization in sleep duration in mammals ", Neuron 90(1):70-85. Gene editing Tissue clearing
GA Sunagawa, K Sumiyama, M Ukai-Tadenuma, D Perrin, H Fujishima, H Ukai, O Nishimura, S Shi, R Ohno, R Narumi, Y Shimizu, D Tone, KL Ode, S Kuraku, HR Ueda (2016). "Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene ", Cell Reports 14(3):662-677. Gene editing
2015
2014
K Tainaka, SI Kubota, TQ Suyama, EA Susaki, D Perrin, M Ukai-Tadenuma, H Ukai, HR Ueda (2014). "Whole-body imaging with single-cell resolution by tissue decolorization ", Cell 159(4):911-924. Tissue clearing
HJ Ruskin, D Perrin, IA Roznovat (2014). "Building cross-scale models of epigenetic mechanisms ", Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 30-37. Misc
CC Jolley, M Ukai-Tadenuma, D Perrin, HR Ueda (2014). "A mammalian circadian clock model incorporating daytime expression elements ", Biophysical Journal 107(6):1462-1473. Misc
EA Susaki, K Tainaka, D Perrin, F Kishino, T Tawara, TM Watanabe, C Yokoyama, H Onoe, M Eguchi, S Yamaguchi, T Abe, H Kiyonari, Y Shimizu, A Miyawaki, H Yokota, HR Ueda (2014). "Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis ", Cell 157(3):726-739.Tissue clearing
Earlier publications
For the complete list of publications from group leader Dimitri Perrin, please refer to
his Google Scholar profile .