Selected Publications | Donnelly Centre for Cellular and Biomolecular Research

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class="paragraph--published"> <div class="m-image"> <div class="m-image-wrap width--100"> <picture> <source srcset="/sites/default/files/styles/landscape_4_3_400/public/cimms.webp?itok=w3NbLCGe 400w, /sites/default/files/styles/landscape_4_3_600/public/cimms.webp?itok=abLLJzHE 600w, /sites/default/files/styles/landscape_4_3_900/public/cimms.webp?itok=Vl3Uwmiz 900w, /sites/default/files/styles/landscape_4_3_1200/public/cimms.webp?itok=8tVSAHnf 1200w, /sites/default/files/styles/landscape_4_3_1500/public/cimms.webp?itok=EKuvCe9X 1500w, /sites/default/files/styles/landscape_4_3_1800/public/cimms.webp?itok=i6czF9t9 1800w" type="image/webp" sizes="(min-width:1280px) 820px, (min-width:900px) 70vw, 100vw - 48px" width="900" height="675"/> <source srcset="/sites/default/files/styles/landscape_4_3_400/public/cimms.jpg?itok=w3NbLCGe 400w, /sites/default/files/styles/landscape_4_3_600/public/cimms.jpg?itok=abLLJzHE 600w, /sites/default/files/styles/landscape_4_3_900/public/cimms.jpg?itok=Vl3Uwmiz 900w, /sites/default/files/styles/landscape_4_3_1200/public/cimms.jpg?itok=8tVSAHnf 1200w, /sites/default/files/styles/landscape_4_3_1500/public/cimms.jpg?itok=EKuvCe9X 1500w, /sites/default/files/styles/landscape_4_3_1800/public/cimms.jpg?itok=i6czF9t9 1800w" type="image/jpeg" sizes="(min-width:1280px) 820px, (min-width:900px) 70vw, 100vw - 48px" width="900" height="675"/> <img width="900" height="675" srcset="/sites/default/files/styles/landscape_4_3_400/public/cimms.jpg?itok=w3NbLCGe 400w, /sites/default/files/styles/landscape_4_3_600/public/cimms.jpg?itok=abLLJzHE 600w, /sites/default/files/styles/landscape_4_3_900/public/cimms.jpg?itok=Vl3Uwmiz 900w, /sites/default/files/styles/landscape_4_3_1200/public/cimms.jpg?itok=8tVSAHnf 1200w, /sites/default/files/styles/landscape_4_3_1500/public/cimms.jpg?itok=EKuvCe9X 1500w, /sites/default/files/styles/landscape_4_3_1800/public/cimms.jpg?itok=i6czF9t9 1800w" sizes="(min-width:1280px) 820px, (min-width:900px) 70vw, 100vw - 48px" src="/sites/default/files/styles/landscape_4_3_1800/public/cimms.jpg?itok=i6czF9t9" alt="Cell invasion in digital microfluidic microgel systems Figure 1" loading="lazy" typeof="foaf:Image" /> </picture> </div> </div> </div> <div class="paragraph--published"> <div class="m-text"> <div class="m-text__content s-wysiwyg"> <div class="s-wysiwyg"><h2>Latest feature: Cell invasion in digital microfluidic microgel systems</h2> In <a href="http://advances.sciencemag.org/content/6/29/eaba9589">this study</a>, researchers used digital microfluidics to develop a novel in vivo-like microgel system for studying cell invasions. This system allows both imaging of extracellular matrix remodeling (an important aspect of metastasis) as well as collection of invading cell subpopulations for RNA-Seq, synthesizing the strengths of the two main existing tools for in vitro studies of cell invasion. The study was conducted in the lab of <a href="http://microfluidics.utoronto.ca/">Aaron Wheeler</a>, based here at U of T in the Donnelly Centre. To establish the performance of this assay for yielding RNA-Seq data, and to compare expression between invading and noninvading cells, libraries were run on the NextSeq500 at the Donnelly Sequencing Centre. <h2>Please make sure to <a href="mailto:dseqcentre@utoronto.ca">shoot us an email</a> when your DSC collaboration is published - we'd like to feature it!</h2> <h3 class="a-heading__h3">2022</h3> Barutcu, A. R., Wu, M., Braunschweig, U., Dyakov, B. J., Luo, Z., Turner, K. M., ... & Blencowe, B. J. (2022). Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns. Molecular Cell, 82(5), 1035-1052. [<a href="https://pubmed.ncbi.nlm.nih.gov/35182477/">Pubmed</a>] Biancolin, A. D., Jeong, H., Mak, K. W., Yuan, Z., & Brubaker, P. L. (2022). Disrupted and elevated circadian secretion of glucagon-like peptide-1 in a murine model of type 2 diabetes. Endocrinology, 163(9); [<a href="https://pubmed.ncbi.nlm.nih.gov/35876276/">Pubmed</a>] Erwood, S., Bily, T. M., Lequyer, J., Yan, J., Gulati, N., Brewer, R. A., ... & Cohn, R. D. (2022). Saturation variant interpretation using CRISPR prime editing. Nature Biotechnology, 1-11; [<a href="https://pubmed.ncbi.nlm.nih.gov/35190686/">Pubmed</a>] Han, H., Mikolajewicz, N., Brown, K., & Moffat, J. (2022). Multi-level cellular and functional annotation of single-cell transcriptomes.[<a href="https://www.biorxiv.org/content/10.1101/2022.03.13.484162v1">Article</a>] Kim, B., Sasaki, A., Murphy, K., & Matthews, S. G. (2022). DNA methylation signatures in human neonatal blood following maternal antenatal corticosteroid treatment. Translational Psychiatry, 12(1), 1-8.[<a href="https://pubmed.ncbi.nlm.nih.gov/35354798/">Pubmed</a>] Kim, S. H., Steere, L., Zhang, Y. K., McGregor, C., Hahne, C., Zhou, Y., ... & Cowen, L. E. (2022). Inhibiting C-4 Methyl Sterol Oxidase with Novel Diazaborines to Target Fungal Plant Pathogens. ACS Chemical Biology, 17(6),1343–1350, [<a href="https://pubmed.ncbi.nlm.nih.gov/35584803/">Pubmed</a>] Li, B. B., Scott, E. Y., Olafsen, N. E., Matthews, J., & Wheeler, A. R. (2022). Analysis of the effects of aryl hydrocarbon receptor expression on cancer cell invasion via three-dimensional microfluidic invasion assays. Lab on a Chip, 22(2), 313-325. [<a href="https://pubmed.ncbi.nlm.nih.gov/34904612/">Pubmed</a>] Martchenko, A., Biancolin, A. D., Martchenko, S. E., & Brubaker, P. L. (2022). Nobiletin ameliorates high fat-induced disruptions in rhythmic glucagon-like peptide-1 secretion. Scientific reports, 12(1), 1-14.[<a href="https://pubmed.ncbi.nlm.nih.gov/35508494/">Pubmed</a>] Peterson, J., McTiernan, C. D., Thome, C., Khaper, N., Lees, S. J., Boreham, D. R., ... & Tharmalingam, S. (2022). Identification of Radiation-Induced miRNA Biomarkers Using the CGL1 Cell Model System. Bioengineering, 9(5), 214. [<a href="https://pubmed.ncbi.nlm.nih.gov/35621492/">Pubmed</a>] Singh, S., Chokshi, C., Tieu, D., Brown, K., Venugopal, C., Rossotti, M., ... & Moffat, J. (2022). Functional discovery of targetable dependencies in recurrent glioblastoma.[<a href="https://assets.researchsquare.com/files/rs-1871890/v1/fc69b8de-284b-4f52-bf03-286e198179da.pdf?c=1666184262">Preprint</a>] Song, J., Nabeel-Shah, S., Pu, S., Lee, H., Braunschweig, U., Ni, Z., ... & Greenblatt, J. F. (2022). Regulation of alternative polyadenylation by the C2H2-zinc-finger protein Sp1. Molecular Cell, 82(17), 3135-3150. [<a href="https://pubmed.ncbi.nlm.nih.gov/35914531/">Pubmed</a>] Khobzey, M. (2022). Exploring different approaches for constructing temperature sensitive alleles of yeast essential genes (Doctoral dissertation, University of Toronto (Canada)). [<a href="https://www.proquest.com/docview/2643991783/CDD9ACB021044EF9PQ/1?accountid=14771">Proquest</a>] Ng, K. (2022). Mapping of the Novel mRNA Acetylation, ac4C, in the HEK293 Transcriptome (Doctoral dissertation, University of Toronto (Canada)). [<a href="https://www.proquest.com/docview/2642353852?pq-origsite=gscholar&fromopenview=true">Proquest</a>] <h3 class="a-heading__h3">2021</h3> Kelil, A., Gallo, E., Banerjee, S., Adams, J. J., & Sidhu, S. S. (2021). CellectSeq: In silico discovery of antibodies targeting integral membrane proteins combining in situ selections and next-generation sequencing. Communications biology, 4(1), 1-13. [<a href="https://pubmed.ncbi.nlm.nih.gov/33980972/">Pubmed</a>] Ma, Y., Chen, K., Xia, F., Atwal, R., Wang, H., Ahmed, S. U., ... & Kelley, S. O. (2021). Phage-Based Profiling of Rare Single Cells Using Nanoparticle-Directed Capture. ACS nano, 15(12), 19202-19210. [<a href="https://pubmed.ncbi.nlm.nih.gov/34813293/">Pubmed</a>] Maino, E., Wojtal, D., Evagelou, S. L., Farheen, A., Wong, T. W., Lindsay, K., ... & Cohn, R. D. (2021). Targeted genome editing in vivo corrects a Dmd duplication restoring wild‐type dystrophin expression. EMBO molecular medicine, 13(5), e13228.[<a href="https://pubmed.ncbi.nlm.nih.gov/33724658/">Pubmed</a>] Nabeel-Shah, S., Lee, H., Ahmed, N., Burke, G., Farhangmehr, S., Ashraf, K., ... & Greenblatt, J. (2021). SARS-CoV-2 nucleocapsid protein attenuates stress granules and interacts with mRNAs to impair host stress response. Iscience, 25(1):103562. [<a href="https://pubmed.ncbi.nlm.nih.gov/34901782/">Pubmed</a>] Pačnik, K., Ogrizović, M., Diepold, M., Eisenberg, T., Žganjar, M., Žun, G., ... & Natter, K. (2021). Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae. BMC genomics, 22(1), 1-15. [<a href="https://pubmed.ncbi.nlm.nih.gov/33563210/">Pubmed</a>] Stokes, K., Nunes, M., Trombley, C., Flôres, D. E., Wu, G., Taleb, Z., ... & Karpowicz, P. (2021). 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Selected Publications | Donnelly Centre for Cellular and Biomolecular Research