Genotype-free demultiplexing of pooled single-cell RNA-seq

Autor: Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett D. McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang, Nathan J. Palpant, Jian Yang, Michael D. Mueller, Alex W. Hewitt, Alice Pébay, Grant W. Montgomery, Joseph E. Powell, Lachlan J.M Coin

Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-12 (2019)

Abstract A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes gen

Externí odkaz: https://doaj.org/article/1b71a24d668b46c094a1546909858b98

Development of Matrix-Embedded Bovine Tracheal Organoids to Study the Innate Immune Response against Bovine Respiratory Disease

Autor: Pin Shie Quah, Bang M. Tran, Vincent D.A. Corbin, Jessie J.-Y. Chang, Chinn Yi Wong, Andrés Diaz-Méndez, Carol A. Hartley, Weiguang Zeng, Eric Hanssen, Zlatan Trifunovic, Patrick C. Reading, David C. Jackson, Elizabeth Vincan, Lachlan J.M. Coin, Georgia Deliyannis

Publikováno v: Organoids, Vol 2, Iss 2, Pp 82-101 (2023)

Bovine respiratory disease (BRD) is the leading cause of morbidity and mortality in feedlot cattle. Bovine herpesvirus-1 (BHV-1) is one of the main culprits of BRD; however, research on BHV-1 is hampered by the lack of suitable models for infection a

Externí odkaz: https://doaj.org/article/ed4322c03eea4e6aaacc8409cdb74018

Long-read RNA sequencing identifies polyadenylation elongation and differential transcript usage of host transcripts during SARS-CoV-2 in vitro infection

Autor: Jessie J.-Y. Chang, Josie Gleeson, Daniel Rawlinson, Miranda E. Pitt, Ricardo De Paoli-Iseppi, Chenxi Zhou, Francesca L. Mordant, Sarah L. Londrigan, Michael B. Clark, Kanta Subbarao, Timothy P. Stinear, Lachlan J.M. Coin

Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections are imperative to help understand and prevent this disease. Here we implemented RNA-sequencing (RNA-seq) using Oxf

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::52a2187eeb04737e84812a33f9cd8609
https://doi.org/10.1101/2021.12.14.472725

Genetic architecture of early childhood growth phenotypes gives insights into their link with later obesity

Autor: N. Maneka G. De Silva, Sylvain Sebert, Alexessander Couto Alves, Ulla Sovio, Shikta Das, Rob Taal, Nicole M. Warrington, Alexandra M. Lewin, Marika Kaakinen, Diana Cousminer, Elisabeth Thiering, Nicholas J. Timpson, Ville Karhunen, Tom Bond, Xavier Estivill, Virpi Lindi, Jonathan P. Bradfield, Frank Geller, Lachlan J.M. Coin, Marie Loh, Sheila J. Barton, Lawrence J. Beilin, Hans Bisgaard, Klaus Bønnelykke, Rohia Alili, Ida J. Hatoum, Katharina Schramm, Rufus Cartwright, Marie-Aline Charles, Vincenzo Salerno, Karine Clément, Cornelia M. van Duijn, Elena Moltchanova, Johan G. Eriksson, Cathy Elks, Bjarke Feenstra, Claudia Flexeder, Stephen Franks, Timothy M. Frayling, Rachel M. Freathy, Paul Elliott, Elisabeth Widén, Hakon Hakonarson, Andrew T. Hattersley, Alina Rodriguez, Marco Banterle, Joachim Heinrich, Barbara Heude, John W. Holloway, Albert Hofman, Elina Hyppönen, Hazel Inskip, Lee M. Kaplan, Asa K. Hedman, Esa Läärä, Holger Prokisch, Harald Grallert, Timo A. Lakka, Debbie A. Lawlor, Mads Melbye, Tarunveer S. Ahluwalia, Marcella Marinelli, Iona Y. Millwood, Lyle J. Palmer, Craig E. Pennell, John R. Perry, Susan M. Ring, Markku Savolainen, Kari Stefansson, Gudmar Thorleifsson, Fernando Rivadeneira, Marie Standl, Jordi Sunyer, Carla M.T. Tiesler, Andre G. Uitterlinden, Inga Prokopenko, Karl-Heinz Herzig, George Davey Smith, Paul O'Reilly, Janine F. Felix, Jessica L. Buxton, Alexandra I.F. Blakemore, Ken K. Ong, Struan F.A. Grant, Vincent W.V. Jaddoe, Mark I. McCarthy, Marjo-Riitta Järvelin

Publikováno v: bioRxiv
bioRxiv The Preprint Server for Biology.

Early childhood growth patterns are associated with adult metabolic health, but the underlying mechanisms are unclear. We performed genome-wide meta-analyses and follow-up in up to 22,769 European children for six early growth phenotypes derived from

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b364b3d95ff7602ee9e18bad1640ac56

Computational analysis and prediction of PE_PGRS proteins using machine learning

Autor: Fuyi Li, Xudong Guo, Dongxu Xiang, Miranda E. Pitt, Arnold Bainomugisa, Lachlan J.M. Coin

Publikováno v: Computational and Structural Biotechnology Journal, Vol 20, Iss , Pp 662-674 (2022)

Mycobacterium tuberculosis genome comprises approximately 10% of two families of poorly characterised genes due to their high GC content and highly repetitive nature. The largest sub-group, the proline-glutamic acid polymorphic guanine-cytosine-rich

Externí odkaz: https://doaj.org/article/166b298210084cd5b21ddd6540563a95