Mike Clark

NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing

Yupei You, Michael B Clark, Heejung Shim

Journal article  |  2022  |  BIOINFORMATICS

MOTIVATION: Long-read sequencing methods have considerable advantages for characterizing RNA isoforms. Oxford Nanopore sequencing ..

Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection

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

Journal article  |  2022  |  FRONTIERS IN IMMUNOLOGY

Better methods to interrogate host-pathogen interactions during Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infec..

Using long-read RNA sequencing to decipher the role of RNA isoforms in disease

Ricardo De Paoli-Iseppi, Shweta Joshi, Tomasz Wrzesinski, Paul J Harrison, Wilfried Haerty, Elizabeth M Tunbridge, Michael B Clark

Journal article  |  2022  |  Pathology

Accurate quantification of genes and their mRNA products is essential to understanding health and disease. In humans, processes su..

Accurate expression quantification from nanopore direct RNA sequencing with NanoCount

Josie Gleeson, Adrien Leger, Yair DJ Prawer, Tracy A Lane, Paul J Harrison, Wilfried Haerty, Michael B Clark

Journal article  |  2021  |  NUCLEIC ACIDS RESEARCH

Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disea..

Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Luyi Tian, Jafar S Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, Mei RM Du, Jakob Schuster, Changqing Wang, Shian Su, Xueyi Dong, Charity W Law, Alexis Lucattini, Yair David Joseph Prawer, Coralina Collar-Fernandez, Jin D Chung, Timur Naim, Audrey Chan, Chi Hai Ly, et al.

Journal article  |  2021  |  GENOME BIOLOGY

A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing toget..

Isoform Age-Splice Isoform Profiling Using Long-Read Technologies (vol 8, 744, 2021)

Ricardo De Paoli-Iseppi, Josie Gleeson, Michael B Clark

Journal article  |  2021  |  FRONTIERS IN MOLECULAR BIOSCIENCES

[This corrects the article DOI: 10.3389/fmolb.2021.711733.].

Isoform Age - Splice Isoform Profiling Using Long-Read Technologies

Ricardo De Paoli-Iseppi, Josie Gleeson, Michael B Clark

Journal article  |  2021  |  Frontiers in Molecular Biosciences

Alternative splicing (AS) of RNA is a key mechanism that results in the expression of multiple transcript isoforms from single gen..

Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories

Alexandra Pokhilko, Adam E Handel, Fabiola Curion, Viola Volpato, Emma S Whiteley, Sunniva Bostrand, Sarah E Newey, Colin J Akerman, Caleb Webber, Michael B Clark, Rory Bowden, M Zameel Cader

Journal article  |  2021  |  GENOME RESEARCH

Single-cell RNA sequencing (scRNA-seq) is a widely used method for identifying cell types and trajectories in biologically heterog..

The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools

Xueyi Dong, Luyi Tian, Quentin Gouil, Hasaru Kariyawasam, Shian Su, Ricardo De Paoli-Iseppi, Yair David Joseph Prawer, Michael B Clark, Kelsey Breslin, Megan Iminitoff, Marnie E Blewitt, Charity W Law, Matthew E Ritchie

Journal article  |  2021  |  NAR Genomics and Bioinformatics

Application of Oxford Nanopore Technologies' long-read sequencing platform to transcriptomic analysis is increasing in popularity...

Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

Jessie J-Y Chang, Daniel Rawlinson, Miranda E Pitt, George Taiaroa, Josie Gleeson, Chenxi Zhou, Francesca L Mordant, Ricardo De Paoli-Iseppi, Leon Caly, Damian FJ Purcell, Timothy P Stinear, Sarah L Londrigan, Michael B Clark, Deborah A Williamson, Kanta Subbarao, Lachlan JM Coin

Journal article  |  2021  |  CELL REPORTS

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication..