UNCOVERING THE ROLE OF HIDDEN GENES IN BRAIN DISORDERS

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

2021-11-25

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

2021-11-11

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

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

2021-06-01

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

2021-06-01

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

2021-05-11

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

CARMN Loss Regulates Smooth Muscle Cells and Accelerates Atherosclerosis in Mice

Francesca Vacante, Julie Rodor, Mukesh K Lalwani, Amira D Mahmoud, Matthew Bennett, Azzurra L De Pace, Eileen Miller, Kim Van Kuijk, Jenny de Bruijn, Marion Gijbels, Thomas C Williams, Michael B Clark, Jessica P Scanlon, Amanda C Doran, Rusty Montgomery, David E Newby, Mauro Giacca, Donal O'Carroll, Patrick WF Hadoke, Laura Denby

2021-04-30

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Multiomic analysis elucidates Complex I deficiency caused by a deep intronic variant in NDUFB10

Guy Helman, Alison G Compton, Daniella H Hock, Marzena Walkiewicz, Gemma R Brett, Lynn Pais, Tiong Y Tan, Ricardo De Paoli-Iseppi, Michael B Clark, John Christodoulou, Susan M White, David R Thorburn, David A Stroud, Zornitza Stark, Cas Simons

2020-11-11

The diagnosis of Mendelian disorders following uninformative exome and genome sequencing remains a challenging and often unmet nee..

Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples

Fabiola Curion, Adam E Handel, Moustafa Attar, Giuseppe Gallone, Rory Bowden, M Zameel Cader, Michael B Clark

2020-06-29

RNA-seq is the standard method for profiling gene expression in many biological systems. Due to the wide dynamic range and complex..

Exploiting the Variability of CACNA1C Splicing to Identify Novel, Brain-Selective Targets for Schizophrenia and Bipolar Disorder

Nicola Hall, Michael B Clark, Tomasz Wrzesinski, Aintzane B Garcia, Syed M Husain, Joel E Kleinman, Thomas Hyde, Daniel R Weinberger, Paul J Harrison, Wilfried Haerty, Elizabeth M Tunbridge

2020-05-01

Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

Michael B Clark, Tomasz Wrzesinski, Aintzane B Garcia, Nicola AL Hall, Joel E Kleinman, Thomas Hyde, Daniel R Weinberger, Paul J Harrison, Wilfried Haerty, Elizabeth M Tunbridge

2020-01-01

RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse i..

Universal Alternative Splicing of Noncoding Exons

Ira W Deveson, Marion E Brunck, James Blackburn, Elizabeth Tseng, Ting Hon, Tyson A Clark, Michael B Clark, Joanna Crawford, Marcel E Dinger, Lars K Nielsen, John S Mattick, Tim R Mercer

2018-02-28

The human transcriptome is so large, diverse, and dynamic that, even after a decade of investigation by RNA sequencing (RNA-seq), ..

Intergenic disease-associated regions are abundant in novel transcripts

N Bartonicek, MB Clark, XC Quek, JR Torpy, AL Pritchard, JLV Maag, BS Gloss, J Crawford, RJ Taft, NK Hayward, GW Montgomery, JS Mattick, TR Mercer, ME Dinger

2017-12-28

BACKGROUND: Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomi..

Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage

Joshua A Betts, Mahdi Moradi Marjaneh, Fares Al-Ejeh, Yi Chieh Lim, Wei Shi, Haran Sivakumaran, Romain Tropee, Ann-Marie Patch, Michael B Clark, Nenad Bartonicek, Adrian P Wiegmans, Kristine M Hillman, Susanne Kaufmann, Amanda L Bain, Brian S Gloss, Joanna Crawford, Stephen Kazakoff, Shivangi Wani, Shu W Wen, Bryan Day

2017-08-03

Breast cancer risk is strongly associated with an intergenic region on 11q13. We have previously shown that the strongest risk-ass..

Improved definition of the mouse transcriptome via targeted RNA sequencing

Giovanni Bussotti, Tommaso Leonardi, Michael B Clark, Tim R Mercer, Joanna Crawford, Lorenzo Malquori, Cedric Notredame, Marcel E Dinger, John S Mattick, Anton J Enright

2016-05-01

Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage,..

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Michael B Clark, Tim R Mercer, Giovanni Bussotti, Tommaso Leonardi, Katelin R Haynes, Joanna Crawford, Marion E Brunck, Kim-Anh Le Cao, Gethin P Thomas, Wendy Y Chen, Ryan J Taft, Lars K Nielsen, Anton J Enright, John S Mattick, Marcel E Dinger

2015-04-01

We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and q..

Genome-wide discovery of human splicing branchpoints

Tim R Mercer, Michael B Clark, Stacey B Andersen, Marion E Brunck, Wilfried Haerty, Joanna Crawford, Ryan J Taft, Lars K Nielsen, Marcel E Dinger, John S Mattick

2015-02-01

During the splicing reaction, the 5' intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate in..

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

Xiu Cheng Quek, Daniel W Thomson, Jesper LV Maag, Nenad Bartonicek, Bethany Signal, Michael B Clark, Brian S Gloss, Marcel E Dinger

2015-01-28

Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for ..