UNCOVERING THE ROLE OF HIDDEN GENES IN BRAIN DISORDERS

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..

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

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

2020-06-29

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

RNA sequencing identifies a cryptic exon caused by a deep intronic variant in NDUFB10 resulting in isolated Complex I deficiency.

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

2020-05-26

The diagnosis of mitochondrial disorders remains a challenging and often unmet need. We sought to investigate a sibling pair with ..

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

2019-01-01

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 ..