Terence Speed

Serum microRNA is a biomarker for post-operative monitoring in glioma

Andrew Morokoff, Jordan Jones, Hong Nguyen, Chenkai Ma, Arian Lasocki, Frank Gaillard, Iwan Bennett, Rod Luwor, Stanley Stylli, Lucia Paradiso, Rachel Koldej, Iddo Paldor, Ramyar Molania, Terence P Speed, Andrew Webb, Guiseppe Infusini, Jason Li, Charles Malpas, Tomas Kalincik, Katharine Drummond, et al.

Journal article  |  2020  |  JOURNAL OF NEURO-ONCOLOGY

PURPOSE: A circulating biomarker has potential to provide more accurate information for glioma progression post treatment, however..

Changes in ferrous iron and glutathione promote ferroptosis and frailty in aging Caenorhabditis elegans

Nicole L Jenkins, Simon A James, Agus Salim, Fransisca Sumardy, Terence P Speed, Marcus Conrad, Des R Richardson, Ashley Bush, Gawain McColl

Journal article  |  2020  |  ELIFE

All eukaryotes require iron. Replication, detoxification, and a cancer-protective form of regulated cell death termed ferroptosis,..

Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells

Melissa M Gresle, Margaret A Jordan, Jim Stankovich, Tim Spelman, Laura J Johnson, Louise Laverick, Alison Hamlett, Letitia D Smith, Vilija G Jokubaitis, Josephine Baker, Jodi Haartsen, Bruce Taylor, Jac Charlesworth, Melanie Bahlo, Terence P Speed, Matthew A Brown, Judith Field, Alan G Baxter, Helmut Butzkueven

Journal article  |  2020  |  LIFE SCIENCE ALLIANCE

At least 200 single-nucleotide polymorphisms (SNPs) are associated with multiple sclerosis (MS) risk. A key function that could me..

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, Terence P Speed, David M Lin, Pengyi Yang, Jean Yee Hwa Yang

Journal article  |  2020  |  MOLECULAR SYSTEMS BIOLOGY

Automated cell type identification is a key computational challenge in single-cell RNA-sequencing (scRNA-seq) data. To capitalise ..

DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data

Chengzhong Ye, Terence P Speed, Agus Salim

Journal article  |  2019  |  BIOINFORMATICS

MOTIVATION: Dropout is a common phenomenon in single-cell RNA-seq (scRNA-seq) data, and when left unaddressed it affects the valid..

Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network

Sue Haupt, Franco Caramia, Alan Herschtal, Thierry Soussi, Guillermina Lozano, Hu Chen, Han Liang, Terence P Speed, Ygal Haupt

Journal article  |  2019  |  NATURE COMMUNICATIONS

The disproportionately high prevalence of male cancer is poorly understood. We tested for sex-disparity in the functional integrit..

A new normalization for Nanostring nCounter gene expression data

Ramyar Molania, Johann A Gagnon-Bartsch, Alexander Dobrovic, Terence P Speed

Journal article  |  2019  |  NUCLEIC ACIDS RESEARCH

The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of ..

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

Yingxin Lin, Shila Ghazanfar, Kevin YX Wang, Johann A Gagnon-Bartsch, Kitty K Lo, Xianbin Su, Ze-Guang Han, John T Ormerod, Terence P Speed, Pengyi Yang, Jean Yee Hwa Yang

Journal article  |  2019  |  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights th..

Using long-read sequencing to detect imprinted DNA methylation

Scott Gigante, Quentin Gouil, Alexis Lucattini, Andrew Keniry, Tamara Beck, Matthew Tinning, Lavinia Gordon, Chris Woodruff, Terence P Speed, Marnie E Blewitt, Matthew E Ritchie

Journal article  |  2019  |  NUCLEIC ACIDS RESEARCH

Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other m..

Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements

Timothy J Peters, Hugh J French, Stephen T Bradford, Ruth Pidsley, Clare Stirzaker, Hilal Varinli, Shalima Nair, Wenjia Qu, Jenny Song, Katherine A Giles, Aaron L Statham, Helen Speirs, Terence P Speed, Susan J Clark

Journal article  |  2019  |  BIOINFORMATICS

MOTIVATION: A synoptic view of the human genome benefits chiefly from the application of nucleic acid sequencing and microarray te..