Terence Speed

Remove unwanted variation retrieves unknown experimental designs

Ingrid M Lonnstedt, Terence P Speed

Journal article  |  2023  |  SCANDINAVIAN JOURNAL OF STATISTICS

Remove unwanted variation (RUV) is an estimation and normalization system in which the underlying correlation structure of a multi..

An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.

Burcu Gurun, Wesley Horton, Dhaarini Murugan, Biqing Zhu, Patrick Leyshock, Sushil Kumar, Katelyn T Byrne, Robert H Vonderheide, Adam A Margolin, Motomi Mori, Paul T Spellman, Lisa M Coussens, Terence P Speed

Journal article  |  2023  |  Res Sq

T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical chang..

Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7.

Andrew J Kueh, Maria I Bergamasco, Anna Quaglieri, Belinda Phipson, Connie SN Li-Wai-Suen, Ingrid M Lönnstedt, Yifang Hu, Zhi-Ping Feng, Chris Woodruff, Rose E May, Stephen Wilcox, Alexandra L Garnham, Michael P Snyder, Gordon K Smyth, Terence P Speed, Tim Thomas, Anne K Voss

Journal article  |  2023  |  Cell Rep

In the conventional model of transcriptional activation, transcription factors bind to response elements and recruit co-factors, i..

Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.

Shaolong Cao, Jennifer R Wang, Shuangxi Ji, Peng Yang, Yaoyi Dai, Shuai Guo, Matthew D Montierth, John Paul Shen, Xiao Zhao, Jingxiao Chen, Jaewon James Lee, Paola A Guerrero, Nicholas Spetsieris, Nikolai Engedal, Sinja Taavitsainen, Kaixian Yu, Julie Livingstone, Vinayak Bhandari, Shawna M Hubert, Najat C Daw, et al.

Journal article  |  2022  |  Nat Biotechnol

Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytic..

Removing unwanted variation from large-scale RNA sequencing data with PRPS

Ramyar Molania, Momeneh Foroutan, Johann A Gagnon-Bartsch, Luke C Gandolfo, Aryan Jain, Abhishek Sinha, Gavriel Olshansky, Alexander Dobrovic, Anthony T Papenfuss, Terence P Speed

Journal article  |  2022  |  NATURE BIOTECHNOLOGY

Accurate identification and effective removal of unwanted variation is essential to derive meaningful biological results from RNA ..

Runx3 drives a CD8( ) T cell tissue residency program that is absent in CD4( ) T cells

Raissa Fonseca, Thomas N Burn, Luke C Gandolfo, Sapna Devi, Simone L Park, Andreas Obers, Maximilien Evrard, Susan N Christo, Frank A Buquicchio, Caleb A Lareau, Keely M McDonald, Sarah K Sandford, Natasha M Zamudio, Nagela G Zanluqui, Ali Zaid, Terence P Speed, Ansuman T Satpathy, Scott N Mueller, Francis R Carbone, Laura K Mackay

Journal article  |  2022  |  NATURE IMMUNOLOGY

Tissue-resident memory T cells (TRM cells) provide rapid and superior control of localized infections. While the transcription fac..

RUV-III-NB: normalization of single cell RNA-seq data

Agus Salim, Ramyar Molania, Jianan Wang, Alysha De Livera, Rachel Thijssen, Terence P Speed

Journal article  |  2022  |  NUCLEIC ACIDS RESEARCH

Normalization of single cell RNA-seq data remains a challenging task. The performance of different methods can vary greatly betwee..

Spectral PCA for MANOVA and data over binary trees

Terence P Speed, Damien G Hicks

Journal article  |  2022  |  JOURNAL OF MULTIVARIATE ANALYSIS

We extend a concept of ANOVA broader than the traditional variance component models to MANOVA. Within this framework we can derive..

A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development

Andrew J Modzelewski, Wanqing Shao, Jingqi Chen, Angus Lee, Xin Qi, Mackenzie Noon, Kristy Tjokro, Gabriele Sales, Anne Biton, Aparna Anand, Terence P Speed, Zhenyu Xuan, Ting Wang, Davide Risso, Lin He

Journal article  |  2021  |  CELL

Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transie..

The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome

Momeneh Foroutan, Ramyar Molania, Aline Pfefferle, Corina Behrenbruch, Sebastian Scheer, Axel Kallies, Terence P Speed, Joseph Cursons, Nicholas D Huntington

Journal article  |  2021  |  CANCER IMMUNOLOGY RESEARCH

Immunotherapy success in colorectal cancer is mainly limited to patients whose tumors exhibit high microsatellite instability (MSI..