Matthew E Ritchie (Matthew Ritchie)

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 47

Top Venues

Nature methods

NAR genomics and bioinformatics

Nature communications

F1000Research

Walter and Eliza Hall Institute of Medical Research

University of Melbourne (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Walter and Eliza Hall Institute of Medical Research Jan 01 2013

Australia

Laboratory Head :: Molecular Medicine

Education History

University of Melbourne - May 04 2005

Australia

PHD :: Medical Biology

Publications

Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Yue You, Yuting Fu, Lanxiang Li, Zhongmin Zhang, Shikai Jia, Shihong Lu, Wenle Ren, Yifang Liu, Yang Xu, Xiaojing Liu, Fuqing Jiang, Guangdun Peng, Abhishek Sampath Kumar, Matthew E Ritchie, Xiaodong Liu, Lu-Yi Tian
Systematic comparison of sequencing-based spatial transcriptomic methods. Nature methods (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Yue You, Yuting Fu, Lanxiang Li, Zhongmin Zhang, Shikai Jia, Shihong Lu, Wenle Ren, Yifang Liu, Yang Xu, Xiaojing Liu, Fuqing Jiang, Guangdun Peng, Abhishek Sampath Kumar, Matthew E Ritchie, Xiaodong Liu, Lu-Yi Tian
Systematic comparison of sequencing-based spatial transcriptomic methods. Nature methods (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Sena A Gocuk, James Lancaster, Shian Su, Jasleen Kaur Jolly, Thomas L Edwards, Doron G Hickey, Matthew E Ritchie, Marnie E Blewitt, Lauren N Ayton, Quentin A Gouil
Measuring X inactivation skew for X-linked diseases with adaptive nanopore sequencing. Genome research (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Lim Chee Liew, Yue You, Lucas Auroux, Marina Oliva, Marta Peirats-Llobet, Sophia Ng, Muluneh Tamiru-Oli, Oliver Berkowitz, Uyen Vu Thuy Hong, Asha Haslem, Tim Stuart, Matthew E Ritchie, George W Bassel, Ryan Lister, James Whelan, Quentin A Gouil, Mathew G Lewsey
Establishment of single-cell transcriptional states during seed germination. Nature plants (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods (2024)
Jakob Schuster, Matthew E Ritchie, Quentin A Gouil
Restrander: rapid orientation and artefact removal for long-read cDNA data. NAR genomics and bioinformatics 5 (4) (2023)
Nusrat Nahar, Greg Tram, Freda E-C Jen, Zachary N Phillips, Lucy A Weinert, Janine T Bossé, Jafar S Jabbari, Quentin A Gouil, Mei R M Du, Matthew E Ritchie, Rory Bowden, Paul R Langford, Alexander W Tucker, Michael P Jennings, Conny Turni, Patrick J Blackall, John M Atack
Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions. Nucleic acids research (2023)
Xueyi Dong, Mei R M Du, Quentin A Gouil, Luyi Tian, Jafar S Jabbari, Rory Bowden, Pedro L Baldoni, Yunshun Chen, Aaron T L Lun, Shanika L Amarasinghe, Charity W Law, Matthew E Ritchie
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Nature methods (2023)
Jakob Schuster, Matthew E Ritchie, Quentin A Gouil
Restrander: rapid orientation and artefact removal for long-read cDNA data. NAR genomics and bioinformatics 5 (4) (2023)
Shanika L Amarasinghe, Phil Yang, Oliver Voogd, Haoyu Yang, Mei R M Du, Shian Su, Daniel V Brown, Jafar S Jabbari, Rory Bowden, Matthew E Ritchie
scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor. NAR genomics and bioinformatics 5 (4) (2023)
Pedro L Baldoni, Yunshun Chen, Soroor Hediyeh-Zadeh, Yang Liao, Xueyi Dong, Matthew E Ritchie, Wei Shi, Aaron T L Lun
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR. Nucleic acids research (2023)
Jakob Schuster, Matthew E Ritchie, Quentin A Gouil
Restrander: rapid orientation and artefact removal for long-read cDNA data. NAR genomics and bioinformatics 5 (4) (2023)
Andres Tapia Del Fierro, Bianca den Hamer, Natalia Benetti, Natasha Jansz, Kelan Chen, Tamara Beck, Hannah Vanyai, Alexandra D Gurzau, Lucia Daxinger, Shifeng Xue, Thanh Thao Nguyen Ly, Iromi Wanigasuriya, Megan Iminitoff, Kelsey A Breslin, Harald Oey, Yvonne D Krom, Dinja van der Hoorn, Linde F Bouwman, Timothy M Johanson, Matthew E Ritchie, Quentin A Gouil, Bruno Reversade, Fabrice Prin, Timothy Mohun, Silvère M van der Maarel, Edwina McGlinn, James G Murphy, Andrew Keniry, Jessica C de Greef, Marnie E Blewitt
SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nature communications 14 (1) (2023)
Nusrat Nahar, Greg Tram, Freda E-C Jen, Zachary N Phillips, Lucy A Weinert, Janine T Bossé, Jafar S Jabbari, Quentin A Gouil, Mei R M Du, Matthew E Ritchie, Rory Bowden, Paul R Langford, Alexander W Tucker, Michael P Jennings, Conny Turni, Patrick J Blackall, John M Atack
Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions. Nucleic acids research (2023)
Iromi Wanigasuriya, Sarah A Kinkel, Tamara Beck, Ellise A Roper, Kelsey A Breslin, Heather J Lee, Andrew Keniry, Matthew E Ritchie, Marnie E Blewitt, Quentin A Gouil
Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation. Epigenetics & chromatin 15 (1) (2022)
Isabella Y Kong, Stephanie Trezise, Amanda Light, Izabela Todorovski, Gisela Mir Arnau, Sreeja Gadipally, David Yoannidis, Kaylene J Simpson, Xueyi Dong, Lachlan Whitehead, Jessica C Tempany, Anthony J Farchione, Amania A Sheikh, Joanna R Groom, Kelly L Rogers, Marco J Herold, Vanessa L Bryant, Matthew E Ritchie, Simon N Willis, Ricky W Johnstone, Philip D Hodgkin, Stephen L Nutt, Stephin J Vervoort, Edwin D Hawkins
Epigenetic modulators of B cell fate identified through coupled phenotype-transcriptome analysis. Cell death and differentiation (2022)
Andrew Keniry, Natasha Jansz, Linden J Gearing, Iromi Wanigasuriya, Joseph Chen, Christian Maximilian Nefzger, Peter F Hickey, Quentin A Gouil, Joy Liu, Kelsey A Breslin, Megan Iminitoff, Tamara Beck, Andres Tapia Del Fierro, Lachlan W Whitehead, Andrew Jarratt, Sarah A Kinkel, Phillippa C Taberlay, Tracy Willson, Miha Pakusch, Matthew E Ritchie, Douglas J Hilton, Mohammad Mahfuz Chowdhury, Marnie E Blewitt
BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation. Nature communications 13 (1) (2022)
Rachel Thijssen, Luyi Tian, Mary Ann Anderson, Christoffer Flensburg, Andrew Jarratt, Alexandra L Garnham, Jafar S Jabbari, Hongke Peng, Thomas E Lew, Charis E Teh, Quentin A Gouil, Angela Georgiou, Tania Tan, Tirta M Djajawi, Constantine S Tam, John Francis Seymour, Piers Blombery, Daniel H D Gray, Ian J Majewski, Matthew E Ritchie, Andrew W Roberts, David Ching Siang Huang
Single-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapy. Blood 140 (20) (2022)
Charis E Teh, Hongke Peng, Meng-Xiao Luo, Tania Tan, Marie Trussart, Lauren J Howson, Chong Chyn Chua, Christine Muttiah, Fiona C Brown, Matthew E Ritchie, Andrew H Wei, Andrew W Roberts, Vanessa L Bryant, Mary Ann Anderson, Geoffrey J Lindeman, David Ching Siang Huang, Rachel Thijssen, Daniel H D Gray
Venetoclax treatment in cancer patients has limited impact on circulating T and NK cells. Blood advances (2022)
Hema Preethi Subas Satish, Kathleen Zeglinski, Rachel T Uren, Stephen L Nutt, Matthew E Ritchie, Quentin A Gouil, Ruth M Kluck
NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells. mAbs 14 (1) (2022)
Hui Jing Lim, Jacinta M Wubben, Cristian Pinero Garcia, Sebastian Cruz-Gomez, Jieru Deng, Jeffrey Y W Mak, Abderrahman Hachani, Regan J Anderson, Gavin A Painter, Jesse Goyette, Shanika L Amarasinghe, Matthew E Ritchie, Antoine Roquilly, David P Fairlie, Katharina Gaus, Jamie Rossjohn, Jose A Villadangos, Hamish E G McWilliam
A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells. The Journal of cell biology 221 (12) (2022)
Xueyi Dong, Luyi Tian, Quentin A 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
The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools. NAR genomics and bioinformatics 3 (2) (2021)
Casey Ah-Cann, Verena C Wimmer, Clare E Weeden, Claire Marceaux, Charity W Law, Laura A Galvis, Caitlin E Filby, Joy Liu, Kelsey Breslin, Tracy Willson, Matthew E Ritchie, Marnie E Blewitt, Marie-Liesse Asselin-Labat
A functional genetic screen identifies aurora kinase b as an essential regulator of Sox9-positive mouse embryonic lung progenitor cells. Development (Cambridge, England) 148 (13) (2021)
Hasaru Kariyawasam, Shian Su, Oliver Voogd, Matthew E Ritchie, Charity W Law
Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0. NAR genomics and bioinformatics 3 (4) (2021)
Luyi Tian, Jafar S Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, Mei R M Du, Jakob Schuster, Changqing Wang, Shian Su, Xueyi Dong, Charity W Law, Alexis Lucattini, Yair David Joseph Prawer, Coralina Collar-Fernández, Jin D Chung, Timur Naim, Audrey Chan, Chi Hai Ly, Gordon S Lynch, James G Ryall, Casey J A Anttila, Hongke Peng, Mary Ann Anderson, Christoffer Flensburg, Ian Majewski, Andrew W Roberts, David C S Huang, Michael B Clark, Matthew E Ritchie
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing. Genome biology 22 (1) (2021)
Yue You, Luyi Tian, Shian Su, Xueyi Dong, Jafar S Jabbari, Peter F Hickey, Matthew E Ritchie
Benchmarking UMI-based single-cell RNA-seq preprocessing workflows. Genome biology 22 (1) (2021)
Nathalie A J Verzele, Brendon Y Chua, Charity W Law, Albert Zhang, Matthew E Ritchie, Oliver Wightman, Isaac N Edwards, Katina D Hulme, Conor J Bloxham, Helle Bielefeldt-Ohmann, Matthew W Trewella, Aung Aung Kywe Moe, Keng Yih Chew, Stuart B Mazzone, Kirsty R Short, Alice E McGovern
The impact of influenza pulmonary infection and inflammation on vagal bronchopulmonary sensory neurons. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 35 (3) (2021)
Dawn S Lin, Lu-Yi Tian, Sara Tomei, Daniela Amann-Zalcenstein, Tracey M Baldwin, Tom S Weber, Jaring Schreuder, Olivia J Stonehouse, Jai Rautela, Nicholas D Huntington, Samir Taoudi, Matthew E Ritchie, Philip D Hodgkin, Ashley P Ng, Stephen L Nutt, Shalin H Naik
Single-cell analyses reveal the clonal and molecular aetiology of Flt3L-induced emergency dendritic cell development. Nature cell biology 23 (3) (2021)
Shian Su, Quentin A Gouil, Marnie E Blewitt, Dianne Cook, Peter F Hickey, Matthew E Ritchie
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data. PLoS computational biology 17 (10) (2021)
Najoua Lalaoui, Delphine Merino, Goknur Giner, François Vaillant, Diep Chau, Lin Liu, Tobias Kratina, Bhupinder Pal, James R Whittle, Nima Etemadi, Jean Berthelet, Julius Gräsel, Cathrine Hall, Matthew E Ritchie, Matthias Ernst, Aaron T L Lun, David L Vaux, Jane E Visvader, Geoffrey J Lindeman, John Silke
Targeting triple-negative breast cancers with the Smac-mimetic birinapant. Cell death and differentiation 27 (10) (2020)
Daniela Amann-Zalcenstein, Lu-Yi Tian, Jaring Schreuder, Sara Tomei, Dawn S Lin, Kirsten A Fairfax, Jessica E Bolden, Mark D McKenzie, Andrew Jarratt, Adrienne Hilton, Jacob T Jackson, Ladina Di Rago, Matthew P McCormack, Carolyn A de Graaf, Olivia Stonehouse, Samir Taoudi, Warren S Alexander, Stephen L Nutt, Matthew E Ritchie, Ashley P Ng, Shalin H Naik
A new lymphoid-primed progenitor marked by Dach1 downregulation identified with single cell multi-omics. Nature immunology 21 (12) (2020)
Kevin X Lau, Elizabeth A Mason, Joshua Kie, David P de Souza, Joachim Kloehn, Dedreia Tull, Malcolm J McConville, Andrew Keniry, Tamara Beck, Marnie E Blewitt, Matthew E Ritchie, Shalin H Naik, Daniela Amann-Zalcenstein, Othmar Korn, Shian Su, Irene Gallego Romero, Catrina Spruce, Christopher L Baker, Tracy C McGarr, Christine A Wells, Martin F Pera
Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal. Nature communications 11 (1) (2020)
Charity W Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Aaron T L Lun, Matthew E Ritchie
A guide to creating design matrices for gene expression experiments. F1000Research 9 (2020)
Stuart Lee, Albert Y Zhang, Shian Su, Ashley P Ng, Aliaksei Z Holik, Marie-Liesse Asselin-Labat, Matthew E Ritchie, Charity W Law
Covering all your bases: incorporating intron signal from RNA-seq data. NAR genomics and bioinformatics 2 (3) (2020)
Sarah A Best, Sheryl Ding, Ariena Kersbergen, Xueyi Dong, Ji-Ying Song, Yi Xie, Boris Reljic, Kaiming Li, James E Vince, Vivek Rathi, Gavin M Wright, Matthew E Ritchie, Kate D Sutherland
Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma. Nature communications 10 (1) (2019)
Cyril Seillet, Kylie Luong, Julie Tellier, Nicolas Jacquelot, Rui Dong Shen, Peter F Hickey, Verena C Wimmer, Lachlan Whitehead, Kelly Rogers, Aaron T L Lun, Alexandra L Garnham, Matthew E Ritchie, Gabrielle T Belz
The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity. Nature immunology 21 (2) (2019)
Stuart B Mazzone, Luyi Tian, Aung Aung Kywe Moe, Matthew W Trewella, Matthew E Ritchie, Alice E McGovern
Transcriptional Profiling of Individual Airway Projecting Vagal Sensory Neurons. Molecular neurobiology 57 (2) (2019)
Lu-Yi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Lê Cao, Shian Su, Abolfazl JalalAbadi, Daniela Amann-Zalcenstein, Tom S Weber, Azadeh Seidi, Jafar S Jabbari, Shalin H Naik, Matthew E Ritchie
Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments. Nature methods 16 (6) (2019)
Shian Su, Vincent J Carey, Lori Shepherd, Matthew E Ritchie, Martin T Morgan, Sean Davis
BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem. F1000Research 8 (2019)
Lu-Yi Tian, Shian Su, Xueyi Dong, Daniela Amann-Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J Hilton, Shalin H Naik, Matthew E Ritchie
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data. PLoS computational biology 14 (8) (2018)
Monther Alhamdoosh, Charity W Law, Luyi Tian, Julie M Sheridan, Milica Ng, Matthew E Ritchie
Easy and efficient ensemble gene set testing with EGSEA. F1000Research 6 (2017)
Charity W Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Lu-Yi Tian, Aaron T L Lun, Matthew E Ritchie
RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR. F1000Research 5 (2016)

Matthew E Ritchie.css-eqlu8i{font-size:small;padding-left:4px;} (Matthew Ritchie)

Publication Activity (10 Years)

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Matthew E Ritchie (Matthew Ritchie)