Publications by authors named "Matthew Ritchie"

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stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data.
Yang Xu, Callum J Sargeant, Yue You, Yupei You, Shian Su, Matthew E Ritchie

NAR Genom Bioinform· December 2025

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-diphtheria toxin receptor mice allow for depletion of antibody-secreting cells and analysis of differentiation kinetics.
KimAnh T Pioli, Matthew Ritchie, Hira Haq, Peter D Pioli

iScience· December 2025

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Jchain-Diphtheria Toxin Receptor Mice Allow for Diphtheria Toxin-Mediated Depletion of Antibody-Secreting Cells and Analysis of Differentiation Kinetics.
KimAnh T Pioli, Matthew Ritchie, Hira Haq, Peter D Pioli

bioRxiv· May 2025

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A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor.
Shian Su, Lucinda Xiao, James Lancaster, Tamara Cameron, Kelsey Breslin, Matthew E Ritchie

F1000Res· May 2025

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TIRE-seq simplifies transcriptomics via integrated RNA capture and library preparation.
Piper O'Keeffe, Yasmin Nouri, Hui Shi Saw, Zachery Moore, Tracey M Baldwin, Matthew E Ritchie

Sci Rep· May 2025

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Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes.
Hongke Peng, Jafar S Jabbari, Luyi Tian, Changqing Wang, Yupei You, Matthew E Ritchie

Genome Res· April 2025

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Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset.
Mei R M Du, Changqing Wang, Charity W Law, Daniela Amann-Zalcenstein, Casey J A Anttila, Matthew E Ritchie

Genome Biol· March 2025

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An Interdisciplinary Overview on Ambient Assisted Living Systems for Health Monitoring at Home: Trade-Offs and Challenges.
Baraa Zieni, Matthew A Ritchie, Anna Maria Mandalari, Francesca Boem

Sensors (Basel)· January 2025

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Venetoclax dose escalation rapidly activates a BAFF/BCL-2 survival axis in chronic lymphocytic leukemia.
Meng-Xiao Luo, Tania Tan, Marie Trussart, Annika Poch, Thi Minh Hanh Nguyen, David Ritchie, Matthew E Ritchie

Blood· December 2024

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A dataset examining technical factors on fixed white blood cell single-cell RNA-seq.
Daniel V Brown, Agnieszka Swierczak, Yue You, Yupei You, Daniela Amann-Zalcenstein, Matthew E Ritchie

Data Brief· December 2024

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Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing.
Sena A Gocuk, James Lancaster, Shian Su, Jasleen K Jolly, Thomas L Edwards, Matthew E Ritchie

Genome Res· November 2024

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A lipid signature of BAK-driven apoptotic pore formation.
Rachel T Uren, Matthew E Ritchie, Agnes W Wong, Justin P Ludeman, Etsuko Uno

bioRxiv· November 2024

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An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing.
Kathleen Zeglinski, Christian Montellese, Matthew E Ritchie, Monther Alhamdoosh, Cédric Vonarburg

Genome Res· November 2024

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VEGF-dependent testicular vascularisation involves MEK1/2 signalling and the essential angiogenesis factors, SOX7 and SOX17.
Rheannon O Blücher, Rachel S Lim, Matthew E Ritchie, Patrick S Western

BMC Biol· October 2024

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Systematic comparison of sequencing-based spatial transcriptomic methods.
Yue You, Yuting Fu, Lanxiang Li, Zhongmin Zhang, Shikai Jia, Matthew E Ritchie

Nat Methods· September 2024

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Establishment of single-cell transcriptional states during seed germination.
Lim Chee Liew, Yue You, Lucas Auroux, Marina Oliva, Marta Peirats-Llobet, Matthew E Ritchie

Nat Plants· September 2024

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An immunohistochemical atlas of necroptotic pathway expression.
Shene Chiou, Aysha H Al-Ani, Yi Pan, Komal M Patel, Isabella Y Kong, Matthew E Ritchie

EMBO Mol Med· July 2024

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Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Matthew E Ritchie

Nat Methods· July 2024

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Flexiplex: a versatile demultiplexer and search tool for omics data.
Oliver Cheng, Min Hao Ling, Changqing Wang, Shuyi Wu, Matthew E Ritchie

Bioinformatics· March 2024

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Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR.
Pedro L Baldoni, Yunshun Chen, Soroor Hediyeh-Zadeh, Yang Liao, Xueyi Dong, Matthew E Ritchie

Nucleic Acids Res· February 2024

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scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor.
Shanika L Amarasinghe, Phil Yang, Oliver Voogd, Haoyu Yang, Mei R M Du, Matthew E Ritchie

NAR Genom Bioinform· December 2023

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FGF-independent MEK1/2 signalling in the developing foetal testis is essential for male germline differentiation in mice.
Rheannon O Blücher, Rachel S Lim, Ellen G Jarred, Matthew E Ritchie, Patrick S Western

BMC Biol· December 2023

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Hookworms dynamically respond to loss of Type 2 immune pressure.
Annabel A Ferguson, Juan M Inclan-Rico, Dihong Lu, Sarah D Bobardt, LiYin Hung, Matthew E Ritchie

PLoS Pathog· December 2023

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Restrander: rapid orientation and artefact removal for long-read cDNA data.
Jakob Schuster, Matthew E Ritchie, Quentin Gouil

NAR Genom Bioinform· December 2023

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Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures.
Xueyi Dong, Mei R M Du, Quentin Gouil, Luyi Tian, Jafar S Jabbari, Matthew E Ritchie

Nat Methods· November 2023

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