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M. Ritchie · SciRah

Researcher profile · Semantic Scholar

M. Ritchie

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M. Ritchie — researcher profile on SciRah

h-index: 49
Works: 176
Citations: 47K

Most-cited papers

Opportunities and challenges in long-read sequencing data analysis
Shanika L. Amarasinghe, S. Su, Xue-Yi Dong, L. Zappia +2 more
2020Genome Biology1,358 citations Open access
Semantic Scholar
Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments
L. Tian, Xue-Yi Dong, S. Freytag, K. Cao +8 more
2019Nature Methods301 citations Open access
Semantic Scholar
The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity
Cyril Seillet, Kylie Luong, Julie Tellier, N. Jacquelot +9 more
2019Nature Immunology209 citations
Semantic Scholar
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, M. Diekhans +83 more
2024Nature Methods207 citations Open access
Semantic Scholar
Synergy between the KEAP1/NRF2 and PI3K Pathways Drives Non-Small-Cell Lung Cancer with an Altered Immune Microenvironment.
S. Best, D. D. de Souza, A. Kersbergen, A. Policheni +7 more
2018Cell Metabolism204 citations Open access
Semantic Scholar
Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing
L. Tian, J. Jabbari, R. Thijssen, Q. Gouil +27 more
2021Genome Biology203 citations Open access
Semantic Scholar
Using long-read sequencing to detect imprinted DNA methylation
S. Gigante, Q. Gouil, Alexis Lucattini, A. Keniry +7 more
2018bioRxiv120 citations Open access
Semantic Scholar
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
L. Tian, S. Su, Xue-Yi Dong, D. Amann-Zalcenstein +5 more
2018PLoS Comput. Biol.103 citations Open access
Semantic Scholar
Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures
Xue-Yi Dong, Mei-Hong Du, Q. Gouil, L. Tian +8 more
2023bioRxiv98 citations Open access
Semantic Scholar
Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters
N. Jansz, A. Keniry, M. Trussart, H. Bildsoe +11 more
2018Nature Structural & Molecular Biology88 citations
Semantic Scholar
Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma
S. Best, S. Ding, A. Kersbergen, Xue-Yi Dong +9 more
2019Nature Communications83 citations Open access
Semantic Scholar
Single-cell multiomics reveal the scale of multilayered adaptations enabling CLL relapse during venetoclax therapy
R. Thijssen, L. Tian, M. Anderson, C. Flensburg +18 more
2022Blood81 citations Open access
Semantic Scholar
Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia.
M. McKenzie, M. Ghisi, Ethan P. Oxley, Steven Ngo +37 more
2019Cell Stem Cell79 citations Open access
Semantic Scholar
Harnessing natural killer immunity in metastatic small cell lung cancer.
S. Best, J. Hess, Fernando Souza-Fonseca-Guimarães, J. Cursons +11 more
2020Journal of Thoracic Oncology62 citations Open access
Semantic Scholar
Single cell transcriptomic analysis reveals BCMA CAR-T cell dynamics in a patient with refractory primary plasma cell leukemia.
Xue Li, Xin Guo, Yu-Qing Zhu, Guo-Qing Wei +19 more
2020Molecular Therapy61 citations Open access
Semantic Scholar
A guide to creating design matrices for gene expression experiments
C. Law, Kathleen Zeglinski, Xue-Yi Dong, M. Alhamdoosh +2 more
2020F1000Research59 citations Open access
Semantic Scholar
Benchmarking UMI-based single-cell RNA-seq preprocessing workflows
Yue You, L. Tian, S. Su, Xue-Yi Dong +3 more
2021Genome Biology54 citations Open access
Semantic Scholar
The EMT modulator SNAI1 contributes to AML pathogenesis via its interaction with LSD1.
C. Carmichael, Jue-Qiong Wang, Thao Nguyen, Oluseyi Kolawole +33 more
2020Blood50 citations Open access
Semantic Scholar
Transcriptional Profiling of Individual Airway Projecting Vagal Sensory Neurons
S. Mazzone, L. Tian, Aung Aung Kywe Moe, Matthew W. Trewella +2 more
2019Molecular Neurobiology50 citations
Semantic Scholar
Targeting triple-negative breast cancers with the Smac-mimetic birinapant
N. Lalaoui, D. Merino, Göknur Giner, F. Vaillant +16 more
2020Cell Death and Differentiation47 citations Open access
Semantic Scholar
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data
Shanika L. Amarasinghe, M. Ritchie, Q. Gouil
2021GigaScience45 citations Open access
Semantic Scholar
The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read differential expression analysis tools
Xue-Yi Dong, L. Tian, Q. Gouil, Hasaru Kariyawasam +9 more
2021NAR Genomics and Bioinformatics45 citations Open access
Semantic Scholar
Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR
Pedro L. Baldoni, Yun-Shun Chen, S. Hediyeh-zadeh, Yang Liao +4 more
2023bioRxiv40 citations Open access
Semantic Scholar
Single-cell analyses reveal the clonal and molecular aetiology of Flt3L-induced emergency dendritic cell development
Dawn S Y Lin, L. Tian, S. Tomei, D. Amann-Zalcenstein +12 more
2021Nature Cell Biology37 citations
Semantic Scholar
Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal
Kevin X. Lau, Elizabeth A. Mason, Joshua Kie, D. D. de Souza +17 more
2020Nature Communications37 citations Open access
Semantic Scholar
Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development.
L. Tian, S. Tomei, J. Schreuder, T. Weber +22 more
2021Immunity36 citations Open access
Semantic Scholar
Establishment of single-cell transcriptional states during seed germination
L. C. Liew, Yue You, Lucas Auroux, Marina Oliva +13 more
2024Nature Plants35 citations Open access
Semantic Scholar
An immunohistochemical atlas of necroptotic pathway expression
Shene Chiou, A. Al-Ani, Yi Pan, K. Patel +35 more
2024bioRxiv32 citations Open access
Semantic Scholar
Flexiplex: a versatile demultiplexer and search tool for omics data
Oliver Y. Cheng, Min-Hao Ling, Changqing Wang, Shu-Yi Wu +4 more
2024bioRxiv29 citations Open access
Semantic Scholar
A new lymphoid-primed progenitor marked by Dach1 downregulation identified with single cell multi-omics
D. Amann-Zalcenstein, L. Tian, J. Schreuder, S. Tomei +17 more
2020Nature Immunology27 citations Open access
Semantic Scholar
NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data
S. Su, Q. Gouil, M. Blewitt, D. Cook +2 more
2021bioRxiv26 citations Open access
Semantic Scholar
Smchd1 is a maternal effect gene required for genomic imprinting
Iromi Wanigasuriya, Q. Gouil, S. Kinkel, Andres Tapia del Fierro +9 more
2020eLife25 citations Open access
Semantic Scholar
CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods
S. Su, L. Tian, Xue-Yi Dong, Peter F. Hickey +2 more
2019Bioinform.25 citations Open access
Semantic Scholar
Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Yue You, Xue-Yi Dong, Y. K. Wee, M. Maxwell +5 more
2023Genome Biology23 citations Open access
Semantic Scholar
The impact of influenza pulmonary infection and inflammation on vagal bronchopulmonary sensory neurons
N. Verzele, B. Chua, C. Law, Albert Y Zhang +12 more
2021The FASEB Journal22 citations Open access
Semantic Scholar
Lung morphogenesis is orchestrated through Grainyhead-like 2 (Grhl2) transcriptional programs.
A. Kersbergen, S. Best, Sebastian Dworkin, Casey Ah-Cann +5 more
2018Developmental Biology22 citations Open access
Semantic Scholar
SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease
Andres Tapia del Fierro, B. den Hamer, Natalia Benetti, N. Jansz +26 more
2021bioRxiv21 citations Open access
Semantic Scholar
CD36 family members are TCR-independent ligands for CD1 antigen-presenting molecules
N. Gherardin, S. Redmond, H. McWilliam, Catarina F. Almeida +13 more
2021Science immunology20 citations Open access
Semantic Scholar
Venetoclax treatment in patients with cancer has limited impact on circulating T and NK cells
Charis E. Teh, Hong-Ke Peng, Maohui Luo, Tania Tan +14 more
2022Blood Advances19 citations Open access
Semantic Scholar
NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells
Hema Preethi Subas Satish, Kathleen Zeglinski, Rachel T. Uren, S. Nutt +3 more
2022bioRxiv17 citations Open access
Semantic Scholar
A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells
Hui-Jing Lim, Jacinta Wubben, C. García, S. Cruz-Gomez +14 more
2022Journal of Cell Biology16 citations Open access
Semantic Scholar
Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
S. A. Gocuk, J. Lancaster, S. Su, J. Jolly +6 more
2024Genome Research15 citations Open access
Semantic Scholar
Community-wide hackathons to identify central themes in single-cell multi-omics
K. Cao, Al J Abadi, Emily F. Davis-Marcisak, Lauren L. Hsu +27 more
2021Genome Biology15 citations Open access
Semantic Scholar
SC-JNMF: single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization
Mikio Shiga, S. Seno, Makoto Onizuka, H. Matsuda +313 more
2020bioRxiv15 citations Open access
Semantic Scholar
Identification and control for the effects of bioinformatic globin depletion on human RNA-seq differential expression analysis
D. Sheerin, F. Lakay, H. Esmail, C. Kinnear +5 more
2023Scientific Reports13 citations Open access
Semantic Scholar
scRNA-seq mixology: towards better benchmarking of single cell RNA-seq protocols and analysis methods
L. Tian, Xue-Yi Dong, S. Freytag, K. Cao +8 more
2018bioRxiv13 citations Open access
Semantic Scholar
Spotlight on 10x Visium: a multi-sample protocol comparison of spatial technologies
Mei-Hong Du, Changqing Wang, C. Law, D. Amann-Zalcenstein +12 more
2024bioRxiv12 citations Open access
Semantic Scholar
Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions
N. Nahar, Greg Tram, F. Jen, Zachary N. Phillips +13 more
2022bioRxiv11 citations Open access
Semantic Scholar
Hookworms dynamically respond to loss of Type 2 immune pressure
Annabel A. Ferguson, Juan M. Inclan-Rico, Dihong Lu, Sarah D. Bobardt +10 more
2023PLoS Pathogens10 citations Open access
Semantic Scholar
BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation
A. Keniry, N. Jansz, L. Gearing, Iromi Wanigasuriya +19 more
2022Nature Communications10 citations Open access
Semantic Scholar

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