Works by Ritchie, Matthew E.

Results: 59

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 3, p. e17, doi. 10.1093/nar/gkp942

By:

Barbosa-Morais, Nuno L.;
Dunning, Mark J.;
Samarajiwa, Shamith A.;
Darot, Jeremy F. J.;
Ritchie, Matthew E.;
Lynch, Andy G.;
Tavaré, Simon

Publication type:

Article

VEGF-dependent testicular vascularisation involves MEK1/2 signalling and the essential angiogenesis factors, SOX7 and SOX17.

Published in:

BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-02003-y

By:

Blücher, Rheannon O.;
Lim, Rachel S.;
Ritchie, Matthew E.;
Western, Patrick S.

Publication type:

Article

FGF-independent MEK1/2 signalling in the developing foetal testis is essential for male germline differentiation in mice.

Published in:

BMC Biology, 2023, v. 21, n. 1, p. 1, doi. 10.1186/s12915-023-01777-x

By:

Blücher, Rheannon O.;
Lim, Rachel S.;
Jarred, Ellen G.;
Ritchie, Matthew E.;
Western, Patrick S.

Publication type:

Article

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data.

Published in:

PLoS Computational Biology, 2018, v. 14, n. 8, p. 1, doi. 10.1371/journal.pcbi.1006361

By:

Tian, Luyi;
Su, Shian;
Dong, Xueyi;
Amann-Zalcenstein, Daniela;
Biben, Christine;
Seidi, Azadeh;
Hilton, Douglas J.;
Naik, Shalin H.;
Ritchie, Matthew E.

Publication type:

Article

Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0.

Published in:

NAR Genomics & Bioinformatics, 2021, v. 3, n. 4, p. 1, doi. 10.1093/nargab/lqab116

By:

Kariyawasam, Hasaru;
Su, Shian;
Voogd, Oliver;
Ritchie, Matthew E;
Law, Charity W

Publication type:

Article

BeadArray Expression Analysis Using Bioconductor.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 12, p. 1, doi. 10.1371/journal.pcbi.1002276

By:

Ritchie, Matthew E.;
Dunning, Mark J.;
Smith, Mike L.;
Wei Shi;
Lynch, Andy G.

Publication type:

Article

Benchmarking spatial transcriptomics technologies with the multi-sample SpatialBenchVisium dataset.

Published in:

Genome Biology, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s13059-025-03543-4

By:

Du, Mei R. M.;
Wang, Changqing;
Law, Charity W.;
Amann-Zalcenstein, Daniela;
Anttila, Casey J. A.;
Ling, Ling;
Hickey, Peter F.;
Sargeant, Callum J.;
Chen, Yunshun;
Ioannidis, Lisa J.;
Rajasekhar, Pradeep;
Yip, Raymond K. H.;
Rogers, Kelly L.;
Hansen, Diana S.;
Bowden, Rory;
Ritchie, Matthew E.

Publication type:

Article

Distinct initiating events underpin the immune and metabolic heterogeneity of KRAS-mutant lung adenocarcinoma.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12164-y

By:

Best, Sarah A.;
Ding, Sheryl;
Kersbergen, Ariena;
Dong, Xueyi;
Song, Ji-Ying;
Xie, Yi;
Reljic, Boris;
Li, Kaiming;
Vince, James E.;
Rathi, Vivek;
Wright, Gavin M.;
Ritchie, Matthew E.;
Sutherland, Kate D.

Publication type:

Article

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing.

Published in:

Epigenetics & Chromatin, 2016, v. 9, p. 1, doi. 10.1186/s13072-016-0064-6

By:

Keniry, Andrew;
Gearing, Linden J.;
Jansz, Natasha;
Liu, Joy;
Holik, Aliaksei Z.;
Hickey, Peter F.;
Kinkel, Sarah A.;
Moore, Darcy L.;
Breslin, Kelsey;
Chen, Kelan;
Ruijie Liu;
Phillips, Catherine;
Pakusch, Miha;
Biben, Christine;
Sheridan, Julie M.;
Kile, Benjamin T.;
Carmichael, Catherine;
Ritchie, Matthew E.;
Hilton, Douglas J.;
Blewitt, Marnie E.

Publication type:

Article

Myocardial Gene Expression Associated with Genetic Cardiac Hypertrophy in the Absence of Hypertension.

Published in:

Hypertension Research, 2008, v. 31, n. 5, p. 941, doi. 10.1291/hypres.31.941

By:

Dwyer, Jeremy P;
Ritchie, Matthew E;
Smyth, Gordon K;
Harrap, Stephen B;
Delbridge, Lea M D;
Domenighetti, Andrea A;
Di Nicolantonio, Robert

Publication type:

Article

Modulation of Vagal Sensory Neurons via High Mobility Group Box-1 and Receptor for Advanced Glycation End Products: Implications for Respiratory Viral Infections.

Published in:

Frontiers in Physiology, 2021, v. 12, p. 1, doi. 10.3389/fphys.2021.744812

By:

Mazzone, Stuart B.;
Yang, Seung-Kwon;
Keller, Jennifer A.;
Simanauskaite, Juste;
Arikkatt, Jaisy;
Fogarty, Matthew J.;
Moe, Aung Aung Kywe;
Chen, Chen;
Trewella, Matthew W.;
Tian, Luyi;
Ritchie, Matthew E.;
Chua, Brendan Y.;
Phipps, Simon;
Short, Kirsty R.;
McGovern, Alice E.

Publication type:

Article

NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells.

Published in:

2022

By:

Subas Satish, Hema Preethi;
Zeglinski, Kathleen;
Uren, Rachel T.;
Nutt, Stephen L.;
Ritchie, Matthew E.;
Gouil, Quentin;
Kluck, Ruth M.

Publication type:

Report

Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data.

Published in:

Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02949-2

By:

You, Yue;
Dong, Xueyi;
Wee, Yong Kiat;
Maxwell, Mhairi J.;
Alhamdoosh, Monther;
Smyth, Gordon K.;
Hickey, Peter F.;
Ritchie, Matthew E.;
Law, Charity W.

Publication type:

Article

Publisher Correction: Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data.

Published in:

2023

By:

You, Yue;
Dong, Xueyi;
Wee, Yong Kiat;
Maxwell, Mhairi J.;
Alhamdoosh, Monther;
Smyth, Gordon K.;
Hickey, Peter F.;
Ritchie, Matthew E.;
Law, Charity W.

Publication type:

Correction Notice

Benchmarking UMI-based single-cell RNA-seq preprocessing workflows.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02552-3

By:

You, Yue;
Tian, Luyi;
Su, Shian;
Dong, Xueyi;
Jabbari, Jafar S.;
Hickey, Peter F.;
Ritchie, Matthew E.

Publication type:

Article

High-LET Radiation Increases Tumor Progression in a K-Ras-Driven Model of Lung Adenocarcinoma.

Published in:

Radiation Research, 2017, v. 188, n. 5, p. 562, doi. 10.1667/RR14794.1

By:

Asselin-Labat, Marie-Liesse;
Rampersad, Rishi;
Xu, Xia;
Ritchie, Matthew E.;
Michalski, Jacob;
Huang, Lingling;
Onaitis, Mark W.

Publication type:

Article

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

Published in:

BMC Genetics, 2010, v. 11, p. 25, doi. 10.1186/1471-2156-11-25

By:

Daelemans, Caroline;
Ritchie, Matthew E.;
Smits, Guillaume;
Abu-Amero, Sayeda;
Sudbery, Ian M.;
Forrest, Matthew S.;
Campino, Susana;
Clark, Taane G.;
Stanier, Philip;
Kwiatkowski, Dominic;
Deloukas, Panos;
Dermitzakis, Emmanouil T.;
Tavaré, Simon;
Moore, Gudrun E.;
Dunham, Ian

Publication type:

Article

Allele-specific expression analysis methods for high-density SNP microarray data.

Published in:

Bioinformatics, 2012, v. 28, n. 8, p. 1102, doi. 10.1093/bioinformatics/bts089

By:

Liu, Ruijie;
Maia, Ana-Teresa;
Russell, Roslin;
Caldas, Carlos;
Ponder, Bruce A.;
Ritchie, Matthew E.

Publication type:

Article

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.

Published in:

Bioinformatics, 2009, v. 25, n. 19, p. 2621, doi. 10.1093/bioinformatics/btp470

By:

Ritchie, Matthew E.;
Carvalho, Benilton S.;
Hetrick, Kurt N.;
Tavaré, Simon;
Irizarry, Rafael A.

Publication type:

Article

A comparison of background correction methods for two-colour microarrays.

Published in:

Bioinformatics, 2007, v. 23, n. 20, p. 2700, doi. 10.1093/bioinformatics/btm412

By:

Ritchie, Matthew E.;
Silver, Jeremy;
Oshlack, Alicia;
Holmes, Melissa;
Diyagama, Dileepa;
Holloway, Andrew;
Smyth, Gordon K.

Publication type:

Article

beadarray: R classes and methods for Illumina bead-based data.

Published in:

Bioinformatics, 2007, v. 23, n. 16, p. 2183, doi. 10.1093/bioinformatics/btm311

By:

Mark J. Dunning;
Mike L. Smith;
Matthew E. Ritchie;
Simon TavarÃ©

Publication type:

Article

CD36 family members are TCR-independent ligands for CD1 antigen–presenting molecules.

Published in:

Science Immunology, 2021, v. 6, n. 60, p. 1, doi. 10.1126/sciimmunol.abg4176

By:

Gherardin, Nicholas A.;
Redmond, Samuel J.;
McWilliam, Hamish E. G.;
Almeida, Catarina F.;
Gourley, Katherine H. A.;
Seneviratna, Rebecca;
Li, Shihan;
De Rose, Robert;
Ross, Fiona J.;
Nguyen-Robertson, Catriona V.;
Su, Shian;
Ritchie, Matthew E.;
Villadangos, Jose A.;
Moody, D. Branch;
Pellicci, Daniel G.;
Uldrich, Adam P.;
Godfrey, Dale I.

Publication type:

Article

Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.

Published in:

Epigenetics & Chromatin, 2022, v. 15, n. 1, p. 1, doi. 10.1186/s13072-022-00458-3

By:

Wanigasuriya, Iromi;
Kinkel, Sarah A.;
Beck, Tamara;
Roper, Ellise A.;
Breslin, Kelsey;
Lee, Heather J.;
Keniry, Andrew;
Ritchie, Matthew E.;
Blewitt, Marnie E.;
Gouil, Quentin

Publication type:

Article

Maternal SMCHD1 controls both imprinted Xist expression and imprinted X chromosome inactivation.

Published in:

Epigenetics & Chromatin, 2022, v. 15, n. 1, p. 1, doi. 10.1186/s13072-022-00458-3

By:

Wanigasuriya, Iromi;
Kinkel, Sarah A.;
Beck, Tamara;
Roper, Ellise A.;
Breslin, Kelsey;
Lee, Heather J.;
Keniry, Andrew;
Ritchie, Matthew E.;
Blewitt, Marnie E.;
Gouil, Quentin

Publication type:

Article

Loss of PUMA ( BBC3) does not prevent thrombocytopenia caused by the loss of BCL- XL ( BCL2L1).

Published in:

British Journal of Haematology, 2016, v. 174, n. 6, p. 962, doi. 10.1111/bjh.14155

By:

Delbridge, Alex R. D.;
Chappaz, Stephane;
Ritchie, Matthew E.;
Kile, Benjamin T.;
Strasser, Andreas;
Grabow, Stephanie

Publication type:

Article

KRLMM: an adaptive genotype calling method for common and low frequency variants.

Published in:

BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-158

By:

Ruijie Liu;
Dai, Zhiyin;
Yeager, Meredith;
Irizarry, Rafael A.;
Ritchie, Matthew E.

Publication type:

Article

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips.

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 68, doi. 10.1186/1471-2105-12-68

By:

Ritchie, Matthew E.;
Ruijie Liu;
Carvalho, Benilton S.;
Irizarry, Rafael A.

Publication type:

Article

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 280, doi. 10.1186/1471-2105-11-280

By:

Ritchie, Matthew E.;
Forrest, Matthew S.;
Dimas, Antigone S.;
Daelemans, Caroline;
Dermitzakis, Emmanouil T.;
Deloukas, Panagiotis;
Tavaré, Simon

Publication type:

Article

Statistical issues in the analysis of Illumina data.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-85

By:

Dunning, Mark J.;
Barbosa-Morais, Nuno L.;
Lynch, Andy G.;
Tavaré, Simon;
Ritchie, Matthew E.

Publication type:

Article

Flexiplex: a versatile demultiplexer and search tool for omics data.

Published in:

Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae102

By:

Cheng, Oliver;
Ling, Min Hao;
Wang, Changqing;
Wu, Shuyi;
Ritchie, Matthew E;
Göke, Jonathan;
Amin, Noorul;
Davidson, Nadia M

Publication type:

Article

CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods.

Published in:

Bioinformatics, 2020, v. 36, n. 7, p. 2288, doi. 10.1093/bioinformatics/btz889

By:

Su, Shian;
Tian, Luyi;
Dong, Xueyi;
Hickey, Peter F;
Freytag, Saskia;
Ritchie, Matthew E

Publication type:

Article

Glimma: interactive graphics for gene expression analysis.

Published in:

Bioinformatics, 2017, v. 33, n. 13, p. 2050, doi. 10.1093/bioinformatics/btx094

By:

Shian Su;
Law, Charity W.;
Ah-Cann, Casey;
Asselin-Labat, Marie-Liesse;
Blewitt, Marnie E.;
Ritchie, Matthew E.

Publication type:

Article

Combining multiple tools outperforms individual methods in gene set enrichment analyses.

Published in:

Bioinformatics, 2017, v. 33, n. 3, p. 414, doi. 10.1093/bioinformatics/btw623

By:

Alhamdoosh, Monther;
Ng, Milica;
Wilson, Nicholas J.;
Sheridan, Julie M.;
Huy Huynh;
Wilson, Michael J.;
Ritchie, Matthew E.

Publication type:

Article

A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells.

Published in:

Journal of Cell Biology, 2022, v. 221, n. 12, p. 1, doi. 10.1083/jcb.202110125

By:

Hui Jing Lim;
Wubben, Jacinta M.;
Garcia, Cristian Pinero;
Cruz-Gomez, Sebastian;
Deng, Jieru;
Mak, Jeffrey Y. W.;
Hachani, Abderrahman;
Anderson, Regan J.;
Painter, Gavin F.;
Goyette, Jesse;
Amarasinghe, Shanika L.;
Ritchie, Matthew E.;
Roquilly, Antoine;
Fairlie, David P.;
Gaus, Katharina;
Rossjohn, Jamie;
Villadangos, Jose A.;
McWilliam, Hamish E. G.

Publication type:

Article

Using long-read sequencing to detect imprinted DNA methylation.

Published in:

Nucleic Acids Research, 2019, v. 47, n. 8, p. e46, doi. 10.1093/nar/gkz107

By:

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

Publication type:

Article

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods.

Published in:

Nucleic Acids Research, 2017, v. 45, n. 5, p. 1, doi. 10.1093/nar/gkw1063

By:

Holik, Aliaksei Z.;
Law, Charity W.;
Ruijie Liu;
Zeya Wang;
Wenyi Wang;
Ahn, Jaeil;
Asselin-Labat, Marie-Liesse;
Smyth, Gordon K.;
Ritchie, Matthew E.

Publication type:

Article

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 15, p. 1, doi. 10.1093/nar/gkv412

By:

Ruijie Liu;
Holik, Aliaksei Z.;
Shian Su;
Jansz, Natasha;
Kelan Chen;
Huei San Leong;
Blewitt, Marnie E.;
Asselin-Labat, Marie-Liesse;
Smyth, Gordon K.;
Ritchie, Matthew E.

Publication type:

Article

limma powers differential expression analyses for RNA-sequencing and microarray studies.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 7, p. e47, doi. 10.1093/nar/gkv007

By:

Ritchie, Matthew E.;
Phipson, Belinda;
Di Wu;
Yifang Hu;
Law, Charity W.;
Wei Shi;
Smyth, Gordon K.

Publication type:

Article

NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data.

Published in:

PLoS Computational Biology, 2021, v. 17, n. 10, p. 1, doi. 10.1371/journal.pcbi.1009524

By:

Su, Shian;
Gouil, Quentin;
Blewitt, Marnie E.;
Cook, Dianne;
Hickey, Peter F.;
Ritchie, Matthew E.

Publication type:

Article

Transcriptional Profiling of Individual Airway Projecting Vagal Sensory Neurons.

Published in:

Molecular Neurobiology, 2020, v. 57, n. 2, p. 949, doi. 10.1007/s12035-019-01782-8

By:

Mazzone, Stuart B.;
Tian, Luyi;
Moe, Aung Aung Kywe;
Trewella, Matthew W.;
Ritchie, Matthew E.;
McGovern, Alice E.

Publication type:

Article

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution.

Published in:

2009

By:

Silver JD;
Ritchie ME;
Smyth GK;
Silver, Jeremy D;
Ritchie, Matthew E;
Smyth, Gordon K

Publication type:

journal article

Microarray background correction: maximum likelihood estimation for the normal-exponential convolution.

Published in:

Biostatistics, 2009, v. 10, n. 2, p. 352, doi. 10.1093/biostatistics/kxn042

By:

Jeremy D. Silver;
Matthew E. Ritchie;
Gordon K. Smyth

Publication type:

Article

long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data.

Published in:

GigaScience, 2021, v. 10, n. 2, p. 1, doi. 10.1093/gigascience/giab003

By:

Amarasinghe, Shanika L;
Ritchie, Matthew E;
Gouil, Quentin

Publication type:

Article

Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16214-8

By:

Lau, Kevin X.;
Mason, Elizabeth A.;
Kie, Joshua;
De Souza, David P.;
Kloehn, Joachim;
Tull, Dedreia;
McConville, Malcolm J.;
Keniry, Andrew;
Beck, Tamara;
Blewitt, Marnie E.;
Ritchie, Matthew E.;
Naik, Shalin H.;
Zalcenstein, Daniela;
Korn, Othmar;
Su, Shian;
Romero, Irene Gallego;
Spruce, Catrina;
Baker, Christopher L.;
McGarr, Tracy C.;
Wells, Christine A.

Publication type:

Article

Opportunities and challenges in long-read sequencing data analysis.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-1935-5

By:

Amarasinghe, Shanika L.;
Su, Shian;
Dong, Xueyi;
Zappia, Luke;
Ritchie, Matthew E.;
Gouil, Quentin

Publication type:

Article

Gene Network Disruptions and Neurogenesis Defects in the Adult Ts1Cje Mouse Model of Down Syndrome.

Published in:

PLoS ONE, 2010, v. 5, n. 7, p. 1, doi. 10.1371/journal.pone.0011561

By:

Hewitt, Chelsee A.;
King-Hwa Ling;
Merson, Tobias D.;
Simpson, Ken M.;
Ritchie, Matthew E.;
King, Sarah L.;
Pritchard, Melanie A.;
Smyth, Gordon K.;
Thomas, Tim;
Scott, Hamish S.;
Voss, Anne K.

Publication type:

Article

Smchd1 is a maternal effect gene required for genomic imprinting.

Published in:

eLife, 2020, p. 1, doi. 10.7554/eLife.55529

By:

Wanigasuriya, Iromi;
Gouil, Quentin;
Kinkel, Sarah A.;
del Fierro, Andrés Tapia;
Beck, Tamara;
Roper, Ellise A.;
Breslin, Kelsey;
Stringer, Jessica;
Hutt, Karla;
Lee, Heather J.;
Keniry, Andrew;
Ritchie, Matthew E.;
Blewitt, Marnie E.

Publication type:

Article

Identification and control for the effects of bioinformatic globin depletion on human RNA-seq differential expression analysis.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-28218-7

By:

Sheerin, Dylan;
Lakay, Francisco;
Esmail, Hanif;
Kinnear, Craig;
Sansom, Bianca;
Glanzmann, Brigitte;
Wilkinson, Robert J.;
Ritchie, Matthew E.;
Coussens, Anna K.

Publication type:

Article

Dividing out quantification uncertainty allows efficient assessment of differential transcript expression with edgeR.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 3, p. e13, doi. 10.1093/nar/gkad1167

By:

Baldoni, Pedro L;
Chen, Yunshun;
Hediyeh-zadeh, Soroor;
Liao, Yang;
Dong, Xueyi;
Ritchie, Matthew E;
Shi, Wei;
Smyth, Gordon K

Publication type:

Article

Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions.

Published in:

Nucleic Acids Research, 2023, v. 51, n. 7, p. 3240, doi. 10.1093/nar/gkad091

By:

Nahar, Nusrat;
Tram, Greg;
Jen, Freda E-C;
Phillips, Zachary N;
Weinert, Lucy A;
Bossé, Janine T;
Jabbari, Jafar S;
Gouil, Quentin;
Du, Mei R M;
Ritchie, Matthew E;
Bowden, Rory;
Langford, Paul R;
Tucker, Alexander W;
Jennings, Michael P;
Turni, Conny;
Blackall, Patrick J;
Atack, John M

Publication type:

Article