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

Su S, Tian L, Dong X, Hickey PF, Freytag S, Ritchie ME.

Bioinformatics. 2019 Nov 28. pii: btz889. doi: 10.1093/bioinformatics/btz889. [Epub ahead of print]


A divergent transcriptional landscape underpins the development and functional branching of MAIT cells.

Koay HF, Su S, Amann-Zalcenstein D, Daley SR, Comerford I, Miosge L, Whyte CE, Konstantinov IE, d'Udekem Y, Baldwin T, Hickey PF, Berzins SP, Mak JYW, Sontani Y, Roots CM, Sidwell T, Kallies A, Chen Z, Nüssing S, Kedzierska K, Mackay LK, McColl SR, Deenick EK, Fairlie DP, McCluskey J, Goodnow CC, Ritchie ME, Belz GT, Naik SH, Pellicci DG, Godfrey DI.

Sci Immunol. 2019 Nov 22;4(41). pii: eaay6039. doi: 10.1126/sciimmunol.aay6039.


Transcriptional Profiling of Individual Airway Projecting Vagal Sensory Neurons.

Mazzone SB, Tian L, Moe AAK, Trewella MW, Ritchie ME, McGovern AE.

Mol Neurobiol. 2019 Oct 19. doi: 10.1007/s12035-019-01782-8. [Epub ahead of print]


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

Best SA, Ding S, Kersbergen A, Dong X, Song JY, Xie Y, Reljic B, Li K, Vince JE, Rathi V, Wright GM, Ritchie ME, Sutherland KD.

Nat Commun. 2019 Sep 13;10(1):4190. doi: 10.1038/s41467-019-12164-y.


Interconversion between Tumorigenic and Differentiated States in Acute Myeloid Leukemia.

McKenzie MD, Ghisi M, Oxley EP, Ngo S, Cimmino L, Esnault C, Liu R, Salmon JM, Bell CC, Ahmed N, Erlichster M, Witkowski MT, Liu GJ, Chopin M, Dakic A, Simankowicz E, Pomilio G, Vu T, Krsmanovic P, Su S, Tian L, Baldwin TM, Zalcenstein DA, DiRago L, Wang S, Metcalf D, Johnstone RW, Croker BA, Lancaster GI, Murphy AJ, Naik SH, Nutt SL, Pospisil V, Schroeder T, Wall M, Dawson MA, Wei AH, de Thé H, Ritchie ME, Zuber J, Dickins RA.

Cell Stem Cell. 2019 Aug 1;25(2):258-272.e9. doi: 10.1016/j.stem.2019.07.001.


Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments.

Tian L, Dong X, Freytag S, Lê Cao KA, Su S, JalalAbadi A, Amann-Zalcenstein D, Weber TS, Seidi A, Jabbari JS, Naik SH, Ritchie ME.

Nat Methods. 2019 Jun;16(6):479-487. doi: 10.1038/s41592-019-0425-8. Epub 2019 May 27.


Cross-boundary human impacts compromise the Serengeti-Mara ecosystem.

Veldhuis MP, Ritchie ME, Ogutu JO, Morrison TA, Beale CM, Estes AB, Mwakilema W, Ojwang GO, Parr CL, Probert J, Wargute PW, Hopcraft JGC, Olff H.

Science. 2019 Mar 29;363(6434):1424-1428. doi: 10.1126/science.aav0564. Epub 2019 Mar 28.


Using long-read sequencing to detect imprinted DNA methylation.

Gigante S, Gouil Q, Lucattini A, Keniry A, Beck T, Tinning M, Gordon L, Woodruff C, Speed TP, Blewitt ME, Ritchie ME.

Nucleic Acids Res. 2019 May 7;47(8):e46. doi: 10.1093/nar/gkz107.


Lung morphogenesis is orchestrated through Grainyhead-like 2 (Grhl2) transcriptional programs.

Kersbergen A, Best SA, Dworkin S, Ah-Cann C, de Vries ME, Asselin-Labat ML, Ritchie ME, Jane SM, Sutherland KD.

Dev Biol. 2018 Nov 1;443(1):1-9. doi: 10.1016/j.ydbio.2018.09.002. Epub 2018 Sep 5.


Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters.

Jansz N, Keniry A, Trussart M, Bildsoe H, Beck T, Tonks ID, Mould AW, Hickey P, Breslin K, Iminitoff M, Ritchie ME, McGlinn E, Kay GF, Murphy JM, Blewitt ME.

Nat Struct Mol Biol. 2018 Sep;25(9):766-777. doi: 10.1038/s41594-018-0111-z. Epub 2018 Aug 20.


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

Tian L, Su S, Dong X, Amann-Zalcenstein D, Biben C, Seidi A, Hilton DJ, Naik SH, Ritchie ME.

PLoS Comput Biol. 2018 Aug 10;14(8):e1006361. doi: 10.1371/journal.pcbi.1006361. eCollection 2018 Aug.


Reaction and diffusion thermodynamics explain optimal temperatures of biochemical reactions.

Ritchie ME.

Sci Rep. 2018 Jul 23;8(1):11105. doi: 10.1038/s41598-018-28833-9.


Identification of a Siglec-F+ granulocyte-macrophage progenitor.

Bolden JE, Lucas EC, Zhou G, O'Sullivan JA, de Graaf CA, McKenzie MD, Di Rago L, Baldwin TM, Shortt J, Alexander WS, Bochner BS, Ritchie ME, Hilton DJ, Fairfax KA.

J Leukoc Biol. 2018 Jul;104(1):123-133. doi: 10.1002/JLB.1MA1217-475R. Epub 2018 Apr 12.


Synergy between the KEAP1/NRF2 and PI3K Pathways Drives Non-Small-Cell Lung Cancer with an Altered Immune Microenvironment.

Best SA, De Souza DP, Kersbergen A, Policheni AN, Dayalan S, Tull D, Rathi V, Gray DH, Ritchie ME, McConville MJ, Sutherland KD.

Cell Metab. 2018 Apr 3;27(4):935-943.e4. doi: 10.1016/j.cmet.2018.02.006. Epub 2018 Mar 8.


Easy and efficient ensemble gene set testing with EGSEA.

Alhamdoosh M, Law CW, Tian L, Sheridan JM, Ng M, Ritchie ME.

F1000Res. 2017 Nov 14;6:2010. doi: 10.12688/f1000research.12544.1. eCollection 2017.


Thymospheres Are Formed by Mesenchymal Cells with the Potential to Generate Adipocytes, but Not Epithelial Cells.

Sheridan JM, Keown A, Policheni A, Roesley SNA, Rivlin N, Kadouri N, Ritchie ME, Jain R, Abramson J, Heng TSP, Gray DHD.

Cell Rep. 2017 Oct 24;21(4):934-942. doi: 10.1016/j.celrep.2017.09.090.


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

Asselin-Labat ML, Rampersad R, Xu X, Ritchie ME, Michalski J, Huang L, Onaitis MW.

Radiat Res. 2017 Nov;188(5):562-570. doi: 10.1667/RR14794.1. Epub 2017 Sep 27.


Cisplatin Increases Sensitivity to FGFR Inhibition in Patient-Derived Xenograft Models of Lung Squamous Cell Carcinoma.

Weeden CE, Holik AZ, Young RJ, Ma SB, Garnier JM, Fox SB, Antippa P, Irving LB, Steinfort DP, Wright GM, Russell PA, Ritchie ME, Burns CJ, Solomon B, Asselin-Labat ML.

Mol Cancer Ther. 2017 Aug;16(8):1610-1622. doi: 10.1158/1535-7163.MCT-17-0174. Epub 2017 Jun 13.


Glimma: interactive graphics for gene expression analysis.

Su S, Law CW, Ah-Cann C, Asselin-Labat ML, Blewitt ME, Ritchie ME.

Bioinformatics. 2017 Jul 1;33(13):2050-2052. doi: 10.1093/bioinformatics/btx094.


Identification of quiescent and spatially restricted mammary stem cells that are hormone responsive.

Fu NY, Rios AC, Pal B, Law CW, Jamieson P, Liu R, Vaillant F, Jackling F, Liu KH, Smyth GK, Lindeman GJ, Ritchie ME, Visvader JE.

Nat Cell Biol. 2017 Mar;19(3):164-176. doi: 10.1038/ncb3471. Epub 2017 Feb 13.


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

Holik AZ, Law CW, Liu R, Wang Z, Wang W, Ahn J, Asselin-Labat ML, Smyth GK, Ritchie ME.

Nucleic Acids Res. 2017 Mar 17;45(5):e30. doi: 10.1093/nar/gkw1063.


High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS).

Yin D, Ritchie ME, Jabbari JS, Beck T, Blewitt ME, Keniry A.

Genom Data. 2016 Oct 6;10:97-100. eCollection 2016 Dec.


Deciphering the Innate Lymphoid Cell Transcriptional Program.

Seillet C, Mielke LA, Amann-Zalcenstein DB, Su S, Gao J, Almeida FF, Shi W, Ritchie ME, Naik SH, Huntington ND, Carotta S, Belz GT.

Cell Rep. 2016 Oct 4;17(2):436-447. doi: 10.1016/j.celrep.2016.09.025.


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

Alhamdoosh M, Ng M, Wilson NJ, Sheridan JM, Huynh H, Wilson MJ, Ritchie ME.

Bioinformatics. 2017 Feb 1;33(3):414-424. doi: 10.1093/bioinformatics/btw623.


RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR.

Law CW, Alhamdoosh M, Su S, Dong X, Tian L, Smyth GK, Ritchie ME.

Version 3. F1000Res. 2016 Jun 17 [revised 2018 Jan 1];5. pii: ISCB Comm J-1408. doi: 10.12688/f1000research.9005.3. eCollection 2016.


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

Delbridge AR, Chappaz S, Ritchie ME, Kile BT, Strasser A, Grabow S.

Br J Haematol. 2016 Sep;174(6):962-9. doi: 10.1111/bjh.14155. Epub 2016 May 25.


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

Keniry A, Gearing LJ, Jansz N, Liu J, Holik AZ, Hickey PF, Kinkel SA, Moore DL, Breslin K, Chen K, Liu R, Phillips C, Pakusch M, Biben C, Sheridan JM, Kile BT, Carmichael C, Ritchie ME, Hilton DJ, Blewitt ME.

Epigenetics Chromatin. 2016 May 18;9:16. doi: 10.1186/s13072-016-0064-6. eCollection 2016.


Transcriptional profiling of the epigenetic regulator Smchd1.

Liu R, Chen K, Jansz N, Blewitt ME, Ritchie ME.

Genom Data. 2015 Dec 31;7:144-7. doi: 10.1016/j.gdata.2015.12.027. eCollection 2016 Mar.


Intraspecific trait variation drives functional responses of old-field plant communities to nutrient enrichment.

Siefert A, Ritchie ME.

Oecologia. 2016 May;181(1):245-55. doi: 10.1007/s00442-016-3563-z. Epub 2016 Jan 29.


Transcriptome and H3K27 tri-methylation profiling of Ezh2-deficient lung epithelium.

Holik AZ, Galvis LA, Lun AT, Ritchie ME, Asselin-Labat ML.

Genom Data. 2015 Jul 16;5:346-51. doi: 10.1016/j.gdata.2015.07.006. eCollection 2015 Sep.


Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation.

Chen K, Hu J, Moore DL, Liu R, Kessans SA, Breslin K, Lucet IS, Keniry A, Leong HS, Parish CL, Hilton DJ, Lemmers RJ, van der Maarel SM, Czabotar PE, Dobson RC, Ritchie ME, Kay GF, Murphy JM, Blewitt ME.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3535-44. doi: 10.1073/pnas.1504232112. Epub 2015 Jun 19.


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

Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME, Asselin-Labat ML, Smyth GK, Ritchie ME.

Nucleic Acids Res. 2015 Sep 3;43(15):e97. doi: 10.1093/nar/gkv412. Epub 2015 Apr 29.


A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.

Sheridan JM, Ritchie ME, Best SA, Jiang K, Beck TJ, Vaillant F, Liu K, Dickins RA, Smyth GK, Lindeman GJ, Visvader JE.

BMC Cancer. 2015 Apr 3;15:221. doi: 10.1186/s12885-015-1187-z.


Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung.

Galvis LA, Holik AZ, Short KM, Pasquet J, Lun AT, Blewitt ME, Smyth IM, Ritchie ME, Asselin-Labat ML.

Development. 2015 Apr 15;142(8):1458-69. doi: 10.1242/dev.122077. Epub 2015 Mar 19.


Contrasting effects of different mammalian herbivores on sagebrush plant communities.

Veblen KE, Nehring KC, McGlone CM, Ritchie ME.

PLoS One. 2015 Feb 11;10(2):e0118016. doi: 10.1371/journal.pone.0118016. eCollection 2015.


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

Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK.

Nucleic Acids Res. 2015 Apr 20;43(7):e47. doi: 10.1093/nar/gkv007. Epub 2015 Jan 20.


Apoptotic caspases suppress mtDNA-induced STING-mediated type I IFN production.

White MJ, McArthur K, Metcalf D, Lane RM, Cambier JC, Herold MJ, van Delft MF, Bedoui S, Lessene G, Ritchie ME, Huang DC, Kile BT.

Cell. 2014 Dec 18;159(7):1549-62. doi: 10.1016/j.cell.2014.11.036.


Community functional responses to soil and climate at multiple spatial scales: when does intraspecific variation matter?

Siefert A, Fridley JD, Ritchie ME.

PLoS One. 2014 Oct 20;9(10):e111189. doi: 10.1371/journal.pone.0111189. eCollection 2014.


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

Liu R, Dai Z, Yeager M, Irizarry RA, Ritchie ME.

BMC Bioinformatics. 2014 May 23;15:158. doi: 10.1186/1471-2105-15-158.


edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens.

Dai Z, Sheridan JM, Gearing LJ, Moore DL, Su S, Wormald S, Wilcox S, O'Connor L, Dickins RA, Blewitt ME, Ritchie ME.

Version 2. F1000Res. 2014 Apr 24 [revised 2014 Jan 1];3:95. doi: 10.12688/f1000research.3928.2. eCollection 2014.


Evidence for shared broad-scale climatic niches of diploid and polyploid plants.

Glennon KL, Ritchie ME, Segraves KA.

Ecol Lett. 2014 May;17(5):574-82.


Multidisciplinary diabetes care with and without bariatric surgery in overweight people: a randomised controlled trial.

Wentworth JM, Playfair J, Laurie C, Ritchie ME, Brown WA, Burton P, Shaw JE, O'Brien PE.

Lancet Diabetes Endocrinol. 2014 Jul;2(7):545-52. doi: 10.1016/S2213-8587(14)70066-X. Epub 2014 Apr 7. Erratum in: Lancet Diabetes Endocrinol. 2014 May;2(5):e12.


The effect of fire on habitat selection of mammalian herbivores: the role of body size and vegetation characteristics.

Eby SL, Anderson TM, Mayemba EP, Ritchie ME.

J Anim Ecol. 2014 Sep;83(5):1196-205. doi: 10.1111/1365-2656.12221. Epub 2014 May 19.


Body size mediated coexistence in swans.

Engelhardt KA, Ritchie ME, Powell JA.

ScientificWorldJournal. 2014 Feb 4;2014:643694. doi: 10.1155/2014/643694. eCollection 2014.


Plant compensation to grazing and soil carbon dynamics in a tropical grassland.

Ritchie ME.

PeerJ. 2014 Jan 28;2:e233. doi: 10.7717/peerj.233. eCollection 2014.


Laparoscopic adjustable gastric banding and progression from impaired fasting glucose to diabetes.

Wentworth JM, Hensman T, Playfair J, Laurie C, Ritchie ME, Brown WA, Skinner S, Shaw JE, O'Brien PE.

Diabetologia. 2014 Mar;57(3):463-8. doi: 10.1007/s00125-013-3129-0. Epub 2013 Dec 7.


Targeting BCL-2 with the BH3 mimetic ABT-199 in estrogen receptor-positive breast cancer.

Vaillant F, Merino D, Lee L, Breslin K, Pal B, Ritchie ME, Smyth GK, Christie M, Phillipson LJ, Burns CJ, Mann GB, Visvader JE, Lindeman GJ.

Cancer Cell. 2013 Jul 8;24(1):120-9. doi: 10.1016/j.ccr.2013.06.002.


Effects of grazing on grassland soil carbon: a global review.

McSherry ME, Ritchie ME.

Glob Chang Biol. 2013 May;19(5):1347-57. doi: 10.1111/gcb.12144. Epub 2013 Feb 26. Review.


The species-rich assemblages of tintinnids (marine planktonic protists) are structured by mouth size.

Dolan JR, Landry MR, Ritchie ME.

ISME J. 2013 Jun;7(6):1237-43. doi: 10.1038/ismej.2013.23. Epub 2013 Feb 21.

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