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Items: 32

1.

Evaluation of variability in human kidney organoids.

Phipson B, Er PX, Combes AN, Forbes TA, Howden SE, Zappia L, Yen HJ, Lawlor KT, Hale LJ, Sun J, Wolvetang E, Takasato M, Oshlack A, Little MH.

Nat Methods. 2019 Jan;16(1):79-87. doi: 10.1038/s41592-018-0253-2. Epub 2018 Dec 20.

PMID:
30573816
2.

3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening.

Hale LJ, Howden SE, Phipson B, Lonsdale A, Er PX, Ghobrial I, Hosawi S, Wilson S, Lawlor KT, Khan S, Oshlack A, Quinlan C, Lennon R, Little MH.

Nat Commun. 2018 Dec 4;9(1):5167. doi: 10.1038/s41467-018-07594-z.

3.

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period.

Krauss RH, Phipson B, Oshlack A, Prasad-Gupta N, Cheung MM, Smolich JJ, Pepe S.

PLoS One. 2018 Sep 19;13(9):e0204038. doi: 10.1371/journal.pone.0204038. eCollection 2018.

4.

STRetch: detecting and discovering pathogenic short tandem repeat expansions.

Dashnow H, Lek M, Phipson B, Halman A, Sadedin S, Lonsdale A, Davis M, Lamont P, Clayton JS, Laing NG, MacArthur DG, Oshlack A.

Genome Biol. 2018 Aug 21;19(1):121. doi: 10.1186/s13059-018-1505-2.

5.

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.

Zappia L, Phipson B, Oshlack A.

PLoS Comput Biol. 2018 Jun 25;14(6):e1006245. doi: 10.1371/journal.pcbi.1006245. eCollection 2018 Jun.

6.

Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms.

Forbes TA, Howden SE, Lawlor K, Phipson B, Maksimovic J, Hale L, Wilson S, Quinlan C, Ho G, Holman K, Bennetts B, Crawford J, Trnka P, Oshlack A, Patel C, Mallett A, Simons C, Little MH.

Am J Hum Genet. 2018 May 3;102(5):816-831. doi: 10.1016/j.ajhg.2018.03.014. Epub 2018 Apr 26.

7.

Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number.

Combes AN, Wilson S, Phipson B, Binnie BB, Ju A, Lawlor KT, Cebrian C, Walton SL, Smyth IM, Moritz KM, Kopan R, Oshlack A, Little MH.

Kidney Int. 2018 Mar;93(3):589-598. doi: 10.1016/j.kint.2017.09.015. Epub 2017 Dec 6.

8.

Splatter: simulation of single-cell RNA sequencing data.

Zappia L, Phipson B, Oshlack A.

Genome Biol. 2017 Sep 12;18(1):174. doi: 10.1186/s13059-017-1305-0.

9.

Gene length and detection bias in single cell RNA sequencing protocols.

Phipson B, Zappia L, Oshlack A.

F1000Res. 2017 Apr 28;6:595. doi: 10.12688/f1000research.11290.1. eCollection 2017.

10.

A cross-package Bioconductor workflow for analysing methylation array data.

Maksimovic J, Phipson B, Oshlack A.

Version 3. F1000Res. 2016 Jun 8 [revised 2017 Jan 1];5:1281. doi: 10.12688/f1000research.8839.3. eCollection 2016.

11.

ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION.

Phipson B, Lee S, Majewski IJ, Alexander WS, Smyth GK.

Ann Appl Stat. 2016 Jun;10(2):946-963. doi: 10.1214/16-AOAS920. Epub 2016 Jul 22.

12.

Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros.

Ng ES, Azzola L, Bruveris FF, Calvanese V, Phipson B, Vlahos K, Hirst C, Jokubaitis VJ, Yu QC, Maksimovic J, Liebscher S, Januar V, Zhang Z, Williams B, Conscience A, Durnall J, Jackson S, Costa M, Elliott D, Haylock DN, Nilsson SK, Saffery R, Schenke-Layland K, Oshlack A, Mikkola HK, Stanley EG, Elefanty AG.

Nat Biotechnol. 2016 Nov;34(11):1168-1179. doi: 10.1038/nbt.3702. Epub 2016 Oct 17.

PMID:
27748754
13.

Functionally distinct roles for different miR-155 expression levels through contrasting effects on gene expression, in acute myeloid leukaemia.

Narayan N, Morenos L, Phipson B, Willis SN, Brumatti G, Eggers S, Lalaoui N, Brown LM, Kosasih HJ, Bartolo RC, Zhou L, Catchpoole D, Saffery R, Oshlack A, Goodall GJ, Ekert PG.

Leukemia. 2017 Apr;31(4):808-820. doi: 10.1038/leu.2016.279. Epub 2016 Oct 14.

PMID:
27740637
14.

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform.

Phipson B, Maksimovic J, Oshlack A.

Bioinformatics. 2016 Jan 15;32(2):286-8. doi: 10.1093/bioinformatics/btv560. Epub 2015 Sep 30.

PMID:
26424855
15.

Early lineage priming by trisomy of Erg leads to myeloproliferation in a Down syndrome model.

Ng AP, Hu Y, Metcalf D, Hyland CD, Ierino H, Phipson B, Wu D, Baldwin TM, Kauppi M, Kiu H, Di Rago L, Hilton DJ, Smyth GK, Alexander WS.

PLoS Genet. 2015 May 14;11(5):e1005211. doi: 10.1371/journal.pgen.1005211. eCollection 2015 May.

16.

MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo.

Sheikh BN, Downer NL, Phipson B, Vanyai HK, Kueh AJ, McCarthy DJ, Smyth GK, Thomas T, Voss AK.

Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):5437-42. doi: 10.1073/pnas.1422872112. Epub 2015 Apr 14.

17.

MOZ (MYST3, KAT6A) inhibits senescence via the INK4A-ARF pathway.

Sheikh BN, Phipson B, El-Saafin F, Vanyai HK, Downer NL, Bird MJ, Kueh AJ, May RE, Smyth GK, Voss AK, Thomas T.

Oncogene. 2015 Nov 19;34(47):5807-20. doi: 10.1038/onc.2015.33. Epub 2015 Mar 16.

PMID:
25772242
18.

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.

19.

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging.

Phipson B, Oshlack A.

Genome Biol. 2014 Sep 23;15(9):465. doi: 10.1186/s13059-014-0465-4.

20.

Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma.

Lee SC, Phipson B, Hyland CD, Leong HS, Allan RS, Lun A, Hilton DJ, Nutt SL, Blewitt ME, Smyth GK, Alexander WS, Majewski IJ.

Blood. 2013 Oct 10;122(15):2654-63. doi: 10.1182/blood-2013-02-484055. Epub 2013 Aug 27.

21.

Neither loss of Bik alone, nor combined loss of Bik and Noxa, accelerate murine lymphoma development or render lymphoma cells resistant to DNA damaging drugs.

Happo L, Phipson B, Smyth GK, Strasser A, Scott CL.

Cell Death Dis. 2012 May 10;3:e306. doi: 10.1038/cddis.2012.42.

22.

Bcl-2, Bcl-x(L), and Bcl-w are not equivalent targets of ABT-737 and navitoclax (ABT-263) in lymphoid and leukemic cells.

Mérino D, Khaw SL, Glaser SP, Anderson DJ, Belmont LD, Wong C, Yue P, Robati M, Phipson B, Fairlie WD, Lee EF, Campbell KJ, Vandenberg CJ, Cory S, Roberts AW, Ludlam MJ, Huang DC, Bouillet P.

Blood. 2012 Jun 14;119(24):5807-16. doi: 10.1182/blood-2011-12-400929. Epub 2012 Apr 26.

23.

Proteomic and metabolomic analyses of mitochondrial complex I-deficient mouse model generated by spontaneous B2 short interspersed nuclear element (SINE) insertion into NADH dehydrogenase (ubiquinone) Fe-S protein 4 (Ndufs4) gene.

Leong DW, Komen JC, Hewitt CA, Arnaud E, McKenzie M, Phipson B, Bahlo M, Laskowski A, Kinkel SA, Davey GM, Heath WR, Voss AK, Zahedi RP, Pitt JJ, Chrast R, Sickmann A, Ryan MT, Smyth GK, Thorburn DR, Scott HS.

J Biol Chem. 2012 Jun 8;287(24):20652-63. doi: 10.1074/jbc.M111.327601. Epub 2012 Apr 25.

24.

Targeting antigen to mouse dendritic cells via Clec9A induces potent CD4 T cell responses biased toward a follicular helper phenotype.

Lahoud MH, Ahmet F, Kitsoulis S, Wan SS, Vremec D, Lee CN, Phipson B, Shi W, Smyth GK, Lew AM, Kato Y, Mueller SN, Davey GM, Heath WR, Shortman K, Caminschi I.

J Immunol. 2011 Jul 15;187(2):842-50. doi: 10.4049/jimmunol.1101176. Epub 2011 Jun 15.

25.

Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance.

Hubert FX, Kinkel SA, Davey GM, Phipson B, Mueller SN, Liston A, Proietto AI, Cannon PZ, Forehan S, Smyth GK, Wu L, Goodnow CC, Carbone FR, Scott HS, Heath WR.

Blood. 2011 Sep 1;118(9):2462-72. doi: 10.1182/blood-2010-06-286393. Epub 2011 Apr 19.

26.

A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility.

Tan IK, Mackin L, Wang N, Papenfuss AT, Elso CM, Ashton MP, Quirk F, Phipson B, Bahlo M, Speed TP, Smyth GK, Morahan G, Brodnicki TC.

Genome Res. 2010 Dec;20(12):1629-38. doi: 10.1101/gr.101881.109. Epub 2010 Nov 4.

27.

Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn.

Phipson B, Smyth GK.

Stat Appl Genet Mol Biol. 2010;9:Article39. doi: 10.2202/1544-6115.1585. Epub 2010 Oct 31.

PMID:
21044043
28.

Maximal killing of lymphoma cells by DNA damage-inducing therapy requires not only the p53 targets Puma and Noxa, but also Bim.

Happo L, Cragg MS, Phipson B, Haga JM, Jansen ES, Herold MJ, Dewson G, Michalak EM, Vandenberg CJ, Smyth GK, Strasser A, Cory S, Scott CL.

Blood. 2010 Dec 9;116(24):5256-67. doi: 10.1182/blood-2010-04-280818. Epub 2010 Sep 9.

29.

Opposing roles of polycomb repressive complexes in hematopoietic stem and progenitor cells.

Majewski IJ, Ritchie ME, Phipson B, Corbin J, Pakusch M, Ebert A, Busslinger M, Koseki H, Hu Y, Smyth GK, Alexander WS, Hilton DJ, Blewitt ME.

Blood. 2010 Aug 5;116(5):731-9. doi: 10.1182/blood-2009-12-260760. Epub 2010 May 5.

30.

Pro-inflammatory CD11c+CD206+ adipose tissue macrophages are associated with insulin resistance in human obesity.

Wentworth JM, Naselli G, Brown WA, Doyle L, Phipson B, Smyth GK, Wabitsch M, O'Brien PE, Harrison LC.

Diabetes. 2010 Jul;59(7):1648-56. doi: 10.2337/db09-0287. Epub 2010 Mar 31.

31.

Murine hematopoietic blast colony-forming cells and their progeny have distinctive membrane marker profiles.

Metcalf D, Ng AP, Loughran SJ, Phipson B, Smyth GK, Di Rago L, Mifsud S.

Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19102-7. doi: 10.1073/pnas.0910354106. Epub 2009 Oct 23.

32.

Molecular dissection of the pea shoot apical meristem.

Liang D, Wong CE, Singh MB, Beveridge CA, Phipson B, Smyth GK, Bhalla PL.

J Exp Bot. 2009;60(14):4201-13. doi: 10.1093/jxb/erp254. Epub 2009 Aug 25.

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