Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 75

1.

Nephron progenitor commitment is a stochastic process influenced by cell migration.

Lawlor KT, Zappia L, Lefevre J, Park JS, Hamilton NA, Oshlack A, Little MH, Combes AN.

Elife. 2019 Jan 24;8. pii: e41156. doi: 10.7554/eLife.41156.

2.

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney.

Combes AN, Zappia L, Er PX, Oshlack A, Little MH.

Genome Med. 2019 Jan 23;11(1):3. doi: 10.1186/s13073-019-0615-0.

3.

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
4.

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.

5.

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.

6.

Ximmer: a system for improving accuracy and consistency of CNV calling from exome data.

Sadedin SP, Ellis JA, Masters SL, Oshlack A.

Gigascience. 2018 Oct 1;7(10). doi: 10.1093/gigascience/giy112.

7.

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.

8.

Clustering trees: a visualization for evaluating clusterings at multiple resolutions.

Zappia L, Oshlack A.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy083.

9.

Clinker: visualizing fusion genes detected in RNA-seq data.

Schmidt BM, Davidson NM, Hawkins ADK, Bartolo R, Majewski IJ, Ekert PG, Oshlack A.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy079.

10.

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.

11.

Cord Blood CD8+ T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner.

Zhang Y, Maksimovic J, Huang B, De Souza DP, Naselli G, Chen H, Zhang L, Weng K, Liang H, Xu Y, Wentworth JM, Huntington ND, Oshlack A, Gong S, Kallies A, Vuillermin P, Yang M, Harrison LC.

Front Immunol. 2018 Apr 25;9:879. doi: 10.3389/fimmu.2018.00879. eCollection 2018.

12.

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

Davidson NM, Oshlack A.

Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy045.

13.

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.

14.

NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network.

Anderson DJ, Kaplan DI, Bell KM, Koutsis K, Haynes JM, Mills RJ, Phelan DG, Qian EL, Leitoguinho AR, Arasaratnam D, Labonne T, Ng ES, Davis RP, Casini S, Passier R, Hudson JE, Porrello ER, Costa MW, Rafii A, Curl CL, Delbridge LM, Harvey RP, Oshlack A, Cheung MM, Mummery CL, Petrou S, Elefanty AG, Stanley EG, Elliott DA.

Nat Commun. 2018 Apr 10;9(1):1373. doi: 10.1038/s41467-018-03714-x.

15.

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.

16.

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.

17.

Erratum to: SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes.

Davidson NM, Hawkins ADK, Oshlack A.

Genome Biol. 2017 Aug 24;18(1):160. doi: 10.1186/s13059-017-1303-2. No abstract available.

18.

A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data.

Stark Z, Dashnow H, Lunke S, Tan TY, Yeung A, Sadedin S, Thorne N, Macciocca I, Gaff C; Melbourne Genomics Health Alliance, Oshlack A, White SM, James PA.

Eur J Hum Genet. 2017 Nov;25(11):1268-1272. doi: 10.1038/ejhg.2017.123. Epub 2017 Aug 23.

19.

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes.

Davidson NM, Hawkins ADK, Oshlack A.

Genome Biol. 2017 Aug 4;18(1):148. doi: 10.1186/s13059-017-1284-1. Erratum in: Genome Biol. 2017 Aug 24;18(1):160.

20.

Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions.

Tan TY, Dillon OJ, Stark Z, Schofield D, Alam K, Shrestha R, Chong B, Phelan D, Brett GR, Creed E, Jarmolowicz A, Yap P, Walsh M, Downie L, Amor DJ, Savarirayan R, McGillivray G, Yeung A, Peters H, Robertson SJ, Robinson AJ, Macciocca I, Sadedin S, Bell K, Oshlack A, Georgeson P, Thorne N, Gaff C, White SM.

JAMA Pediatr. 2017 Sep 1;171(9):855-862. doi: 10.1001/jamapediatrics.2017.1755.

21.

Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing.

Farlie PG, Davidson NM, Baker NL, Raabus M, Roeszler KN, Hirst C, Major A, Mariette MM, Lambert DM, Oshlack A, Smith CA.

Nat Commun. 2017 Jul 25;8(1):132. doi: 10.1038/s41467-017-00112-7.

22.

Transcriptional profiles for distinct aggregation states of mutant Huntingtin exon 1 protein unmask new Huntington's disease pathways.

Moily NS, Ormsby AR, Stojilovic A, Ramdzan YM, Diesch J, Hannan RD, Zajac MS, Hannan AJ, Oshlack A, Hatters DM.

Mol Cell Neurosci. 2017 Sep;83:103-112. doi: 10.1016/j.mcn.2017.07.004. Epub 2017 Jul 23.

PMID:
28743452
23.

MCM3AP in recessive Charcot-Marie-Tooth neuropathy and mild intellectual disability.

Ylikallio E, Woldegebriel R, Tumiati M, Isohanni P, Ryan MM, Stark Z, Walsh M, Sawyer SL, Bell KM, Oshlack A, Lockhart PJ, Shcherbii M, Estrada-Cuzcano A, Atkinson D, Hartley T, Tetreault M, Cuppen I, van der Pol WL, Candayan A, Battaloglu E, Parman Y, van Gassen KLI, van den Boogaard MH, Boycott KM, Kauppi L, Jordanova A, Lönnqvist T, Tyynismaa H.

Brain. 2017 Aug 1;140(8):2093-2103. doi: 10.1093/brain/awx138.

PMID:
28633435
24.

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.

25.

Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy.

Walsh M, Bell KM, Chong B, Creed E, Brett GR, Pope K, Thorne NP, Sadedin S, Georgeson P, Phelan DG, Day T, Taylor JA, Sexton A, Lockhart PJ, Kiers L, Fahey M, Macciocca I, Gaff CL, Oshlack A, Yiu EM, James PA, Stark Z, Ryan MM; Melbourne Genomics Health Alliance.

Ann Clin Transl Neurol. 2017 Apr 26;4(5):318-325. doi: 10.1002/acn3.409. eCollection 2017 May.

26.

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.

27.

Limb patterning genes and heterochronic development of the emu wing bud.

Smith CA, Farlie PG, Davidson NM, Roeszler KN, Hirst C, Oshlack A, Lambert DM.

Evodevo. 2016 Dec 20;7:26. doi: 10.1186/s13227-016-0063-5. eCollection 2016.

28.

Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort.

Eggers S, Sadedin S, van den Bergen JA, Robevska G, Ohnesorg T, Hewitt J, Lambeth L, Bouty A, Knarston IM, Tan TY, Cameron F, Werther G, Hutson J, O'Connell M, Grover SR, Heloury Y, Zacharin M, Bergman P, Kimber C, Brown J, Webb N, Hunter MF, Srinivasan S, Titmuss A, Verge CF, Mowat D, Smith G, Smith J, Ewans L, Shalhoub C, Crock P, Cowell C, Leong GM, Ono M, Lafferty AR, Huynh T, Visser U, Choong CS, McKenzie F, Pachter N, Thompson EM, Couper J, Baxendale A, Gecz J, Wheeler BJ, Jefferies C, MacKenzie K, Hofman P, Carter P, King RI, Krausz C, van Ravenswaaij-Arts CM, Looijenga L, Drop S, Riedl S, Cools M, Dawson A, Juniarto AZ, Khadilkar V, Khadilkar A, Bhatia V, Dũng VC, Atta I, Raza J, Thi Diem Chi N, Hao TK, Harley V, Koopman P, Warne G, Faradz S, Oshlack A, Ayers KL, Sinclair AH.

Genome Biol. 2016 Nov 29;17(1):243.

29.

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
30.

A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders.

Stark Z, Tan TY, Chong B, Brett GR, Yap P, Walsh M, Yeung A, Peters H, Mordaunt D, Cowie S, Amor DJ, Savarirayan R, McGillivray G, Downie L, Ekert PG, Theda C, James PA, Yaplito-Lee J, Ryan MM, Leventer RJ, Creed E, Macciocca I, Bell KM, Oshlack A, Sadedin S, Georgeson P, Anderson C, Thorne N, Melbourne Genomics Health Alliance, Gaff C, White SM.

Genet Med. 2016 Nov;18(11):1090-1096. doi: 10.1038/gim.2016.1. Epub 2016 Mar 3.

PMID:
26938784
31.

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
32.

Erratum to: 'Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq'.

Ayers KL, Lambeth LS, Davidson NM, Sinclair AH, Oshlack A, Smith CA.

BMC Genomics. 2016 Mar 2;17:169. doi: 10.1186/s12864-016-2439-2. No abstract available.

33.

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
34.

Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq.

Ayers KL, Lambeth LS, Davidson NM, Sinclair AH, Oshlack A, Smith CA.

BMC Genomics. 2015 Sep 16;16:704. doi: 10.1186/s12864-015-1886-5. Erratum in: BMC Genomics. 2016;17:169.

35.

Cpipe: a shared variant detection pipeline designed for diagnostic settings.

Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM; Melbourne Genomics Health Alliance, Taylor G, Gaff C, Oshlack A, Thorne NP.

Genome Med. 2015 Jul 10;7(1):68. doi: 10.1186/s13073-015-0191-x. eCollection 2015.

36.

JAFFA: High sensitivity transcriptome-focused fusion gene detection.

Davidson NM, Majewski IJ, Oshlack A.

Genome Med. 2015 May 11;7(1):43. doi: 10.1186/s13073-015-0167-x. eCollection 2015.

37.

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data.

Maksimovic J, Gagnon-Bartsch JA, Speed TP, Oshlack A.

Nucleic Acids Res. 2015 Sep 18;43(16):e106. doi: 10.1093/nar/gkv526. Epub 2015 May 18.

38.

Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells.

McClelland KS, Bell K, Larney C, Harley VR, Sinclair AH, Oshlack A, Koopman P, Bowles J.

Biol Reprod. 2015 Jun;92(6):145. doi: 10.1095/biolreprod.115.128918. Epub 2015 Apr 8.

PMID:
25855264
39.

Jarid2 regulates hematopoietic stem cell function by acting with polycomb repressive complex 2.

Kinkel SA, Galeev R, Flensburg C, Keniry A, Breslin K, Gilan O, Lee S, Liu J, Chen K, Gearing LJ, Moore DL, Alexander WS, Dawson M, Majewski IJ, Oshlack A, Larsson J, Blewitt ME.

Blood. 2015 Mar 19;125(12):1890-900. doi: 10.1182/blood-2014-10-603969. Epub 2015 Feb 2.

40.

A comparison of control samples for ChIP-seq of histone modifications.

Flensburg C, Kinkel SA, Keniry A, Blewitt ME, Oshlack A.

Front Genet. 2014 Sep 25;5:329. doi: 10.3389/fgene.2014.00329. eCollection 2014.

41.

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.

42.

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes.

Davidson NM, Oshlack A.

Genome Biol. 2014 Jul 26;15(7):410. doi: 10.1186/s13059-014-0410-6.

43.

The polycomb repressive complex 2 governs life and death of peripheral T cells.

Zhang Y, Kinkel S, Maksimovic J, Bandala-Sanchez E, Tanzer MC, Naselli G, Zhang JG, Zhan Y, Lew AM, Silke J, Oshlack A, Blewitt ME, Harrison LC.

Blood. 2014 Jul 31;124(5):737-49. doi: 10.1182/blood-2013-12-544106. Epub 2014 Jun 20.

44.

Identification, expression, and regulation of anti-Müllerian hormone type-II receptor in the embryonic chicken gonad.

Cutting AD, Ayers K, Davidson N, Oshlack A, Doran T, Sinclair AH, Tizard M, Smith CA.

Biol Reprod. 2014 May;90(5):106. doi: 10.1095/biolreprod.113.116491. Epub 2014 Mar 12.

PMID:
24621923
45.

Susceptibility to acute rheumatic fever based on differential expression of genes involved in cytotoxicity, chemotaxis, and apoptosis.

Bryant PA, Smyth GK, Gooding T, Oshlack A, Harrington Z, Currie B, Carapetis JR, Robins-Browne R, Curtis N.

Infect Immun. 2014 Feb;82(2):753-61. doi: 10.1128/IAI.01152-13. Epub 2013 Dec 2.

46.

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy.

Cruickshank MN, Oshlack A, Theda C, Davis PG, Martino D, Sheehan P, Dai Y, Saffery R, Doyle LW, Craig JM.

Genome Med. 2013 Oct 18;5(10):96. doi: 10.1186/gm500. eCollection 2013.

47.

Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes.

Kim JH, Zhang T, Wong NC, Davidson N, Maksimovic J, Oshlack A, Earnshaw WC, Kalitsis P, Hudson DF.

Nat Commun. 2013;4:2537. doi: 10.1038/ncomms3537.

48.

Cell-type-specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological, and environmental demands.

Pasricha S, Payne M, Canovas D, Pase L, Ngaosuwankul N, Beard S, Oshlack A, Smyth GK, Chaiyaroj SC, Boyce KJ, Andrianopoulos A.

G3 (Bethesda). 2013 Nov 6;3(11):1997-2014. doi: 10.1534/g3.113.006809.

49.

Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells.

Zhang Y, Maksimovic J, Naselli G, Qian J, Chopin M, Blewitt ME, Oshlack A, Harrison LC.

Blood. 2013 Oct 17;122(16):2823-36. doi: 10.1182/blood-2013-02-481788. Epub 2013 Aug 23.

50.

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing.

Majewski IJ, Mittempergher L, Davidson NM, Bosma A, Willems SM, Horlings HM, de Rink I, Greger L, Hooijer GK, Peters D, Nederlof PM, Hofland I, de Jong J, Wesseling J, Kluin RJ, Brugman W, Kerkhoven R, Nieboer F, Roepman P, Broeks A, Muley TR, Jassem J, Niklinski J, van Zandwijk N, Brazma A, Oshlack A, van den Heuvel M, Bernards R.

J Pathol. 2013 Jul;230(3):270-6. doi: 10.1002/path.4209.

PMID:
23661334

Supplemental Content

Loading ...
Support Center