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Items: 1 to 50 of 107

1.

Index suffix-prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression.

Liu Y, Yu Y, Dinger ME, Li J.

Bioinformatics. 2018 Nov 8. doi: 10.1093/bioinformatics/bty936. [Epub ahead of print]

PMID:
30407482
2.

The Medical Genome Reference Bank: a whole-genome data resource of 4000 healthy elderly individuals. Rationale and cohort design.

Lacaze P, Pinese M, Kaplan W, Stone A, Brion MJ, Woods RL, McNamara M, McNeil JJ, Dinger ME, Thomas DM.

Eur J Hum Genet. 2018 Oct 24. doi: 10.1038/s41431-018-0279-z. [Epub ahead of print]

PMID:
30353151
3.

Response to Brodehl et al.

Minoche AE, Horvat C, Johnson R, Gayevskiy V, Morton SU, Drew AP, Woo K, Statham AL, Lundie B, Bagnall RD, Ingles J, Semsarian C, Seidman JG, Seidman CE, Dinger ME, Cowley MJ, Fatkin D.

Genet Med. 2018 Sep 28. doi: 10.1038/s41436-018-0292-1. [Epub ahead of print] No abstract available.

PMID:
30262924
4.

Selection of Antibody Fragments Against Structured DNA by Phage Display.

Zeraati M, Dinger ME, Christ D.

Methods Mol Biol. 2018;1827:197-209. doi: 10.1007/978-1-4939-8648-4_11.

PMID:
30196499
5.

Expanding the spectrum of PEX16 mutations and novel insights into disease mechanisms.

Kumar KR, Wali G, Davis RL, Mallawaarachchi AC, Palmer EE, Gayevskiy V, Minoche AE, Veivers D, Dinger ME, Mackay-Sim A, Cowley MJ, Sue CM.

Mol Genet Metab Rep. 2018 Jul 20;16:46-51. doi: 10.1016/j.ymgmr.2018.07.003. eCollection 2018 Sep.

6.

Realizing the significance of noncoding functionality in clinical genomics.

Gloss BS, Dinger ME.

Exp Mol Med. 2018 Aug 7;50(8):97. doi: 10.1038/s12276-018-0087-0. Review.

7.

Whole Genome Sequencing Improves Outcomes of Genetic Testing in Patients With Hypertrophic Cardiomyopathy.

Bagnall RD, Ingles J, Dinger ME, Cowley MJ, Ross SB, Minoche AE, Lal S, Turner C, Colley A, Rajagopalan S, Berman Y, Ronan A, Fatkin D, Semsarian C.

J Am Coll Cardiol. 2018 Jul 24;72(4):419-429. doi: 10.1016/j.jacc.2018.04.078.

PMID:
30025578
8.

Genome sequencing as a first-line genetic test in familial dilated cardiomyopathy.

Minoche AE, Horvat C, Johnson R, Gayevskiy V, Morton SU, Drew AP, Woo K, Statham AL, Lundie B, Bagnall RD, Ingles J, Semsarian C, Seidman JG, Seidman CE, Dinger ME, Cowley MJ, Fatkin D.

Genet Med. 2018 Jul 2. doi: 10.1038/s41436-018-0084-7. [Epub ahead of print]

PMID:
29961767
9.

I-motif DNA structures are formed in the nuclei of human cells.

Zeraati M, Langley DB, Schofield P, Moye AL, Rouet R, Hughes WE, Bryan TM, Dinger ME, Christ D.

Nat Chem. 2018 Jun;10(6):631-637. doi: 10.1038/s41557-018-0046-3. Epub 2018 Apr 23.

PMID:
29686376
10.

Evidence that TLR4 Is Not a Receptor for Saturated Fatty Acids but Mediates Lipid-Induced Inflammation by Reprogramming Macrophage Metabolism.

Lancaster GI, Langley KG, Berglund NA, Kammoun HL, Reibe S, Estevez E, Weir J, Mellett NA, Pernes G, Conway JRW, Lee MKS, Timpson P, Murphy AJ, Masters SL, Gerondakis S, Bartonicek N, Kaczorowski DC, Dinger ME, Meikle PJ, Bond PJ, Febbraio MA.

Cell Metab. 2018 May 1;27(5):1096-1110.e5. doi: 10.1016/j.cmet.2018.03.014. Epub 2018 Apr 19.

PMID:
29681442
11.

Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders.

Ewans LJ, Schofield D, Shrestha R, Zhu Y, Gayevskiy V, Ying K, Walsh C, Lee E, Kirk EP, Colley A, Ellaway C, Turner A, Mowat D, Worgan L, Freckmann ML, Lipke M, Sachdev R, Miller D, Field M, Dinger ME, Buckley MF, Cowley MJ, Roscioli T.

Genet Med. 2018 Mar 29. doi: 10.1038/gim.2018.39. [Epub ahead of print]

PMID:
29595814
12.

A Mild PUM1 Mutation Is Associated with Adult-Onset Ataxia, whereas Haploinsufficiency Causes Developmental Delay and Seizures.

Gennarino VA, Palmer EE, McDonell LM, Wang L, Adamski CJ, Koire A, See L, Chen CA, Schaaf CP, Rosenfeld JA, Panzer JA, Moog U, Hao S, Bye A, Kirk EP, Stankiewicz P, Breman AM, McBride A, Kandula T, Dubbs HA, Macintosh R, Cardamone M, Zhu Y, Ying K, Dias KR, Cho MT, Henderson LB, Baskin B, Morris P, Tao J, Cowley MJ, Dinger ME, Roscioli T, Caluseriu O, Suchowersky O, Sachdev RK, Lichtarge O, Tang J, Boycott KM, Holder JL Jr, Zoghbi HY.

Cell. 2018 Feb 22;172(5):924-936.e11. doi: 10.1016/j.cell.2018.02.006.

PMID:
29474920
13.

Universal Alternative Splicing of Noncoding Exons.

Deveson IW, Brunck ME, Blackburn J, Tseng E, Hon T, Clark TA, Clark MB, Crawford J, Dinger ME, Nielsen LK, Mattick JS, Mercer TR.

Cell Syst. 2018 Feb 28;6(2):245-255.e5. doi: 10.1016/j.cels.2017.12.005. Epub 2018 Jan 24.

PMID:
29396323
14.

Integrating exome sequencing into a diagnostic pathway for epileptic encephalopathy: Evidence of clinical utility and cost effectiveness.

Palmer EE, Schofield D, Shrestha R, Kandula T, Macintosh R, Lawson JA, Andrews I, Sampaio H, Johnson AM, Farrar MA, Cardamone M, Mowat D, Elakis G, Lo W, Zhu Y, Ying K, Morris P, Tao J, Dias KR, Buckley M, Dinger ME, Cowley MJ, Roscioli T, Kirk EP, Bye A, Sachdev RK.

Mol Genet Genomic Med. 2018 Mar;6(2):186-199. doi: 10.1002/mgg3.355. Epub 2018 Jan 4.

15.

Intergenic disease-associated regions are abundant in novel transcripts.

Bartonicek N, Clark MB, Quek XC, Torpy JR, Pritchard AL, Maag JLV, Gloss BS, Crawford J, Taft RJ, Hayward NK, Montgomery GW, Mattick JS, Mercer TR, Dinger ME.

Genome Biol. 2017 Dec 28;18(1):241. doi: 10.1186/s13059-017-1363-3.

16.

CCR6 Defines Memory B Cell Precursors in Mouse and Human Germinal Centers, Revealing Light-Zone Location and Predominant Low Antigen Affinity.

Suan D, Kräutler NJ, Maag JLV, Butt D, Bourne K, Hermes JR, Avery DT, Young C, Statham A, Elliott M, Dinger ME, Basten A, Tangye SG, Brink R.

Immunity. 2017 Dec 19;47(6):1142-1153.e4. doi: 10.1016/j.immuni.2017.11.022.

PMID:
29262350
17.

Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework.

Baynam G, Bowman F, Lister K, Walker CE, Pachter N, Goldblatt J, Boycott KM, Gahl WA, Kosaki K, Adachi T, Ishii K, Mahede T, McKenzie F, Townshend S, Slee J, Kiraly-Borri C, Vasudevan A, Hawkins A, Broley S, Schofield L, Verhoef H, Groza T, Zankl A, Robinson PN, Haendel M, Brudno M, Mattick JS, Dinger ME, Roscioli T, Cowley MJ, Olry A, Hanauer M, Alkuraya FS, Taruscio D, Posada de la Paz M, Lochmüller H, Bushby K, Thompson R, Hedley V, Lasko P, Mina K, Beilby J, Tifft C, Davis M, Laing NG, Julkowska D, Le Cam Y, Terry SF, Kaufmann P, Eerola I, Norstedt I, Rath A, Suematsu M, Groft SC, Austin CP, Draghia-Akli R, Weeramanthri TS, Molster C, Dawkins HJS.

Adv Exp Med Biol. 2017;1031:55-94. doi: 10.1007/978-3-319-67144-4_4. Review.

PMID:
29214566
18.

NMNAT1 variants cause cone and cone-rod dystrophy.

Nash BM, Symes R, Goel H, Dinger ME, Bennetts B, Grigg JR, Jamieson RV.

Eur J Hum Genet. 2018 Mar;26(3):428-433. doi: 10.1038/s41431-017-0029-7. Epub 2017 Nov 28.

PMID:
29184169
19.

Somatic mutations in salivary duct carcinoma and potential therapeutic targets.

Khoo TK, Yu B, Smith JA, Clarke AJ, Luk PP, Selinger CI, Mahon KL, Kraitsek S, Palme C, Boyer MJ, Dinger ME, Cowley MJ, O'Toole SA, Clark JR, Gupta R.

Oncotarget. 2017 May 25;8(44):75893-75903. doi: 10.18632/oncotarget.18173. eCollection 2017 Sep 29.

20.

Machine learning annotation of human branchpoints.

Signal B, Gloss BS, Dinger ME, Mercer TR.

Bioinformatics. 2018 Mar 15;34(6):920-927. doi: 10.1093/bioinformatics/btx688.

PMID:
29092009
21.

A De Novo Mutation in the Sodium-Activated Potassium Channel KCNT2 Alters Ion Selectivity and Causes Epileptic Encephalopathy.

Gururaj S, Palmer EE, Sheehan GD, Kandula T, Macintosh R, Ying K, Morris P, Tao J, Dias KR, Zhu Y, Dinger ME, Cowley MJ, Kirk EP, Roscioli T, Sachdev R, Duffey ME, Bye A, Bhattacharjee A.

Cell Rep. 2017 Oct 24;21(4):926-933. doi: 10.1016/j.celrep.2017.09.088.

22.

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers.

Hoang VLT, Tom LN, Quek XC, Tan JM, Payne EJ, Lin LL, Sinnya S, Raphael AP, Lambie D, Frazer IH, Dinger ME, Soyer HP, Prow TW.

PeerJ. 2017 Aug 21;5:e3631. doi: 10.7717/peerj.3631. eCollection 2017.

23.

Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage.

Betts JA, Moradi Marjaneh M, Al-Ejeh F, Lim YC, Shi W, Sivakumaran H, Tropée R, Patch AM, Clark MB, Bartonicek N, Wiegmans AP, Hillman KM, Kaufmann S, Bain AL, Gloss BS, Crawford J, Kazakoff S, Wani S, Wen SW, Day B, Möller A, Cloonan N, Pearson J, Brown MA, Mercer TR, Waddell N, Khanna KK, Dray E, Dinger ME, Edwards SL, French JD.

Am J Hum Genet. 2017 Aug 3;101(2):255-266. doi: 10.1016/j.ajhg.2017.07.007.

24.

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci.

Gloss BS, Signal B, Cheetham SW, Gruhl F, Kaczorowski DC, Perkins AC, Dinger ME.

Sci Rep. 2017 Jul 27;7(1):6731. doi: 10.1038/s41598-017-06110-5.

25.

Novel Aberrations Uncovered in Barrett's Esophagus and Esophageal Adenocarcinoma Using Whole Transcriptome Sequencing.

Maag JLV, Fisher OM, Levert-Mignon A, Kaczorowski DC, Thomas ML, Hussey DJ, Watson DI, Wettstein A, Bobryshev YV, Edwards M, Dinger ME, Lord RV.

Mol Cancer Res. 2017 Nov;15(11):1558-1569. doi: 10.1158/1541-7786.MCR-17-0332. Epub 2017 Jul 27.

26.

Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data.

Everaert C, Luypaert M, Maag JLV, Cheng QX, Dinger ME, Hellemans J, Mestdagh P.

Sci Rep. 2017 May 8;7(1):1559. doi: 10.1038/s41598-017-01617-3.

27.

Initiating an undiagnosed diseases program in the Western Australian public health system.

Baynam G, Broley S, Bauskis A, Pachter N, McKenzie F, Townshend S, Slee J, Kiraly-Borri C, Vasudevan A, Hawkins A, Schofield L, Helmholz P, Palmer R, Kung S, Walker CE, Molster C, Lewis B, Mina K, Beilby J, Pathak G, Poulton C, Groza T, Zankl A, Roscioli T, Dinger ME, Mattick JS, Gahl W, Groft S, Tifft C, Taruscio D, Lasko P, Kosaki K, Wilhelm H, Melegh B, Carapetis J, Jana S, Chaney G, Johns A, Owen PW, Daly F, Weeramanthri T, Dawkins H, Goldblatt J.

Orphanet J Rare Dis. 2017 May 3;12(1):83. doi: 10.1186/s13023-017-0619-z.

28.

Cancer-associated noncoding mutations affect RNA G-quadruplex-mediated regulation of gene expression.

Zeraati M, Moye AL, Wong JWH, Perera D, Cowley MJ, Christ DU, Bryan TM, Dinger ME.

Sci Rep. 2017 Apr 6;7(1):708. doi: 10.1038/s41598-017-00739-y.

29.

Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo.

Maag JL, Kaczorowski DC, Panja D, Peters TJ, Bramham CR, Wibrand K, Dinger ME.

BMC Genomics. 2017 Mar 23;18(1):250. doi: 10.1186/s12864-017-3621-x.

30.

Gonadal mosaicism of a novel IQSEC2 variant causing female limited intellectual disability and epilepsy.

Ewans LJ, Field M, Zhu Y, Turner G, Leffler M, Dinger ME, Cowley MJ, Buckley MF, Scheffer IE, Jackson MR, Roscioli T, Shoubridge C.

Eur J Hum Genet. 2017 Jun;25(6):763-767. doi: 10.1038/ejhg.2017.29. Epub 2017 Mar 15.

31.

Germline variants in familial pituitary tumour syndrome genes are common in young patients and families with additional endocrine tumours.

De Sousa SM, McCabe MJ, Wu K, Roscioli T, Gayevskiy V, Brook K, Rawlings L, Scott HS, Thompson TJ, Earls P, Gill AJ, Cowley MJ, Dinger ME, McCormack AI.

Eur J Endocrinol. 2017 May;176(5):635-644. doi: 10.1530/EJE-16-0944. Epub 2017 Feb 20.

PMID:
28220018
32.

Endometriosis risk alleles at 1p36.12 act through inverse regulation of CDC42 and LINC00339.

Powell JE, Fung JN, Shakhbazov K, Sapkota Y, Cloonan N, Hemani G, Hillman KM, Kaufmann S, Luong HT, Bowdler L, Painter JN, Holdsworth-Carson SJ, Visscher PM, Dinger ME, Healey M, Nyholt DR, French JD, Edwards SL, Rogers PA, Montgomery GW.

Hum Mol Genet. 2016 Nov 15;25(22):5046-5058. doi: 10.1093/hmg/ddw320.

PMID:
28171565
33.

The regulatory role of long noncoding RNAs in cancer.

Tang Y, Cheung BB, Atmadibrata B, Marshall GM, Dinger ME, Liu PY, Liu T.

Cancer Lett. 2017 Apr 10;391:12-19. doi: 10.1016/j.canlet.2017.01.010. Epub 2017 Jan 19. Review.

PMID:
28111137
34.

The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states.

Barry G, Briggs JA, Hwang DW, Nayler SP, Fortuna PR, Jonkhout N, Dachet F, Maag JL, Mestdagh P, Singh EM, Avesson L, Kaczorowski DC, Ozturk E, Jones NC, Vetter I, Arriola-Martinez L, Hu J, Franco GR, Warn VM, Gong A, Dinger ME, Rigo F, Lipovich L, Morris MJ, O'Brien TJ, Lee DS, Loeb JA, Blackshaw S, Mattick JS, Wolvetang EJ.

Sci Rep. 2017 Jan 5;7:40127. doi: 10.1038/srep40127.

35.

The BET bromodomain inhibitor exerts the most potent synergistic anticancer effects with quinone-containing compounds and anti-microtubule drugs.

Liu PY, Sokolowski N, Guo ST, Siddiqi F, Atmadibrata B, Telfer TJ, Sun Y, Zhang L, Yu D, Mccarroll J, Liu B, Yang RH, Guo XY, Tee AE, Itoh K, Wang J, Kavallaris M, Haber M, Norris MD, Cheung BB, Byrne JA, Ziegler DS, Marshall GM, Dinger ME, Codd R, Zhang XD, Liu T.

Oncotarget. 2016 Nov 29;7(48):79217-79232. doi: 10.18632/oncotarget.12640.

36.

Defining the genetic basis of early onset hereditary spastic paraplegia using whole genome sequencing.

Kumar KR, Wali GM, Kamate M, Wali G, Minoche AE, Puttick C, Pinese M, Gayevskiy V, Dinger ME, Roscioli T, Sue CM, Cowley MJ.

Neurogenetics. 2016 Oct;17(4):265-270. Epub 2016 Sep 28.

37.

Computational Approaches for Functional Prediction and Characterisation of Long Noncoding RNAs.

Signal B, Gloss BS, Dinger ME.

Trends Genet. 2016 Oct;32(10):620-637. doi: 10.1016/j.tig.2016.08.004. Epub 2016 Sep 1. Review.

PMID:
27592414
38.

Corrigendum: Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity.

Maag JL, Panja D, Sporild I, Patil SS, Kaczorowski DC, Bramham CR, Dinger ME, Wibrand K.

Front Neurosci. 2016 Jul 27;10:354. doi: 10.3389/fnins.2016.00354. eCollection 2016.

39.

Long noncoding RNAs in cancer: mechanisms of action and technological advancements.

Bartonicek N, Maag JL, Dinger ME.

Mol Cancer. 2016 May 27;15(1):43. doi: 10.1186/s12943-016-0530-6. Review.

40.

The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation.

Bell CC, Amaral PP, Kalsbeek A, Magor GW, Gillinder KR, Tangermann P, di Lisio L, Cheetham SW, Gruhl F, Frith J, Tallack MR, Ru KL, Crawford J, Mattick JS, Dinger ME, Perkins AC.

Sci Rep. 2016 May 26;6:26657. doi: 10.1038/srep26657.

41.

Improved definition of the mouse transcriptome via targeted RNA sequencing.

Bussotti G, Leonardi T, Clark MB, Mercer TR, Crawford J, Malquori L, Notredame C, Dinger ME, Mattick JS, Enright AJ.

Genome Res. 2016 May;26(5):705-16. doi: 10.1101/gr.199760.115.

42.

Whole-genome sequencing overcomes pseudogene homology to diagnose autosomal dominant polycystic kidney disease.

Mallawaarachchi AC, Hort Y, Cowley MJ, McCabe MJ, Minoche A, Dinger ME, Shine J, Furlong TJ.

Eur J Hum Genet. 2016 Nov;24(11):1584-1590. doi: 10.1038/ejhg.2016.48. Epub 2016 May 11.

43.

Endogenous microRNA sponges: evidence and controversy.

Thomson DW, Dinger ME.

Nat Rev Genet. 2016 May;17(5):272-83. doi: 10.1038/nrg.2016.20. Epub 2016 Apr 4. Review.

PMID:
27040487
44.

Comparison of whole-exome sequencing of matched fresh and formalin fixed paraffin embedded melanoma tumours: implications for clinical decision making.

De Paoli-Iseppi R, Johansson PA, Menzies AM, Dias KR, Pupo GM, Kakavand H, Wilmott JS, Mann GJ, Hayward NK, Dinger ME, Long GV, Scolyer RA.

Pathology. 2016 Apr;48(3):261-6. doi: 10.1016/j.pathol.2016.01.001. Epub 2016 Mar 9.

PMID:
27020503
45.

Gonadotropin suppression in men leads to a reduction in claudin-11 at the Sertoli cell tight junction.

McCabe MJ, Tarulli GA, Laven-Law G, Matthiesson KL, Meachem SJ, McLachlan RI, Dinger ME, Stanton PG.

Hum Reprod. 2016 Apr;31(4):875-86. doi: 10.1093/humrep/dew009. Epub 2016 Feb 18.

PMID:
26908839
46.

Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents.

Merlevede J, Droin N, Qin T, Meldi K, Yoshida K, Morabito M, Chautard E, Auboeuf D, Fenaux P, Braun T, Itzykson R, de Botton S, Quesnel B, Commes T, Jourdan E, Vainchenker W, Bernard O, Pata-Merci N, Solier S, Gayevskiy V, Dinger ME, Cowley MJ, Selimoglu-Buet D, Meyer V, Artiguenave F, Deleuze JF, Preudhomme C, Stratton MR, Alexandrov LB, Padron E, Ogawa S, Koscielny S, Figueroa M, Solary E.

Nat Commun. 2016 Feb 24;7:10767. doi: 10.1038/ncomms10767.

47.

The long noncoding RNA MALAT1 promotes tumor-driven angiogenesis by up-regulating pro-angiogenic gene expression.

Tee AE, Liu B, Song R, Li J, Pasquier E, Cheung BB, Jiang C, Marshall GM, Haber M, Norris MD, Fletcher JI, Dinger ME, Liu T.

Oncotarget. 2016 Feb 23;7(8):8663-75. doi: 10.18632/oncotarget.6675.

48.

The Long Noncoding RNA SPRIGHTLY Regulates Cell Proliferation in Primary Human Melanocytes.

Zhao W, Mazar J, Lee B, Sawada J, Li JL, Shelley J, Govindarajan S, Towler D, Mattick JS, Komatsu M, Dinger ME, Perera RJ.

J Invest Dermatol. 2016 Apr;136(4):819-28. doi: 10.1016/j.jid.2016.01.018. Epub 2016 Jan 29.

49.

Claudin-11 and occludin are major contributors to Sertoli cell tight junction function, in vitro.

McCabe MJ, Foo CF, Dinger ME, Smooker PM, Stanton PG.

Asian J Androl. 2016 Jul-Aug;18(4):620-6. doi: 10.4103/1008-682X.163189.

50.

Identification of a novel fusion transcript between human relaxin-1 (RLN1) and human relaxin-2 (RLN2) in prostate cancer.

Tevz G, McGrath S, Demeter R, Magrini V, Jeet V, Rockstroh A, McPherson S, Lai J, Bartonicek N, An J, Batra J, Dinger ME, Lehman ML, Williams ED, Nelson CC.

Mol Cell Endocrinol. 2016 Jan 15;420:159-68. doi: 10.1016/j.mce.2015.10.011. Epub 2015 Oct 21.

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