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Items: 49

1.

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis.

Hardwick SA, Chen WY, Wong T, Kanakamedala BS, Deveson IW, Ongley SE, Santini NS, Marcellin E, Smith MA, Nielsen LK, Lovelock CE, Neilan BA, Mercer TR.

Nat Commun. 2018 Aug 6;9(1):3096. doi: 10.1038/s41467-018-05555-0.

2.

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.

3.

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.

4.

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
5.

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.

6.

Phosphoproteomic Profiling Reveals ALK and MET as Novel Actionable Targets across Synovial Sarcoma Subtypes.

Fleuren EDG, Vlenterie M, van der Graaf WTA, Hillebrandt-Roeffen MHS, Blackburn J, Ma X, Chan H, Magias MC, van Erp A, van Houdt L, Cebeci SAS, van de Ven A, Flucke UE, Heyer EE, Thomas DM, Lord CJ, Marini KD, Vaghjiani V, Mercer TR, Cain JE, Wu J, Versleijen-Jonkers YMH, Daly RJ.

Cancer Res. 2017 Aug 15;77(16):4279-4292. doi: 10.1158/0008-5472.CAN-16-2550. Epub 2017 Jun 20.

7.

Reference standards for next-generation sequencing.

Hardwick SA, Deveson IW, Mercer TR.

Nat Rev Genet. 2017 Aug;18(8):473-484. doi: 10.1038/nrg.2017.44. Epub 2017 Jun 19. Review.

PMID:
28626224
8.

The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome.

Deveson IW, Hardwick SA, Mercer TR, Mattick JS.

Trends Genet. 2017 Jul;33(7):464-478. doi: 10.1016/j.tig.2017.04.004. Epub 2017 May 20. Review.

PMID:
28535931
9.

ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing.

Wong T, Deveson IW, Hardwick SA, Mercer TR.

Bioinformatics. 2017 Jun 1;33(11):1723-1724. doi: 10.1093/bioinformatics/btx038.

PMID:
28130232
10.

Spliced synthetic genes as internal controls in RNA sequencing experiments.

Hardwick SA, Chen WY, Wong T, Deveson IW, Blackburn J, Andersen SB, Nielsen LK, Mattick JS, Mercer TR.

Nat Methods. 2016 Sep;13(9):792-8. doi: 10.1038/nmeth.3958. Epub 2016 Aug 8.

PMID:
27502218
11.

Representing genetic variation with synthetic DNA standards.

Deveson IW, Chen WY, Wong T, Hardwick SA, Andersen SB, Nielsen LK, Mattick JS, Mercer TR.

Nat Methods. 2016 Sep;13(9):784-91. doi: 10.1038/nmeth.3957. Epub 2016 Aug 8.

PMID:
27502217
12.

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.

13.

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME.

Nat Methods. 2015 Apr;12(4):339-42. doi: 10.1038/nmeth.3321. Epub 2015 Mar 9.

PMID:
25751143
14.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

15.

Genome-wide discovery of human splicing branchpoints.

Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS.

Genome Res. 2015 Feb;25(2):290-303. doi: 10.1101/gr.182899.114. Epub 2015 Jan 5.

16.

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells.

Cossetti C, Iraci N, Mercer TR, Leonardi T, Alpi E, Drago D, Alfaro-Cervello C, Saini HK, Davis MP, Schaeffer J, Vega B, Stefanini M, Zhao C, Muller W, Garcia-Verdugo JM, Mathivanan S, Bachi A, Enright AJ, Mattick JS, Pluchino S.

Mol Cell. 2014 Oct 23;56(2):193-204. doi: 10.1016/j.molcel.2014.08.020. Epub 2014 Sep 18. Erratum in: Mol Cell. 2014 Nov 20;56(4):609.

17.

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS.

Nat Protoc. 2014 May;9(5):989-1009. doi: 10.1038/nprot.2014.058. Epub 2014 Apr 3.

PMID:
24705597
18.

Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting.

Liu G, Mercer TR, Shearwood AM, Siira SJ, Hibbs ME, Mattick JS, Rackham O, Filipovska A.

Cell Rep. 2013 Nov 14;5(3):839-48. doi: 10.1016/j.celrep.2013.09.036. Epub 2013 Oct 31.

19.

Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach.

Marcellin E, Licona-Cassani C, Mercer TR, Palfreyman RW, Nielsen LK.

BMC Genomics. 2013 Oct 11;14:699. doi: 10.1186/1471-2164-14-699.

20.

Understanding the regulatory and transcriptional complexity of the genome through structure.

Mercer TR, Mattick JS.

Genome Res. 2013 Jul;23(7):1081-8. doi: 10.1101/gr.156612.113. Review.

21.

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.

Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA.

Nat Genet. 2013 Aug;45(8):852-9. doi: 10.1038/ng.2677. Epub 2013 Jun 23.

22.

Structure and function of long noncoding RNAs in epigenetic regulation.

Mercer TR, Mattick JS.

Nat Struct Mol Biol. 2013 Mar;20(3):300-7. doi: 10.1038/nsmb.2480. Review.

PMID:
23463315
23.

Saccharopolyspora erythraea's genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch.

Marcellin E, Mercer TR, Licona-Cassani C, Palfreyman RW, Dinger ME, Steen JA, Mattick JS, Nielsen LK.

BMC Genomics. 2013 Jan 16;14:15. doi: 10.1186/1471-2164-14-15.

24.

The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression.

Rackham O, Mercer TR, Filipovska A.

Wiley Interdiscip Rev RNA. 2012 Sep-Oct;3(5):675-95. doi: 10.1002/wrna.1128. Epub 2012 Jul 9. Review.

PMID:
22777840
25.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL.

Nat Biotechnol. 2011 Nov 13;30(1):99-104. doi: 10.1038/nbt.2024.

26.

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins.

Rackham O, Shearwood AM, Mercer TR, Davies SM, Mattick JS, Filipovska A.

RNA. 2011 Dec;17(12):2085-93. doi: 10.1261/rna.029405.111. Epub 2011 Oct 25.

27.

Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling.

Thiagarajan RD, Cloonan N, Gardiner BB, Mercer TR, Kolle G, Nourbakhsh E, Wani S, Tang D, Krishnan K, Georgas KM, Rumballe BA, Chiu HS, Steen JA, Mattick JS, Little MH, Grimmond SM.

BMC Genomics. 2011 Sep 5;12:441. doi: 10.1186/1471-2164-12-441.

28.

RNA processing in human mitochondria.

Sanchez MI, Mercer TR, Davies SM, Shearwood AM, Nygård KK, Richman TR, Mattick JS, Rackham O, Filipovska A.

Cell Cycle. 2011 Sep 1;10(17):2904-16. Epub 2011 Sep 1.

PMID:
21857155
29.

The human mitochondrial transcriptome.

Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA, Filipovska A, Mattick JS.

Cell. 2011 Aug 19;146(4):645-58. doi: 10.1016/j.cell.2011.06.051.

30.

SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer.

Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, Dinger ME, Mattick JS.

RNA. 2011 May;17(5):878-91. doi: 10.1261/rna.2528811. Epub 2011 Apr 1.

31.

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage.

Bracken CP, Szubert JM, Mercer TR, Dinger ME, Thomson DW, Mattick JS, Michael MZ, Goodall GJ.

Nucleic Acids Res. 2011 Jul;39(13):5658-68. doi: 10.1093/nar/gkr110. Epub 2011 Mar 22.

32.

Expression of distinct RNAs from 3' untranslated regions.

Mercer TR, Wilhelm D, Dinger ME, Soldà G, Korbie DJ, Glazov EA, Truong V, Schwenke M, Simons C, Matthaei KI, Saint R, Koopman P, Mattick JS.

Nucleic Acids Res. 2011 Mar;39(6):2393-403. doi: 10.1093/nar/gkq1158. Epub 2010 Nov 12.

33.

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome.

Mercer TR, Dinger ME, Bracken CP, Kolle G, Szubert JM, Korbie DJ, Askarian-Amiri ME, Gardiner BB, Goodall GJ, Grimmond SM, Mattick JS.

Genome Res. 2010 Dec;20(12):1639-50. doi: 10.1101/gr.112128.110. Epub 2010 Nov 2.

34.

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.

Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ, Rasko JE, Rokhsar DS, Degnan BM, Mattick JS.

Nat Struct Mol Biol. 2010 Aug;17(8):1030-4. doi: 10.1038/nsmb.1841. Epub 2010 Jul 11.

PMID:
20622877
35.

A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells.

Lai J, Lehman ML, Dinger ME, Hendy SC, Mercer TR, Seim I, Lawrence MG, Mattick JS, Clements JA, Nelson CC.

RNA. 2010 Jun;16(6):1156-66. doi: 10.1261/rna.2019810. Epub 2010 Apr 20.

36.

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation.

Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF.

BMC Neurosci. 2010 Feb 5;11:14. doi: 10.1186/1471-2202-11-14.

37.

Non-coding RNAs: regulators of disease.

Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS.

J Pathol. 2010 Jan;220(2):126-39. doi: 10.1002/path.2638. Review.

PMID:
19882673
38.

Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications.

Dinger ME, Amaral PP, Mercer TR, Mattick JS.

Brief Funct Genomic Proteomic. 2009 Nov;8(6):407-23. doi: 10.1093/bfgp/elp038. Epub 2009 Sep 21.

PMID:
19770204
39.

Genome-wide identification of long noncoding RNAs in CD8+ T cells.

Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, Mattick JS.

J Immunol. 2009 Jun 15;182(12):7738-48. doi: 10.4049/jimmunol.0900603.

40.

Long non-coding RNAs: insights into functions.

Mercer TR, Dinger ME, Mattick JS.

Nat Rev Genet. 2009 Mar;10(3):155-9. doi: 10.1038/nrg2521. Review.

PMID:
19188922
41.

RNA regulation of epigenetic processes.

Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF.

Bioessays. 2009 Jan;31(1):51-9. doi: 10.1002/bies.080099. Review.

PMID:
19154003
42.

Differentiating protein-coding and noncoding RNA: challenges and ambiguities.

Dinger ME, Pang KC, Mercer TR, Mattick JS.

PLoS Comput Biol. 2008 Nov;4(11):e1000176. doi: 10.1371/journal.pcbi.1000176. Epub 2008 Nov 28. Review.

43.

Noncoding RNAs in Long-Term Memory Formation.

Mercer TR, Dinger ME, Mariani J, Kosik KS, Mehler MF, Mattick JS.

Neuroscientist. 2008 Oct;14(5):434-45. doi: 10.1177/1073858408319187. Review.

PMID:
18997122
44.

NRED: a database of long noncoding RNA expression.

Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS.

Nucleic Acids Res. 2009 Jan;37(Database issue):D122-6. doi: 10.1093/nar/gkn617. Epub 2008 Oct 1.

45.

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation.

Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC, Mattick JS.

Genome Res. 2008 Sep;18(9):1433-45. doi: 10.1101/gr.078378.108. Epub 2008 Jun 18.

46.

RNAs as extracellular signaling molecules.

Dinger ME, Mercer TR, Mattick JS.

J Mol Endocrinol. 2008 Apr;40(4):151-9. doi: 10.1677/JME-07-0160. Review.

PMID:
18372404
47.

The eukaryotic genome as an RNA machine.

Amaral PP, Dinger ME, Mercer TR, Mattick JS.

Science. 2008 Mar 28;319(5871):1787-9. doi: 10.1126/science.1155472.

PMID:
18369136
48.

Specific expression of long noncoding RNAs in the mouse brain.

Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS.

Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):716-21. doi: 10.1073/pnas.0706729105. Epub 2008 Jan 9.

49.

Association of a common complement receptor 2 haplotype with increased risk of systemic lupus erythematosus.

Wu H, Boackle SA, Hanvivadhanakul P, Ulgiati D, Grossman JM, Lee Y, Shen N, Abraham LJ, Mercer TR, Park E, Hebert LA, Rovin BH, Birmingham DJ, Chang DM, Chen CJ, McCurdy D, Badsha HM, Thong BY, Chng HH, Arnett FC, Wallace DJ, Yu CY, Hahn BH, Cantor RM, Tsao BP.

Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3961-6. Epub 2007 Feb 22.

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