By Associate Professor Timothy Robert Mercer

Journal articles

Deveson IW; Chen WY; Wong T; Hardwick SA; Andersen SB; Nielsen LK; Mattick JS; Mercer TR, 2016, 'Representing genetic variation with synthetic DNA standards', Nature Methods, 13, pp. 784 - 791, http://dx.doi.org/10.1038/nmeth.3957

Hardwick SA; Chen WY; Wong T; Deveson IW; Blackburn J; Andersen SB; Nielsen LK; Mattick JS; Mercer TR, 2016, 'Spliced synthetic genes as internal controls in RNA sequencing experiments', Nature Methods, 13, pp. 792 - 798, http://dx.doi.org/10.1038/nmeth.3958

Bussotti G; Leonardi T; Clark MB; Mercer TR; Crawford J; Malquori L; Notredame C; Dinger ME; Mattick JS; Enright AJ, 2016, 'Improved definition of the mouse transcriptome via targeted RNA sequencing', Genome Research, 26, pp. 705 - 716, http://dx.doi.org/10.1101/gr.199760.115

Clark MB; Mercer TR; Bussotti G; Leonardi T; Haynes KR; Crawford J; Brunck ME; Cao KAL; Thomas GP; Chen WY; Taft RJ; Nielsen LK; Enright AJ; Mattick JS; Dinger ME, 2015, 'Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing', Nature Methods, 12, pp. 339 - 342, http://dx.doi.org/10.1038/nmeth.3321

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 SJM; 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, 2015, 'Integrative analysis of 111 reference human epigenomes', Nature, 518, pp. 317 - 329, http://dx.doi.org/10.1038/nature14248

Mercer TR; Clark MB; Andersen SB; Brunck ME; Haerty W; Crawford J; Taft RJ; Nielsen LK; Dinger ME; Mattick JS, 2015, 'Genome-wide discovery of human splicing branchpoints', Genome Research, 25, pp. 290 - 303, http://dx.doi.org/10.1101/gr.182899.114

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 CJ; Muller W; Garcia-Verdugo JM; Mathivanan S; Bachi A; Enright AJ; Mattick JS; Pluchino S, 2014, 'Extracellular Vesicles from Neural Stem Cells Transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells', Molecular Cell, 56, pp. 609, http://dx.doi.org/10.1016/j.molcel.2014.11.009

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 CJ; Muller W; Garcia-Verdugo JM; Mathivanan S; Bachi A; Enright AJ; Mattick JS; Pluchino S, 2014, 'Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells', Molecular Cell, 56, pp. 193 - 204, http://dx.doi.org/10.1016/j.molcel.2014.08.020

Mercer TR; Clark MB; Crawford J; Brunck ME; Gerhardt DJ; Taft RJ; Nielsen LK; Dinger ME; Mattick JS, 2014, 'Targeted sequencing for gene discovery and quantification using RNA CaptureSeq', Nature Protocols, 9, pp. 989 - 1009, http://dx.doi.org/10.1038/nprot.2014.058

Liu G; Mercer TR; Shearwood AMJ; Siira SJ; Hibbs ME; Mattick JS; Rackham O; Filipovska A, 2013, 'Mapping of mitochondrial RNA-protein interactions by digital rnase footprinting', Cell Reports, 5, pp. 839 - 848, http://dx.doi.org/10.1016/j.celrep.2013.09.036

Marcellin E; Licona-Cassani C; Mercer TR; Palfreyman RW; Nielsen LK, 2013, 'Re-annotation of the Saccharopolyspora erythraea genome using a systems biology approach', BMC Genomics, 14, http://dx.doi.org/10.1186/1471-2164-14-699

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, 2013, 'DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements', Nature Genetics, 45, pp. 852 - 859, http://dx.doi.org/10.1038/ng.2677

Mercer TR; Mattick JS, 2013, 'Understanding the regulatory and transcriptional complexity of the genome through structure', Genome Research, 23, pp. 1081 - 1088, http://dx.doi.org/10.1101/gr.156612.113

Marcellin E; Mercer TR; Licona-Cassani C; Palfreyman RW; Dinger ME; Steen JA; Mattick JS; Nielsen LK, 2013, 'Saccharopolyspora erythraea’s genome is organised in high-order transcriptional regions mediated by targeted degradation at the metabolic switch', BMC Genomics, 14, pp. 15 - 25, http://dx.doi.org/10.1186/1471-2164-14-15

Mercer TR; Mattick JS, 2013, 'Structure and function of long noncoding RNAs in epigenetic regulation', Nature Structural & Molecular Biology, 20, pp. 300 - 307, http://dx.doi.org/10.1038/nsmb.2480

Cruickshank MN; Karimi M; Mason RL; Fenwick E; Mercer T; Tsao BP; Boackle SA; Ulgiati D, 2012, 'Transcriptional effects of a lupus-associated polymorphism in the 5' untranslated region (UTR) of human complement receptor 2 (CR2/CD21)', Molecular Immunology, 52, pp. 165 - 173, http://dx.doi.org/10.1016/j.molimm.2012.04.013

Rackham O; Mercer TR; Filipovska A, 2012, 'The human mitochondrial transcriptome and the rna-binding proteins that regulate its expression', Wiley Interdisciplinary Reviews: RNA, 3, pp. 675 - 695, http://dx.doi.org/10.1002/wrna.1128

Mercer TR; Gerhardt DJ; Dinger ME; Crawford J; Trapnell C; Jeddeloh JA; Mattick JS; Rinn JL, 2012, 'Targeted RNA sequencing reveals the deep complexity of the human transcriptome', Nature Biotechnology, 30, pp. 99 - 104, http://dx.doi.org/10.1038/nbt.2024

Rackham O; Shearwood AMJ; Mercer TR; Davies SMK; Mattick JS; Filipovska A, 2011, 'Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins', RNA, 17, pp. 2085 - 2093, http://dx.doi.org/10.1261/rna.029405.111

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, 2011, 'Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling', BMC Genomics, 12, http://dx.doi.org/10.1186/1471-2164-12-441

Lopez Sanchez MIG; Mercer TR; Davies SMK; Shearwood AMJ; Nygård KKA; Richman TR; Mattick JS; Rackham O; Filipovska A, 2011, 'RNA processing in human mitochondria', Cell Cycle, 10, pp. 2904 - 2916, http://dx.doi.org/10.4161/cc.10.17.17060

Mercer TR; Neph S; Dinger ME; Crawford J; Smith MA; Shearwood AMJ; Haugen E; Bracken CP; Rackham O; Stamatoyannopoulos JA; Filipovska A; Mattick JS, 2011, 'The human mitochondrial transcriptome', Cell, 146, pp. 645 - 658, http://dx.doi.org/10.1016/j.cell.2011.06.051

Bracken CP; Szubert JM; Mercer TR; Dinger ME; Thomson DW; Mattick JS; Michael MZ; Goodall GJ, 2011, 'Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage', Nucleic Acids Research, 39, pp. 5658 - 5668, http://dx.doi.org/10.1093/nar/gkr110

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, 2011, 'SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer', RNA, 17, pp. 878 - 891, http://dx.doi.org/10.1261/rna.2528811

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, 2011, 'Expression of distinct RNAs from 3′ untranslated regions', Nucleic Acids Research, 39, pp. 2393 - 2403, http://dx.doi.org/10.1093/nar/gkq1158

Mercer TR; Dinger ME; Bracken CP; Kolle G; Szubert JM; Korbie DJ; Askarian-Amiri ME; Gardiner BB; Goodall GJ; Grimmond SM; Mattick JS, 2010, 'Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome', Genome Research, 20, pp. 1639 - 1650, http://dx.doi.org/10.1101/gr.112128.110

Taft RJ; Simons C; Nahkuri S; Oey H; Korbie DJ; Mercer TR; Holst J; Ritchie W; Wong JJL; Rasko JEJ; Rokhsar DS; Degnan BM; Mattick JS, 2010, 'Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans', Nature Structural and Molecular Biology, 17, pp. 1030 - 1034, http://dx.doi.org/10.1038/nsmb.1841

Lai J; Lehman ML; Dinger ME; Hendy SC; Mercer TR; Seim I; Lawrence MG; Mattick JS; Clements JA; Nelson CC, 2010, 'A variant of the KLK4 gene is expressed as a cis sense-antisense chimeric transcript in prostate cancer cells', RNA, 16, pp. 1156 - 1166, http://dx.doi.org/10.1261/rna.2019810

Mercer TR; Qureshi IA; Gokhan S; Dinger ME; Li G; Mattick JS; Mehler MF, 2010, 'Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation', BMC Neuroscience, 11, http://dx.doi.org/10.1186/1471-2202-11-14

Taft RJ; Pang KC; Mercer TR; Dinger M; Mattick JS, 2010, 'Non-coding RNAs: Regulators of disease', Journal of Pathology, 220, pp. 126 - 139, http://dx.doi.org/10.1002/path.2638

Dinger ME; Amaral PP; Mercer TR; Mattick JS, 2009, 'Pervasive transcription of the eukaryotic genome: Functional indices and conceptual implications', Briefings in Functional Genomics and Proteomics, 8, pp. 407 - 423, http://dx.doi.org/10.1093/bfgp/elp038

Pang KC; Dinger ME; Mercer TR; Malquori L; Grimmond SM; Chen W; Mattick JS, 2009, 'Genome-wide identification of long noncoding RNAs in CD8⁺ T cells', Journal of Immunology, 182, pp. 7738 - 7748, http://dx.doi.org/10.4049/jimmunol.0900603

Mercer TR; Dinger ME; Mattick JS, 2009, 'Long non-coding RNAs: Insights into functions', Nature Reviews Genetics, 10, pp. 155 - 159, http://dx.doi.org/10.1038/nrg2521

Mattick JS; Amaral PP; Dinger ME; Mercer TR; Mehler MF, 2009, 'RNA regulation of epigenetic processes', BioEssays, 31, pp. 51 - 59, http://dx.doi.org/10.1002/bies.080099

Dinger ME; Pang KC; Mercer TR; Crowe ML; Grimmond SM; Mattick JS, 2009, 'NRED: A database of long noncoding RNA expression', Nucleic Acids Research, 37, http://dx.doi.org/10.1093/nar/gkn617

Mercer TR; Dinger ME; Mariani J; Kosik KS; Mehler MF; Mattick JS, 2008, 'Noncoding RNAs in long-term memory formation', Neuroscientist, 14, pp. 434 - 445, http://dx.doi.org/10.1177/1073858408319187

Dinger ME; Amara 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, 2008, 'Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation', Genome Research, 18, pp. 1433 - 1445, http://dx.doi.org/10.1101/gr.078378.108

Mattick JS; Croft LJ; Pheasant M; Mercer TR; Dinger ME, 2008, 'The mammalian genome as an RNA machine', FASEB JOURNAL, 22, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000208467805697&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Amaral PP; Dinger ME; Mercer TR; Mattick JS, 2008, 'The eukaryotic genome as an RNA machine', Science, 319, pp. 1787 - 1789, http://dx.doi.org/10.1126/science.1155472

Dinger ME; Mercer TR; Mattick JS, 2008, 'RNAs as extracellular signaling molecules', Journal of Molecular Endocrinology, 40, pp. 151 - 159, http://dx.doi.org/10.1677/JME-07-0160

Mercer TR; Dinger ME; Sunkin SM; Mehler MF; Mattick JS, 2008, 'Specific expression of long noncoding RNAs in the mouse brain', Proceedings of the National Academy of Sciences of the United States of America, 105, pp. 716 - 721, http://dx.doi.org/10.1073/pnas.0706729105

Dinger ME; Pang KC; Mercer TR; Mattick JS, 2008, 'Differentiating protein-coding and noncoding RNA: Challenges and ambiguities', PLoS Computational Biology, 4, http://dx.doi.org/10.1371/journal.pcbi.1000176

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; Chung JC; McCurdy D; Badsha HM; Thong BYH; Chng HH; Arnett FC; Wallace DJ; Yu CY; Hahn BH; Cantor RM; Tsao BP, 2007, 'Association of a common complement receptor 2 haplotype with increased risk of systemic lupus erythematosus', Proceedings of the National Academy of Sciences of the United States of America, 104, pp. 3961 - 3966, http://dx.doi.org/10.1073/pnas.0609101104

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