Papers.

Towards accurate and reliable resolution of structural variants for clinical diagnosis. Liu Z, Roberts R, Mercer TR, Xu J, Sedlazeck FJ, Tong W. Genome Biology. 2022 Mar 3;23(1):68

The potential of long noncoding RNA therapies. Mercer TR, Munro T, Mattick JS. Trends in Pharmacological Science. 2022 Feb 10

Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome. Reis ALM, Deveson IW, Madala BS, Wong T, Barker C, Xu J, Lennon N, Tong W, Mercer TR; SEQC2 Consortium. Genome Biology. 2022 Jan 12;23(1):19.

The splicing effect of variants at branchpoint elements in cancer genes. Canson DM, Dumenil T, Parsons MT, O’Mara TA, Davidson AL, Okano S, Signal B, Mercer TR, Glubb DM, Spurdle AB. Genetic Medicine. 2022 Feb;24(2):398-409.

Emerging technologies and their impact on regulatory science. Experimental Biology and Medicine. Anklam E, Bahl MI, Ball R, et al. 2022;247(1):1-75.

Testing at scale during the COVID-19 pandemic. Mercer TR, Salit M. Nature Review Genetics. 2021 May 4.

Ultra-deep Sequencing Data from a Liquid Biopsy Proficiency Study Demonstrating Analytic Validity. Binsheng Gong, Ira Deveson, Timothy Mercer, Donald Johann Jr, Wendell Jones, Weida Tong, and Joshua Xu  Scientific Data (2022)

Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests. Madala BS, Reis ALM, Deveson IW, Rawlinson W, Mercer TR. Scientific Reports. 2021 Jan 29;11(1):2636.

A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency. W. Jones, B. Gong, N. Novoradovskaya, D. Li, R. Kusko, T. A. Richmond, D. J. Johann, H. Bisgin, S. M. E. Sahraeian, P. R. Bushel, M. Pirooznia, K. Wilkins, M. Chierici, W. Bao, L. S. Basehore, A. B. Lucas, D. Burgess, D. J. Butler, S. Cawley, C.-J. Chang, G. Chen, T. Chen, Y.-C. Chen, D. J. Craig, A. del Pozo, J. Foox, M. Francescatto, Y. Fu, C. Furlanello, K. Giorda, K. P. Grist, M. Guan, Y. Hao, S. Happe, G. Hariani, N. Haseley, J. Jasper, G. Jurman, D. P. Kreil, P. Łabaj, K. Lai, J. Li, Q.-Z. Li, Y. Li, Z. Li, Z. Liu, M. S. López, K. Miclaus, R. Miller, V. K. Mittal, M. Mohiyuddin, C. Pabón-Peña, B. L. Parsons, F. Qiu, A. Scherer, T. Shi, S. Stiegelmeyer, C. Suo, N. Tom, D. Wang, Z. Wen, L. Wu, W. Xiao, C. Xu, Y. Yu, J. Zhang, Y. Zhang, Z. Zhang, Y. Zheng, C. E. Mason, J. C. Willey, W. Tong, L. Shi, J. Xu, Genome Biology. 2021 221. 22, 1–38 (2021).

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. B. Gong, D. Li, R. Kusko, N. Novoradovskaya, Y. Zhang, S. Wang, C. Pabón-Peña, Z. Zhang, K. Lai, W. Cai, J. S. LoCoco, E. Lader, T. A. Richmond, V. K. Mittal, L.-C. Liu, D. J. Johann, J. C. Willey, P. R. Bushel, Y. Yu, C. Xu, G. Chen, D. Burgess, S. Cawley, K. Giorda, N. Haseley, F. Qiu, K. Wilkins, H. Arib, C. Attwooll, K. Babson, L. Bao, W. Bao, A. B. Lucas, H. Best, A. Bhandari, H. Bisgin, J. Blackburn, T. M. Blomquist, L. Boardman, B. Burgher, D. J. Butler, C.-J. Chang, A. Chaubey, T. Chen, M. Chierici, C. R. Chin, D. Close, J. Conroy, J. C. Coleman, D. J. Craig, E. Crawford, A. del Pozo, I. W. Deveson, D. Duncan, A. K. Eterovic, X. Fan, J. Foox, C. Furlanello, A. Ghosal, S. Glenn, M. Guan, C. Haag, X. Hang, S. Happe, B. Hennigan, J. Hipp, H. Hong, K. Horvath, J. Hu, L.-Y. Hung, M. Jarosz, J. Kerkhof, B. Kipp, D. P. Kreil, P. Łabaj, P. Lapunzina, P. Li, Q.-Z. Li, W. Li, Z. Li, Y. Liang, S. Liu, Z. Liu, C. Ma, N. Marella, R. Martín-Arenas, D. B. Megherbi, Q. Meng, P. A. Mieczkowski, T. Morrison, D. Muzny, B. Ning, B. L. Parsons, C. P. Paweletz, M. Pirooznia, W. Qu, A. Raymond, P. Rindler, R. Ringler, B. Sadikovic, A. Scherer, E. Schulze, R. Sebra, R. Shaknovich, Q. Shi, T. Shi, J. C. Silla-Castro, M. Smith, M. S. López, P. Song, D. Stetson, M. Strahl, A. Stuart, J. Supplee, P. Szankasi, H. Tan, L. Tang, Y. Tao, S. Thakkar, D. Thierry-Mieg, J. Thierry-Mieg, V. J. Thodima, D. Thomas, B. Tichý, N. Tom, E. V. Garcia, S. Verma, K. Walker, C. Wang, J. Wang, Y. Wang, Z. Wen, V. Wirta, L. Wu, C. Xiao, W. Xiao, S. Xu, M. Yang, J. Ying, S. H. Yip, G. Zhang, S. Zhang, M. Zhao, Y. Zheng, X. Zhou, C. E. Mason, T. Mercer, W. Tong, L. Shi, W. Jones, J. Xu,  Genome Biology. 2021 221. 22, 1–23 (2021).

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. W. Xiao, L. Ren, Z. Chen, L. T. Fang, Y. Zhao, J. Lack, M. Guan, B. Zhu, E. Jaeger, L. Kerrigan, T. M. Blomquist, T. Hung, M. Sultan, K. Idler, C. Lu, A. Scherer, R. Kusko, M. Moos, C. Xiao, S. T. Sherry, O. D. Abaan, W. Chen, X. Chen, J. Nordlund, U. Liljedahl, R. Maestro, M. Polano, J. Drabek, P. Vojta, S. Kõks, E. Reimann, B. S. Madala, T. Mercer, C. Miller, H. Jacob, T. Truong, A. Moshrefi, A. Natarajan, A. Granat, G. P. Schroth, R. Kalamegham, E. Peters, V. Petitjean, A. Walton, T.-W. Shen, K. Talsania, C. J. Vera, K. Langenbach, M. de Mars, J. A. Hipp, J. C. Willey, J. Wang, J. Shetty, Y. Kriga, A. Raziuddin, B. Tran, Y. Zheng, Y. Yu, M. Cam, P. Jailwala, C. Nguyen, D. Meerzaman, Q. Chen, C. Yan, B. Ernest, U. Mehra, R. V. Jensen, W. Jones, J.-L. Li, B. N. Papas, M. Pirooznia, Y.-C. Chen, F. Seifuddin, Z. Li, X. Liu, W. Resch, J. Wang, L. Wu, G. Yavas, C. Miles, B. Ning, W. Tong, C. E. Mason, E. Donaldson, S. Lababidi, L. M. Staudt, Z. Tezak, H. Hong, C. Wang, L. Shi,  Nature. Biotechnology. 2021 399. 39, 1141–1150 (2021).

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome.  R.-L. Troskie, Y. Jafrani, T. R. Mercer, A. D. Ewing, G. J. Faulkner, S. W. Cheetham, Genome Biology. 22 (2021), doi:10.1186/s13059-021-02369-0.

A Clinical Laboratory-Developed {LSC}17 Stemness Score Assay for Rapid Risk Assessment of Acute Myeloid Leukemia Patients. S. W. K. Ng, T. Murphy, I. King, T. Zhang, M. Mah, Z. Lu, N. Stickle, N. Ibrahimova, A. Arruda, A. Mitchell, M. Mai, R. He, B. S. Madala, D. S. Viswanatha, J. E. Dick, S. M. C. Chan, C. Virtanen, M. D. Minden, T. R. Mercer, T. L. Stockley, J. C. Y. Wang,  Blood Advances. (2021)

Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z,Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J,Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, MieczkowskiPA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, BestH, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D,Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K,Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE,Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A,Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M,Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, ZhangS, Zhang Y, Shi L, Tong W, Johann DJ Jr, Mercer TR, Xu J; SEQC2 OncopanelSequencing Working Group. Nature Biotechnology. 2021 Apr 12.

Reporting guidelines for human microbiome research: the STORMS checklist. Mirzayi C, Renson A; Genomic Standards Consortium; Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L. Nature Medecine. 2021 Nov;27(11):1885-1892.

The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine. Mercer TR, Xu J, Mason CE, Tong W; MAQC/SEQC2 Consortium. Genome Biology. 2021 Nov 8;22(1):306.

Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA. Willey, James C., Morrison, Thomas, Austermiller, Brad, Crawford, Erin L., Craig, Daniel J., Blomquist, Thomas M., Jones, wendell D., Wali, Aminah, Lococo, Jennifer S., Haseley, Nathan, Richmond, Todd A., Novoradovskaya, Natalia, Kusko, Rebecca, Chen, Guangchun, Li, Quan-Zhen, Johann, Don, Deveson, Ira W., Mercer, Tim, Wu, Leihong, and Xu, Joshua Cell Reports, 2021 

A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features. Reis ALM, Deveson IW, Wong T, Madala BS, Barker C, Blackburn J, Marcellin E, Mercer TR. Nature Communications. 2020 Jul 17;11(1):3609.

Use of synthetic DNA spike-in controls (sequins) for human genome sequencing. Blackburn J, Wong T, Madala BS, Barker C, Hardwick SA, Reis ALM, Deveson IW, Mercer TR. Nature Protocols. 2019 Jul;14(7):2119-2151.

Crizotinib and Surgery for Long-Term Disease Control in Children and Adolescents With ALK-Positive Inflammatory Myofibroblastic Tumors. Trahair T, Gifford AJ, Fordham A, Mayoh C, Fadia M, Lukeis R, Wood AC, Valvi S, Walker RD, Blackburn J, Heyer EE, Mercer TR, Barbaric D, Marshall GM, MacKenzie KL. C JCO Precision Oncology. 2019 May 16;3:PO.18.00297.

TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa. Blackburn J, Vecchiarelli S, Heyer EE, Patrick SM, Lyons RJ, Jaratlerdsiri W, van Zyl S, Bornman MSR, Mercer TR, Hayes VM. Prostate. 2019 Jul;79(10):1191-1196.

Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions. Hardwick SA, Bassett SD, Kaczorowski D, Blackburn J, Barton K, Bartonicek N, Carswell SL, Tilgner HU, Loy C, Halliday G, Mercer TR, Smith MA, Mattick JS. Frontiers in Genetics. 2019 Apr 12;10:309.

Diagnosis of fusion genes using targeted RNA sequencing. Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O’Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR, Blackburn J.  Nature Communications. 2019 Mar 27;10(1):1388.

Chiral DNA sequences as commutable controls for clinical genomics. Deveson IW, Madala BS, Blackburn J, Barker C, Wong T, Barton KM, Smith MA, Watkins DN, Mercer TR. Nature Communications. 2019 Mar 22;10(1):1342. doi: 10.1038/s41467-019-09272-0.

Synthetic microbe communities provide internal reference standards formetagenome 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, MercerTR. Nature Communications. 2018 Aug 6;9(1):3096.

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 Systems. 2018 Feb 28;6(2):245-255.e5.

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, DingerME. Genome Biology. 2017 Dec 28;18(1):241.

Machine learning annotation of human branchpoints. Signal B, Gloss BS, Dinger ME, Mercer TR. Bioinformatics. 2018 Mar 15;34(6):920-927.

Long Noncoding RNAs CUPID1 and CUPID2 Mediate BreastCancer 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, BainAL, Gloss BS, Crawford J, Kazakoff S, Wani S, Wen SW, Day B, Möller A, CloonanN, Pearson J, Brown MA, Mercer TR, Waddell N, Khanna KK, Dray E, Dinger ME,Edwards SL, French JD. American Journal of Human Genetics. 2017 Aug 3;101(2):255-266.

Phosphoproteomic ProfilingReveals ALK and MET as Novel Actionable Targets across Synovial SarcomaSubtypes. 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 deVen A, Flucke UE, Heyer EE, Thomas DM, Lord CJ, Marini KD, Vaghjiani V, MercerTR, Cain JE, Wu J, Versleijen-Jonkers YMH, Daly RJ. Cancer Research. 2017 Aug 15;77(16):4279-4292.

Reference standards for next-generationsequencing. Hardwick SA, Deveson IW, Mercer TR. Nature Reviews Genetics. 2017 Aug;18(8):473-484.

The Dimensions, Dynamics,and Relevance of the Mammalian Noncoding Transcriptome. Deveson IW, Hardwick SA, Mercer TR, Mattick JS.  Trends in Genetics. 2017 Jul;33(7):464-478.

ANAQUIN: a software toolkit forthe 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.

Spliced synthetic genes as internal controls in RNAsequencing experiments. Hardwick SA, Chen WY, Wong T, Deveson IW, Blackburn J, Andersen SB, NielsenLK, Mattick JS, Mercer TR. Nature Methods. 2016 Sep;13(9):792-8.

Representing genetic variation with synthetic DNA standards. Deveson IW, Chen WY, Wong T, Hardwick SA, Andersen SB, Nielsen LK, MattickJS, Mercer TR. Nature Methods. 2016 Sep;13(9):784-91.

Improved definition of the mousetranscriptome 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 Research. 2016 May;26(5):705-16.

 

Quantitative gene profiling of long noncoding RNAs with targeted RNAsequencing. Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, BrunckME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS,Dinger ME. Nature Methods. 2015 Apr;12(4):339-42.

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, WuYC, 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, TlstyTD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, CostelloJF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, StamatoyannopoulosJA, Wang T, Kellis M. 2015 Nature. Feb 19;518(7539):317-30.

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

 

Extracellular vesicles from neural stem cells transfer IFN-γ via Ifngr1 toactivate Stat1 signaling in target cells. Cossetti C, Iraci N, Mercer TR, Leonardi T, Alpi E, Drago D, Alfaro-CervelloC, 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. Molecular Cell. 2014 Oct 23;56(2):193-204.

Targeted sequencing for gene discovery andquantification using RNA CaptureSeq. Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt DJ, Taft RJ, NielsenLK, Dinger ME, Mattick JS. Nature Protocols. 2014 May;9(5):989-1009.

Mapping of mitochondrial RNA-protein interactions by digital RNasefootprinting. Liu G, Mercer TR, Shearwood AM, Siira SJ, Hibbs ME, Mattick JS, Rackham O,Filipovska A. Cell Reports. 2013 Nov 14;5(3):839-48.

Re-annotation of the Saccharopolyspora erythraea genome using a systems biologyapproach. Marcellin E, Licona-Cassani C, Mercer TR, Palfreyman RW, Nielsen LK. BMC Genomics. 2013 Oct 11;14:699.

Understanding the regulatory and transcriptional complexity of the genome through structure. Mercer TR, Mattick JS.  Genome Research. 2013 Jul;23(7):1081-8.

DNase I-hypersensitive exons colocalize with promoters and distal regulatoryelements. 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, StamatoyannopoulosJA. Nature Genetics. 2013 Aug;45(8):852-9.

Structure and function of long noncoding RNAs inepigenetic regulation. Mercer TR, Mattick JS. Nature Structural Molecular Biology. 2013 Mar;20(3):300-7.

Saccharopolyspora erythraea’s genome is organised inhigh-order transcriptional regions mediated by targeted degradation at themetabolic switch. Marcellin E, Mercer TR, Licona-Cassani C, Palfreyman RW, Dinger ME, SteenJA, Mattick JS, Nielsen LK. BMC Genomics. 2013 Jan 16;14:15.

The human mitochondrial transcriptome and the RNA-binding proteins that regulate its expression. Rackham O, Mercer TR, Filipovska A. Wiley Interdisciplinary Review RNA. 2012 Sep-Oct;3(5):675-95.

Targeted RNA sequencing reveals the deep complexity of thehuman transcriptome. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA,Mattick JS, Rinn JL. Nature Biotechnology. 2011 Nov 13;30(1):99-104.

Long noncoding RNAs are generated from the mitochondrial genome and regulated bynuclear-encoded proteins. Rackham O, Shearwood AM, Mercer TR, Davies SM, Mattick JS, Filipovska A. RNA. 2011 Dec;17(12):2085-93.

Refining transcriptional programs in kidneydevelopment by integration of deep RNA-sequencing and array-based spatialprofiling. 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, MattickJS, Little MH, Grimmond SM. BMC Genomics. 2011 Sep 5;12:441.

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.

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.

SNORD-host RNA Zfas1 is a regulator of mammary development and apotential marker for breast cancer. Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, RuK, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, DingerME, Mattick JS. RNA. 2011 May;17(5):878-91.

Global analysis of the mammalian RNA degradome revealswidespread 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 Research. 2011 Jul;39(13):5658-68.

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 Research. 2011Mar;39(6):2393-403.

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 Research. 2010 Dec;20(12):1639-50.

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. Nature Structural Molecular Biology. 2010 Aug;17(8):1030-4.

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.

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 Neuroscience. 2010 Feb 5;11:14.

Non-coding RNAs:regulators of disease. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. Journal of Pathology. 2010 Jan;220(2):126-39.

Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Dinger ME, Amaral PP, Mercer TR, Mattick JS.  Briefings in Functional Genomics and Proteomics. 2009 Nov;8(6):407-23.

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. Journal of Immunology. 2009 Jun 15;182(12):7738-48.

Long non-coding RNAs: insights into functions. Mercer TR, Dinger ME, Mattick JS.  Nature Review Genetics. 2009 Mar;10(3):155-9.

RNA regulation of epigenetic processes. Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF. Bioessays. 2009 Jan;31(1):51-9.

Differentiating protein-coding and noncoding RNA: challenges and ambiguities. Dinger ME, Pang KC, Mercer TR, Mattick JS. PLoS Computational Biology. 2008 Nov;4(11):e1000176.

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.

NRED: a database of long noncoding RNA expression. Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS. Nucleic Acids Research. 2009 Jan;37(Database issue):D122-6.

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 Research. 2008 Sep;18(9):1433-45.

RNAs as extracellular signaling molecules. Dinger ME, Mercer TR, Mattick JS. Journal of Molecular Endocrinology. 2008 Apr;40(4):151-9.

The eukaryotic genome as an RNA machine. Amaral PP, Dinger ME, Mercer TR, Mattick JS. Science. 2008 Mar 28;319(5871):1787-9.

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.

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