Associate Professor Timothy Mercer

Mattick JS; Amaral PP; Carninci P; Carpenter S; Chang HY; Chen LL; Chen R; Dean C; Dinger ME; Fitzgerald KA; Gingeras TR; Guttman M; Hirose T; Huarte M; Johnson R; Kanduri C; Kapranov P; Lawrence JB; Lee JT; Mendell JT; Mercer TR; Moore KJ; Nakagawa S; Rinn JL; Spector DL; Ulitsky I; Wan Y; Wilusz JE; Wu M, 2023, 'Long non-coding RNAs: definitions, functions, challenges and recommendations', Nature Reviews Molecular Cell Biology, http://dx.doi.org/10.1038/s41580-022-00566-8

Anklam E; Bahl MI; Ball R; Beger RD; Cohen J; Fitzpatrick S; Girard P; Halamoda-Kenzaoui B; Hinton D; Hirose A; Hoeveler A; Honma M; Hugas M; Ishida S; Kass GEN; Kojima H; Krefting I; Liachenko S; Liu Y; Masters S; Marx U; McCarthy T; Mercer T; Patri A; Pelaez C; Pirmohamed M; Platz S; Ribeiro AJS; Rodricks JV; Rusyn I; Salek RM; Schoonjans R; Silva P; Svendsen CN; Sumner S; Sung K; Tagle D; Tong L; Tong W; Eijnden-van-Raaij JVD; Vary N; Wang T; Waterton J; Wang M; Wen H; Wishart D; Yuan Y; Slikker W, 2022, 'Emerging technologies and their impact on regulatory science', Experimental Biology and Medicine, vol. 247, pp. 1 - 75, http://dx.doi.org/10.1177/15353702211052280

Canson DM; Dumenil T; Parsons MT; O'Mara TA; Davidson AL; Okano S; Signal B; Mercer TR; Glubb DM; Spurdle AB, 2022, 'The splicing effect of variants at branchpoint elements in cancer genes', Genetics in Medicine, vol. 24, pp. 398 - 409, http://dx.doi.org/10.1016/j.gim.2021.09.020

Gong B; Deveson IW; Mercer T; Johann DJ; Jones W; Tong W; Xu J, 2022, 'Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity', Scientific Data, vol. 9, http://dx.doi.org/10.1038/s41597-022-01276-8

Gunter HM; Youlten SE; Madala BS; Reis ALM; Stevanovski I; Wong T; Kummerfield SK; Deveson IW; Santini NS; Marcellin E; Mercer TR, 2022, 'Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing', Nature Communications, vol. 13, pp. 6437, http://dx.doi.org/10.1038/s41467-022-34028-8

Liu Z; Roberts R; Mercer TR; Xu J; Sedlazeck FJ; Tong W, 2022, 'Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis (Genome Biology, (2022), 23, 1, (68), 10.1186/s13059-022-02636-8)', Genome Biology, vol. 23, http://dx.doi.org/10.1186/s13059-022-02773-0

Liu Z; Roberts R; Mercer TR; Xu J; Sedlazeck FJ; Tong W, 2022, 'Towards accurate and reliable resolution of structural variants for clinical diagnosis', Genome Biology, vol. 23, pp. 68, http://dx.doi.org/10.1186/s13059-022-02636-8

Mercer T; Almond N; Crone MA; Chain PSG; Deshpande A; Eveleigh D; Freemont P; Fuchs S; Garlick R; Huggett J; Kammel M; Li PE; Milavec M; Marlowe EM; O’Sullivan DM; Page M; Pestano GA; Suliman S; Simen B; Sninsky JJ; Sopchak L; Tato CM; Vallone PM; Vandesompele J; White TJ; Zeichhardt H; Salit M, 2022, 'The Coronavirus Standards Working Group’s roadmap for improved population testing', Nature Biotechnology, vol. 40, pp. 1563 - 1568, http://dx.doi.org/10.1038/s41587-022-01538-1

Mercer TR; Munro T; Mattick JS, 2022, 'The potential of long noncoding RNA therapies', Trends in Pharmacological Sciences, vol. 43, pp. 269 - 280, http://dx.doi.org/10.1016/j.tips.2022.01.008

Ng SWK; Murphy T; King I; Zhang T; Mah M; Lu Z; Stickle N; Ibrahimova N; Arruda A; Mitchell A; Mai M; He R; Madala BS; Viswanatha DS; Dick JE; Chan S; Virtanen C; Minden MD; Mercer T; Stockley T; Wang JCY, 2022, 'A clinical laboratory–developed LSC17 stemness score assay for rapid risk assessment of patients with acute myeloid leukemia', Blood Advances, vol. 6, pp. 1064 - 1073, http://dx.doi.org/10.1182/bloodadvances.2021005741

Reis ALM; Deveson IW; Madala BS; Wong T; Barker C; Xu J; Lennon N; Tong W; Mercer TR, 2022, 'Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome', Genome Biology, vol. 23, http://dx.doi.org/10.1186/s13059-021-02579-6

Wei W; Zhao Q; Wang Z; Liau WS; Basic D; Ren H; Marshall PR; Zajaczkowski EL; Leighton LJ; Madugalle SU; Musgrove M; Periyakaruppiah A; Shi J; Zhang J; Mattick JS; Mercer TR; Spitale RC; Li X; Bredy TW, 2022, 'ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3', Cell Reports, vol. 38, http://dx.doi.org/10.1016/j.celrep.2022.110546

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; Mieczkowski PA; Qiu F; Sebra R; Stetson D; Sun L; Szankasi P; Tan H; Tang LY; Arib H; Best H; 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; Zhang S; Zhang Y; Shi L; Tong W; Johann DJ; Mercer TR; Xu J, 2021, 'Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology', Nature Biotechnology, vol. 39, pp. 1115 - 1128, http://dx.doi.org/10.1038/s41587-021-00857-z

Gong B; Li D; Kusko R; Novoradovskaya N; Zhang Y; Wang S; Pabón-Peña C; Zhang Z; Lai K; Cai W; LoCoco JS; Lader E; Richmond TA; Mittal VK; Liu LC; Johann DJ; Willey JC; Bushel PR; Yu Y; Xu C; Chen G; Burgess D; Cawley S; Giorda K; Haseley N; Qiu F; Wilkins K; Arib H; Attwooll C; Babson K; Bao L; Bao W; Lucas AB; Best H; Bhandari A; Bisgin H; Blackburn J; Blomquist TM; Boardman L; Burgher B; Butler DJ; Chang CJ; Chaubey A; Chen T; Chierici M; Chin CR; Close D; Conroy J; Coleman JC; Craig DJ; Crawford E; del Pozo A; Deveson IW; Duncan D; Eterovic AK; Fan X; Foox J; Furlanello C; Ghosal A; Glenn S; Guan M; Haag C; Hang X; Happe S; Hennigan B; Hipp J; Hong H; Horvath K; Hu J; Hung LY; Jarosz M; Kerkhof J; Kipp B; Kreil DP; Łabaj P; Lapunzina P; Li P; Li QZ; Li W; Li Z; Liang Y; Liu S; Liu Z; Ma C; Marella N; Martín-Arenas R; Megherbi DB; Meng Q; Mieczkowski PA; Morrison T; Muzny D; Ning B; Parsons BL; Paweletz CP; Pirooznia M; Qu W; Raymond A; Rindler P; Ringler R; Sadikovic B, 2021, 'Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions', Genome Biology, vol. 22, pp. 109, http://dx.doi.org/10.1186/s13059-021-02315-0

Madala BS; Reis ALM; Deveson IW; Rawlinson W; Mercer TR, 2021, 'Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests', Scientific Reports, vol. 11, http://dx.doi.org/10.1038/s41598-021-81760-0

Mercer TR; Salit M, 2021, 'Testing at scale during the COVID-19 pandemic', Nature Reviews Genetics, vol. 22, pp. 415 - 426, http://dx.doi.org/10.1038/s41576-021-00360-w

Mercer TR; Xu J; Mason CE; Tong W, 2021, 'The Sequencing Quality Control 2 study: establishing community standards for sequencing in precision medicine', Genome Biology, vol. 22, http://dx.doi.org/10.1186/s13059-021-02528-3

Mirzayi C; Renson A; Furlanello C; Sansone SA; 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; 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; Scherer A; Shi L; Thakkar S; Tong W; Wolfinger R; Hunter C, 2021, 'Reporting guidelines for human microbiome research: the STORMS checklist', Nature Medicine, vol. 27, pp. 1885 - 1892, http://dx.doi.org/10.1038/s41591-021-01552-x

Troskie RL; Jafrani Y; Mercer TR; Ewing AD; Faulkner GJ; Cheetham SW, 2021, 'Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome', Genome Biology, vol. 22, http://dx.doi.org/10.1186/s13059-021-02369-0

Willey JC; Morrison TB; Austermiller B; Crawford EL; Craig DJ; Blomquist TM; Jones WD; Wali A; Lococo JS; Haseley N; Richmond TA; Novoradovskaya N; Kusko R; Chen G; Li QZ; Johann DJ; Deveson IW; Mercer TR; Wu L; Xu J, 2021, 'Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA', Cell Reports Methods, vol. 1, pp. 100106 - 100106, http://dx.doi.org/10.1016/j.crmeth.2021.100106

Xiao W; Ren L; Chen Z; Fang LT; Zhao Y; Lack J; Guan M; Zhu B; Jaeger E; Kerrigan L; Blomquist TM; Hung T; Sultan M; Idler K; Lu C; Scherer A; Kusko R; Moos M; Xiao C; Sherry ST; Abaan OD; Chen W; Chen X; Nordlund J; Liljedahl U; Maestro R; Polano M; Drabek J; Vojta P; Kõks S; Reimann E; Madala BS; Mercer T; Miller C; Jacob H; Truong T; Moshrefi A; Natarajan A; Granat A; Schroth GP; Kalamegham R; Peters E; Petitjean V; Walton A; Shen TW; Talsania K; Vera CJ; Langenbach K; de Mars M; Hipp JA; Willey JC; Wang J; Shetty J; Kriga Y; Raziuddin A; Tran B; Zheng Y; Yu Y; Cam M; Jailwala P; Nguyen C; Meerzaman D; Chen Q; Yan C; Ernest B; Mehra U; Jensen RV; Jones W; Li JL; Papas BN; Pirooznia M; Chen YC; Seifuddin F; Li Z; Liu X; Resch W; Wang J; Wu L; Yavas G; Miles C; Ning B; Tong W; Mason CE; Donaldson E; Lababidi S; Staudt LM; Tezak Z; Hong H; Wang C; Shi L, 2021, 'Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing', Nature Biotechnology, vol. 39, pp. 1141 - 1150, http://dx.doi.org/10.1038/s41587-021-00994-5

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, 2020, 'Author Correction: Diagnosis of fusion genes using targeted RNA sequencing (Nature Communications, (2019), 10, 1, (1388), 10.1038/s41467-019-09374-9)', Nature Communications, vol. 11, http://dx.doi.org/10.1038/s41467-020-15697-9

Reis ALM; Deveson IW; Wong T; Madala BS; Barker C; Blackburn J; Marcellin E; Mercer TR, 2020, 'A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features', Nature Communications, vol. 11, http://dx.doi.org/10.1038/s41467-020-17445-5

Singh M; Jackson KJL; Wang JJ; Schofield P; Field MA; Koppstein D; Peters TJ; Burnett DL; Rizzetto S; Nevoltris D; Masle-Farquhar E; Faulks ML; Russell A; Gokal D; Hanioka A; Horikawa K; Colella AD; Chataway TK; Blackburn J; Mercer TR; Langley DB; Goodall DM; Jefferis R; Gangadharan Komala M; Kelleher AD; Suan D; Rischmueller M; Christ D; Brink R; Luciani F; Gordon TP; Goodnow CC; Reed JH, 2020, 'Lymphoma Driver Mutations in the Pathogenic Evolution of an Iconic Human Autoantibody', Cell, vol. 180, pp. 878 - 894.e19, http://dx.doi.org/10.1016/j.cell.2020.01.029

Blackburn J; Vecchiarelli S; Heyer EE; Patrick SM; Lyons RJ; Jaratlerdsiri W; van Zyl S; Bornman MSR; Mercer TR; Hayes VM, 2019, 'TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa', Prostate, vol. 79, pp. 1191 - 1196, http://dx.doi.org/10.1002/pros.23823

Blackburn J; Wong T; Madala BS; Barker C; Hardwick SA; Reis ALM; Deveson IW; Mercer TR, 2019, 'Use of synthetic DNA spike-in controls (sequins) for human genome sequencing', Nature Protocols, vol. 14, pp. 2119 - 2151, http://dx.doi.org/10.1038/s41596-019-0175-1

Deveson IW; Madala BS; Blackburn J; Barker C; Wong T; Barton KM; Smith MA; Watkins DN; Mercer TR, 2019, 'Chiral DNA sequences as commutable controls for clinical genomics', Nature Communications, vol. 10, pp. 1342, http://dx.doi.org/10.1038/s41467-019-09272-0

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, 2019, 'Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions', Frontiers in Genetics, vol. 10, http://dx.doi.org/10.3389/fgene.2019.00309

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, 2019, 'Diagnosis of fusion genes using targeted RNA sequencing', Nature Communications, vol. 10, http://dx.doi.org/10.1038/s41467-019-09374-9

Santini NS; Lovelock CE; Hua Q; Zawadzki A; Mazumder D; Mercer TR; Muñoz-Rojas M; Hardwick SA; Madala BS; Cornwell W; Thomas T; Marzinelli EM; Adam P; Paul S; Vergés A, 2019, 'Natural and Regenerated Saltmarshes Exhibit Similar Soil and Belowground Organic Carbon Stocks, Root Production and Soil Respiration', Ecosystems, vol. 22, pp. 1803 - 1822, http://dx.doi.org/10.1007/s10021-019-00373-x

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, 2019, 'Crizotinib and surgery for long-term disease control in children and adolescents with ALK-positive inflammatory myofibroblastic tumors', JCO Precision Oncology, vol. 3, pp. 1 - 11, http://dx.doi.org/10.1200/PO.18.00297

Deveson I; Madala BS; Blackburn J; Barker C; Wong T; Barton K; Smith M; Watkins N; Mercer T, 2018, 'Chiral DNA sequences as commutable reference standards for clinical genomics', BIORXIV, http://dx.doi.org/10.1101/404285

Deveson IW; Brunck ME; Blackburn J; Tseng E; Hon T; Clark TA; Clark MB; Crawford J; Dinger ME; Nielsen LK; Mattick JS; Mercer TR, 2018, 'Universal Alternative Splicing of Noncoding Exons', Cell Systems, vol. 6, pp. 245 - 255.e5, http://dx.doi.org/10.1016/j.cels.2017.12.005

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, 2018, 'Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis', Nature Communications, vol. 9, http://dx.doi.org/10.1038/s41467-018-05555-0

Signal B; Gloss BS; Dinger ME; Mercer TR, 2018, 'Machine learning annotation of human branchpoints', Bioinformatics, vol. 34, pp. 920 - 927, http://dx.doi.org/10.1093/bioinformatics/btx688

Sowlati T; Sarkar S; Perumana BG; Chan WL; Papio Toda A; Afshar B; Boers M; Shin D; Mercer TR; Chen WH; Grau Besoli A; Yoon S; Kyriazidou S; Yang P; Aggarwal V; Vakilian N; Rozenblit D; Kahrizi M; Zhang J; Wang A; Sen P; Murphy D; Sajjadi A; Mehrabani A; Kornaros E; Low K; Kimura K; Roussel V; Xie H; Kodavati V, 2018, 'A 60-GHz 144-element phased-array transceiver for backhaul application', IEEE Journal of Solid-State Circuits, vol. 53, pp. 3640 - 3659, http://dx.doi.org/10.1109/JSSC.2018.2874048

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, 2017, 'Intergenic disease-associated regions are abundant in novel transcripts', Genome Biology, vol. 18, http://dx.doi.org/10.1186/s13059-017-1363-3

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, 2017, 'Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage', American Journal of Human Genetics, vol. 101, pp. 255 - 266, http://dx.doi.org/10.1016/j.ajhg.2017.07.007

Deveson IW; Hardwick SA; Mercer TR; Mattick JS, 2017, 'The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome', Trends in Genetics, vol. 33, pp. 464 - 478, http://dx.doi.org/10.1016/j.tig.2017.04.004

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, 2017, 'Phosphoproteomic profiling reveals ALK and MET as novel actionable targets across synovial sarcoma subtypes', Cancer Research, vol. 77, pp. 4279 - 4292, http://dx.doi.org/10.1158/0008-5472.CAN-16-2550

Hardwick SA; Deveson IW; Mercer TR, 2017, 'Reference standards for next-generation sequencing', Nature Reviews Genetics, vol. 18, pp. 473 - 484, http://dx.doi.org/10.1038/nrg.2017.44

Wong T; Deveson IW; Hardwick SA; Mercer TR, 2017, 'ANAQUIN: A software toolkit for the analysis of spike-in controls for next generation sequencing', Bioinformatics, vol. 33, pp. 1723 - 1724, http://dx.doi.org/10.1093/bioinformatics/btx038

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, vol. 26, pp. 705 - 716, http://dx.doi.org/10.1101/gr.199760.115

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, vol. 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, vol. 13, pp. 792 - 798, http://dx.doi.org/10.1038/nmeth.3958

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, vol. 12, pp. 339 - 342, http://dx.doi.org/10.1038/nmeth.3321

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, vol. 25, pp. 290 - 303, http://dx.doi.org/10.1101/gr.182899.114

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, vol. 518, pp. 317 - 329, http://dx.doi.org/10.1038/nature14248

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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 14, http://dx.doi.org/10.1186/1471-2164-14-699

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, vol. 14, pp. 15 - 25, http://dx.doi.org/10.1186/1471-2164-14-15

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, vol. 45, pp. 852 - 859, http://dx.doi.org/10.1038/ng.2677

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

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

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, vol. 52, pp. 165 - 173, http://dx.doi.org/10.1016/j.molimm.2012.04.013

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, vol. 30, pp. 99 - 104, http://dx.doi.org/10.1038/nbt.2024

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

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, vol. 17, pp. 878 - 891, http://dx.doi.org/10.1261/rna.2528811

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, vol. 39, pp. 5658 - 5668, http://dx.doi.org/10.1093/nar/gkr110

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, vol. 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, vol. 146, pp. 645 - 658, http://dx.doi.org/10.1016/j.cell.2011.06.051

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, vol. 39, pp. 2393 - 2403, http://dx.doi.org/10.1093/nar/gkq1158

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, vol. 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, vol. 12, http://dx.doi.org/10.1186/1471-2164-12-441

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, vol. 16, pp. 1156 - 1166, http://dx.doi.org/10.1261/rna.2019810

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, vol. 20, pp. 1639 - 1650, http://dx.doi.org/10.1101/gr.112128.110

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, vol. 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, vol. 220, pp. 126 - 139, http://dx.doi.org/10.1002/path.2638

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, vol. 17, pp. 1030 - 1034, http://dx.doi.org/10.1038/nsmb.1841

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, vol. 8, pp. 407 - 423, http://dx.doi.org/10.1093/bfgp/elp038

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

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

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

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, vol. 182, pp. 7738 - 7748, http://dx.doi.org/10.4049/jimmunol.0900603

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

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, vol. 18, pp. 1433 - 1445, http://dx.doi.org/10.1101/gr.078378.108

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

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

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

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, vol. 105, pp. 716 - 721, http://dx.doi.org/10.1073/pnas.0706729105

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, vol. 104, pp. 3961 - 3966, http://dx.doi.org/10.1073/pnas.0609101104

Giles K; Phipps A; Cashion J; Huskins S; Mercer T; Robinson M; Woodhouse A; Taberlay P, 2022, H3K4me3 enrichment defines neuronal age, while a youthful H3K27ac signature is recapitulated in aged neurons, http://dx.doi.org/10.21203/rs.3.rs-1367459/v1

Williams T; Kroukamp H; Xu X; Wightman E; Llorente B; Borneman A; Carpenter A; Van Wyk N; Espinosa M; Daniel E; Walker R; Cai Y; Nevalainen H; Curach N; Deveson I; Mercer T; Johnson D; Mitchell L; Bader J; Stracquadanio G; Boeke J; Goold H; Pretorius I; Paulsen I, 2022, Laboratory evolution and polyploid SCRaMbLE reveal genomic plasticity to synthetic chromosome defects and rearrangements, http://dx.doi.org/10.1101/2022.07.22.501046

Giles KA; Phipps AJ; Cashion JM; Huskins SN; Mercer TR; Robinson MD; Woodhouse A; Taberlay PC, 2021, H3K4me3 enrichment defines neuronal age, while a youthful H3K27ac signature is recapitulated in aged neurons, http://dx.doi.org/10.1101/2021.11.11.467877

Li X; Zhao Q; Wang Z; Liau W-S; Basic D; Ren H; Marshall PR; Zajaczkowski EL; Leighton LJ; Madugalle SU; Musgrove M; Periyakaruppiah A; Shi J; Zhang J; Mattick JS; Mercer TR; Wei W; Bredy TW, 2021, On the discovery of ADRAM, an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3, http://dx.doi.org/10.1101/2021.08.01.454607

Sowlati T; Sarkar S; Perumana B; Chan WL; Afshar B; Boers M; Shin D; Mercer T; Chen WH; Toda AP; Besoli AG; Yoon S; Kyriazidou S; Yang P; Aggarwal V; Vakilian N; Rozenblit D; Kahrizi M; Zhang J; Wang A; Sen P; Murphy D; Mikhemar M; Sajjadi A; Mehrabani A; Ibrahim B; Pan B; Juan K; Xu S; Guan C; Geshvindman G; Low K; Kocaman N; Eberhart H; Kimura K; Elgorriaga I; Roussel V; Xie H; Shi L; Kodavati V, 2018, 'A 60GHz 144-element phased-array transceiver with 51dBm maximum EIRP and ±60° beam steering for backhaul application', in Digest of Technical Papers - IEEE International Solid-State Circuits Conference, pp. 66 - 68, http://dx.doi.org/10.1109/ISSCC.2018.8310186

Signal B; Gloss BS; Dinger ME; Mercer TR, 2016, Machine-learning annotation of human splicing branchpoints, http://dx.doi.org/10.1101/094003

Analui B; Mercer T; Mandegaran S; Goel A; Hashemi H, 2014, 'A 50 MHz-6 GHz, 2 × 2 MIMO, reconfigurable architecture, software-defined radio in 130nm CMOS', in Digest of Papers - IEEE Radio Frequency Integrated Circuits Symposium, pp. 329 - 332, http://dx.doi.org/10.1109/RFIC.2014.6851733

Clark MB; Mercer TR; Leonardi T; Bussotti G; Crawford J; Nielsen LK; Enright AJ; Ponting CP; Dinger ME; Mattick JS, 2014, 'Quantitative gene expression profiling with targeted RNA sequencing', in FEBS JOURNAL, WILEY-BLACKWELL, FRANCE, Paris, pp. 45 - 45, presented at FEBS EMBO 2014 Conference, FRANCE, Paris, 30 August 2014 - 04 September 2014, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000359666800141&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Chang SH; Chu TS; Roderick J; Du C; Mercer T; Burdick JW; Hashemi H, 2011, 'UWB human detection radar system: A RF CMOS chip and algorithm integrated sensor', in Proceedings - IEEE International Conference on Ultra-Wideband, pp. 355 - 359, http://dx.doi.org/10.1109/ICUWB.2011.6058863

Chu TS; Roderick J; Chang SH; Mercer T; Du C; Hashemi H, 2011, 'A short-range UWB impulse-radio CMOS sensor for human feature detection', in Digest of Technical Papers - IEEE International Solid-State Circuits Conference, pp. 294 - 295, http://dx.doi.org/10.1109/ISSCC.2011.5746325