By Professor John Stanley Mattick

Journal articles

Ersavas T; Smith MA; Mattick JS, 2024, 'Novel applications of Convolutional Neural Networks in the age of Transformers', Scientific Reports, 14, http://dx.doi.org/10.1038/s41598-024-60709-z

Mattick JSA; Bromley RE; Watson KJ; Adkins RS; Holt CI; Lebov JF; Sparklin BC; Tyson TS; Rasko DA; Dunning Hotopp JC, 2024, 'Deciphering transcript architectural complexity in bacteria and archaea.', mBio, 15, pp. e0235924, http://dx.doi.org/10.1128/mbio.02359-24

Werner A; Kanhere A; Wahlestedt C; Mattick JS, 2024, 'Natural antisense transcripts as versatile regulators of gene expression', Nature Reviews Genetics, 25, pp. 730 - 744, http://dx.doi.org/10.1038/s41576-024-00723-z

Mattick J, 2024, 'Never underestimate RNA: how a molecule went from bit player to star of the show', Nature, 632, pp. 250 - 251, http://dx.doi.org/10.1038/d41586-024-02537-9

Cummins M; Watson C; Edwards RJ; Mattick JS, 2024, 'The Evolution of Ultraconserved Elements in Vertebrates.', Mol Biol Evol, 41, http://dx.doi.org/10.1093/molbev/msae146

Cummins M; Watson C; Edwards RJ; Mattick JS, 2024, 'The Evolution of Ultraconserved Elements in Vertebrates', Molecular Biology and Evolution, 41, pp. msae146, http://dx.doi.org/10.1093/molbev/msae146

Mattick JS, 2023, 'A Kuhnian revolution in molecular biology: Most genes in complex organisms express regulatory RNAs', BioEssays, 45, http://dx.doi.org/10.1002/bies.202300080

Mattick JS, 2023, 'Enhancers are genes that express organizational RNAs', Frontiers in RNA Research, 1, http://dx.doi.org/10.3389/frnar.2023.1194526

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, 24, pp. 430 - 447, http://dx.doi.org/10.1038/s41580-022-00566-8

Enguita FJ; Leitão AL; Mattick JS, 2023, 'RNA Regulatory Networks 2.0', International Journal of Molecular Sciences, 24, http://dx.doi.org/10.3390/ijms24109001

Mattick JS, 2023, 'RNA out of the mist', Trends in Genetics, 39, pp. 187 - 207, http://dx.doi.org/10.1016/j.tig.2022.11.001

Begik O; Diensthuber G; Liu H; Delgado-Tejedor A; Kontur C; Niazi AM; Valen E; Giraldez AJ; Beaudoin JD; Mattick JS; Novoa EM, 2023, 'Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing', Nature Methods, 20, pp. 75 - 85, http://dx.doi.org/10.1038/s41592-022-01714-w

Begik O; Mattick JS; Novoa EM, 2022, 'Exploring the epitranscriptome by native RNA sequencing', RNA, 28, pp. 1430 - 1439, http://dx.doi.org/10.1261/rna.079404.122

Mattick J; Amaral P, 2022, 'RNA, the Epicenter of Genetic Information', , http://dx.doi.org/10.1201/9781003109242

Bartonicek N; Rouet R; Warren J; Loetsch C; Rodriguez GS; Walters S; Lin F; Zahra D; Blackburn J; Hammond JM; Reis ALM; Deveson IW; Zammit N; Zeraati M; Grey S; Christ D; Mattick JS; Chtanova T; Brink R; Dinger ME; Weatheritt RJ; Sprent J; King C, 2022, 'The retroelement Lx9 puts a brake on the immune response to virus infection', Nature, 608, pp. 757 - 765, http://dx.doi.org/10.1038/s41586-022-05054-9

Tvedte ES; Gasser M; Zhao X; Tallon LJ; Sadzewicz L; Bromley RE; Chung M; Mattick J; Sparklin BC; Dunning Hotopp JC, 2022, 'Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement.', Curr Biol, 32, pp. 2786 - 2795.e5, http://dx.doi.org/10.1016/j.cub.2022.05.024

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

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, 38, http://dx.doi.org/10.1016/j.celrep.2022.110546

Dey P; Mattick JS, 2021, 'High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs', Epigenetics and Chromatin, 14, http://dx.doi.org/10.1186/s13072-021-00419-2

Begik O; Lucas MC; Pryszcz LP; Ramirez JM; Medina R; Milenkovic I; Cruciani S; Liu H; Vieira HGS; Sas-Chen A; Mattick JS; Schwartz S; Novoa EM, 2021, 'Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing', Nature Biotechnology, 39, pp. 1278 - 1291, http://dx.doi.org/10.1038/s41587-021-00915-6

Werner A; Clark JE; Samaranayake C; Casement J; Zinad HS; Sadeq S; Al-Hashimi S; Smith M; Kotaja N; Mattick JS, 2021, 'Widespread formation of double-stranded RNAs in testis', Genome Research, 31, pp. 1174 - 1186, http://dx.doi.org/10.1101/gr.265603.120

Chung M; Adkins RS; Mattick JSA; Bradwell KR; Shetty AC; Sadzewicz L; Tallon LJ; Fraser CM; Rasko DA; Mahurkar A; Dunning Hotopp JC, 2021, 'FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses.', mSystems, 6, http://dx.doi.org/10.1128/mSystems.00917-20

Jonkhout N; Cruciani S; Santos Vieira HG; Tran J; Liu H; Liu G; Pickford R; Kaczorowski D; Franco GR; Vauti F; Camacho N; Abedini SS; Najmabadi H; Ribas de Pouplana L; Christ D; Schonrock N; Mattick JS; Novoa EM, 2021, 'Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation', RNA Biology, 18, pp. 1905 - 1919, http://dx.doi.org/10.1080/15476286.2021.1881291

Mattick J; Libro S; Bromley R; Chaicumpa W; Chung M; Cook D; Khan MB; Kumar N; Lau Y-L; Misra-Bhattacharya S; Rao R; Sadzewicz L; Saeung A; Shahab M; Sparklin BC; Steven A; Turner JD; Tallon LJ; Taylor MJ; Moorhead AR; Michalski M; Foster JM; Dunning Hotopp JC, 2021, 'X-treme loss of sequence diversity linked to neo-X chromosomes in filarial nematodes.', PLoS Negl Trop Dis, 15, pp. e0009838, http://dx.doi.org/10.1371/journal.pntd.0009838

Lebov JF; Mattick J; Libro S; Sparklin BC; Chung M; Bromley RE; Nadendla S; Zhao X; Ott S; Sadzewicz L; Tallon LJ; Michalski ML; Foster JM; Dunning Hotopp JC, 2020, 'Complete Genome Sequence of wBp, the Wolbachia Endosymbiont of Brugia pahangi FR3.', Microbiol Resour Announc, 9, http://dx.doi.org/10.1128/MRA.00480-20

Mattick J; Libro S; Sparklin BC; Chung M; Bromley RE; Nadendla S; Zhao X; Ott S; Sadzewicz L; Tallon LJ; Michalski ML; Foster JM; Dunning Hotopp JC, 2020, 'Nearly Complete Genome Sequence of Brugia pahangi FR3.', Microbiol Resour Announc, 9, http://dx.doi.org/10.1128/MRA.00479-20

Doble B; Schofield D; Evans CA; Groza T; Mattick JS; Field M; Roscioli T, 2020, 'Impacts of genomics on the health and social costs of intellectual disability', Journal of Medical Genetics, 57, pp. 479 - 486, http://dx.doi.org/10.1136/jmedgenet-2019-106445

Tracey A; Foster JM; Paulini M; Grote A; Mattick J; Tsai Y-C; Chung M; Cotton JA; Clark TA; Geber A; Holroyd N; Korlach J; Libro S; Lustigman S; Michalski ML; Rogers MB; Twaddle A; Dunning Hotopp JC; Berriman M; Ghedin E, 2020, 'Nearly Complete Genome Sequence of Brugia malayi Strain FR3.', Microbiol Resour Announc, 9, http://dx.doi.org/10.1128/MRA.00154-20

Pineda SS; Chin YKY; Undheim EAB; Senff S; Mobli M; Dauly C; Escoubas P; Nicholson GM; Kaas Q; Guo S; Herzig V; Mattick JS; King GF, 2020, 'Structural venomics reveals evolution of a complex venom by duplication and diversification of an ancient peptide-encoding gene', Proceedings of the National Academy of Sciences of the United States of America, 117, http://dx.doi.org/10.1073/pnas.1914536117

Begik O; Lucas MC; Liu H; Ramirez JM; Mattick JS; Novoa EM, 2020, 'Integrative analyses of the RNA modification machinery reveal tissue- And cancer-specific signatures', Genome Biology, 21, pp. 97, http://dx.doi.org/10.1186/s13059-020-02009-z

Foster JM; Grote A; Mattick J; Tracey A; Tsai Y-C; Chung M; Cotton JA; Clark TA; Geber A; Holroyd N; Korlach J; Li Y; Libro S; Lustigman S; Michalski ML; Paulini M; Rogers MB; Teigen L; Twaddle A; Welch L; Berriman M; Dunning Hotopp JC; Ghedin E, 2020, 'Sex chromosome evolution in parasitic nematodes of humans.', Nat Commun, 11, pp. 1964, http://dx.doi.org/10.1038/s41467-020-15654-6

Liu H; Begik O; Lucas MC; Ramirez JM; Mason CE; Wiener D; Schwartz S; Mattick JS; Smith MA; Novoa EM; Novoa Pardo EM, 2019, 'Accurate detection of m⁶A RNA modifications in native RNA sequences', Nature Communications, 10, pp. 4079, http://dx.doi.org/10.1038/s41467-019-11713-9

Habic A; Mattick JS; Calin GA; Krese R; Konc J; Kunej T, 2019, 'Genetic Variations of Ultraconserved Elements in the Human Genome', OMICS A Journal of Integrative Biology, 23, pp. 549 - 559, http://dx.doi.org/10.1089/omi.2019.0156

Ke YD; Chan G; Stefanoska K; Au C; Bi M; Müller J; Przybyla M; Feiten A; Prikas E; Halliday GM; Piguet O; Kiernan MC; Kassiou M; Hodges JR; Loy CT; Mattick JS; Ittner A; Kril JJ; Sutherland GT; Ittner LM, 2019, 'CNS cell type-specific gene profiling of P301S tau transgenic mice identifies genes dysregulated by progressive tau accumulation', Journal of Biological Chemistry, 294, pp. 14149 - 14162, http://dx.doi.org/10.1074/jbc.RA118.005263

Liu H; Begik O; Lucas M; Mason C; Schwartz S; Mattick J; Smith M; Novoa EM, 2019, 'Accurate detection of m6A RNA modifications in native RNA sequences', Nature Communications, 10, http://dx.doi.org/10.1101/525741

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, 10, pp. 309, http://dx.doi.org/10.3389/fgene.2019.00309

Dong X; Liao Z; Gritsch D; Hadzhiev Y; Bai Y; Locascio JJ; Guennewig B; Liu G; Blauwendraat C; Wang T; Adler CH; Hedreen JC; Faull RLM; Frosch MP; Nelson PT; Rizzu P; Cooper AA; Heutink P; Beach TG; Mattick JS; Müller F; Scherzer CR, 2018, 'Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease', Nature Neuroscience, 21, pp. 1482 - 1492, http://dx.doi.org/10.1038/s41593-018-0223-0

Mattick JS, 2018, 'The state of long non-coding RNA biology', Non-coding RNA, 4, pp. 17, http://dx.doi.org/10.3390/ncrna4030017

Mladenova D; Barry G; Konen LM; Pineda SS; Guennewig B; Avesson L; Zinn R; Schonrock N; Bitar M; Jonkhout N; Crumlish L; Kaczorowski DC; Gong A; Pinese M; Franco GR; Walkley CR; Vissel B; Mattick JS, 2018, 'Adar3 is involved in learning and memory in mice', Frontiers in Neuroscience, 12, pp. 243, http://dx.doi.org/10.3389/fnins.2018.00243

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, 6, pp. 245 - 255.e5, http://dx.doi.org/10.1016/j.cels.2017.12.005

Mattick J, 2018, 'Four ways precision medicine is making a difference', The Conversation

Hobbs M; Ender C; Baillie GJ; Crawford J; Ru K; Taft RJ; Mattick J, 2018, 'Transcription initiation RNAs are associated with chromatin activation mark H3K4me3', BIORXIV, http://dx.doi.org/10.1101/265827

Mattick JS; Dinger M; Schonrock N; Cowley M, 2018, 'Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing', Medical Journal of Australia, 209, pp. 197, http://dx.doi.org/10.5694/mja17.01176

Smith MA; Seemann SE; Quek XC; Mattick JS, 2017, 'DotAligner: Identification and clustering of RNA structure motifs', Genome Biology, 18, http://dx.doi.org/10.1186/s13059-017-1371-3

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, 18, pp. 241, http://dx.doi.org/10.1186/s13059-017-1363-3

Doble B; Schofield DJ; Roscioli T; Mattick JS, 2017, 'Prioritising the application of genomic medicine', npj Genomic Medicine, 2, http://dx.doi.org/10.1038/s41525-017-0037-0

Jonkhout N; Tran J; Smith MA; Schonrock N; Mattick JS; Novoa Pardo EM, 2017, 'The RNA modification landscape in human disease', RNA, 23, pp. 1754 - 1769, http://dx.doi.org/10.1261/rna.063503.117

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

Novoa Pardo EM; Mason CE; Mattick JS, 2017, 'Charting the unknown epitranscriptome', Nature Reviews Molecular Cell Biology, 18, pp. 339 - 340, http://dx.doi.org/10.1038/nrm.2017.49

Deveson IW; Holleley CE; Blackburn J; Marshall Graves JA; Mattick JS; Waters PD; Georges A, 2017, 'Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination', Science Advances, 3, pp. e1700731, http://dx.doi.org/10.1126/sciadv.1700731

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