By Professor John Stanley Mattick

Conference Papers

Mattick J, 2008, 'A NEW UNDERSTANDING OF THE HUMAN GENOME', in Arthur J; Ng SK (ed.), GENOME INFORMATICS 2008, VOL 21, IMPERIAL COLLEGE PRESS, AUSTRALIA, Gold Coast, pp. 233 - 234, presented at 19th International Conference on Genome Informatics, AUSTRALIA, Gold Coast, 01 December 2008 - 03 December 2008, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000263559100024&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mattick JS; Croft LJ; Dinger ME; Pheasant M; Makunin IV; Amiri MA; Mercer TR; Pang KC; Simons C; Taft RJ, 2007, 'The human genome as an RNA machine', in FEBS JOURNAL, BLACKWELL PUBLISHING, AUSTRIA, Vienna, pp. 15 - 15, presented at 32nd Congress of the Federation-of-European-Biochemical-Societies (FEBS), AUSTRIA, Vienna, 07 July 2007 - 12 July 2007, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000253283800024&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Simons C; Pheasant M; Makunin I; Mattick JS, 2006, 'Transposon-free regions in mammalian genomes', in Kolchanov N; Hofestadt R (ed.), PROCEEDINGS OF THE FIFTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE, VOL 3, RUSSIAN ACAD SCI SIBERIAN BRANCH, RUSSIA, Novosibirsk, pp. 233 - +, presented at 5th International Conference on Bioinformatics of Genome Regulation and Structure, RUSSIA, Novosibirsk, 16 July 2006 - 22 July 2006

Hallinan JS; Bradley DR; Mattick JS; Wiles J, 2006, 'Effects of an RNA control layer on the state space of Boolean models of genetic regulatory networks', in 2006 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1-6, IEEE, CANADA, Vancouver, pp. 2536 - 2540, presented at IEEE Congress on Evolutionary Computation, CANADA, Vancouver, 16 July 2006 - 21 July 2006, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000245414204044&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mattick JS, 2006, 'The majority of the human genome encodes a hidden RNA regulatory system that controls differentiation and development', in HYPERTENSION, LIPPINCOTT WILLIAMS & WILKINS, AUSTRALIA, pp. 1472 - 1472, presented at Annual Scientific Meeting of the High-Blood-Pressure-Research-Council-of-Australia, AUSTRALIA, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000246720800094&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Wiles J; Geard N; Watson J; Willadsen K; Mattick J; Bradley D; Hallinan J, 2005, 'There s more to a model than code: understanding and formalizing in silico modeling experience', in Gecco 2005 Genetic and Evolutionary Computation Conference, pp. 281 - 288, http://dx.doi.org/10.1145/1102256.1102318

Makunin I; Stephen S; Pheasant M; Bejerano G; Kent JW; Haussler H; Mattick JS, 2004, 'Extremely conserved non-coding sequences in vertebrate genomes', in PROCEEDINGS OF THE FOURTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE, VOL 1, RUSSIAN ACAD SCI SIBERIAN BRANCH, RUSSIA, Novosibirsk, pp. 138 - 140, presented at 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2004), RUSSIA, Novosibirsk, 25 July 2004 - 30 July 2004, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000242399100034&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Mattick JS, 2004, 'Programming of the autopoietic development of complex organisms: The hidden layer of noncoding RNA', in CYTOMETRY PART A, WILEY-LISS, FRANCE, Montpellier, pp. 110 - 110, presented at 22nd Congress of the International-Society-for-Analytical-Cytology, FRANCE, Montpellier, 22 May 2004 - 27 May 2004, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000221319900252&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Utama B; Hartmann B; Mattick J; Ru K; Wang XL; Kennedy D, 2003, 'Nrap, a novel nucleolar protein which interacts with B23/Nucleophosmin during ribosomal biogenesis', in FASEB JOURNAL, FEDERATION AMER SOC EXP BIOL, CALIFORNIA, SAN DIEGO, pp. A180 - A180, presented at Experimental Biology 2003 Meeting, CALIFORNIA, SAN DIEGO, 11 April 2003 - 15 April 2003, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000181733100867&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

TSUKAMOTO Y; WONG H; WAKIL SJ; MATTICK JS, 1982, 'THE ARCHITECTURE OF ANIMAL FATTY-ACID SYNTHETASE', in FEDERATION PROCEEDINGS, FEDERATION AMER SOC EXP BIOL, pp. 1026 - 1026, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1982NG28400943&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

MATTICK JS; AHRENS D; WONG H, 1981, 'MONOCLONAL-ANTIBODIES AGAINST CHICKEN FATTY-ACID SYNTHETASE', in FEDERATION PROCEEDINGS, FEDERATION AMER SOC EXP BIOL, pp. 1596 - 1596, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1981LM15800330&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

ZEHNER ZE; MATTICK JS; STUART RR; WAKIL SJ, 1979, 'ISOLATION AND CHARACTERIZATION OF FATTY-ACID SYNTHETASE MESSENGER-RNA', in FEDERATION PROCEEDINGS, FEDERATION AMER SOC EXP BIOL, pp. 299 - 299, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1979GL65500402&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Conference Abstracts

Zhao W; Mazar J; Lee B; Sawada J; Li J-L; Shelley J; Govindarajani S; Towler D; Mattick JS; Komatsu M; Dinger ME; Perera RJ, 2015, 'The long noncoding RNA SPRIGHTLY regulates cell proliferation in primary human melanocytes', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, MA, Boston, Vol. 76, presented at AACR Special Conference on Noncoding RNAs and Cancer - Mechanisms to Medicines, MA, Boston, 04 December 2015 - 07 December 2015, http://dx.doi.org/10.1158/1538-7445.NONRNA15-A09

Reports

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, 2019, Erratum to: Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease (Nature Neuroscience, (2018), 21, 10, (1482-1492), 10.1038/s41593-018-0223-0), http://dx.doi.org/10.1038/s41593-018-0277-z

Working Papers

Begik O; Mattick JS; Novoa EM, 2020, Decoding ribosomal RNA modification dynamics at single molecule resolution, http://dx.doi.org10.1101/2020.07.06.189969, https://www.biorxiv.org/content/10.1101/2020.07.06.189969v2

Begik O; Lucas MC; Liu H; Ramirez JM; Mattick JS; Novoa EM, Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/830968

Preprints

Cummins M; Mattick J, 2025, Frequent functional orthology of long noncoding RNAs and genomic loci associated with complex traits and disorders, http://dx.doi.org/10.1101/2025.10.31.25339260

Mattick JSA; Bromley RE; Watson KJ; Adkins RS; Holt CI; Lebov JF; Sparklin BC; Tyson TS; Rasko DA; Hotopp JCD, 2024, Deciphering Bacterial and Archaeal Transcriptional Dark Matter and Its Architectural Complexity., http://dx.doi.org/10.1101/2024.04.02.587803

Gaonac’h-Lovejoy V; Mattick J; Sauvageau M; Smith M, 2024, ECSfinder : Optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences, http://dx.doi.org/10.1101/2024.09.14.612549

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

Pineda SS; Chin YK-Y; Undheim EAB; Senff S; Mobli M; Dauly C; Escoubas P; Nicholson GM; Kaas Q; Mattick JS; King GF, 2018, Structural venomics: evolution of a complex chemical arsenal by massive duplication and neofunctionalization of a single ancestral fold, http://dx.doi.org/10.1101/485722

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, http://dx.doi.org/10.1101/265827

Gagen MJ; Mattick JS, 2005, Accelerating, hyper-accelerating, and decelerating probabilistic networks, http://dx.doi.org/10.48550/arxiv.q-bio/0502013

Gagen MJ; Mattick JS, 2004, Failed "nonaccelerating" models of prokaryote gene regulatory networks, http://dx.doi.org/10.48550/arxiv.q-bio/0312022

Gagen MJ; Mattick JS, 2004, Inherent size constraints on prokaryote gene networks due to "accelerating" growth, http://dx.doi.org/10.48550/arxiv.q-bio/0312021

Croft LJ; Lercher MJ; Gagen MJ; Mattick JS, 2003, Is prokaryotic complexity limited by accelerated growth in regulatory overhead?, http://dx.doi.org/10.48550/arxiv.q-bio/0311021

Liu H; Begik O; Lucas MC; Mason CE; Schwartz S; Mattick JS; Smith MA; Novoa EM, Accurate detection of m6A RNA modifications in native RNA sequences, http://dx.doi.org/10.1101/525741

Novoa EM; Beaudoin J-D; Giraldez AJ; Mattick JS; Kellis M, Best practices for genome-wide RNA structure analysis: combination of mutational profiles and drop-off information, http://dx.doi.org/10.1101/176883

Begik O; Diensthuber G; Borovska I; Mattick JS; Incarnato D; Novoa EM, FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling, http://dx.doi.org/10.1101/2025.04.22.649934

Begik O; Diensthuber G; Liu H; Delgado-Tejedor A; Kontur C; Niazi AM; Valen E; Giraldez AJ; Beaudoin J-D; Mattick JS; Novoa EM, Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing, http://dx.doi.org/10.1101/2021.09.22.461331

Ersavas T; Smith MA; Mattick JS, Novel applications of Convolutional Neural Networks in the age of Transformers, http://dx.doi.org/10.21203/rs.3.rs-3868861/v1

Cox LB; Mattick JS; Middleton IA; Rizzuto FJ; Thordarson P, Specificity of the stabilising interaction between intrinsically disordered protein sequences and G-quadruplexes in RNA, http://dx.doi.org/10.1101/2025.10.19.683336

Jonkhout N; Cruciani S; Vieira HGS; Tran J; Liu H; Liu G; Pickford R; Kaczorowski D; Franco GR; Vauti F; Camacho N; Abedini SS; Najmabadi H; de Pouplana LR; Christ D; Schonrock N; Mattick JS; Novoa EM, Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation, http://dx.doi.org/10.1101/2020.10.17.343772

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, Targeted, High-resolution RNA Sequencing of Non-coding Genomic Regions Associated with Neuropsychiatric Functions, http://dx.doi.org/10.1101/539882

Jung S; Cummins MJ; Altaf S; Heggen RJ; Poljak A; Ferguson L; Clemens K; Delerue F; Ittner LM; Mattick JS, The long noncoding RNA Dory is required for female but not male spatial learning and memory, http://dx.doi.org/10.64898/2026.04.01.715990

Deveson IW; Brunck ME; Blackburn J; Tseng E; Hon T; Clark TA; Clark MB; Crawford J; Dinger ME; Nielsen LK; Mattick JS; Mercer TR, Universal alternative splicing of noncoding exons, http://dx.doi.org/10.1101/136275

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