By Dr James Blackburn

Journal articles

Wagner S; Whiteley SL; Castelli M; Patel HR; Deveson IW; Blackburn J; Holleley CE; Marshall Graves JA; Georges A, 2023, 'Gene expression of male pathway genes sox9 and amh during early sex differentiation in a reptile departs from the classical amniote model', BMC Genomics, 24, http://dx.doi.org/10.1186/s12864-023-09334-0

Vargas AC; Heyer EE; Cheah AL; Bonar F; Jones M; Maclean FM; Gill AJ; Blackburn J, 2023, 'Improving sarcoma classification by using RNA hybridisation capture sequencing in sarcomas of uncertain histogenesis of young individuals', Pathology, 55, pp. 478 - 485, http://dx.doi.org/10.1016/j.pathol.2022.11.012

Epstein RJ; Lin FPY; Brink RA; Blackburn J, 2023, 'Synonymous alterations of cancer-associated Trp53 CpG mutational hotspots cause fatal developmental jaw malocclusions but no tumors in knock-in mice', PLoS ONE, 18, http://dx.doi.org/10.1371/journal.pone.0284327

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

Bournazos AM; Riley LG; Bommireddipalli S; Ades L; Akesson LS; Al-Shinnag M; Alexander SI; Archibald AD; Balasubramaniam S; Berman Y; Beshay V; Boggs K; Bojadzieva J; Brown NJ; Bryen SJ; Buckley MF; Chong B; Davis MR; Dawes R; Delatycki M; Donaldson L; Downie L; Edwards C; Edwards M; Engel A; Ewans LJ; Faiz F; Fennell A; Field M; Freckmann ML; Gallacher L; Gear R; Goel H; Goh S; Goodwin L; Hanna B; Harraway J; Higgins M; Ho G; Hopper BK; Horton AE; Hunter MF; Huq AJ; Josephi-Taylor S; Joshi H; Kirk E; Krzesinski E; Kumar KR; Lemckert F; Leventer RJ; Lindsey-Temple SE; Lunke S; Ma A; Macaskill S; Mallawaarachchi A; Marty M; Marum JE; McCarthy HJ; Menezes MP; McLean A; Milnes D; Mohammad S; Mowat D; Niaz A; Palmer EE; Patel C; Patel SG; Phelan D; Pinner JR; Rajagopalan S; Regan M; Rodgers J; Rodrigues M; Roxburgh RH; Sachdev R; Roscioli T; Samarasekera R; Sandaradura SA; Savva E; Schindler T; Shah M; Sinnerbrink IB; Smith JM; Smith RJ; Springer A; Stark Z; Strom SP; Sue CM; Tan K; Tan TY; Tantsis E; Tchan MC; Thompson BA; Trainer AH; van Spaendonck-Zwarts K; Walsh R; Warwick L; White S; White SM; Williams MG, 2022, 'Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants', Genetics in Medicine, 24, pp. 130 - 145, http://dx.doi.org/10.1016/j.gim.2021.09.001

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; Mercer T; Thomas D, 2021, 'Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions', Genome Biology, 22, pp. 109, http://dx.doi.org/10.1186/s13059-021-02315-0

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, 39, pp. 1115 - 1128, http://dx.doi.org/10.1038/s41587-021-00857-z

Whiteley SL; Holleley CE; Wagner S; Blackburn J; Deveson IW; Marshall Graves JA; Georges A, 2021, 'Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination', PLoS Genetics, 17, http://dx.doi.org/10.1371/journal.pgen.1009465

Whiteley S; Holleley C; Wagner S; Blackburn J; Deveson I; Graves JM; Georges A, 2021, 'Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination', , http://dx.doi.org/10.1101/2021.02.03.429474

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, 11, http://dx.doi.org/10.1038/s41467-020-17445-5

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; O'Toole S, 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, 11, pp. 1810, http://dx.doi.org/10.1038/s41467-020-15697-9

Mueller SA; Gauthier MEA; Blackburn J; Grady JP; Kraitsek S; Hajdu E; Dettmer MS; Dahlstrom JE; Lee CS; Luk PP; Yu B; Giger R; Kummerfeld S; Clark JR; Gupta R; Cowley MJ, 2020, 'Molecular patterns in salivary duct carcinoma identify prognostic subgroups', Modern Pathology, 33, pp. 1896 - 1909, http://dx.doi.org/10.1038/s41379-020-0576-2

Yamada A; Kawasaki M; Miake Y; Yamada Y; Blackburn J; Kawasaki K; Trakanant S; Nagai T; Nihara J; Kudo T; Meguro F; Schmidt-Ullrich R; Liu B; Hu Y; Page A; Ramírez Á; Sharpe PT; Maeda T; Takagi R; Ohazama A, 2020, 'Overactivation of the NF-κB pathway impairs molar enamel formation', Oral Diseases, 26, pp. 1513 - 1522, http://dx.doi.org/10.1111/odi.13384

Heyer EE; Blackburn J, 2020, 'Sequencing Strategies for Fusion Gene Detection', BioEssays, 42, http://dx.doi.org/10.1002/bies.202000016

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, 180, pp. 878 - 894.e19, http://dx.doi.org/10.1016/j.cell.2020.01.029

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, 10, http://dx.doi.org/10.1038/s41467-019-09272-0

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; O'Toole S, 2019, 'Diagnosis of fusion genes using targeted RNA sequencing', Nature Communications, 10, pp. 1388, http://dx.doi.org/10.1038/s41467-019-09374-9

Singh M; Al-Eryani G; Carswell S; Ferguson JM; Blackburn J; Barton K; Roden D; Luciani F; Giang Phan T; Junankar S; Jackson K; Goodnow CC; Smith MA; Swarbrick A, 2019, 'High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-11049-4

Joffrin E; Abduallev S; Abhangi M; Abreu P; Afanasev V; Afzal M; Aggarwal KM; Ahlgren T; Aho-Mantila L; Aiba N; Airila M; Alarcon T; Albanese R; Alegre D; Aleiferis S; Alessi E; Aleynikov P; Alkseev A; Allinson M; Alper B; Alves E; Ambrosino G; Ambrosino R; Amosov V; Andersson Sundén E; Andrews R; Angelone M; Anghel M; Angioni C; Appel L; Appelbee C; Arena P; Ariola M; Arshad S; Artaud J; Arter W; Ash A; Ashikawa N; Aslanyan V; Asunta O; Asztalos O; Auriemma F; Austin Y; Avotina L; Axton M; Ayres C; Baciero A; Baiao D; Balboa I; Balden M; Balshaw N; Bandaru VK; Banks J; Baranov YF; Barcellona C; Barnard T; Barnes M; Barnsley R; Baron Wiechec A; Barrera Orte L; Baruzzo M; Basiuk V; Bassan M; Bastow R; Batista A; Batistoni P; Baumane L; Bauvir B; Baylor L; Beaumont PS; Beckers M; Beckett B; Bekris N; Beldishevski M; Bell K; Belli F; Belonohy E; Benayas J; Bergsaker H; Bernardo J; Bernert M; Berry M; Bertalot L; Besiliu C; Betar H; Beurskens M; Bielecki J; Biewer T; Bilato R; Biletskyi O; Bilková P; Binda F; Birkenmeier G; Bizarro JPS; Björkas C; Blackburn J; Blackman TR; Blanchard P; Blatchford P; Bobkov V, 2019, 'Overview of the JET preparation for deuterium-tritium operation with the ITER like-wall', Nuclear Fusion, 59, http://dx.doi.org/10.1088/1741-4326/ab2276

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, 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, 14, pp. 2119 - 2151, http://dx.doi.org/10.1038/s41596-019-0175-1

Nagai T; Trakanant S; Kawasaki M; Kawasaki K; Yamada Y; Watanabe M; Blackburn J; Otsuka-Tanaka Y; Hishinuma M; Kitatmura A; Meguro F; Yamada A; Kodama Y; Maeda T; Zhou Q; Saijo Y; Yasue A; Sharpe PT; Hindges R; Takagi R; Ohazama A, 2019, 'MicroRNAs control eyelid development through regulating Wnt signaling', Developmental Dynamics, 248, pp. 201 - 210, http://dx.doi.org/10.1002/dvdy.10

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, 3, pp. 1 - 11, http://dx.doi.org/10.1200/PO.18.00297

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

Mueller SA; Grady J; Dettmer M; Gauthier M-EA; Hajdu E; Blackburn J; Giger R; Dahlstrom JE; Luk P; Lee S; Kratisek S; Yu B; Clark JR; Cowley MJ; Gupta R, 2019, 'The targetable genomic landscape of salivary duct carcinoma', Pathology, 51, pp. S83 - S83, http://dx.doi.org/10.1016/j.pathol.2018.12.210

Kawasaki M; Kawasaki K; Meguro F; Yamada A; Ishikawa R; Porntaveetus T; Blackburn J; Otsuka-Tanaka Y; Saito N; Ota MS; Sharpe PT; Kessler JA; Herz J; Cobourne MT; Maeda T; Ohazama A, 2018, 'Lrp4/Wise regulates palatal rugae development through turing-type reaction-diffusion mechanisms', PLoS ONE, 13, http://dx.doi.org/10.1371/journal.pone.0204126

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

Singh M; Al-Eryani G; Carswell S; Ferguson J; Blackburn J; Barton K; Roden D; Luciani F; Phan T; Junankar S; Jackson K; Goodnow C; Smith M; Swarbrick A, 2018, 'High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes', , http://dx.doi.org/10.1101/424945

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, 77, pp. 4279 - 4292, http://dx.doi.org/10.1158/0008-5472.CAN-16-2550

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

Blackburn J; Roden DL; Ng R; Wu J; Bosman A; Epstein RJ, 2016, 'Damage-inducible intragenic demethylation of the human TP53 tumor suppressor gene is associated with transcription from an alternative intronic promoter', Molecular Carcinogenesis, 55, pp. 1940 - 1951, http://dx.doi.org/10.1002/mc.22441

Kawasaki M; Kawasaki K; Oommen S; Blackburn J; Watanabe M; Nagai T; Kitamura A; Maeda T; Liu B; Schmidt-Ullrich R; Akiyama T; Inoue JI; Hammond NL; Sharpe PT; Ohazama A, 2016, 'Regional regulation of Filiform tongue papillae development by Ikkα/Irf6', Developmental Dynamics, 245, pp. 937 - 946, http://dx.doi.org/10.1002/dvdy.24427

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

Watanabe M; Kawasaki K; Kawasaki M; Portaveetus T; Oommen S; Blackburn J; Nagai T; Kitamura A; Nishikawa A; Kodama Y; Takagi R; Maeda T; Sharpe PT; Ohazama A, 2016, 'Spatio-temporal expression of Sox genes in murine palatogenesis', Gene Expression Patterns, 21, pp. 111 - 118, http://dx.doi.org/10.1016/j.gep.2016.05.002

Blackburn J; Kawasaki K; Porntaveetus T; Kawasaki M; Otsuka-Tanaka Y; Miake Y; Ota MS; Watanabe M; Hishinuma M; Nomoto T; Oommen S; Ghafoor S; Harada F; Nozawa-Inoue K; Maeda T; Peterková R; Lesot H; Inoue J; Akiyama T; Schmidt-Ullrich R; Liu B; Hu Y; Page A; Ramírez ; Sharpe PT; Ohazama A, 2015, 'Excess NF-κB induces ectopic odontogenesis in embryonic incisor epithelium', Journal of Dental Research, 94, pp. 121 - 128, http://dx.doi.org/10.1177/0022034514556707

Kawasaki K; Porntaveetus T; Oommen S; Ghafoor S; Kawasaki M; Otsuka-Tanaka Y; Blackburn J; Kessler JA; Sharpe PT; Ohazama A, 2012, 'Bmp signalling in filiform tongue papillae development', Archives of Oral Biology, 57, pp. 805 - 813, http://dx.doi.org/10.1016/j.archoralbio.2011.11.014

Blackburn J; Ohazama A; Kawasaki K; Otsuka-Tanaka Y; Liu B; Honda K; Rountree RB; Hu Y; Kawasaki M; Birchmeier W; Schmidt-Ullrich R; Kinoshita A; Schutte BC; Hammond NL; Dixon MJ; Sharpe PT, 2012, 'The role of Irf6 in tooth epithelial invagination', Developmental Biology, 365, pp. 61 - 70, http://dx.doi.org/10.1016/j.ydbio.2012.02.009

Ohazama A; Blackburn J; Porntaveetus T; Ota MS; Choi HY; Johnson EB; Myers P; Oommen S; Eto K; Kessler JA; Kondo T; Fraser GJ; Streelman JT; Pardiñas UFJ; Tucker AS; Ortiz PE; Charles C; Viriot L; Herz J; Sharpe PT, 2010, 'A role for suppressed incisor cuspal morphogenesis in the evolution of mammalian heterodont dentition', Proceedings of the National Academy of Sciences of the United States of America, 107, pp. 92 - 97, http://dx.doi.org/10.1073/pnas.0907236107

Ohazama A; Haycraft CJ; Seppala M; Blackburn J; Ghafoor S; Cobourne M; Martinelli DC; Fan CM; Peterkova R; Lesot H; Yoder BK; Sharpe PT, 2009, 'Primary cilia regulate Shh activity in the control of molar tooth number', Development, 136, pp. 897 - 903, http://dx.doi.org/10.1242/dev.027979

Matalová E; š etková J; Míšek I; Blackburn J; Sharpe PT, 2006, 'CD 95 mediated apoptosis in embryogenesis: Implication in tooth development', Orthodontics and Craniofacial Research, 9, pp. 123 - 128, http://dx.doi.org/10.1111/j.1601-6343.2006.00365.x

Courtney JM; Blackburn J; Sharpe PT, 2005, 'The Ectodysplasin and NFκB signalling pathways in odontogenesis', Archives of Oral Biology, 50, pp. 159 - 163, http://dx.doi.org/10.1016/j.archoralbio.2004.11.019

Blackburn J; Tarttelin EE; Gregory-Evans CY; Moosajee M; Gregory-Evans K, 2003, 'Transcriptional Regulation and Expression of the Dominant Drusen Gene FBLN3 (EFEMP1) in Mammalian Retina', Investigative Ophthalmology and Visual Science, 44, pp. 4613 - 4621, http://dx.doi.org/10.1167/iovs.03-0112

Tarttelin EE; Gregory-Evans CY; Bird AC; Weleber RG; Klein ML; Blackburn J; Gregory-Evans K, 2001, 'Molecular genetic heterogeneity in autosomal dominant drusen', Journal of Medical Genetics, 38, pp. 381 - 384, http://dx.doi.org/10.1136/jmg.38.6.381

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