By Associate Professor Martin Smith

Journal articles

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, 9, http://dx.doi.org/10.1038/s41467-018-05555-0

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

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

Smith MA; Mattick JS, 2017, 'Structural and functional annotation of long noncoding RNAs', , 1526, pp. 65 - 85, http://dx.doi.org/10.1007/978-1-4939-6613-4_4

Lu Z; Zhang QC; Lee B; Flynn RA; Smith MA; Robinson JT; Davidovich C; Gooding AR; Goodrich KJ; Mattick JS; Mesirov JP; Cech TR; Chang HY, 2016, 'RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure', Cell, 165, pp. 1267 - 1279, http://dx.doi.org/10.1016/j.cell.2016.04.028

Gonzalez-Estrada A; Cuervo-Pardo L; Ghosh B; Smith M; Pazheri F; Zell K; Wang X-F; Lang DM, 2015, 'Popular on YouTube: A critical appraisal of the educational quality of information regarding asthma', Allergy & Asthma Proceedings, 36, pp. 121 - 126, http://dx.doi.org/10.2500/aap.2015.36.3890

Suryani S; Carol H; Chonghaile TN; Frismantas V; Sarmah C; High L; Bornhauser B; Cowley MJ; Szymanska B; Evans K; Boehm I; Tonna E; Jones L; Manesh DM; Kurmasheva RT; Billups C; Kaplan W; Letai A; Bourquin J-P; Houghton PJ; Smith MA; Lock RB, 2014, 'Cell and molecular determinants of in vivo efficacy of the BH3 mimetic ABT-263 against pediatric acute lymphoblastic leukemia xenografts.', Clin Cancer Res, 20, pp. 4520 - 4531, http://dx.doi.org/10.1158/1078-0432.CCR-14-0259

Buske FA; French HJ; Smith MA; Clark SJ; Bauer DC, 2014, 'NGSANE: a lightweight production informatics framework for high-throughput data analysis.', Bioinformatics, 30, pp. 1471 - 1472, http://dx.doi.org/10.1093/bioinformatics/btu036

Joseph L; Casanegra AI; Dhariwal M; Smith MA; Raju MG; Militello MA; Gomes MP; Gornik HL; Bartholomew JR, 2014, 'Bivalirudin for the treatment of patients with confirmed or suspected heparin‐induced thrombocytopenia', Journal of Thrombosis and Haemostasis, 12, pp. 1044 - 1053, http://dx.doi.org/10.1111/jth.12592

WEBBER M; HALLAMS E; SMITH MA, 2014, 'Repairing NATO's motors', International Affairs, 90, pp. 773 - 793, http://dx.doi.org/10.1111/1468-2346.12140

Smith MA; Gesell T; Stadler PF; Mattick JS, 2013, 'Widespread purifying selection on RNA structure in mammals', Nucleic Acids Research, 41, pp. 8220 - 8236, http://dx.doi.org/10.1093/nar/gkt596

Clark MB; Choudhary A; Smith MA; Taft RJ; Mattick JS, 2013, 'The dark matter rises: The expanding world of regulatory RNAs', Essays in Biochemistry, 54, pp. 1 - 16, http://dx.doi.org/10.1042/BSE0540001

Smith MA, 2013, 'Russia and multipolarity since the end of the Cold War', East European Politics, 29, pp. 36 - 51, http://dx.doi.org/10.1080/21599165.2013.764481

Shore AN; Kabotyanski EB; Roarty K; Smith MA; Zhang Y; Creighton CJ; Dinger ME; Rosen JM, 2012, 'Pregnancy-induced noncoding RNA (PINC) associates with polycomb repressive complex 2 and regulates mammary epithelial differentiation', Plos Genetics, 8, pp. e1002840, http://dx.doi.org/10.1371/journal.pgen.1002840

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

Smith MJ, 2011, 'Tsars, leadership and innovation in the public sector', Policy & Politics, 39, pp. 343 - 359, http://dx.doi.org/10.1332/030557310x520289

Khaitan D; Dinger ME; Mazar J; Crawford J; Smith MA; Mattick JS; Perera RJ, 2011, 'The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion', Cancer Research, 71, pp. 3852 - 3862, http://dx.doi.org/10.1158/0008-5472.CAN-10-4460

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

Smith MA, 2011, 'British nuclear weapons and NATO in the Cold War and beyond', INTERNATIONAL AFFAIRS, 87, pp. 1385 - +, http://dx.doi.org/10.1111/j.1468-2346.2011.01042.x

Smith MJ, 2010, 'From Big Government to Big Society: Changing the State–Society Balance', Parliamentary Affairs, 63, pp. 818 - 833, http://dx.doi.org/10.1093/pa/gsq023

Müller M; Padmanabhan PK; Rochette A; Mukherjee D; Smith M; Dumas C; Papadopoulou B, 2010, 'Rapid decay of unstable Leishmania mRNAs bearing a conserved retroposon signature 3'-UTR motif is initiated by a site-specific endonucleolytic cleavage without prior deadenylation', Nucleic Acids Research, 38, pp. 5867 - 5883, http://dx.doi.org/10.1093/nar/gkq349

Smith MA, 2010, 'AFGHANISTAN IN CONTEXT: NATO OUT-OF-AREA DEBATES IN THE 1990S', REVISTA UNISCI, pp. 16 - 32

Smith MJ, 2010, 'Innovation and Dialogue in Contemporary Political Science Preface', Political Studies, 58, pp. 235 - 237, http://dx.doi.org/10.1111/j.1467-9248.2009.00839.x

Smith MA, 2010, 'Law and Practice of the United Nations: Documents and Commentary', INTERNATIONAL PEACEKEEPING, 17, pp. 424 - 426

Smith M; Bringaud F; Papadopoulou B, 2009, 'Organization and evolution of two SIDER retroposon subfamilies and their impact on the Leishmania genome', BMC Genomics, 10, http://dx.doi.org/10.1186/1471-2164-10-240

Rochette A; Raymond F; Ubeda JM; Smith M; Messier N; Boisvert S; Rigault P; Corbeil J; Ouellette M; Papadopoulou B, 2008, 'Genome-wide gene expression profiling analysis of Leishmania major and Leishmania infantum developmental stages reveals substantial differences between the two species', BMC Genomics, 9, http://dx.doi.org/10.1186/1471-2164-9-255

Smith M; Blanchette M; Papadopoulou B, 2008, 'Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania', BMC Bioinformatics, 9, http://dx.doi.org/10.1186/1471-2105-9-158

Smith MJ, 2008, 'Re-Centring British Government: Beliefs, Traditions and Dilemmas in Political Science', Political Studies Review, 6, pp. 143 - 154, http://dx.doi.org/10.1111/j.1478-9302.2008.00148.x

Bringaud F; Müller M; Cerqueira GC; Smith M; Rochette A; El-Sayed NMA; Papadopoulou B; Ghedin E, 2007, 'Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania', Plos Pathogens, 3, pp. 1291 - 1307, http://dx.doi.org/10.1371/journal.ppat.0030136

Smith MA, 2007, 'The EU-NATO relationship: A legal and political perspective', JCMS-JOURNAL OF COMMON MARKET STUDIES, 45, pp. 753 - 754, http://dx.doi.org/10.1111/j.1468-5965.2007.00735_9.x

Kolln J; Ren H-M; Da R-R; Zhang Y; Spillner E; Olek M; Hermanowicz N; Hilgenberg LG; Smith MA; van den Noort S; Qin Y, 2006, 'Triosephosphate Isomerase- and Glyceraldehyde-3-Phosphate Dehydrogenase-Reactive Autoantibodies in the Cerebrospinal Fluid of Patients with Multiple Sclerosis', The Journal of Immunology, 177, pp. 5652 - 5658, http://dx.doi.org/10.4049/jimmunol.177.8.5652

Zhang Y; Da R-R; Guo W; Ren H-M; Hilgenberg LG; Sobel RA; Tourtellotte WW; Smith MA; Olek M; Gupta S; Robertson RT; Nagra R; Noort SVD; Qin Y, 2005, 'Axon Reactive B Cells Clonally Expanded in the Cerebrospinal Fluid of Patients with Multiple Sclerosis', Journal of Clinical Immunology, 25, pp. 254 - 264, http://dx.doi.org/10.1007/s10875-005-4083-5

Zhang Y; Da R-R; Hilgenberg LG; Tourtellotte WW; Sobel RA; Smith MA; Olek M; Nagra R; Sudhir G; van den Noort S; Qin Y, 2005, 'Clonal expansion of IgA-positive plasma cells and axon-reactive antibodies in MS lesions', Journal of Neuroimmunology, 167, pp. 120 - 130, http://dx.doi.org/10.1016/j.jneuroim.2005.05.006

Smith MA; Schroer BC, 'Could We Discontinue All Asthma Medications in a Third of Adult Asthmatics?', JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE, 5, pp. 1471 - 1472, http://dx.doi.org/10.1016/j.jaip.2017.04.023

Conference Papers

Smith MA; Newton LP; Newton D; Cho L; Blanch MAB; Pardo LC; Wang X; Li M; Lang DM, 2018, 'Risk Factors for Anaphylactoid Reaction to Low Osmolar Contrast During Cardiac Catheterization', in JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, MOSBY-ELSEVIER, FL, Orlando, pp. AB32 - AB32, presented at American-Academy-of-Allergy-Asthma-and-Immunology / World-Allergy-Organization Joint Congress, FL, Orlando, 02 March 2018 - 08 March 2018, http://dx.doi.org/10.1016/j.jaci.2017.12.103

Smith MA; Gonzalez-Estrada A; Siles RI, 2015, 'Are We Doing Enough to Protect Asthmatic Patients from Pneumococcal Disease?', in JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, MOSBY-ELSEVIER, TX, Houston, pp. AB50 - AB50, presented at Annual Meeting of the American-Academy-of-Allergy-Asthma-and-Immunology (AAAAI), TX, Houston, 20 February 2015 - 24 February 2015, http://dx.doi.org/10.1016/j.jaci.2014.12.1094

Joseph L; Casanegra A; Dhariwal M; Smith MA; Raju M; Militelo M; Gomes M; Gornik H; Bartholomew J, 2014, 'BIVALIRUDIN FOR THE TREATMENT OF HEPARIN-INDUCED THROMBOCYTOPENIA: A 9 YEAR, 461 PATIENT EXPERIENCE', in Journal of the American College of Cardiology, Elsevier, pp. a2046, http://dx.doi.org/10.1016/s0735-1097(14)62049-0

RUTLEDGE JL; DRUCE HM; GLADNEY JH; BOYD JH; SMITH MA; BATES D, 1992, 'AN ACADEMIC COMPREHENSIVE SINUS CLINIC', in JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, MOSBY-YEAR BOOK INC, pp. 368 - 368

Working Papers

Smith MA; Ersavas T; Ferguson JM; Liu H; Lucas MC; Begik O; Bojarski L; Barton K; Novoa EM, Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/864322

Du Q; Smith GC; Luu PL; Ferguson JM; Armstrong NJ; Caldon CE; Campbell E; Nair SS; Zotenko E; Gould CM; Buckley M; Kaczorowski D; Barton K; Deveson IW; Smith MA; Powell JE; Skvortsova K; Stirzaker C; Achinger-Kawecka J; Clark SJ, DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity, Cold Spring Harbor Laboratory, http://dx.doi.org10.1101/2020.10.15.338855

Preprints

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

Benoit P; Jolicoeur G; Point F; Normand K; Soucy C; Morency-Potvin P; Gagnon S; Kaufmann DE; Tremblay C; Coutlée F; Harrigan PR; Hardy I; Smith M; Savard P; Lapierre SG, 2022, On-Demand Hospital-Based SARS-CoV-2 Genomic Epidemiology to Support Nosocomial Outbreak Investigations: A Prospective Molecular Epidemiology Study in Montreal, http://dx.doi.org/10.2139/ssrn.4199208

Gamaarachchi H; Lam CW; Jayatilaka G; Samarakoon H; Simpson J; Smith M; Parameswaran S, 2019, GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis, http://dx.doi.org/10.1101/756122

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, http://dx.doi.org/10.1101/404285

Gamaarachchi H; Parameswaran S; Smith M, 2018, Featherweight long read alignment using partitioned reference indexes, http://dx.doi.org/10.1101/386847

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

Sagniez M; Budhraja A; Paré B; Simpson SM; Vinet-Ouellette C; Rozendaal M; Smith MA, Assembly Arena: Benchmarking RNA isoform reconstruction algorithms for nanopore sequencing, http://dx.doi.org/10.1101/2024.03.21.586080

Mostefai F; Gamache I; Huang J; N’Guessan A; Pelletier J; Pesaranghader A; Hamelin D; Murall CL; Poujol R; Grenier J-C; Smith M; Caron E; Craig M; Shapiro J; Wolf G; Krishnaswamy S; Hussin JG, Data-driven approaches for genetic characterization of SARS-CoV-2 lineages, http://dx.doi.org/10.1101/2021.09.28.462270

Raad S; David A; Sagniez M; Orfi Z; Dumont NA; Smith M; Faure C, Directed differentiation of EA/TEF patient-derived induced pluripotent stem cells into esophageal epithelial organoids reveal SOX2 dysregulation at the anterior foregut stage, http://dx.doi.org/10.1101/2022.02.14.480418

Paré B; Rozendaal M; Morin S; Poujol R; Mostefai F; Grenier J-C; Kaufmann L; Xing H; Sanchez M; Yechouron A; Racette R; Hussin J; Wolf G; Pavlov I; Smith MA, Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec, http://dx.doi.org/10.1101/2021.05.29.21257760

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