Publications
protected_59901_Valdmanis_081919_P_Web.mp4A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools.
2024
Elizabeth G Plender, Timofey Prodanov, PingHsun Hsieh, Evangelos Nizamis, William T Harvey, Arvis Sulovari, Katherine M Munson, Eli Kaufman, Wanda K O'Neal, Paul N Valdmanis, Tobias Marschall, Jesse D. Bloom, Evan E Eichler. Structural and genetic diversity in the secreted mucins, MUC5AC and MUC5B bioRxiv 2024.03.18 (Preprint)
Jadhav VS, Stair JG, Eck RJ, Smukowski SN, Currey HN, Toscano LG, Hincks JC, Latimer CS, Valdmanis PN, Kraemer BC, Liachko NF. Transcriptomic evaluation of tau and TDP-43 synergism shows tauopathy predominance and reveals potential modulating targets. Neurobiol Dis. 2024 Feb 18:193:106441.
Kiianitsa K, Lukes ME, Hayes BJ, Brutman J, Valdmanis PN, Bird TD, Raskind WH, Korvatska O. TREM2 variants that cause early dementia and increase Alzheimer's disease risk affect gene splicing. Brain 2024 Jan 16.
2023
Fernando A. Villanea, David Peede, Eli J. Kaufman, Valeria Añorve-Garibay, Kelsey E. Witt, Viridiana Villa-Islas, Roberta Zeloni, Davide Marnetto, Priya Moorjani, Flora Jay, Paul N. Valdmanis, María C. Ávila-Arcos, Emilia Huerta-Sánchez. The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection. bioRxiv 2023 (Preprint)
Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci. 2023 Oct 31:ETLS20230074.
Lee S, Kim J, Valdmanis PN, Kim HK. Emerging roles of tRNA-derived small RNAs in cancer biology. Exp Mol Med. 2023 Jul;55(7):1293-1304.
Park J, Kaufman E, Valdmanis PN, Bafna V. TRviz: a python library for decomposing and visualizing tandem repeat sequences. Bioinformatics Advances 2023 Apr 26;3(1):vbad058.
Course, MM, Gudsnuk, K, Keene, CD, Bird TD Jayadev S, Valdmanis PN. Aberrant splicing of PSEN2, but not PSEN1, in individuals with sporadic Alzheimer's disease. Brain 2023 Feb 13;146(2):507-518.
2022
Smukowski SN, Maioli H, Latimer CS, Bird TD, Jayadev S, Valdmanis PN. Progress in Amyotrophic Lateral Sclerosis Gene Discovery: Reflecting on Classic Approaches and Leveraging Emerging Technologies. Neurology: Genetics 2022 Apr 27;8(3):e669.
2021
Smith AST, Chun C, Hesson J, Mathieu J, Valdmanis PN, Mack DL, Choi B-O, Kim D-H, Bothwell MA. Human Induced Pluripotent Stem Cell-Derived TDP-43 Mutant Neurons Exhibit Consistent Functional Phenotypes Across Multiple Gene Edited Lines Despite Transcriptomic and Splicing Discrepancies. Frontiers in Cell and Developmental Biology 2021 Sep 29;9:728707.
Course MM, Gudsnuk K, Sulovari A, Eichler EE, Valdmanis PN. Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats. Genome Research. 2021 Aug; 31(8):1313-1324.
Monti G, Kjolby M, Jensen AMG, Allen M, Reiche J, Møller PL, Comaposada-Baró R, Zolkowski BE, Vieira C, Jørgensen MM, Holm IE, Valdmanis PN, Wellner N, Vægter CB, Lincoln SJ, Nykjær A, Ertekin-Taner N, Young JE, Nyegaard M, Andersen OM. Expression of an alternatively spliced variant of SORL1 in neuronal dendrites is decreased in patients with Alzheimer's disease. Acta Neuropathol Commun. 2021 Mar 16;9(1):43.
2020
Course, MM, Gudsnuk, K, Smukowski, SN, Winston, K, Desai, N, Ross, JP, Sulovari, A, Bourassa, CV, Spiegelman, D, Couthouis, J, Yu, C-E, Tsuang, DW, Jayadev, S, Kay, MA, Gitler, AD, Dupre, N, Eichler, EE, Dion PA, Rouleau, GA, Valdmanis, PN. Evolution of a human-specific tandem repeat associated with ALS. American Journal of Human Genetics. 2020 Sep 3;107(3):445-460.
Li C, Course MM, Drescher CW, Valdmanis PN, Lieber A. Prophylactic in vivo hematopoietic stem cell gene therapy with an immune checkpoint inhibitor reverses tumor growth in a syngeneic mouse tumor model. Cancer Research. 2020 Feb 1;80(3):549-560.
de Alencastro G, Pekrun K, Valdmanis P, Tiffany M, Xu J, Kay MA. Tracking adeno-associated virus capsid evolution by high-throughput sequencing. Human Gene Therapy. 2020 Feb 5.
2019
Course MM, Gudsnuk K, Desai N, Chamberlain JR, Valdmanis PN. Endogenous MicroRNA Competition as a Mechanism of shRNA-Induced Cardiotoxicity. Molecular Therapy Nucleic Acids. 2019 Dec 18;19:572-580.
Kim HK, Xu J, Chu K, Park H, Jang H, Li P, Valdmanis PN, Zhang QC, Kay MA. A tRNA-Derived Small RNA Regulates Ribosomal Protein S28 Protein Levels after Translation Initiation in Humans and Mice. Cell Reports. 2019 Dec 17;29(12):3816-3824.e4
Course MM, Gudsnuk K, Valdmanis PN. A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools. Journal of Visualized Experiments. 2019 Aug 21; 150: e59901.
Braggin JE, Bucks SA, Course MM, Smith C, Sopher B, Osnis L, Domoto-Reilly K, Caso C, Kinoshita C, Scherpelz KP, Cross C, Grabowski T, Nik SH, Newman M, Garden GA, Leverenz J, Tsuang D, Latimer C, Gonzalez-Cuyar LF, Keene CD, Morrison RS, Rhoads K, Dorschner MO, Lardelli M, Young JE, Valdmanis PN, Bird TD, Jayadev S. Alternative splicing in a presenilin 2 variant associated with Alzheimer disease. Annals of Clinical and Translational Neurology. 2019 Mar 10; 6(4):762-777.
2018
Valdmanis PN, Kim HK, Chu K, Zhang F, Xu J, Munding EM, Shen J, Kay MA. Removal of miR-122 in the liver activates imprinted microRNAs and enables more effective microRNA-mediated gene repression. Nature Communications 2018 Dec 14, 9. Article 5321.
2017
Valdmanis PN, Kay MA. Future of rAAV Gene Therapy: Platform for RNAi, Gene Editing, and Beyond. Human Gene Therapy. 2017 Apr;28(4):361-372.
2016
Picher-Martel V, Valdmanis PN, Gould PV, Julien JP, Dupré N. From animal models to human disease: a genetic approach for personalized medicine in ALS. Acta Neuropathol. Commun. 2016 Jul 11;4(1):70.
Valdmanis PN, Gu S, Chu K, Jin L, Zhang F, Munding EM, Huang Y, Kutay H, Ghoshal K, Lisowski L, Kay MA. RNA interference-induced hepatotoxicity results from loss of the first synthesized isoform of microRNA-122 in mice. Nature Medicine 2016 May;22(5)557-62.
2015
Valdmanis PN, Roy-Chaudhuri B, Kim HK, Sayles LC, Zheng Y, Chuang CH, Caswell DR, Chu K, Zhang Y, Winslow MM, Sweet-Cordero EA, Kay MA. Upregulation of the microRNA cluster at the Dlk1-Dio3 locus in lung adenocarcinoma. Oncogene. 2015 Jan 2;34(1):94-103.
Barzel A, Paulk NK, Shi Y, Huang Y, Chu K, Zhang F, Valdmanis PN, Spector, LP, Porteus MH, Gaensler KM, Kay MA. Promoterless gene targeting without nucleases ameliorates haemophilia B in mice. Nature 2015 Jan 15;517(7534):360-4.
2014
Roy-Chaudhuri B, Valdmanis PN, Zhang Y, Wang Q, Luo QJ, Kay MA. Regulation of microRNA-mediated gene silencing by microRNA precursors. Nature Structural & Molecular Biology 2014 Sep;21(9):825-32.
2013
Valdmanis PN, Kay MA. The expanding repertoire of circularRNAs. Molecular Therapy 2013 Jun;21(6):1112-4.
Kabashi E, El Oussini H, Bercier V, Gros-Louis F, Valdmanis PN, McDearmid J, Mejier IA, Dion PA, Dupre N, Hollinger D, Sinniger J, Dirrig-Grosch S, Camu W, Meininger V, Loeffler JP, René F, Drapeau P, Rouleau GA, Dupuis L. Investigating the contribution of VAPB/ALS8 loss of function in amyotrophic lateral sclerosis. Human Molecular Genetics 2013 Jun 15;22(12):2350-60.
2012
Valdmanis PN, Lisowski L, Kay MA. rAAV-mediated tumorigenesis: still unresolved after an AAV assault. Molecular Therapy 2012 Nov;20(11):2014-7.
Gu S, Jin L, Zhang Y, Huang Y, Zhang F, Valdmanis PN, Kay MA. The loop position of shRNAs and pre-miRNAs is critical for the accuracy of dicer processing in vivo. Cell 2012 Nov 9;151(4):900-11.
Valdmanis PN, Gu S, Schüermann N, Sethupathy P, Grimm D, Kay MA. Expression determinants of mammalian argonaute proteins in mediating gene silencing. Nucleic Acids Research 2012 Apr;40(8):3704-13.
Corcia P, Valdmanis P, Millecamps S, Lionnet C, Blasco H, Mouzat K, Daoud H, Belzil V, Morales R, Pageot N, Danel-Brunaud V, Vandenberghe N, Pradat PF, Couratier P, Salachas F, Lumbroso S, Rouleau GA, Meininger V, Camu W. Phenotype and genotype analysis in amyotrophic lateral sclerosis with TARDBP gene mutations. Neurology. 2012 May 8;78(19):1519-26.
2011
Daoud H, Valdmanis PN, Gros-Louis F, Belzil V, Spiegelman D, Henrion E, Diallo O, Desjarlais A, Gauthier J, Camu W, Dion PA, Rouleau GA. Resequencing of 29 candidate genes in patients with familial and sporadic amyotrophic lateral sclerosis. Archives of Neurology 2011 May;68(5):587-93.
Valdmanis PN, Dupré N, Lachance M, Stochmanski S, Belzil VV, P.A. Dion PA, I. Thiffault, B. Brais, L. Weston, L. Saint-Amant, M.E. Samuels and Rouleau GA. A mutation in the RNF170 gene causes autosomal dominant sensory ataxia. Brain 2011 Feb;134(Pt 2):602-7.
2010
Kudo LC, Parfenova L, Li N, Lau K, Pomakian J, Valdmanis P, Rouleau GA, Vinters HV, Wiedau-Pazos M, Karsten SL. Integrative gene-tissue microarray-based approach for identification of human disease biomarkers: application to amyotrophic lateral sclerosis. Human Molecular Genetics. 2010 Aug 15;19(16):3233-53.
Daoud H, Valdmanis PN, Dion PA, Rouleau GA. Analysis of DPP6 and FGGY as candidate genes for amyotrophic lateral sclerosis. Amyotrophic Lateral Sclerosis 2010 Aug; 11(4):389-91.
Felbecker A, Camu W, Valdmanis PN, Sperfeld AD, Waibel S, Steinbach P, Rouleau GA, Ludolph AC, Andersen PM. Four familial ALS pedigrees discordant for two SOD1 mutations: are all SOD1 mutations pathogenic? Journal of Neurology, Neurosurgery and Psychiatry. 2010 May; 81(5):572-7.
2009
Valdmanis PN, Belzil VV, Lee J, Dion PA, St-Onge J, Hince P, Funalot B, Couratier P, Clavelou P, Camu W, Rouleau GA. A Mutation that Creates a Pseudoexon in SOD1 Causes Familial ALS. Annals of Human Genetics 2009 Nov; 73(Pt 6)652-7.
Belzil VV∗, Valdmanis PN∗, Dion PA, Daoud H, Kabashi E, Noreau A, Gauthier J, Hince P, Desjarlais A, Bouchard J-P, Lacomblez L, Pochigayeva K, Salachas F, Pradat P-F, Camu W, Meininger V, Dupré N, Rouleau GA. Mutations in FUS cause FALS and SALS in French and French Canadian populations. Neurology 2009 Oct 13;73.
Laforce R, Valdmanis PN, Dupré N, Rouleau GA, Turgeon AF, Savard M. A novel TYMP mutation in a French Canadian patient with mitochondrial neurogastrointestinal encephalomyopathy. Clinical Neurol Neurosurg 2009 Oct; 111(8):691-4.
Valdmanis PN, H. Daoud, Dion PA, and Rouleau GA. Recent advances in the genetics of amyotrophic lateral sclerosis. Current Neurology and Neuroscience Reports 2009 May; 9(3):198-205
Wills A-M, Cronin S, Slowik A, Kasperaviciute D, Van Es MA, Morahan JM, Valdmanis PN, Meininger V, Melki J, Shaw CE, Rouleau GA, Fisher EMC, Pamphlett R, Figlewicz DA, Andersen P, Al-Chalabi A, Hardiman O, Landers JE, Brown RH Jr. A meta-analysis of paraoxonase gene polymorphisms in sporadic ALS. Neurology 2009 Jul 7;73(1):16-24.
Valdmanis PN, Verlaan DJ and Rouleau GA. The proportion of mutations predicted to have a deleterious effect differs between gain and loss of function genes in neurodegenerative disease. Human Mutation 2009 Mar;30(3):E481-9.
Kwiatkowski TJ Jr, Bosco DA, Leclerc AL, Tamrazian E, Vanderburg CR, Russ C, Davis A, Gilchrist J, Kasarskis EJ, Munsat T, Valdmanis P, Rouleau GA, Hosler BA, Cortelli P, de Jong PJ, Yoshinaga Y, Haines JL, Pericak-Vance MA, Yan J, Ticozzi N, Siddique T, McKenna-Yasek D, Sapp PC, Horvitz HR, Landers JE, Brown RH Jr. Mutations in the FUS gene on chromosome 16 cause familial amyotrophic lateral sclerosis. Science 2009 Feb 27;323(5918):1205-8.
Kabashi E, Daoud H, Riviere JB, Valdmanis PN, Bourgouin P, Provencher P, Pourcher E, Dion P, Dupré N, Rouleau GA. No TARDBP mutations in a French Canadian population of patients with Parkinson disease. Archives of Neurology 2009 Feb;66(2):281-2.
Dupré N and Valdmanis PN. Genome wide association studies in amyotrophic lateral sclerosis European Journal of Human Genetics 2009 Feb;17(2):137-8.
Daoud H, Valdmanis PN, Kabashi E, Dion P, Dupre N, Camu W, Meininger V and Rouleau GA. Contribution of TARDBP mutations to sporadic amyotrophic lateral sclerosis. Journal of Medical Genetics 2009 Feb:46(2):112-4.
2008
Moeller JJ, Macaulay RJB, Valdmanis PN, Weston LE, Rouleau GA and Dupré N. Neuropathology of Autosomal Dominant Sensory Ataxia: Neuroaxonal Dystrophy and Granulomatous Myositis. Acta Neuropathologica 2008 Sep;116(3):331-6.
Valdmanis PN, Kabashi E, Dyck A, Hince P, Lee J, Dion PA, D’Amour M, Souchon F, Bouchard J-P, Lacomblez L, Pochigayeva K, Salachas F, Pradat P-F, Meininger V, Andersen P, Camu W, Dupré N and Rouleau GA. Association of paraoxonase gene cluster polymorphisms with ALS in France, Quebec and Sweden. Neurology 2008 Aug 12; 71(7):514-20.
Chrestian N, Valdmanis PN, Echahidi N, Brunet D, Gould P, Rouleau GA, J. Champagne, and Dupré N. A novel mutation in a French-Canadian family with LGMD1B. Canadian Journal of Neurological Sciences 2008; 35: 331-334.
Broom WJ, Greenway M, Sadri-Vakili G, Russ C, Auwarter KE, Glajch KE, Dupre N, Swingler RJ, Purcell S, Hayward C, Sapp PC, McKenna-Yasek D, Valdmanis PN, Bouchard JP, Meininger V, Hosler BA, Glass JD, Polack M, Rouleau GA, Cha JH, Hardiman O, Brown RH Jr. 50bp deletion in the promoter for superoxide dismutase 1 (SOD1) reduces SOD1 expression in vitro and may correlate with increased age of onset of sporadic amyotrophic lateral sclerosis. Amyotrophic Lateral Sclerosis 2008 Aug;9(4):229-37.
Kabashi E*, Valdmanis PN*, Dion PA, Spiegelman D, McConkey BJ, Vande Velde C, Bouchard J-P, Lacomblez L, Pochigayeva K, Salachas F, Pradat P-F, Camu W, Meininger V, Dupré N and Rouleau GA. TARDBP mutations in sporadic and familial ALS patients. Nature Genetics 2008 May; 40(5):572-4.
Valdmanis PN, Dupré N, and Rouleau GA. A locus for primary lateral sclerosis maps to chromosome 4ptel-4p16.1. Archives of Neurology 2008;65(3):383-386.
Valdmanis PN, Kabashi E, Dion PA and Rouleau GA. Knock NOX, who’s there? SOD1 mice still are. European Journal of Human Genetics. 2008 Feb; 16(2):140-2.
Valdmanis PN and Rouleau GA. Genetics of familial amyotrophic lateral sclerosis. Neurology 2008 Jan 8; 70(2):144-52.
2007
Kabashi E, Valdmanis PN, Dion P and Rouleau GA. Oxidized/misfolded superoxide dismutase-1: the cause of all amyotrophic lateral sclerosis? Annals of Neurology 2007 Dec;62(6):553-9.
Dupré N, Valdmanis PN, Bouchard J-P, and Rouleau GA. Autosomal Dominant Primary Lateral Sclerosis. Neurology 2007 Apr 3; 68(14):1156-7.
Valdmanis PN, Dupré N, Bouchard J-P, Camu W, Meininger V, Strong MJ and Rouleau GA. Three ALS/FTD families with evidence of linkage to chromosome 9p. Archives of Neurology 2007;64:240-245.
Valdmanis PN*, Meijer IA*, Reynolds A, Lei A, MacLeod P, Schlesinger D, Zatz M, Reid E, Dion PA, Drapeau P, and Rouleau GA. Mutations in the KIAA0196 gene at the SPG8 locus cause Hereditary Spastic Paraplegia. American Journal of Human Genetics 2007 Jan; 80(1): 152-61.
2006
Valdmanis PN, Brunet D, St-Onge J, Weston L, Rouleau GA, and Dupré N. A founder haplotype for autosomal dominant sensory ataxia in Eastern Canada. Neurology 2006 Dec 26; 67(12): 2239-42.
2004
Valdmanis PN, Simoes Lopes AA, Gros-Louis F, Stewart JD, Rouleau GA, and Dupré N. A novel neurodegenerative disease characterized by posterior column ataxia and pyramidal tract involvement maps to chromosome 8p12-8q12.1. Journal of Medical Genetics 2004 Aug 1; 41(8): 634-639.
* - equal contributing authors