Cancer transcriptomics and splicing in cancer


MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer. Quesnel-Vallières M, Jewell S, Lynch KW, Thomas-Tikhonenko A, Barash Y Nucleic Acids Research


CHESSBOARD: a Bayesian model for unsupervised detection of alternative splicing based subtypes in heterogeneous cancers. Wang D, Quesnel-Vallières M, Jewell P, Elzubeir M, Lynch KW, Thomas-Tikhonenko A, Barash Y Nature Communications


High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance.
Cortés-López M, Schulz L, Enculescu M, Paret C, Spiekermann B, Busch A, Orekhova A, Kielisch F, Quesnel-Vallières M, Torres-Diz M, Faber J, Barash Y, Thomas- Tikhonenko A, Zarnack K, Legewie S, König J
Nature Communications

Identifying common transcriptome signatures of cancer by interpreting deep learning models.
Jha A*#, Quesnel-Vallières M*#, Thomas-Tikhonenko A, Lynch KW, Barash Y#
Genome Biology
* co-first authors # corresponding authors

Modulation of CD22 protein expression in childhood leukemia by pervasive splicing aberrations: implications for CD22-directed immunotherapies.
Zheng S, Gillespie E, Naqvi A, Hayer K, Ang Z, Torres-Diz M, Quesnel-Vallières M, Hottman D, Bagashev A, Chukinas J, Asnani M, Shraim R, Schmidt C, Taylor DM, Rheingold S.R, O’Brien MM, Singh N, Lynch K.W, Ruella M, Barash Y, Tasian SK, Thomas-Tikhonenko A
Blood Cancer Discovery


Alternative splicing redefines landscape of commonly mutated genes in acute myeloid leukemia.
Rivera OD, Mallory MJ, Quesnel-Vallières M, Schultz D.C, Carroll M, Barash Y, Cherry S, Lynch KW

Alternative splicing in autism spectrum disorders


Autism-misregulated eIF4G microexons control synaptic translation and higher order cognitive functions.
Gonatopoulos-Pournatzis T, Niibori R, Salter EW, Weatheritt RJ, Tsang B, Farhangmehr S, Liang X, Braunschweig U, Roth J, Zhang S, Henderson T, Sharma E, Quesnel- Vallières M, Permanyer J, Maier S, Georgiou J, Irimia M, Sonenberg N, Forman-Kay JD, Gingras AC, Collingridge GL, Woodin MA, Cordes SP, Blencowe BJ
Molecular Cell


Autism Spectrum Disorder: Insights into convergent mechanisms from transcriptomics.
Quesnel-Vallières M#, Weatheritt RJ, Cordes SP#, and Blencowe BJ#
Nature Reviews Genetics
# corresponding authors
Cover article: NRG_cover


Misregulation of an activity-dependent splicing network as a common mechanism underlying autism spectrum disorders.
Quesnel-Vallières M, Dargaei Z, Irimia M, Gonatopoulos-Pournatzis T, Ip J, Wu M, Sterne-Weiler T, Nakagawa S, Woodin MA, Blencowe BJ, and Cordes SP
Molecular Cell
Article covered by The Globe and Mail: Globe


Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development.
Quesnel-Vallières M, Irimia M, Cordes SP, and Blencowe BJ
Genes and Development


A highly conserved program of neuronal microexons is misregulated in autistic brains.
Irimia M, Weatheritt RJ, Ellis J, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O’Hanlon D, Barrios-Rodiles M, Sternberg MJ, Cordes SP, Roth FP, Wrana JL, Geschwind DH, and Blencowe BJ
Article highlighted in a Preview in Cell, an Editor’s Choice in Science and a Research Highlights in Nature Genetics; covered by international media (e.g Toronto Star, The Scientist)

Other work


The Tumor Suppressor Adenomatous Polyposis Coli (apc) Is Required for Neural Crest-Dependent Craniofacial Development in Zebrafish. Liu X, Jones WD, Quesnel-Vallières M, Devadiga SA, Lorent K, Valvezan AJ, Myers RL, Li N, Lengner CJ, Barash Y, Pack M, Klein PS. Journal of Developmental Biology


Identification and characterization of RBM12 as a novel regulator of fetal hemoglobin expression.
Wakabayashi A, Kihiu M, Sharma M, Thrasher AJ, Saari MS, Quesnel-Vallières M, Abdulmalik O, Chou ST, Peslak SA, Khandros E, Keller CA, Giardine BM, Hardison RC, Shi J, Blobel GA
Blood Advances


Rapid and scalable profiling of nascent RNA with fastGRO.
Barbieri E, Hill C, Quesnel-Vallières M, Zucco AJ, Barash Y, Gardini A
Cell Reports


Missense mutations in NKAP cause a disorder of transcriptional regulation characterized by marfanoid habitus and cognitive impairment
Fiordaliso SK, Iwata-Otsubo A, Ritter AL, Quesnel-Vallières M, Fujiki K, Nishi E, Hancarova M, Miyake N, Morton JEV, Lee S, Hackmann K, Bando M, Masuda K, Nakato R, Arakawa M, Bhoj E, Li D, Hakonarson H, Takeda R, Harr M, Keena B, Zackai EH, Okamoto N, Mizuno S, Ko JM, Valachova A, Prchalova D, Vlckova M, Pippucci T, Seiler C, Choi M, Matsumoto N, Di Donato N, Barash Y, Sedlacek Z, Shirahige K, Izumi K
American Journal of Human Genetics


An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms.
Tapial J, Ha KCH, Sterne-Weiler T, Gohr A, Braunschweig U, Hermoso-Pulido A, Quesnel-Vallières M, Permanyer J, Sodaei R, Marquez Y, Cozzuto L, Wang X, Gómez- Velázquez M, Rayon T, Manzanares M, Ponomarenko J, Blencowe BJ, and Irimia M
Genome Research


Seronegative Hepatitis C Virus infection in a child infected via mother-to-child transmission.
Larouche A, Gaëtan G, El-Bilali N, Quesnel-Vallières M, Martin SR, Alvarez F, Shoukry NH, and Soudeyns H
Journal of Clinical Microbiology


Novel HIV-1 recombinant forms in antenatal cohort, Montreal, Quebec, Canada.
Quesnel-Vallières M, Kouzayha I, Tran E, Barry I, Lasgi C, Mérindol N, Monteil V, Ransy DG, Boucher M, Lapointe N, and Soudeyns H
Emerging Infectious Diseases


HCV quasispecies evolution during treatment with interferon alfa-2b and ribavirin in two children coinfected with HCV and HIV-1.
Quesnel-Vallières M, Lemay M, Lapointe N, Martin SR, and Soudeyns H
Journal of Clinical Virology