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Motif models for RNA-binding proteins.

Sasse A, Laverty KU, Hughes TR, Morris QD.

Curr Opin Struct Biol. 2018 Aug 29;53:115-123. doi: 10.1016/ [Epub ahead of print] Review.


A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B).

François-Moutal L, Jahanbakhsh S, Nelson ADL, Ray D, Scott DD, Hennefarth MR, Moutal A, Perez-Miller S, Ambrose AJ, Al-Shamari A, Coursodon P, Meechoovet B, Reiman R, Lyons E, Beilstein M, Chapman E, Morris QD, Van Keuren-Jensen K, Hughes TR, Khanna R, Koehler C, Jen J, Gokhale V, Khanna M.

ACS Chem Biol. 2018 Sep 6. doi: 10.1021/acschembio.8b00745. [Epub ahead of print]


GeneMANIA update 2018.

Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q.

Nucleic Acids Res. 2018 Jul 2;46(W1):W60-W64. doi: 10.1093/nar/gky311.


The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression.

Espiritu SMG, Liu LY, Rubanova Y, Bhandari V, Holgersen EM, Szyca LM, Fox NS, Chua MLK, Yamaguchi TN, Heisler LE, Livingstone J, Wintersinger J, Yousif F, Lalonde E, Rouette A, Salcedo A, Houlahan KE, Li CH, Huang V, Fraser M, van der Kwast T, Morris QD, Bristow RG, Boutros PC.

Cell. 2018 May 3;173(4):1003-1013.e15. doi: 10.1016/j.cell.2018.03.029. Epub 2018 Apr 19.


QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data.

Ha KCH, Blencowe BJ, Morris Q.

Genome Biol. 2018 Mar 28;19(1):45. doi: 10.1186/s13059-018-1414-4.


High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.

Youn JY, Dunham WH, Hong SJ, Knight JDR, Bashkurov M, Chen GI, Bagci H, Rathod B, MacLeod G, Eng SWM, Angers S, Morris Q, Fabian M, Côté JF, Gingras AC.

Mol Cell. 2018 Feb 1;69(3):517-532.e11. doi: 10.1016/j.molcel.2017.12.020. Epub 2018 Jan 25.


Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma.

Dang H, Takai A, Forgues M, Pomyen Y, Mou H, Xue W, Ray D, Ha KCH, Morris QD, Hughes TR, Wang XW.

Cancer Cell. 2017 Jul 10;32(1):101-114.e8. doi: 10.1016/j.ccell.2017.06.002.


RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.

Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD.

Methods. 2017 Aug 15;126:18-28. doi: 10.1016/j.ymeth.2017.06.024. Epub 2017 Jun 24.


An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion.

Collins KM, Kainov YA, Christodolou E, Ray D, Morris Q, Hughes T, Taylor IA, Makeyev EV, Ramos A.

Nucleic Acids Res. 2017 Jun 20;45(11):6761-6774. doi: 10.1093/nar/gkx225.


Using the Electronic Medical Record to Identify Patients at High Risk for Frequent Emergency Department Visits and High System Costs.

Frost DW, Vembu S, Wang J, Tu K, Morris Q, Abrams HB.

Am J Med. 2017 May;130(5):601.e17-601.e22. doi: 10.1016/j.amjmed.2016.12.008. Epub 2017 Jan 5.


RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins.

Ray D, Ha KCH, Nie K, Zheng H, Hughes TR, Morris QD.

Methods. 2017 Apr 15;118-119:3-15. doi: 10.1016/j.ymeth.2016.12.003. Epub 2016 Dec 10.


Machine learning and computer vision approaches for phenotypic profiling.

Grys BT, Lo DS, Sahin N, Kraus OZ, Morris Q, Boone C, Andrews BJ.

J Cell Biol. 2017 Jan 2;216(1):65-71. doi: 10.1083/jcb.201610026. Epub 2016 Dec 9. Review.


MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs.

Rodrigues DC, Kim DS, Yang G, Zaslavsky K, Ha KC, Mok RS, Ross PJ, Zhao M, Piekna A, Wei W, Blencowe BJ, Morris Q, Ellis J.

Cell Rep. 2016 Oct 11;17(3):720-734. doi: 10.1016/j.celrep.2016.09.049.


Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians.

Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N.

Elife. 2016 Aug 9;5. pii: e16797. doi: 10.7554/eLife.16797.


Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis.

Cui A, Quon G, Rosenberg AM, Yeung RS, Morris Q; BBOP Study Consortium.

PLoS One. 2016 May 31;11(5):e0156055. doi: 10.1371/journal.pone.0156055. eCollection 2016.


The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation.

Loedige I, Jakob L, Treiber T, Ray D, Stotz M, Treiber N, Hennig J, Cook KB, Morris Q, Hughes TR, Engelmann JC, Krahn MP, Meister G.

Cell Rep. 2015 Nov 10;13(6):1206-1220. doi: 10.1016/j.celrep.2015.09.068. Epub 2015 Oct 29.


ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.

Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC.

BMC Bioinformatics. 2015 May 14;16:156. doi: 10.1186/s12859-015-0597-x.


Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition.

Laver JD, Li X, Ray D, Cook KB, Hahn NA, Nabeel-Shah S, Kekis M, Luo H, Marsolais AJ, Fung KY, Hughes TR, Westwood JT, Sidhu SS, Morris Q, Lipshitz HD, Smibert CA.

Genome Biol. 2015 May 12;16:94. doi: 10.1186/s13059-015-0659-4.


PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.

Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q.

Genome Biol. 2015 Feb 13;16:35. doi: 10.1186/s13059-015-0602-8.


Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

Deshwar AG, Vembu S, Morris Q.

Pac Symp Biocomput. 2015:20-31.

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