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Neutral tumor evolution?

Tarabichi M, Martincorena I, Gerstung M, Leroi AM, Markowetz F; PCAWG Evolution and Heterogeneity Working Group, Spellman PT, Morris QD, Lingjærde OC, Wedge DC, Van Loo P.

Nat Genet. 2018 Dec;50(12):1630-1633. doi: 10.1038/s41588-018-0258-x. No abstract available.


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 Oct 19;13(10):3000-3010. doi: 10.1021/acschembio.8b00745. Epub 2018 Sep 6.


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.


RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ.

Science. 2015 Jan 9;347(6218):1254806. doi: 10.1126/science.1254806. Epub 2014 Dec 18.


High-throughput characterization of protein-RNA interactions.

Cook KB, Hughes TR, Morris QD.

Brief Funct Genomics. 2015 Jan;14(1):74-89. doi: 10.1093/bfgp/elu047. Epub 2014 Dec 13. Review.


Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli.

Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M.

Bioinformatics. 2015 Feb 1;31(3):306-10. doi: 10.1093/bioinformatics/btu671. Epub 2014 Oct 13.


GeneMANIA: Fast gene network construction and function prediction for Cytoscape.

Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q.

F1000Res. 2014 Jul 1;3:153. doi: 10.12688/f1000research.4572.1. eCollection 2014.


The biologic basis of clinical heterogeneity in juvenile idiopathic arthritis.

Eng SW, Duong TT, Rosenberg AM, Morris Q, Yeung RS; REACCH OUT and BBOP Research Consortia.

Arthritis Rheumatol. 2014 Dec;66(12):3463-75. doi: 10.1002/art.38875.


A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types.

Norris AD, Gao S, Norris ML, Ray D, Ramani AK, Fraser AG, Morris Q, Hughes TR, Zhen M, Calarco JA.

Mol Cell. 2014 Jun 19;54(6):946-59. doi: 10.1016/j.molcel.2014.05.004. Epub 2014 Jun 5.


Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction.

Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q.

Front Genet. 2014 May 16;5:123. doi: 10.3389/fgene.2014.00123. eCollection 2014.


RNA-protein interactions: an overview.

Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT.

Methods Mol Biol. 2014;1097:491-521. doi: 10.1007/978-1-62703-709-9_23. Review.


Inferring clonal evolution of tumors from single nucleotide somatic mutations.

Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q.

BMC Bioinformatics. 2014 Feb 1;15:35. doi: 10.1186/1471-2105-15-35.


Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein.

Chen L, Dumelie JG, Li X, Cheng MH, Yang Z, Laver JD, Siddiqui NU, Westwood JT, Morris Q, Lipshitz HD, Smibert CA.

Genome Biol. 2014 Jan 7;15(1):R4. doi: 10.1186/gb-2014-15-1-r4.


Staufen2 regulates neuronal target RNAs.

Heraud-Farlow JE, Sharangdhar T, Li X, Pfeifer P, Tauber S, Orozco D, Hörmann A, Thomas S, Bakosova A, Farlow AR, Edbauer D, Lipshitz HD, Morris QD, Bilban M, Doyle M, Kiebler MA.

Cell Rep. 2013 Dec 26;5(6):1511-8. doi: 10.1016/j.celrep.2013.11.039. Epub 2013 Dec 19.


Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish.

Musso G, Tasan M, Mosimann C, Beaver JE, Plovie E, Carr LA, Chua HN, Dunham J, Zuberi K, Rodriguez H, Morris Q, Zon L, Roth FP, MacRae CA.

Development. 2014 Jan;141(1):224-35. doi: 10.1242/dev.099796.


Personalized medicine: from genotypes and molecular phenotypes towards therapy- session introduction.

Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L.

Pac Symp Biocomput. 2014;19:224-8. doi: 10.1142/9789814583220_0022. No abstract available.


Finding the target sites of RNA-binding proteins.

Li X, Kazan H, Lipshitz HD, Morris QD.

Wiley Interdiscip Rev RNA. 2014 Jan-Feb;5(1):111-30. doi: 10.1002/wrna.1201. Epub 2013 Nov 11. Review.


A unified model for yeast transcript definition.

de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR.

Genome Res. 2014 Jan;24(1):154-66. doi: 10.1101/gr.164327.113. Epub 2013 Oct 29.


PLIDA: cross-platform gene expression normalization using perturbed topic models.

Deshwar AG, Morris Q.

Bioinformatics. 2014 Apr 1;30(7):956-61. doi: 10.1093/bioinformatics/btt574. Epub 2013 Oct 11.


Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression.

Mezlini AM, Wang B, Deshwar A, Morris Q, Goldenberg A.

PLoS One. 2013 Oct 2;8(10):e73168. doi: 10.1371/journal.pone.0073168. eCollection 2013.


BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles.

Radfar H, Wong W, Morris Q.

BMC Genomics. 2013 Aug 30;14:592. doi: 10.1186/1471-2164-14-592.


Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity.

Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD.

Nucleic Acids Res. 2013 Nov;41(20):9438-60. doi: 10.1093/nar/gkt702. Epub 2013 Aug 13.


A compendium of RNA-binding motifs for decoding gene regulation.

Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.


GeneMANIA prediction server 2013 update.

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

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W115-22. doi: 10.1093/nar/gkt533.


RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins.

Kazan H, Morris Q.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W180-6. doi: 10.1093/nar/gkt463. Epub 2013 Jun 10.


Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction.

Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q.

Genome Med. 2013 Mar 28;5(3):29. doi: 10.1186/gm433.


The future of genome-based medicine.

Morris Q, Brenner SE, Listgarten J, Stegle O.

Pac Symp Biocomput. 2013:456-8. No abstract available.



Stegle O, Brenner SE, Morris Q, Listgarten J.

Pac Symp Biocomput. 2013;18:171-174. No abstract available.


Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27.


Labeling nodes using three degrees of propagation.

Mostafavi S, Goldenberg A, Morris Q.

PLoS One. 2012;7(12):e51947. doi: 10.1371/journal.pone.0051947. Epub 2012 Dec 28.


PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.

Qiao W, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW.

PLoS Comput Biol. 2012;8(12):e1002838. doi: 10.1371/journal.pcbi.1002838. Epub 2012 Dec 20.

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