Quaid Morris - Publications

University of Toronto, Toronto, ON, Canada 
Computational biology

118 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Dentro SC, Leshchiner I, Haase K, Tarabichi M, Wintersinger J, Deshwar AG, Yu K, Rubanova Y, Macintyre G, Demeulemeester J, Vázquez-García I, Kleinheinz K, Livitz DG, Malikic S, Donmez N, ... ... Morris QD, et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell. PMID 33831375 DOI: 10.1016/j.cell.2021.03.009  0.48
2020 Liu LY, Bhandari V, Salcedo A, Espiritu SMG, Morris QD, Kislinger T, Boutros PC. Quantifying the influence of mutation detection on tumour subclonal reconstruction. Nature Communications. 11: 6247. PMID 33288765 DOI: 10.1038/s41467-020-20055-w  0.48
2020 Kosti A, de Araujo PR, Li WQ, Guardia GDA, Chiou J, Yi C, Ray D, Meliso F, Li YM, Delambre T, Qiao M, Burns SS, Lorbeer FK, Georgi F, Flosbach M, ... ... Morris QD, et al. The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation. Genome Biology. 21: 195. PMID 32762776 DOI: 10.1186/S13059-020-02115-Y  0.44
2020 Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, ... ... Morris QD, et al. The evolutionary history of 2,658 cancers. Nature. 578: 122-128. PMID 32025013 DOI: 10.1038/S41586-019-1907-7  0.48
2020 Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, ... ... Morris Q, et al. A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology. 38: 97-107. PMID 31919445 DOI: 10.1038/S41587-019-0364-Z  0.48
2019 Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, ... ... Morris QD, et al. ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development. Nucleic Acids Research. PMID 30698747 DOI: 10.1093/Nar/Gkz010  0.44
2018 Davis GM, Tu S, Anderson JWT, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, et al. The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in . Elife. 7. PMID 30575518 DOI: 10.7554/Elife.35478  0.44
2018 Francois-Moutal L, Jahanbakhsh S, Nelson A, Ray D, Scott DD, Hennefarth M, Moutal A, Perez-Miller S, Ambrose AJ, Al-Shamari A, Coursodon P, Meechoovet B, Reiman R, Lyons E, Beilstein M, ... ... Morris QD, et al. A Chemical Biology Approach to Model Pontocerebellar Hypoplasia Type 1B (PCH1B). Acs Chemical Biology. PMID 30141626 DOI: 10.1021/Acschembio.8B00745  0.44
2018 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, ... ... Morris QD, et al. The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression. Cell. PMID 29681457 DOI: 10.1016/J.Cell.2018.03.029  0.48
2018 Davis GM, Tu S, Anderson JW, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, et al. Author response: The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans Elife. DOI: 10.7554/Elife.35478.032  0.44
2018 Jolly C, Gerstung M, Leshchiner I, Dentro SC, Gonzalez S, Mitchell TJ, Rubanova Y, Anur P, Rosebrock D, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vásquez-García I, ... ... Morris QD, et al. Abstract 218: The evolutionary history of 2,658 cancers Cancer Research. 78: 218-218. DOI: 10.1158/1538-7445.Am2018-218  0.48
2017 Dang H, Takai A, Forgues M, Pomyen Y, Mou H, Xue W, Ray D, Ha KCH, Morris QD, Hughes TR, Wang XW. Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma. Cancer Cell. 32: 101-114.e8. PMID 28697339 DOI: 10.1016/J.Ccell.2017.06.002  0.44
2017 Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD. RNAcompete-S: combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection. Methods (San Diego, Calif.). PMID 28651966 DOI: 10.1016/j.ymeth.2017.06.024  0.44
2017 Collins KM, Kainov YA, Christodolou E, Ray D, Morris Q, Hughes T, Taylor IA, Makeyev EV, Ramos A. An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion. Nucleic Acids Research. PMID 28379442 DOI: 10.1093/Nar/Gkx225  0.44
2016 Ray D, C H Ha K, Nie K, Zheng H, Hughes TR, Morris QD. RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins. Methods (San Diego, Calif.). PMID 27956239 DOI: 10.1016/j.ymeth.2016.12.003  0.44
2016 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. MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs. Cell Reports. 17: 720-734. PMID 27732849 DOI: 10.1016/j.celrep.2016.09.049  0.92
2016 Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N. Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. Elife. 5. PMID 27502555 DOI: 10.7554/eLife.16797  0.44
2016 Cui A, Quon G, Rosenberg AM, Yeung RS, Morris Q. Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis. Plos One. 11: e0156055. PMID 27244050 DOI: 10.1371/Journal.Pone.0156055  0.92
2015 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. The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation. Cell Reports. PMID 26527002 DOI: 10.1016/j.celrep.2015.09.068  0.92
2015 Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC. ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. Bmc Bioinformatics. 16: 156. PMID 25972088 DOI: 10.1186/S12859-015-0597-X  0.88
2015 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, et al. Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition. Genome Biology. 16: 94. PMID 25962635 DOI: 10.1186/S13059-015-0659-4  0.92
2015 Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q. PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biology. 16: 35. PMID 25786235 DOI: 10.1186/s13059-015-0602-8  0.92
2015 Deshwar AG, Vembu S, Morris Q. Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 20-31. PMID 25592565  0.48
2015 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, et al. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science (New York, N.Y.). 347: 1254806. PMID 25525159 DOI: 10.1126/Science.1254806  0.92
2015 Cook KB, Hughes TR, Morris QD. High-throughput characterization of protein-RNA interactions. Briefings in Functional Genomics. 14: 74-89. PMID 25504152 DOI: 10.1093/bfgp/elu047  0.92
2015 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, ... ... Morris Q, et al. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinformatics (Oxford, England). 31: 306-10. PMID 25316676 DOI: 10.1093/Bioinformatics/Btu671  0.92
2015 Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC. ISOpureR: An R implementation of a computational purification algorithm of mixed tumour profiles Bmc Bioinformatics. DOI: 10.1186/s12859-015-0597-x  0.92
2015 Deshwar AG, Boyles L, Wintersinger J, Boutros PC, Teh YW, Morris Q. Abstract B2-59: PhyloSpan: Using multi-mutation reads to resolve subclonal architectures from heterogeneous tumor samples Cancer Research. 75: 4865-4865. DOI: 10.1158/1538-7445.Compsysbio-B2-59  0.48
2015 Deshwar AG, Boyles L, Wintersinger J, Boutros PC, Teh YW, Morris Q. Abstract 4865: PhyloSpan: using multi-mutation reads to resolve subclonal architectures from heterogeneous tumor samples Molecular and Cellular Biology. DOI: 10.1158/1538-7445.Am2015-4865  0.48
2014 Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q. GeneMANIA: Fast gene network construction and function prediction for Cytoscape. F1000research. 3: 153. PMID 25254104 DOI: 10.12688/f1000research.4572.1  0.92
2014 Eng SW, Duong TT, Rosenberg AM, Morris Q, Yeung RS. The biologic basis of clinical heterogeneity in juvenile idiopathic arthritis. Arthritis & Rheumatology (Hoboken, N.J.). 66: 3463-75. PMID 25200124 DOI: 10.1002/art.38875  0.92
2014 Norris AD, Gao S, Norris ML, Ray D, Ramani AK, Fraser AG, Morris Q, Hughes TR, Zhen M, Calarco JA. A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types. Molecular Cell. 54: 946-59. PMID 24910101 DOI: 10.1016/J.Molcel.2014.05.004  0.92
2014 Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q. Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction. Frontiers in Genetics. 5: 123. PMID 24904632 DOI: 10.3389/fgene.2014.00123  0.92
2014 Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT. RNA-protein interactions: an overview. Methods in Molecular Biology (Clifton, N.J.). 1097: 491-521. PMID 24639174 DOI: 10.1007/978-1-62703-709-9_23  0.92
2014 Jiao W, Vembu S, Deshwar AG, Stein L, Morris Q. Inferring clonal evolution of tumors from single nucleotide somatic mutations. Bmc Bioinformatics. 15: 35. PMID 24484323 DOI: 10.1186/1471-2105-15-35  0.92
2014 Chen L, Dumelie JG, Li X, Cheng MH, Yang Z, Laver JD, Siddiqui NU, Westwood JT, Morris Q, Lipshitz HD, Smibert CA. Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. Genome Biology. 15: R4. PMID 24393533 DOI: 10.1186/Gb-2014-15-1-R4  0.92
2014 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. Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish. Development (Cambridge, England). 141: 224-35. PMID 24346703 DOI: 10.1242/Dev.099796  0.92
2014 Vembu S, Morris Q. An efficient algorithm to integrate network and attribute data for gene function prediction. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 388-99. PMID 24297564  0.92
2014 Li X, Kazan H, Lipshitz HD, Morris QD. Finding the target sites of RNA-binding proteins. Wiley Interdisciplinary Reviews. Rna. 5: 111-30. PMID 24217996 DOI: 10.1002/Wrna.1201  0.92
2014 de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR. A unified model for yeast transcript definition. Genome Research. 24: 154-66. PMID 24170600 DOI: 10.1101/Gr.164327.113  0.92
2014 Deshwar AG, Morris Q. PLIDA: cross-platform gene expression normalization using perturbed topic models. Bioinformatics (Oxford, England). 30: 956-61. PMID 24123674 DOI: 10.1093/bioinformatics/btt574  0.92
2014 Re A, Joshi T, Kulberkyte E, Morris Q, Workman CT. RNA–protein interactions: An overview Methods in Molecular Biology. 1097: 491-521. DOI: 10.1007/978-1-62703-709-9__23  0.92
2014 Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L. Personalized medicine: From genotypes and molecular phenotypes towards therapy 19th Pacific Symposium On Biocomputing, Psb 2014. 247-249.  0.92
2013 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, et al. Staufen2 regulates neuronal target RNAs. Cell Reports. 5: 1511-8. PMID 24360961 DOI: 10.1016/J.Celrep.2013.11.039  0.92
2013 Mezlini AM, Wang B, Deshwar A, Morris Q, Goldenberg A. Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression. Plos One. 8: e73168. PMID 24098326 DOI: 10.1371/Journal.Pone.0073168  0.92
2013 Radfar H, Wong W, Morris Q. BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles. Bmc Genomics. 14: 592. PMID 24001276 DOI: 10.1186/1471-2164-14-592  0.92
2013 Laver JD, Li X, Ancevicius K, Westwood JT, Smibert CA, Morris QD, Lipshitz HD. Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. Nucleic Acids Research. 41: 9438-60. PMID 23945942 DOI: 10.1093/Nar/Gkt702  0.92
2013 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, ... ... Morris QD, et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 499: 172-7. PMID 23846655 DOI: 10.1038/Nature12311  0.92
2013 Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q. GeneMANIA prediction server 2013 update. Nucleic Acids Research. 41: W115-22. PMID 23794635 DOI: 10.1093/nar/gkt533  0.92
2013 Kazan H, Morris Q. RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. Nucleic Acids Research. 41: W180-6. PMID 23754853 DOI: 10.1093/Nar/Gkt463  0.92
2013 Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q. Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction. Genome Medicine. 5: 29. PMID 23537167 DOI: 10.1186/Gm433  0.92
2013 Morris Q, Brenner SE, Listgarten J, Stegle O. The future of genome-based medicine. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 456-8. PMID 23424151  0.92
2012 Mostafavi S, Goldenberg A, Morris Q. Labeling nodes using three degrees of propagation. Plos One. 7: e51947. PMID 23284828 DOI: 10.1371/Journal.Pone.0051947  0.92
2012 Qiao W, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW. PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions. Plos Computational Biology. 8: e1002838. PMID 23284283 DOI: 10.1371/journal.pcbi.1002838  0.92
2012 Wilbert ML, Huelga SC, Kapeli K, Stark TJ, Liang TY, Chen SX, Yan BY, Nathanson JL, Hutt KR, Lovci MT, Kazan H, Vu AQ, Massirer KB, Morris Q, Hoon S, et al. LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. Molecular Cell. 48: 195-206. PMID 22959275 DOI: 10.1016/J.Molcel.2012.08.004  0.92
2012 Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. Bmc Systems Biology. 6: 112. PMID 22929553 DOI: 10.1186/1752-0509-6-112  0.92
2012 Mostafavi S, Morris Q. Combining many interaction networks to predict gene function and analyze gene lists. Proteomics. 12: 1687-96. PMID 22589215 DOI: 10.1002/Pmic.201100607  0.92
2012 Chen CY, Morris Q, Mitchell JA. Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. Bmc Genomics. 13: 152. PMID 22537144 DOI: 10.1186/1471-2164-13-152  0.92
2012 Siddiqui NU, Li X, Luo H, Karaiskakis A, Hou H, Kislinger T, Westwood JT, Morris Q, Lipshitz HD. Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells. Genome Biology. 13: R11. PMID 22348290 DOI: 10.1186/Gb-2012-13-2-R11  0.92
2012 Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping in GWAS. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 363-74. PMID 22174291  0.92
2011 Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics (Oxford, England). 27: 3166-72. PMID 21965819 DOI: 10.1093/Bioinformatics/Btr533  0.92
2011 Mostafavi S, Goldenberg A, Morris Q. Predicting node characteristics from molecular networks. Methods in Molecular Biology (Clifton, N.J.). 781: 399-414. PMID 21877293 DOI: 10.1007/978-1-61779-276-2_20  0.92
2011 Radfar MH, Wong W, Morris Q. Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms. Plos One. 6: e19312. PMID 21694770 DOI: 10.1371/Journal.Pone.0019312  0.92
2011 Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription factor specificity. Nature Biotechnology. 29: 483-4. PMID 21654663 DOI: 10.1038/Nbt.1892  0.92
2011 Ramani AK, Calarco JA, Pan Q, Mavandadi S, Wang Y, Nelson AC, Lee LJ, Morris Q, Blencowe BJ, Zhen M, Fraser AG. Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Research. 21: 342-8. PMID 21177968 DOI: 10.1101/Gr.114645.110  0.92
2011 Schimmer BP, Tsao J, Cordova M, Mostafavi S, Morris Q, Scheys JO. Contributions of steroidogenic factor 1 to the transcription landscape of Y1 mouse adrenocortical tumor cells. Molecular and Cellular Endocrinology. 336: 85-91. PMID 21111771 DOI: 10.1016/J.Mce.2010.11.024  0.92
2011 Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Research. 39: D301-8. PMID 21036867 DOI: 10.1093/Nar/Gkq1069  0.92
2011 Quon G, Haider S, Boutros PC, Morris QD. Abstract 4847: Purifying tumor gene expression profiles leads to predictive models of patient outcome Cancer Research. 71: 4847-4847. DOI: 10.1158/1538-7445.Am2011-4847  0.88
2010 Radfar M, Wong W, Morris QD. Predicting the target genes of intronic microRNAs using large-scale gene expression data. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2010: 791-4. PMID 21096111 DOI: 10.1109/IEMBS.2010.5626505  0.92
2010 Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics (Oxford, England). 26: 2927-8. PMID 20926419 DOI: 10.1093/bioinformatics/btq562  0.92
2010 Kazan H, Ray D, Chan ET, Hughes TR, Morris Q. RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. Plos Computational Biology. 6: e1000832. PMID 20617199 DOI: 10.1371/Journal.Pcbi.1000832  0.92
2010 Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, ... ... Morris Q, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research. 38: W214-20. PMID 20576703 DOI: 10.1093/Nar/Gkq537  0.92
2010 Mostafavi S, Morris Q. Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinformatics (Oxford, England). 26: 1759-65. PMID 20507895 DOI: 10.1093/Bioinformatics/Btq262  0.92
2010 Li X, Quon G, Lipshitz HD, Morris Q. Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. Rna (New York, N.Y.). 16: 1096-107. PMID 20418358 DOI: 10.1261/Rna.2017210  0.92
2010 Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, ... ... Morris QD, et al. The genetic landscape of a cell. Science (New York, N.Y.). 327: 425-31. PMID 20093466 DOI: 10.1126/Science.1180823  0.92
2009 Miller BW, Lau G, Grouios C, Mollica E, Barrios-Rodiles M, Liu Y, Datti A, Morris Q, Wrana JL, Attisano L. Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway. Molecular Systems Biology. 5: 315. PMID 19888210 DOI: 10.1038/Msb.2009.72  0.92
2009 Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR. Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nature Biotechnology. 27: 667-70. PMID 19561594 DOI: 10.1038/Nbt.1550  0.92
2009 Quon G, Morris Q. ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinformatics (Oxford, England). 25: 2882-9. PMID 19542156 DOI: 10.1093/bioinformatics/btp378  0.92
2009 Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, et al. Diversity and complexity in DNA recognition by transcription factors. Science (New York, N.Y.). 324: 1720-3. PMID 19443739 DOI: 10.1126/Science.1162327  0.92
2009 Chan ET, Quon GT, Chua G, Babak T, Trochesset M, Zirngibl RA, Aubin J, Ratcliffe MJ, Wilde A, Brudno M, Morris QD, Hughes TR. Conservation of core gene expression in vertebrate tissues. Journal of Biology. 8: 33. PMID 19371447 DOI: 10.1186/Jbiol130  0.92
2009 Blencowe B, Brenner S, Hughes T, Morris Q. Post-transcriptional gene regulation: RNA-protein interactions, RNA processing, mRNA stability and localization. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 545-8. PMID 19209730  0.92
2009 Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nature Biotechnology. 27: 199-204. PMID 19182785 DOI: 10.1038/Nbt.1522  0.92
2009 Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR. Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics (Oxford, England). 25: 1012-8. PMID 19088121 DOI: 10.1093/Bioinformatics/Btn645  0.92
2009 Quon G, Teh YW, Chan E, Hughes T, Brudno M, Morris Q. A mixture model for the evolution of gene expression in non-homogeneous datasets Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference. 1297-1304.  0.92
2009 Mostafavi S, Morris Q. Using the Gene Ontology hierarchy when predicting gene function Proceedings of the 25th Conference On Uncertainty in Artificial Intelligence, Uai 2009. 419-427.  0.92
2008 Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biology. 9: S4. PMID 18613948 DOI: 10.1186/Gb-2008-9-S1-S4  0.92
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, ... ... Morris Q, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/Gb-2008-9-S1-S2  0.92
2008 Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell. 133: 1266-76. PMID 18585359 DOI: 10.1016/J.Cell.2008.05.024  0.92
2008 Huang JC, Frey BJ, Morris QD. Comparing sequence and expression for predicting microRNA targets using GenMiR3. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 52-63. PMID 18229676 DOI: 10.1142/9789812776136_0007  0.92
2008 Andrews EAM, Morris Q, Bonner AJ. Neural networks approaches for discovering the learnable correlation between gene function and gene expression in mouse Neurocomputing. 71: 3168-3175. DOI: 10.1016/j.neucom.2008.04.035  0.92
2007 Walker E, Ohishi M, Davey RE, Zhang W, Cassar PA, Tanaka TS, Der SD, Morris Q, Hughes TR, Zandstra PW, Stanford WL. Prediction and testing of novel transcriptional networks regulating embryonic stem cell self-renewal and commitment. Cell Stem Cell. 1: 71-86. PMID 18371337 DOI: 10.1016/J.Stem.2007.04.002  0.92
2007 Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD. Using expression profiling data to identify human microRNA targets. Nature Methods. 4: 1045-9. PMID 18026111 DOI: 10.1038/Nmeth1130  0.92
2007 Huang JC, Morris QD, Frey BJ. Bayesian inference of MicroRNA targets from sequence and expression data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 550-63. PMID 17683260 DOI: 10.1089/Cmb.2007.R002  0.92
2007 Chen X, Hughes TR, Morris Q. RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics (Oxford, England). 23: i72-9. PMID 17646348 DOI: 10.1093/bioinformatics/btm224  0.92
2007 Schimmer BP, Cordova M, Cheng H, Tsao A, Morris Q. A genome-wide assessment of adrenocorticotropin action in the Y1 mouse adrenal tumor cell line. Molecular and Cellular Endocrinology. 265: 102-7. PMID 17207920 DOI: 10.1016/J.Mce.2006.12.024  0.92
2007 Chechik G, Leslie C, Noble WS, Rätsch G, Morris Q, Tsuda K. NIPS workshop on new problems and methods in computational biology Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S10-S1  0.92
2006 Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, Hughes TR. Identifying transcription factor functions and targets by phenotypic activation. Proceedings of the National Academy of Sciences of the United States of America. 103: 12045-50. PMID 16880382 DOI: 10.1073/Pnas.0605140103  0.92
2006 Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell. 125: 173-86. PMID 16615898 DOI: 10.1016/J.Cell.2006.01.044  0.92
2006 Frey BJ, Morris QD, Hughes TR. GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 200-14. PMID 16597235 DOI: 10.1089/Cmb.2006.13.200  0.92
2006 Schimmer BP, Cordova M, Cheng H, Tsao A, Goryachev AB, Schimmer AD, Morris Q. Global profiles of gene expression induced by adrenocorticotropin in Y1 mouse adrenal cells. Endocrinology. 147: 2357-67. PMID 16484322 DOI: 10.1210/En.2005-1526  0.92
2006 Shai O, Morris QD, Blencowe BJ, Frey BJ. Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics (Oxford, England). 22: 606-13. PMID 16403798 DOI: 10.1093/Bioinformatics/Btk028  0.92
2006 Shenouda EA, Morris Q, Bonner AJ. Connectionist approaches for predicting mouse gene function from gene expression Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4232: 280-289.  0.92
2006 Huang JC, Morris QD, Frey BJ. Detecting MicroRNA targets by linking sequence, MicroRNA and gene expression data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 114-129.  0.92
2005 Roy PJ, Morris Q. Network news: functional modules revealed during early embryogenesis in C. elegans. Developmental Cell. 9: 307-8. PMID 16139218 DOI: 10.1016/j.devcel.2005.08.008  0.92
2005 Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, Mnaimneh S, Chang R, Pan Q, Sat E, Rossant J, Bruneau BG, Aubin JE, Blencowe BJ, Hughes TR. Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nature Genetics. 37: 991-6. PMID 16127451 DOI: 10.1038/Ng1630  0.92
2005 Huang JC, Morris QD, Hughes TR, Frey BJ. GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. Bioinformatics (Oxford, England). 21: i222-31. PMID 15961461 DOI: 10.1093/Bioinformatics/Bti1045  0.92
2005 Dueck D, Morris QD, Frey BJ. Multi-way clustering of microarray data using probabilistic sparse matrix factorization. Bioinformatics (Oxford, England). 21: i144-51. PMID 15961451 DOI: 10.1093/Bioinformatics/Bti1041  0.92
2005 Frey BJ, Morris QD, Zhang W, Mohammad N, Hughes TR. Genrate: a generative model that finds and scores new genes and exons in genomic microarray data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 495-506. PMID 15759654  0.92
2005 Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends in Genetics : Tig. 21: 73-7. PMID 15661351 DOI: 10.1016/J.Tig.2004.12.004  0.92
2005 Hiley SL, Jackman J, Babak T, Trochesset M, Morris QD, Phizicky E, Hughes TR. Detection and discovery of RNA modifications using microarrays. Nucleic Acids Research. 33: e2. PMID 15640439 DOI: 10.1093/Nar/Gni002  0.92
2005 Frey BJ, Morris QD, Robinson M, Hughes TR. Finding novel transcripts in high-resolution genome-wide microarray data using the GenRate model Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3500: 66-82.  0.92
2005 Shai O, Frey BJ, Morris QD, Pan Q, Misquitta C, Blencowe BJ. Probabilistic inference of alternative splicing events in microarray data Advances in Neural Information Processing Systems 0.92
2004 Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Molecular Cell. 16: 929-41. PMID 15610736 DOI: 10.1016/J.Molcel.2004.12.004  0.92
2004 Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, et al. The functional landscape of mouse gene expression. Journal of Biology. 3: 21. PMID 15588312 DOI: 10.1186/Jbiol16  0.92
2004 Chua G, Robinson MD, Morris Q, Hughes TR. Transcriptional networks: reverse-engineering gene regulation on a global scale. Current Opinion in Microbiology. 7: 638-46. PMID 15556037 DOI: 10.1016/j.mib.2004.10.009  0.92
2004 Babak T, Zhang W, Morris Q, Blencowe BJ, Hughes TR. Probing microRNAs with microarrays: tissue specificity and functional inference. Rna (New York, N.Y.). 10: 1813-9. PMID 15496526 DOI: 10.1261/rna.7119904  0.92
2004 Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A, Trochesset M, Morse D, Krogan NJ, Hiley SL, Li Z, ... Morris Q, et al. Exploration of essential gene functions via titratable promoter alleles. Cell. 118: 31-44. PMID 15242642 DOI: 10.1016/J.Cell.2004.06.013  0.92
2004 Morris QD, Frey BJ, Paige CJ. Denoising and untangling graphs using degree priors Advances in Neural Information Processing Systems 0.92
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