Quaid Morris,
Associate Professor in the Donnelly Centre
Director of the Collaborative Program in Genome Biology and Bioinformatics
University of Toronto, Toronto, Ontario
____________________________________________________________________________
University of Toronto
Donnelly Centre for Cellular and
Biomolecular Research
160 College St., Room 616
Toronto, ON M5S 3E1
Tel:
416-978-8568
Fax: 416-978-8287
Email: quaid.morris@utoronto.ca
Website: http://morrislab.med.utoronto.ca
RESEARCH SPECIALIZATION KEYWORDS
Molecular and Cellular Biology, Genetics, Information Technology: Computer Science, Molecular
and Cellular Biology, Electrical and Electronic Engineering, Genetics, Cancer/Oncology
ACADEMIC AND TRAINING BACKGROUND
2003-2005
2002-2003
1999-2001
1996-2002
1991-1996
Post Doctoral Fellow in Computational Biology, BBDMR and Dept of ECE,
University of Toronto
Post Doctoral Fellow, Ontario Cancer Institute, Princess Margaret Hospital and
Dept of ECE, University of Toronto
Graduate training and research in machine learning, Gatsby Unit in University
College London, England
PhD in Brain and Cognitive Sciences (specialization Computational
Neuroscience), Massachusetts Institute of Technology (MIT), Cambridge, USA
Honours B.Sc.: Dept of Computer Science, University of Toronto
WORK EXPERIENCE
2010-Present
2012-Present
2006-2010
2005-2010
2005-2010
Associate Professor, Banting and Best Department of Medical Research and
cross-appointed in: Department of Molecular Genetics, Faculty of Medicine;
and Department of Computer Science, Faculty of Arts and Sciences, University
of Toronto
Associate Professor, cross-appointed Department of Electrical and Computer
Engineering, Faculty of Applied Sciences, University of Toronto
Assistant Professor, cross-appointed, Department of Molecular Genetics,
Faculty of Medicine, University of Toronto
Assistant Professor, Banting & Best Department of Medical Research, Faculty
of Medicine, University of Toronto
Assistant Professor, cross-appointed, Department of Computer Science,
Faculty of Arts and Sciences, University of Toronto
SELECTED ACCOMPLISHMENTS AND HONOURS
2010-2014
Early Researcher Award, Ontario Ministry of Research and Innovation
1
SELECTED PEER-REVIEWED PUBLICATIONS IN LAST FIVE YEARS
* indicates co-first author; † indicates co-corresponding author; underline indicates QM’s trainee or staff; listed
computer science conference proceedings publications are peer-reviewed, in highly selective conferences that have
as much impact as journal publications in computer science. Conference publications from PSB and IEEE Eng Med
Biol Soc are Pubmed-listed. Of the non-Pubmed listed publications, only those from the following top-tier
conferences are included: RECOMB, ISMB, NIPS, UAI, ICML
2014
1.
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 Biol. 2014 Jan
7;15(1):R4. [Epub ahead of print] PubMed PMID: 24393533.
2.
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.
2014 Jan;141(1):224-35. doi: 10.1242/dev.099796. PubMed PMID: 24346703; PubMed
Central PMCID: PMC3865760.
3.
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 Res. 2014 Jan;24(1):154-66. doi:
10.1101/gr.164327.113. Epub 2013 Oct 29. PubMed PMID: 24170600; PubMed Central
PMCID: PMC3875857.
4.
Vembu S, Morris Q. An efficient algorithm to integrate network and attribute data for
gene function prediction. Pac Symp Biocomput. 2014;19:388-99. PubMed PMID:
24297564.
5.
Listgarten J, Stegle O, Morris Q, Brenner SE, Parts L. Personalized medicine: from
genotypes and molecular phenotypes towards therapy- session introduction. Pac Symp
Biocomput. 2014;19:224-8. PubMed PMID: 24297549.
6.
Li X, Kazan H, Lipshitz HD, Morris QD. Finding the target sites of RNA-binding proteins.
Wiley Interdiscip Rev RNA. 2014 Jan;5(1):111-30. doi: 10.1002/wrna.1201. Epub 2013
Nov 11. PubMed PMID: 24217996.
7.
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. Staufen2 Regulates Neuronal Target RNAs. Cell Rep. 2013 Dec
26;5(6):1511-8. doi: 10.1016/j.celrep.2013.11.039. Epub 2013 Dec 19. PubMed PMID:
24360961.
8.
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 Res. 2013 Nov 1;41(20):9438-60. doi:
10.1093/nar/gkt702. Epub 2013 Aug 13. PubMed PMID: 23945942; PubMed Central
PMCID: PMC3814352.
9.
Deshwar AG, Morris Q. PLIDA: Cross-platform gene expression normalization using
perturbed topic models. Bioinformatics. 2013 Oct 11. [Epub ahead of print] PubMed
PMID: 24123674.
2013
2
10.
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. 2013 Oct 2;8(10):e73168. doi:
10.1371/journal.pone.0073168. PubMed PMID: 24098326; PubMed Central PMCID:
PMC3788788.
11.
Radfar H, Wong W, Morris Q. BayMiR: inferring evidence for endogenous miRNAinduced gene repression from mRNA expression profiles. BMC Genomics. 2013 Aug
30;14(1):592. [Epub ahead of print] PubMed PMID: 24001276.
12.
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†. A compendium of RNA-binding motifs for
decoding gene regulation. Nature. 2013 Jul 11;499(7457):172-7. doi:
10.1038/nature12311. PubMed PMID: 23846655.
13.
Zuberi K*, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q.
GeneMANIA prediction server 2013 update. Nucleic Acids Res. 2013 Jul;41(Web Server
issue):W115-22. doi: 10.1093/nar/gkt533. PubMed PMID: 23794635; PubMed Central
PMCID: PMC3692113. IF: 8.026
14.
Kazan H, Morris Q. RBPmotif: a web server for the discovery of sequence and structure
preferences of RNA-binding proteins. Nucleic Acids Res. 2013 Jul;41(Web Server
issue):W180-6. doi: 10.1093/nar/gkt463. Epub 2013 Jun 10. PubMed PMID: 23754853;
PubMed Central PMCID: PMC3692078.
15.
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 Med. 2013 Mar 28;5(3):29. doi: 10.1186/gm433.
PubMed PMID: 23537167; PubMed Central PMCID: PMC3706990.
17.
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. Evaluation of methods for modeling transcription factor
sequence specificity. Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486.
Epub 2013 Jan 27. PubMed PMID: 23354101; PubMed Central PMCID: PMC3687085.
18.
Morris Q, Brenner SE, Listgarten J, Stegle O. The future of genome-based medicine.
Pac Symp Biocomput. 2013:456-8. PubMed PMID: 23424151.
19.
Mostafavi S, Goldenberg A, Morris Q. Labeling nodes using three degrees of
propagation. PLoS One. 2012;7(12):e51947. doi: 10.1371/journal.pone.0051947. Epub
2012 Dec 28. PubMed PMID: 23284828; PubMed Central PMCID: PMC3532359. IF:
4.092
20.
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, Yeo GW.
LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor
Abundance. Mol Cell. 2012 Sep 5. [Epub ahead of print] PubMed PMID: 22959275. IF:
14.178
2012
3
21.
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 Syst Biol. 2012 Aug 28;6(1):112. [Epub ahead of print] PubMed PMID: 22929553.
IF: 3.148
22.
Mostafavi S, Morris Q. Combining many interaction networks to predict gene function
and analyze gene lists. Proteomics. 2012 May;12(10):1687-96. doi:
10.1002/pmic.201100607. Review. PubMed PMID: 22589215.
23.
Chen CY, Morris Q, Mitchell JA. Enhancer identification in mouse embryonic stem cells
using integrative modeling of chromatin and genomic features. BMC Genomics. 2012 Apr
26;13:152. doi: 10.1186/1471-2164-13-152. PubMed PMID: 22537144; PubMed Central
PMCID: PMC3406964.
24.
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 Biol. 2012 Feb 20;13(2):R11. doi: 10.1186/gb-2012-13-2r11. PubMed PMID: 22348290; PubMed Central PMCID: PMC3334568.
25.
Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping
in GWAS. Pac Symp Biocomput. 2012:363-74. PubMed PMID: 22174291.
26.
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 Comput Biol. 2012 Dec;8(12):e1002838. doi:
10.1371/journal.pcbi.1002838. Epub 2012 Dec 20. PubMed PMID: 23284283; PubMed
Central PMCID: PMC3527275. IF: 5.215
27.
Mostafavi S, Goldenberg A, Morris Q. Labeling nodes using three degrees of
propagation. PLoS One. 2012;7(12):e51947. doi: 10.1371/journal.pone.0051947. Epub
2012 Dec 28. PubMed PMID: 23284828; PubMed Central PMCID: PMC3532359. IF:
4.092
28.
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, Yeo GW.
LIN28 Binds Messenger RNAs at GGAGA Motifs and Regulates Splicing Factor
Abundance. Mol Cell. 2012 Sep 5. [Epub ahead of print] PubMed PMID: 22959275. IF:
14.178
29.
Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris Q. Unsupervised detection of
genes of influence in lung cancer using biological networks. Bioinformatics. 2011 Nov
15;27(22):3166-72. Epub 2011 Sep 28. IF: 5.468
30.
Radfar MH, Wong W, Morris Q. Computational prediction of intronic microRNA targets
using host gene expression reveals novel regulatory mechanisms. PLoS One.
2011;6(6):e19312. Epub 2011 Jun 9. IF: 4.092
31.
Morris Q, Bulyk ML, Hughes TR. Jury remains out on simple models of transcription
factor specificity. Nat Biotechnol. 2011 Jun 7;29(6):483-4. doi: 10.1038/nbt.1892. IF:
23.268
2011
4
32.
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. Mol Cell Endocrinol. 2011 Apr 10;336(1-2):85-91. Epub 2010 Nov 25. IF: 4.192
33.
Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL,
Toufighi K, Mostafavi S, [37 names], Morris QD, Kim PM, Kaiser CA, Myers CL,
Andrews BJ, Boone C. The genetic landscape of a cell. Science. 2010 Jan
22;327(5964):425-31. PubMed PMID: 20093466. IF: 31.201
34.
Radfar MH, Wong W, Morris Q. Predicting the target genes of intronic microRNAs using
large-scale gene expression data. Conf Proc IEEE Eng Med Biol Soc. 2010;1:791-4
35.
Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNAbinding specificities. Nucleic Acids Res. 2010 Oct 29. IF: 8.026
36.
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. 2010 Nov 15;26(22):2927-8. IF: 5.468
37.
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 Res. 2011 Feb;21(2):342-8. Epub 2010 Dec 22. IF:
13.608
38.
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: an
interactive web-based network browser. Bioinformatics. 2010;26(18): 2347-2348. IF:
5.468
39.
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,
Bader GD, Morris Q. The GeneMANIA prediction server: biological network integration
for gene prioritization and predicting gene function. Nucleic Acids Res. 2010 Jul 1;38
Suppl:W214-20. IF: 8.026
40.
S Mostafavi, Q Morris, Fast Integration of Multiple Networks for Predicting Protein
Function with Limited Annotatio., Bioinformatics 2010;26(14):1759-65. IF: 5.468
41.
M Costanzo, A Baryshnikova, J Bellay, Y Kim, ED Spear, CS Sevier, H Ding, JL Koh, K
Toufighi, S Mostafavi (+ 37 authors), QD Morris, PM Kim, CA Kaiser, CL Myers, BJ
Andrews, C Boone, Science. 2010 Jan 22;327(5964). IF: 31.201
42.
X Li, G Quon, HD Lipshitz, Q Morris, Target site accessibility predicts in vivo binding of
RNA-binding proteins. RNA. 2010 Jun; 16(6)
43.
H Kazan, D Ray, ET Chan, TR Hughes, and Q Morris. Learning the sequence and
structure binding preferences of RNA-binding proteins from noisy affinity data. PLoS
Comput Biol. 2010 Jul 1;6:e1000832. IF:5.215
44.
D Ray*, H Kazan*, ET Chan, L Peña Castillo, S Chaudhry, S Talukder, BJ Blencowe, †Q
Morris, and †TR Hughes*. Rapid and systematic analysis of the RNA recognition
specificities of RNA-binding proteins. Nature Biotechnology 27:667-70. IF:23.268
2010
2009
5
45.
BW Miller, G Lau, C Grouios, E Mollica, M Barrios-Rodiles, Y Liu, A Datti, Q Morris, JL
Wrana and L Attisano. Application of an integrated physical and functional screening
approach to identify inhibitors of the Wnt pathway. Molecular Systems Biology
M2009;5:315. IF: 8.626
46.
G Quon, Q Morris. ISOLATE: A computational strategy for identifying the primary origin
of cancers using high throughput sequencing. Bioinformatics Epub 2009 June 19. IF:
5.468
47.
S Mostafavi, Q Morris. Using hierarchical information in predicting gene function.
Proceedings of the Association for Uncertainty in Artificial Intelligence (UAI) Conference
2009
48.
IW Taylor, R Linding, D Warde-Farley, Y Liu, C Pesquita, D Faria, S Bull, T Pawson, Q
Morris, JL Wrana. Dynamic modularity in protein interaction networks predicts breast
cancer outcome. Nat Biotechnol. 2009 Feb;27(2):199-204. Epub 2009 Feb 1. IF: 23.268
49.
*G Badis, *MF Berger, *AA Philippakis, *S Talukder, *AR Gehrke, *SA Jaeger, *ET Chan,
G Metzler, A Vedenko, X Chen, H Kuznetsov, C-F Wang, D Coburn, DE. Newburger, Q
Morris, †TR. Hughes, †ML. Bulyk, Diversity and Complexity in DNA Recognition by
Transcription Factors, Science 324:1720. IF: 31.201
50.
ET Chan, GT Quon, G Chua, T Babak, M Trochesset, RA Zirngibl, J Aubin, MJ Ratcliffe,
A Wilde, M Brudno, †QD Morris, †TR Hughes. Conservation of core gene expression in
vertebrate tissues, Journal of Biology 2009 Apr 16;8(3):33.
2008
51.
TM Alleyne, L Peña-Castillo, G Badis, S Talukder, MF Berger, AR Gehrke, AA
Philippakis, ML Bulyk, QD Morris, TR Hughes. Predicting the binding preference of
transcription factors to individual DNA k-mers. Bioinformatics. 2009 Apr 15;25(8):1012-8.
Epub 2008 Dec 16. IF: 5.468
52.
S Mostafavi, D Ray, D Warde-Farley, C Grouios, and QD Morris. GeneMANIA: A realtime Multiple Affinity Network Integration Algorithm for predicting gene function. Genome
Biology 2008;9 Suppl 1:S4. IF: 9.036
53.
L Peña-Castillo, … (37 authors in total including S Mostafavi, D Ray, D Warde-Farley, C
Grouios, QD Morris), … TR Hughes, F Roth. A critical assessment of M. musculus gene
function prediction using integrated genomics evidence. Genome Biology 9 Suppl 1:S2.
IF: 9.036
54.
*MF Berger, … (13 authors in total) QD Morris, †ML Bulyk, †TR Hughes. Variation in
homeodomain DNA binding revealed by high-resolution analysis of sequence
preferences. Cell Jun 27; 133(7). IF: 32.403
55.
G Quon, YW Teh, E Chan, T Hughes, M Brudno, Q Morris. A Mixture Model for the
Evolution of Gene Expression in Non-homogeneous Datasets, NIPS Dec 13;21
56.
JC Huang, BJ Frey, QD Morris. Comparing sequence and expression for predicting
microRNA targets using GenMiR3. Pac Symp Biocomput. (PSB) 52-63.
6
ACTIVITIES AND CONTRIBUTIONS
Invited Seminar & Conference Presentations (>50 in total since 2004):
Keynote 1 hour seminars RECOMB Cancer Computational Biology (2011), ORNL Bioinformatics
conference (Memphis, Tennessee) (2011), McGill-Toronto Bioinformatics Workshop (2013)
Invited 1 hour seminars in Canada, USA, UK, Spain, and Germany including European
Bioinformatics Institute, Fields Institute Toronto, UC Berkeley, Harvard Medical School, CMU,
University of Edinburgh, University of Freiburg, University of Washington, Microsoft Research
Redmond and Cambridge, ICML Computational Biology workshop (given in place of Brendan
Frey))
Invited 15 minute conference or workshop presentations include Pacific Symposium on
Biocomputing (2012, 2014), RECOMB Regulatory Genomics satellite (2010, 2011, 2012),
Riboclub Sherbrooke (2010), ISMB AS-SIG (2009, 2010), ISMB Techtrack (2010), ISMB
Workshops (2013 x2), McGill Barbados Bioinformatics Conference (2005, 2008, 2012, 2013),
ISMB (2007), Cold Spring Harbor Laboratory mRNA processing conference (2009, 2013), CIHR
integrating physical and biological sciences workshop (2008), NHGRI Proteomic Sequence &
Function Workshop (2008)
Editorial and Advisory Boards: Associate Editor: PLoS Computational Biology (2013), BMC
Bioinformatics (2010-2013); Guest Associate Editor: PLoS Computational Biology (2009); Coeditor of BMC Bioinformatics Special Issue (2006); Scientific Advisory Board: Univ of
Sherbrooke Genome Canada project (2007-2009)
Grant Review Panels: Canadian Breast Cancer Foundation, Panel A (Feb 2012); CIHR
Genomics (guest 2008, full member March 2009, Sept 2009, March 2010, March 2011, March
2013); NSF (2007, 2013); Ad hoc reviewer NSERC (2006, 2008, 2011, five grants in total);
Burroughs Wellcome Fund (2009), W.M. Keck (2009)
Symposium and Workshop Organization: Co-organizer Personalized medicine session @
Pacific Symposium on Biocomputing (2012-2014), Machine Learning in Computational Biology
workshop @ NIPS (2006-2008), Post-transcriptional regulation workshop @ Pacific Symposium
on Biocomputing 2009, Session Chair: International Conference on Machine Learning 2006
Reviewing for Journals and Conferences (~20-30 manuscripts / year): Journals include Nature,
Nature Biotechnology, Nature Genetics, Nature Methods, Molecular Systems Biology, Genome
Biology, Genome Research, PLoS Computational Biology, Bioinformatics, BMC Bioinformatics,
IEEE Transactions on Pattern Analysis and Machine Intelligence. Conferences include Pacific
Symposium on Biocomputing (PSB), International Conference on Intelligent Systems for
Molecular Biology (ISMB), Artificial Intelligence and Statistics (AISTATS), Advances in Neural
Information Processing Systems (NIPS), International Conference of Machine Learning (ICML),
RECOMB regulatory genomics and systems biology satellite.
Outreach: Faculty lecturer for Canadian Bioinformatics Workshop (1 or 2 workshops / year since
2008)
7