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ORCIDQuaid Morris
Quaid D. Morris
Person information
- affiliation: Memorial Sloan Kettering Cancer Center, New York City, USA
- affiliation: University of Toronto, Canada
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Journal Articles
- 2022
[j29]Ruian Shi, Haoran Zhang
, Quaid Morris:
PAN-cODE: COVID-19 forecasting using conditional latent ODEs. J. Am. Medical Informatics Assoc. 29(12): 2089-2095 (2022)- [j28]Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan:
Regional mutational signature activities in cancer genomes. PLoS Comput. Biol. 18(12): 1010733 (2022) - 2021
- [j27]Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris:
Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. PLoS Comput. Biol. 17(1) (2021) - 2020
- [j26]Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit G. Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff MacIntyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Marek Cmero, Jonas Demeulemeester, Steven E. Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. L. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, Süleyman Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D. Morris, David J. Adams, Peter J. Campbell, Shaolong Cao, Elizabeth L. Christie, Yupeng Cun, Kevin J. Dawson, Ruben M. Drews, Roland Eils, Matthew Fittall, Dale W. Garsed, Gavin Ha, Henry Lee-Six, Iñigo Martincorena, Layla Oesper, Myron Peto, Benjamin J. Raphael, Daniel T. Rosebrock, Adriana Salcedo, Ruian Shi, Seung Jun Shin, Oliver Spiro, Lincoln D. Stein, Shankar Vembu, David A. Wheeler, Tsun-Po Yang, Paul T. Spellman, David C. Wedge, Peter Van Loo:
The evolutionary history of 2,658 cancers. Nat. 578(7793): 122-128 (2020) - 2018
- [j25]Max Franz, Harold Rodriguez, Christian Tannus Lopes, Khalid Zuberi, Jason Montojo, Gary D. Bader, Quaid Morris:
GeneMANIA update 2018. Nucleic Acids Res. 46(Webserver-Issue): W60-W64 (2018) - 2015
- [j24]James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary D. Bader, Mohan Babu:
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinform. 31(3): 306-310 (2015) - [j23]Catalina V. Anghel, Gerald T. Quon, Syed Haider, Francis Nguyen, Amit G. Deshwar, Quaid Morris, Paul C. Boutros:
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. BMC Bioinform. 16: 156:1-156:11 (2015) - 2014
- [j22]Amit G. Deshwar, Quaid Morris:
PLIDA: cross-platform gene expression normalization using perturbed topic models. Bioinform. 30(7): 956-961 (2014) - [j21]Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris:
Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinform. 15: 35 (2014) - 2013
- [j20]Khalid Zuberi, Max Franz, Harold Rodriguez, Jason Montojo, Christian Tannus Lopes, Gary D. Bader, Quaid Morris:
GeneMANIA Prediction Server 2013 Update. Nucleic Acids Res. 41(Webserver-Issue): 115-122 (2013) - [j19]Hilal Kazan, Quaid Morris:
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res. 41(Webserver-Issue): 180-186 (2013) - [j18]Debashish Ray, Hilal Kazan, Kate B. Cook, Matthew T. Weirauch, Hamed S. Najafabadi, Xiao Li, Serge Gueroussov, Mihai Albu, Hong Zheng, Ally Yang, Hong Na, Manuel Irimia, Leah H. Matzat, Ryan K. Dale, Sarah A. Smith, Christopher A. Yarosh, Seth M. Kelly, Behnam Nabet, Desirea Mecenas, Weimin Li, Rakesh S. Laishram, Mei Qiao, Howard D. Lipshitz, Fabio Piano, Anita H. Corbett, Russ P. Carstens, Brendan J. Frey, Richard A. Anderson, Kristen W. Lynch, Luiz O. F. Penalva, Elissa P. Lei, Andrew G. Fraser, Benjamin J. Blencowe, Quaid Morris, Timothy R. Hughes:
A compendium of RNA-binding motifs for decoding gene regulation. Nat. 499(7457): 172-177 (2013) - 2012
- [j17]Mohammed Alshalalfa, Gary D. Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj:
Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst. Biol. 6: 112 (2012) - [j16]Wenlian Qiao, Gerald T. Quon, Elizabeth Csaszar, Mei Yu, Quaid Morris, Peter W. Zandstra:
PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions. PLoS Comput. Biol. 8(12) (2012) - 2011
- [j15]Anna Goldenberg, Sara Mostafavi, Gerald T. Quon, Paul C. Boutros, Quaid Morris:
Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinform. 27(22): 3166-3172 (2011) - [j14]Amit G. Deshwar, Gerald T. Quon, Quaid Morris:
Computational purification of tumor gene expression data. BMC Bioinform. 12(S-11): A9 (2011) - [j13]Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, Timothy R. Hughes:
RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. 39(Database-Issue): 301-308 (2011) - 2010
- [j12]Sara Mostafavi, Quaid Morris:
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinform. 26(14): 1759-1765 (2010) - [j11]Christian Tannus Lopes, Max Franz, Farzana Kazi, Sylva L. Donaldson, Quaid Morris, Gary D. Bader:
Cytoscape Web: an interactive web-based network browser. Bioinform. 26(18): 2347-2348 (2010) - [j10]Jason Montojo, Khalid Zuberi, Harold Rodriguez, Farzana Kazi, George Wright, Sylva L. Donaldson, Quaid Morris, Gary D. Bader:
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinform. 26(22): 2927-2928 (2010) - [j9]David Warde-Farley, Sylva L. Donaldson, Ovi Comes, Khalid Zuberi, Rashad Badrawi, Pauline Chao, Max Franz, Chris Grouios, Farzana Kazi, Christian Tannus Lopes, Anson Maitland, Sara Mostafavi, Jason Montojo, Quentin Shao, George Wright, Gary D. Bader, Quaid Morris:
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 38(Web-Server-Issue): 214-220 (2010) - [j8]Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris:
RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins. PLoS Comput. Biol. 6(7) (2010) - 2009
- [j7]Trevis M. Alleyne, Lourdes Peña Castillo, Gwenael Badis, Shaheynoor Talukder, Michael F. Berger, Andrew R. Gehrke, Anthony A. Philippakis, Martha L. Bulyk, Quaid Morris, Timothy R. Hughes:
Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinform. 25(8): 1012-1018 (2009) - [j6]Gerald T. Quon, Quaid Morris:
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinform. 25(21): 2882-2889 (2009) - 2008
- [j5]Emad A. M. Andrews, Quaid Morris, Anthony J. Bonner:
Neural networks approaches for discovering the learnable correlation between gene function and gene expression in mouse. Neurocomputing 71(16-18): 3168-3175 (2008) - 2007
- [j4]Gal Chechik, Christina S. Leslie, William Stafford Noble, Gunnar Rätsch, Quaid Morris, Koji Tsuda:
NIPS workshop on New Problems and Methods in Computational Biology. BMC Bioinform. 8(S-10) (2007) - [j3]Jim C. Huang, Quaid Morris, Brendan J. Frey:
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. J. Comput. Biol. 14(5): 550-563 (2007) - 2006
- [j2]Ofer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey:
Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinform. 22(5): 606-613 (2006) - [j1]Brendan J. Frey, Quaid Morris, Timothy R. Hughes:
GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data. J. Comput. Biol. 13(2): 200-214 (2006)
Conference and Workshop Papers
- 2022
- [c33]Abdurrahman Elbasir, Ying Ye, Daniel E. Schäffer, Jayamanna Wickramasinghe, Xue Hao, Paul M. Lieberman, Quaid Morris, Rugang Zhang, Alejandro A. Schäffer, Noam Auslander:
Characterizing The Landscape Of Viral Expression In Cancer By Deep Learning. BIBM 2022: 3801-3803 - 2021
- [c32]Haoran Zhang, Natalie Dullerud, Laleh Seyyed-Kalantari, Quaid Morris, Shalmali Joshi, Marzyeh Ghassemi:
An empirical framework for domain generalization in clinical settings. CHIL 2021: 279-290 - [c31]Ruian Shi, Quaid Morris:
Segmenting Hybrid Trajectories using Latent ODEs. ICML 2021: 9569-9579 - [c30]Haoran Zhang, Quaid Morris, Berk Ustun, Marzyeh Ghassemi:
Learning Optimal Predictive Checklists. NeurIPS 2021: 1215-1229 - 2020
- [c29]Amir Hosein Khas Ahmadi, Kaveh Hassani, Parsa Moradi, Leo Lee, Quaid Morris:
Memory-Based Graph Networks. ICLR 2020 - [c28]Haoran Zhang, Elisa Candido, Andrew S. Wilton, Raquel Duchen, Liisa Jaakkimainen, Walter P. Wodchis, Quaid Morris:
Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary CarePhysicians. PSB 2020: 127-138 - [c27]Caitlin F. Harrigan, Yulia Rubanova, Quaid Morris, Alina Selega:
TrackSigFreq: Subclonal Reconstructions Based on Mutation Signatures and Allele Frequencies. PSB 2020: 238-249 - [c26]Adamo Young, Jacob Chmura, Yoon-Sik Park, Quaid Morris, Gurnit Atwal:
Genome Gerrymandering: Optimal Division of the Genome into Regions with Cancer Type SpecificDifferences in Mutation Rates. PSB 2020: 274-285 - 2018
- [c25]Yulia Rubanova, Ruian Shi, Roujia Li, Jeff Wintersinger, Amit G. Deshwar, Nil Sahin, Quaid Morris:
Reconstructing evolutionary trajectories of mutations in cancer. ICLR (Workshop) 2018 - 2017
- [c24]Chris Cremer, Quaid Morris, David Duvenaud:
Reinterpreting Importance-Weighted Autoencoders. ICLR (Workshop) 2017 - 2016
- [c23]Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris:
Session Introduction. PSB 2016: 429-432 - 2015
- [c22]Amit G. Deshwar, Shankar Vembu, Quaid Morris:
Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. Pacific Symposium on Biocomputing 2015: 20-31 - 2014
- [c21]Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts:
Session introduction. Pacific Symposium on Biocomputing 2014: 247-249 - [c20]Shankar Vembu, Quaid Morris:
An Efficient Algorithm to Integrate Network and Attribute Data for Gene Function Prediction. Pacific Symposium on Biocomputing 2014: 388-399 - 2013
- [c19]Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten:
Session introduction. Pacific Symposium on Biocomputing 2013: 171-174 - [c18]Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle:
The Future of Genome-Based Medicine. Pacific Symposium on Biocomputing 2013: 456-458 - 2012
- [c17]Oliver Stegle, Frederick P. Roth, Quaid Morris, Jennifer Listgarten:
Session introduction. Pacific Symposium on Biocomputing 2012: 323-326 - [c16]David Warde-Farley, Michael Brudno, Quaid Morris, Anna Goldenberg:
Mixture Model for Sub-Phenotyping in GWAS. Pacific Symposium on Biocomputing 2012: 363-374 - 2009
- [c15]Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris:
Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. Pacific Symposium on Biocomputing 2009: 545-548 - [c14]Sara Mostafavi, Quaid Morris:
Using the Gene Ontology Hierarchy when Predicting Gene Function. UAI 2009: 419-427 - 2008
- [c13]Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris:
A mixture model for the evolution of gene expression in non-homogeneous datasets. NIPS 2008: 1297-1304 - [c12]Jim C. Huang, Brendan J. Frey, Quaid Morris:
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. Pacific Symposium on Biocomputing 2008: 52-63 - 2007
- [c11]Xiaoyu Chen, Timothy R. Hughes, Quaid Morris:
RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. ISMB/ECCB (Supplement of Bioinformatics) 2007: 72-79 - 2006
- [c10]Emad A. M. Andrews Shenouda, Quaid Morris, Anthony J. Bonner:
Connectionist Approaches for Predicting Mouse Gene Function from Gene Expression. ICONIP (1) 2006: 280-289 - [c9]Jim C. Huang, Quaid Morris, Brendan J. Frey:
Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. RECOMB 2006: 114-129 - 2005
- [c8]Delbert Dueck, Quaid Morris, Brendan J. Frey:
Multi-way clustering of microarray data using probabilistic sparse matrix factorization. ISMB (Supplement of Bioinformatics) 2005: 144-151 - [c7]Jim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey:
GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. ISMB (Supplement of Bioinformatics) 2005: 222-231 - [c6]Brendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes:
GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data. Pacific Symposium on Biocomputing 2005 - [c5]Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes:
Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. RECOMB 2005: 66-82 - 2004
- [c4]Ofer Shai, Brendan J. Frey, Quaid Morris, Qun Pan, Christine Misquitta, Benjamin J. Blencowe:
Probabilistic Inference of Alternative Splicing Events in Microarray Data. NIPS 2004: 1241-1248 - 2003
- [c3]Quaid Morris, Brendan J. Frey:
Denoising and Untangling Graphs Using Degree Priors. NIPS 2003: 385-392 - 2001
- [c2]Quaid Morris:
Recognition Networks for Approximate Inference in BN20 Networks. UAI 2001: 370-377 - 1996
- [c1]Jeffrey Mark Siskind, Quaid Morris:
A Maximum-Likelihood Approach to Visual Event Classification. ECCV (2) 1996: 347-360
Informal and Other Publications
- 2021
- [i9]Haoran Zhang, Natalie Dullerud, Laleh Seyyed-Kalantari, Quaid Morris, Shalmali Joshi, Marzyeh Ghassemi:
An Empirical Framework for Domain Generalization in Clinical Settings. CoRR abs/2103.11163 (2021) - [i8]Ruian Shi, Quaid Morris:
Segmenting Hybrid Trajectories using Latent ODEs. CoRR abs/2105.03835 (2021) - [i7]Haoran Zhang, Quaid Morris, Berk Ustun, Marzyeh Ghassemi:
Learning Optimal Predictive Checklists. CoRR abs/2112.01020 (2021) - 2020
- [i6]Amir Hosein Khas Ahmadi, Kaveh Hassani, Parsa Moradi, Leo Lee, Quaid Morris:
Memory-Based Graph Networks. CoRR abs/2002.09518 (2020) - 2014
- [i5]Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris:
Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. CoRR abs/1406.7250 (2014) - [i4]Amit G. Deshwar, Shankar Vembu, Quaid Morris:
Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. CoRR abs/1408.2552 (2014) - 2013
- [i3]Quaid Morris:
Recognition Networks for Approximate Inference in BN20 Networks. CoRR abs/1301.2295 (2013) - 2012
- [i2]Sara Mostafavi, Quaid Morris:
Using the Gene Ontology Hierarchy when Predicting Gene Function. CoRR abs/1205.2622 (2012) - [i1]Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris:
Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data. CoRR abs/1210.3384 (2012)
Coauthor Index
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last updated on 2023-10-01 22:26 CEST by the dblp team
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