Quaid Morris

Publication Activity (10 Years)

Years Active: 1996-2022
Publications (10 Years): 19

Top Topics

Nonparametric Bayesian

Gene Regulatory

Evolutionary Process

Top Venues

Pacific Symposium on Biocomputing

Nucleic Acids Res.

Publications

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)
Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan
Regional mutational signature activities in cancer genomes. PLoS Comput. Biol. 18 (12) (2022)
Ruian Shi, Haoran Zhang, Quaid Morris
PAN-cODE: COVID-19 forecasting using conditional latent ODEs. J. Am. Medical Informatics Assoc. 29 (12) (2022)
Haoran Zhang, Natalie Dullerud, Laleh Seyyed-Kalantari, Quaid Morris, Shalmali Joshi, Marzyeh Ghassemi
An Empirical Framework for Domain Generalization in Clinical Settings. CoRR (2021)
Haoran Zhang, Quaid Morris, Berk Ustun, Marzyeh Ghassemi
Learning Optimal Predictive Checklists. CoRR (2021)
Haoran Zhang, Natalie Dullerud, Laleh Seyyed-Kalantari, Quaid Morris, Shalmali Joshi, Marzyeh Ghassemi
An empirical framework for domain generalization in clinical settings. CHIL (2021)
Ruian Shi, Quaid Morris
Segmenting Hybrid Trajectories using Latent ODEs. ICML (2021)
Ruian Shi, Quaid Morris
Segmenting Hybrid Trajectories using Latent ODEs. CoRR (2021)
Haoran Zhang, Quaid Morris, Berk Ustun, Marzyeh Ghassemi
Learning Optimal Predictive Checklists. NeurIPS (2021)
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)
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)
Amir Hosein Khas Ahmadi, Kaveh Hassani, Parsa Moradi, Leo Lee, Quaid Morris
Memory-Based Graph Networks. CoRR (2020)
Amir Hosein Khas Ahmadi, Kaveh Hassani, Parsa Moradi, Leo Lee, Quaid Morris
Memory-Based Graph Networks. ICLR (2020)
Caitlin F. Harrigan, Yulia Rubanova, Quaid Morris, Alina Selega
TrackSigFreq: Subclonal Reconstructions Based on Mutation Signatures and Allele Frequencies. PSB (2020)
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)
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)
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) (2018)
Chris Cremer, Quaid Morris, David Duvenaud
Reinterpreting Importance-Weighted Autoencoders. ICLR (Workshop) (2017)
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
Session Introduction. PSB (2016)
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 (2015)
Amit G. Deshwar, Shankar Vembu, Quaid Morris
Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. Pacific Symposium on Biocomputing (2015)
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
. Bioinform. 31 (3) (2015)
Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts
Session introduction. Pacific Symposium on Biocomputing (2014)
Amit G. Deshwar, Shankar Vembu, Quaid Morris
Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. CoRR (2014)
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 (2014)
Shankar Vembu, Quaid Morris
An Efficient Algorithm to Integrate Network and Attribute Data for Gene Function Prediction. Pacific Symposium on Biocomputing (2014)
Amit G. Deshwar, Quaid Morris
PLIDA: cross-platform gene expression normalization using perturbed topic models. Bioinform. 30 (7) (2014)
Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris
Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinform. 15 (2014)
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) (2013)
Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten
Session introduction. Pacific Symposium on Biocomputing (2013)
Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle
The Future of Genome-Based Medicine. Pacific Symposium on Biocomputing (2013)
Quaid Morris
Recognition Networks for Approximate Inference in BN20 Networks CoRR (2013)
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) (2013)
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) (2013)
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)
Sara Mostafavi, Quaid Morris
Using the Gene Ontology Hierarchy when Predicting Gene Function CoRR (2012)
David Warde-Farley, Michael Brudno, Quaid Morris, Anna Goldenberg
Mixture Model for Sub-Phenotyping in GWAS. Pacific Symposium on Biocomputing (2012)
Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris
Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data CoRR (2012)
Oliver Stegle, Frederick P. Roth, Quaid Morris, Jennifer Listgarten
Session introduction. Pacific Symposium on Biocomputing (2012)
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 (2012)
Amit G. Deshwar, Gerald T. Quon, Quaid Morris
Computational purification of tumor gene expression data. BMC Bioinform. 12 (S-11) (2011)
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) (2011)
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) (2011)
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) (2010)
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)
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) (2010)
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) (2010)
Sara Mostafavi, Quaid Morris
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinform. 26 (14) (2010)
Sara Mostafavi, Quaid Morris
Using the Gene Ontology Hierarchy when Predicting Gene Function. UAI (2009)
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
-mers. Bioinform. 25 (8) (2009)
Gerald T. Quon, Quaid Morris
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinform. 25 (21) (2009)
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)
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) (2008)
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)
Jim C. Huang, Brendan J. Frey, Quaid Morris
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. Pacific Symposium on Biocomputing (2008)
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)
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)
Jim C. Huang, Quaid Morris, Brendan J. Frey
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. J. Comput. Biol. 14 (5) (2007)
Emad A. M. Andrews Shenouda, Quaid Morris, Anthony J. Bonner
Connectionist Approaches for Predicting Mouse Gene Function from Gene Expression. ICONIP (1) (2006)
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) (2006)
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) (2006)
Jim C. Huang, Quaid Morris, Brendan J. Frey
Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. RECOMB (2006)
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)
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)
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)
Delbert Dueck, Quaid Morris, Brendan J. Frey
Multi-way clustering of microarray data using probabilistic sparse matrix factorization. ISMB (Supplement of Bioinformatics) (2005)
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)
Quaid Morris, Brendan J. Frey
Denoising and Untangling Graphs Using Degree Priors. NIPS (2003)
Quaid Morris
Recognition Networks for Approximate Inference in BN20 Networks. UAI (2001)
Jeffrey Mark Siskind, Quaid Morris
A Maximum-Likelihood Approach to Visual Event Classification. ECCV (2) (1996)