Quaid Morris - RankMe

72 papers A* 3A 2B 2Misc 14Journal 39Unranked 12

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Associative Memory and Generative Diffusion in the Zero-noise Limit. CoRR Joshua Hess, Quaid Morris
2024	J	`jnl`	Orchard: Building large cancer phylogenies using stochastic combinatorial search. PLoS Comput. Biol. Ethan Kulman, Rui Kuang, Quaid Morris
2022	—	`conf`	Characterizing The Landscape Of Viral Expression In Cancer By Deep Learning. BIBM Abdurrahman Elbasir, Ying Ye, Daniel E. Schäffer, Jayamanna Wickramasinghe, Xue Hao, Paul M. Lieberman, Quaid Morris, Rugang Zhang, Alejandro A. Schäffer, Noam Auslander
2022	J	`jnl`	PAN-cODE: COVID-19 forecasting using conditional latent ODEs. J. Am. Medical Informatics Assoc. Ruian Shi, Haoran Zhang, Quaid Morris
2022	J	`jnl`	Regional mutational signature activities in cancer genomes. PLoS Comput. Biol. Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan
2021	J	`jnl`	An Empirical Framework for Domain Generalization in Clinical Settings. CoRR Haoran Zhang, Natalie Dullerud, Laleh Seyyed-Kalantari, Quaid Morris, Shalmali Joshi, Marzyeh Ghassemi
2021	—	`conf`	An empirical framework for domain generalization in clinical settings. CHIL Haoran Zhang, Natalie Dullerud, Laleh Seyyed-Kalantari, Quaid Morris, Shalmali Joshi, Marzyeh Ghassemi
2021	A*	`conf`	Learning Optimal Predictive Checklists. NeurIPS Haoran Zhang, Quaid Morris, Berk Ustun, Marzyeh Ghassemi
2021	J	`jnl`	Learning Optimal Predictive Checklists. CoRR Haoran Zhang, Quaid Morris, Berk Ustun, Marzyeh Ghassemi
2021	J	`jnl`	Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. PLoS Comput. Biol. Linda K. Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris
2021	A*	`conf`	Segmenting Hybrid Trajectories using Latent ODEs. ICML Ruian Shi, Quaid Morris
2021	J	`jnl`	Segmenting Hybrid Trajectories using Latent ODEs. CoRR Ruian Shi, Quaid Morris
2020	Misc	`conf`	Genome Gerrymandering: Optimal Division of the Genome into Regions with Cancer Type SpecificDifferences in Mutation Rates. PSB Adamo Young, Jacob Chmura, Yoon-Sik Park, Quaid Morris, Gurnit Atwal
2020	Misc	`conf`	Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary CarePhysicians. PSB Haoran Zhang, Elisa Candido, Andrew S. Wilton, Raquel Duchen, Liisa Jaakkimainen, Walter P. Wodchis, Quaid Morris
2020	A*	`conf`	Memory-Based Graph Networks. ICLR Amir Hosein Khas Ahmadi, Kaveh Hassani, Parsa Moradi, Leo Lee, Quaid Morris
2020	J	`jnl`	Memory-Based Graph Networks. CoRR Amir Hosein Khas Ahmadi, Kaveh Hassani, Parsa Moradi, Leo Lee, Quaid Morris
2020	Misc	`conf`	TrackSigFreq: Subclonal Reconstructions Based on Mutation Signatures and Allele Frequencies. PSB Caitlin F. Harrigan, Yulia Rubanova, Quaid Morris, Alina Selega
2018	J	`jnl`	GeneMANIA update 2018. Nucleic Acids Res. Max Franz, Harold Rodriguez, Christian Tannus Lopes, Khalid Zuberi, Jason Montojo, Gary D. Bader, Quaid Morris
2018	—	`conf`	Reconstructing evolutionary trajectories of mutations in cancer. ICLR (Workshop) Yulia Rubanova, Ruian Shi, Roujia Li, Jeff Wintersinger, Amit G. Deshwar, Nil Sahin, Quaid Morris
2017	—	`conf`	Reinterpreting Importance-Weighted Autoencoders. ICLR (Workshop) Chris Cremer, Quaid Morris, David Duvenaud
2016	Misc	`conf`	Session Introduction. PSB Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
2015	Misc	`conf`	Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. Pacific Symposium on Biocomputing Amit G. Deshwar, Shankar Vembu, Quaid Morris
2015	J	`jnl`	ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. BMC Bioinform. Catalina V. Anghel, Gerald T. Quon, Syed Haider, Francis Nguyen, Amit G. Deshwar, Quaid Morris, Paul C. Boutros
2015	J	`jnl`	Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Bioinform. 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
2014	Misc	`conf`	An Efficient Algorithm to Integrate Network and Attribute Data for Gene Function Prediction. Pacific Symposium on Biocomputing Shankar Vembu, Quaid Morris
2014	J	`jnl`	Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. CoRR Amit G. Deshwar, Shankar Vembu, Quaid Morris
2014	J	`jnl`	Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinform. Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris
2014	J	`jnl`	PLIDA: cross-platform gene expression normalization using perturbed topic models. Bioinform. Amit G. Deshwar, Quaid Morris
2014	J	`jnl`	Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. CoRR Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang, Lincoln Stein, Quaid Morris
2014	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Jennifer Listgarten, Oliver Stegle, Quaid Morris, Steven E. Brenner, Leopold Parts
2013	J	`jnl`	A compendium of RNA-binding motifs for decoding gene regulation. Nat. 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
2013	J	`jnl`	GeneMANIA Prediction Server 2013 Update. Nucleic Acids Res. Khalid Zuberi, Max Franz, Harold Rodriguez, Jason Montojo, Christian Tannus Lopes, Gary D. Bader, Quaid Morris
2013	J	`jnl`	RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res. Hilal Kazan, Quaid Morris
2013	J	`jnl`	Recognition Networks for Approximate Inference in BN20 Networks CoRR Quaid Morris
2013	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Oliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten
2013	Misc	`conf`	The Future of Genome-Based Medicine. Pacific Symposium on Biocomputing Quaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle
2012	J	`jnl`	Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst. Biol. Mohammed Alshalalfa, Gary D. Bader, Anna Goldenberg, Quaid Morris, Reda Alhajj
2012	Misc	`conf`	Mixture Model for Sub-Phenotyping in GWAS. Pacific Symposium on Biocomputing David Warde-Farley, Michael Brudno, Quaid Morris, Anna Goldenberg
2012	J	`jnl`	Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data CoRR Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein, Quaid Morris
2012	J	`jnl`	PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions. PLoS Comput. Biol. Wenlian Qiao, Gerald T. Quon, Elizabeth Csaszar, Mei Yu, Quaid Morris, Peter W. Zandstra
2012	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Oliver Stegle, Frederick P. Roth, Quaid Morris, Jennifer Listgarten
2012	J	`jnl`	Using the Gene Ontology Hierarchy when Predicting Gene Function CoRR Sara Mostafavi, Quaid Morris
2011	J	`jnl`	Computational purification of tumor gene expression data. BMC Bioinform. Amit G. Deshwar, Gerald T. Quon, Quaid Morris
2011	J	`jnl`	RBPDB: a database of RNA-binding specificities. Nucleic Acids Res. Kate B. Cook, Hilal Kazan, Khalid Zuberi, Quaid Morris, Timothy R. Hughes
2011	J	`jnl`	Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinform. Anna Goldenberg, Sara Mostafavi, Gerald T. Quon, Paul C. Boutros, Quaid Morris
2010	J	`jnl`	Cytoscape Web: an interactive web-based network browser. Bioinform. Christian Tannus Lopes, Max Franz, Farzana Kazi, Sylva L. Donaldson, Quaid Morris, Gary D. Bader
2010	J	`jnl`	Fast integration of heterogeneous data sources for predicting gene function with limited annotation. Bioinform. Sara Mostafavi, Quaid Morris
2010	J	`jnl`	GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinform. Jason Montojo, Khalid Zuberi, Harold Rodriguez, Farzana Kazi, George Wright, Sylva L. Donaldson, Quaid Morris, Gary D. Bader
2010	J	`jnl`	RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins. PLoS Comput. Biol. Hilal Kazan, Debashish Ray, Esther T. Chan, Timothy R. Hughes, Quaid Morris
2010	J	`jnl`	The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 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
2009	J	`jnl`	ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. Bioinform. Gerald T. Quon, Quaid Morris
2009	Misc	`conf`	Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. Pacific Symposium on Biocomputing Benjamin J. Blencowe, Steven E. Brenner, Timothy R. Hughes, Quaid Morris
2009	J	`jnl`	Predicting the binding preference of transcription factors to individual DNA Bioinform. 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
2009	A	`conf`	Using the Gene Ontology Hierarchy when Predicting Gene Function. UAI Sara Mostafavi, Quaid Morris
2008	—	`conf`	A mixture model for the evolution of gene expression in non-homogeneous datasets. NIPS Gerald T. Quon, Yee Whye Teh, Esther T. Chan, Timothy R. Hughes, Michael Brudno, Quaid Morris
2008	Misc	`conf`	Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. Pacific Symposium on Biocomputing Jim C. Huang, Brendan J. Frey, Quaid Morris
2008	J	`jnl`	Neural networks approaches for discovering the learnable correlation between gene function and gene expression in mouse. Neurocomputing Emad A. M. Andrews, Quaid Morris, Anthony J. Bonner
2007	J	`jnl`	Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. J. Comput. Biol. Jim C. Huang, Quaid Morris, Brendan J. Frey
2007	J	`jnl`	NIPS workshop on New Problems and Methods in Computational Biology. BMC Bioinform. Gal Chechik, Christina S. Leslie, William Stafford Noble, Gunnar Rätsch, Quaid Morris, Koji Tsuda
2007	—	`conf`	RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. ISMB/ECCB (Supplement of Bioinformatics) Xiaoyu Chen, Timothy R. Hughes, Quaid Morris
2006	—	`conf`	Connectionist Approaches for Predicting Mouse Gene Function from Gene Expression. ICONIP (1) Emad A. M. Andrews Shenouda, Quaid Morris, Anthony J. Bonner
2006	B	`conf`	Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. RECOMB Jim C. Huang, Quaid Morris, Brendan J. Frey
2006	J	`jnl`	GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data. J. Comput. Biol. Brendan J. Frey, Quaid Morris, Timothy R. Hughes
2006	J	`jnl`	Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinform. Ofer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey
2005	B	`conf`	Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. RECOMB Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes
2005	Misc	`conf`	GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data. Pacific Symposium on Biocomputing Brendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes
2005	—	`conf`	GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. ISMB (Supplement of Bioinformatics) Jim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey
2005	—	`conf`	Multi-way clustering of microarray data using probabilistic sparse matrix factorization. ISMB (Supplement of Bioinformatics) Delbert Dueck, Quaid Morris, Brendan J. Frey
2004	—	`conf`	Probabilistic Inference of Alternative Splicing Events in Microarray Data. NIPS Ofer Shai, Brendan J. Frey, Quaid Morris, Qun Pan, Christine Misquitta, Benjamin J. Blencowe
2003	—	`conf`	Denoising and Untangling Graphs Using Degree Priors. NIPS Quaid Morris, Brendan J. Frey
2001	A	`conf`	Recognition Networks for Approximate Inference in BN20 Networks. UAI Quaid Morris
1996	—	`conf`	A Maximum-Likelihood Approach to Visual Event Classification. ECCV (2) Jeffrey Mark Siskind, Quaid Morris