A Maximum-Likelihood Approach to Visual Event Classification. - Jeffrey Mark Siskind; Quaid Morris (ECCV (2), 1996)

Recognition Networks for Approximate Inference in BN20 Networks. - Quaid Morris (UAI, 2001)

Denoising and Untangling Graphs Using Degree Priors. - Quaid Morris; Brendan J. Frey (NIPS, 2003)

Probabilistic Inference of Alternative Splicing Events in Microarray Data. - Ofer Shai; Brendan J. Frey; Quaid Morris; Qun Pan 001; Christine Misquitta; Benjamin J. Blencowe (NIPS, 2004)

Multi-way clustering of microarray data using probabilistic sparse matrix factorization. - Delbert Dueck; Quaid Morris; Brendan J. Frey (ISMB (Supplement of Bioinformatics), 2005)

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. - Jim C. Huang; Quaid Morris; Timothy R. Hughes; Brendan J. Frey (ISMB (Supplement of Bioinformatics), 2005)

GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data. - Brendan J. Frey; Quaid Morris; Wen Zhang; Naveed Mohammad; Timothy R. Hughes (Pacific Symposium on Biocomputing, 2005)

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. - Brendan J. Frey; Quaid Morris; Mark D. Robinson; Timothy R. Hughes (RECOMB, 2005)

Connectionist Approaches for Predicting Mouse Gene Function from Gene Expression. - Emad A. M. Andrews Shenouda; Quaid Morris; Anthony J. Bonner (ICONIP (1), 2006)

Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. - Jim C. Huang; Quaid Morris; Brendan J. Frey (RECOMB, 2006)

Inferring global levels of alternative splicing isoforms using a generative model of microarray data. - Ofer Shai; Quaid Morris; Benjamin J. Blencowe; Brendan J. Frey (Bioinform., 2006)

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data. - Brendan J. Frey; Quaid Morris; Timothy R. Hughes (J. Comput. Biol., 2006)

RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. - Xiaoyu Chen; Timothy R. Hughes; Quaid Morris (ISMB/ECCB (Supplement of Bioinformatics), 2007)

NIPS workshop on New Problems and Methods in Computational Biology. - Gal Chechik; Christina S. Leslie; William Stafford Noble; Gunnar Rätsch; Quaid Morris; Koji Tsuda (BMC Bioinform., 2007)

Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. - Jim C. Huang; Quaid Morris; Brendan J. Frey (J. Comput. Biol., 2007)

A mixture model for the evolution of gene expression in non-homogeneous datasets. - Gerald T. Quon; Yee Whye Teh; Esther T. Chan; Timothy R. Hughes; Michael Brudno; Quaid Morris (NIPS, 2008)

Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. - Jim C. Huang; Brendan J. Frey; Quaid Morris (Pacific Symposium on Biocomputing, 2008)

Neural networks approaches for discovering the learnable correlation between gene function and gene expression in mouse. - Emad A. M. Andrews; Quaid Morris; Anthony J. Bonner (Neurocomputing, 2008)

Post-Transcriptional Gene Regulation: RNA-Protein Interactions, RNA Processing, mRNA Stability and Localization. - Benjamin J. Blencowe; Steven E. Brenner; Timothy R. Hughes; Quaid Morris (Pacific Symposium on Biocomputing, 2009)

Using the Gene Ontology Hierarchy when Predicting Gene Function. - Sara Mostafavi; Quaid Morris (UAI, 2009)

Predicting the binding preference of transcription factors to individual DNA k-mers. - 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 (Bioinform., 2009)

ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing. - Gerald T. Quon; Quaid Morris (Bioinform., 2009)

Cytoscape Web: an interactive web-based network browser. - Christian Tannus Lopes; Max Franz; Farzana Kazi; Sylva L. Donaldson; Quaid Morris; Gary D. Bader (Bioinform., 2010)

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. - Jason Montojo; Khalid Zuberi; Harold Rodriguez; Farzana Kazi; George Wright; Sylva L. Donaldson; Quaid Morris; Gary D. Bader (Bioinform., 2010)

Fast integration of heterogeneous data sources for predicting gene function with limited annotation. - Sara Mostafavi; Quaid Morris (Bioinform., 2010)

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. - 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; et al. (Nucleic Acids Res., 2010)

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins. - Hilal Kazan; Debashish Ray; Esther T. Chan; Timothy R. Hughes; Quaid Morris (PLoS Comput. Biol., 2010)

Unsupervised detection of genes of influence in lung cancer using biological networks. - Anna Goldenberg; Sara Mostafavi; Gerald T. Quon; Paul C. Boutros; Quaid Morris (Bioinform., 2011)

Computational purification of tumor gene expression data. - Amit G. Deshwar; Gerald T. Quon; Quaid Morris (BMC Bioinform., 2011)

RBPDB: a database of RNA-binding specificities. - Kate B. Cook; Hilal Kazan; Khalid Zuberi; Quaid Morris; Timothy R. Hughes (Nucleic Acids Res., 2011)

Session introduction. - Oliver Stegle; Frederick P. Roth; Quaid Morris; Jennifer Listgarten (Pacific Symposium on Biocomputing, 2012)

Mixture Model for Sub-Phenotyping in GWAS. - David Warde-Farley; Michael Brudno; Quaid Morris; Anna Goldenberg (Pacific Symposium on Biocomputing, 2012)

Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. - Mohammed Alshalalfa; Gary D. Bader; Anna Goldenberg; Quaid Morris; Reda Alhajj (BMC Syst. Biol., 2012)

Modeling the Clonal Evolution of Cancer from Next Generation Sequencing Data - Wei Jiao; Shankar Vembu; Amit G. Deshwar; Lincoln Stein; Quaid Morris (CoRR, 2012)

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions. - Wenlian Qiao; Gerald T. Quon; Elizabeth Csaszar; Mei Yu; Quaid Morris; Peter W. Zandstra (PLoS Comput. Biol., 2012)

The Future of Genome-Based Medicine. - Quaid Morris; Steven E. Brenner; Jennifer Listgarten; Oliver Stegle (Pacific Symposium on Biocomputing, 2013)

Session introduction. - Oliver Stegle; Steven E. Brenner; Quaid Morris; Jennifer Listgarten (Pacific Symposium on Biocomputing, 2013)

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. - Hilal Kazan; Quaid Morris (Nucleic Acids Res., 2013)

GeneMANIA Prediction Server 2013 Update. - Khalid Zuberi; Max Franz; Harold Rodriguez; Jason Montojo; Christian Tannus Lopes; Gary D. Bader; Quaid Morris (Nucleic Acids Res., 2013)

A compendium of RNA-binding motifs for decoding gene regulation. - 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; et al. (Nat., 2013)

Session introduction. - Jennifer Listgarten; Oliver Stegle; Quaid Morris; Steven E. Brenner; Leopold Parts (Pacific Symposium on Biocomputing, 2014)

An Efficient Algorithm to Integrate Network and Attribute Data for Gene Function Prediction. - Shankar Vembu; Quaid Morris (Pacific Symposium on Biocomputing, 2014)

PLIDA: cross-platform gene expression normalization using perturbed topic models. - Amit G. Deshwar; Quaid Morris (Bioinform., 2014)

Inferring clonal evolution of tumors from single nucleotide somatic mutations. - Wei Jiao; Shankar Vembu; Amit G. Deshwar; Lincoln Stein; Quaid Morris (BMC Bioinform., 2014)

Reconstructing subclonal composition and evolution from whole genome sequencing of tumors. - Amit G. Deshwar; Shankar Vembu; Christina K. Yung; Gun Ho Jang; Lincoln Stein; Quaid Morris (CoRR, 2014)

Comparing Nonparametric Bayesian Tree Priors for Clonal Reconstruction of Tumors. - Amit G. Deshwar; Shankar Vembu; Quaid Morris (Pacific Symposium on Biocomputing, 2015)

Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. - James Vlasblom; Khalid Zuberi; Harold Rodriguez; Roland Arnold; Alla Gagarinova; Viktor Deineko; Ashwani Kumar; Elisa Leung; Kamran Rizzolo; Bahram Samanfar; Luke Chang; Sadhna Phanse; et al. (Bioinform., 2015)

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles. - Catalina V. Anghel; Gerald T. Quon; Syed Haider; Francis Nguyen; Amit G. Deshwar; Quaid Morris; Paul C. Boutros (BMC Bioinform., 2015)

Session Introduction. - Drena Dobbs; Steven E. Brenner; Vasant G. Honavar; Robert L. Jernigan; Alain Laederach; Quaid Morris (PSB, 2016)

Reinterpreting Importance-Weighted Autoencoders. - Chris Cremer; Quaid Morris; David Duvenaud (ICLR (Workshop), 2017)

Reconstructing evolutionary trajectories of mutations in cancer. - Yulia Rubanova; Ruian Shi; Roujia Li; Jeff Wintersinger; Amit G. Deshwar; Nil Sahin; Quaid Morris (ICLR (Workshop), 2018)

GeneMANIA update 2018. - Max Franz; Harold Rodriguez; Christian Tannus Lopes; Khalid Zuberi; Jason Montojo; Gary D. Bader; Quaid Morris (Nucleic Acids Res., 2018)

Memory-Based Graph Networks. - Amir Hosein Khas Ahmadi; Kaveh Hassani; Parsa Moradi; Leo Lee; Quaid Morris (ICLR, 2020)

TrackSigFreq: Subclonal Reconstructions Based on Mutation Signatures and Allele Frequencies. - Caitlin F. Harrigan; Yulia Rubanova; Quaid Morris; Alina Selega (PSB, 2020)

Genome Gerrymandering: Optimal Division of the Genome into Regions with Cancer Type SpecificDifferences in Mutation Rates. - Adamo Young; Jacob Chmura; Yoon-Sik Park; Quaid Morris; Gurnit Atwal (PSB, 2020)

Identifying Transitional High Cost Users from Unstructured Patient Profiles Written by Primary CarePhysicians. - Haoran Zhang; Elisa Candido; Andrew S. Wilton; Raquel Duchen; Liisa Jaakkimainen; Walter P. Wodchis; Quaid Morris (PSB, 2020)

The evolutionary history of 2,658 cancers. - 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; et al. (Nat., 2020)

An empirical framework for domain generalization in clinical settings. - Haoran Zhang 003; Natalie Dullerud; Laleh Seyyed-Kalantari; Quaid Morris; Shalmali Joshi; Marzyeh Ghassemi (CHIL, 2021)

Segmenting Hybrid Trajectories using Latent ODEs. - Ruian Shi; Quaid Morris (ICML, 2021)

Learning Optimal Predictive Checklists. - Haoran Zhang 003; Quaid Morris; Berk Ustun; Marzyeh Ghassemi (NeurIPS, 2021)

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine. - Linda K. Sundermann; Jeff Wintersinger; Gunnar Rätsch; Jens Stoye; Quaid Morris (PLoS Comput. Biol., 2021)

Characterizing The Landscape Of Viral Expression In Cancer By Deep Learning. - Abdurrahman Elbasir; Ying Ye; Daniel E. Schäffer; Jayamanna Wickramasinghe; Xue Hao; Paul M. Lieberman; Quaid Morris; Rugang Zhang; Alejandro A. Schäffer; Noam Auslander (BIBM, 2022)

PAN-cODE: COVID-19 forecasting using conditional latent ODEs. - Ruian Shi; Haoran Zhang 003; Quaid Morris (J. Am. Medical Informatics Assoc., 2022)

Regional mutational signature activities in cancer genomes. - Caitlin Timmons; Quaid Morris; Caitlin F. Harrigan (PLoS Comput. Biol., 2022)

Orchard: Building large cancer phylogenies using stochastic combinatorial search. - Ethan Kulman; Rui Kuang; Quaid Morris (PLoS Comput. Biol., 2024)

Associative Memory and Generative Diffusion in the Zero-noise Limit. - Joshua Hess; Quaid Morris (CoRR, 2025)