B. Frey

Brendan J. Frey, Nebojsa Jojic, B. Frey, 2001, Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001.

Probabilistic Sparse Matrix Factorization

B. Frey, D. Dueck, 2004 .

Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3

Brendan J. Frey, Quaid Morris, Jim C. Huang, 2007, Pacific Symposium on Biocomputing.

Bayesian Learning of MicroRNA Targets from Sequence and Expression Data

B. Frey, Q. Morris, Jim C. Huang, 2006 .

Using expression profiling data to identify human microRNA targets

B. Frey, T. Hughes, Q. Morris, 2007, Nature Methods.

Factor Graphs and Algorithms

Brendan J. Frey, Frank R. Kschischang, Hans-Andrea Loeliger, 2008 .

Bayesian Painting by Numbers: Flexible Priors for Colour-Invariant Object Recognition

Brendan J. Frey, Ryan P. Adams, Inmar E. Givoni, 2013, Machine Learning for Computer Vision.

Turbo Factor Analysis

B. Frey, 1999 .

Model-based detection of alternative splicing signals

Brendan J. Frey, Yoseph Barash, Benjamin J. Blencowe, 2010, Bioinform..

Probabilistic sparse matrix factorization with an application to discovering gene functions in mouse mRNA expression data

B. Frey, Q. Morris, D. Dueck, 2004 .

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform.

B. Frey, T. Hughes, Q. Morris, 2004, Molecular cell.

Balancing rewrapping error and smoothness in two dimensional phase unwrapping problems

Brendan J. Frey, Ralf Koetter, David C. Munson, 2002, IEEE International Geoscience and Remote Sensing Symposium.

Continuous Sigmoidal Belief Networks Trained using Slice Sampling

Brendan J. Frey, B. Frey, 1996, NIPS.

Concurrent turbo-decoding

Brendan J. Frey, Frank R. Kschischang, P. G. Gulak, 1997, Proceedings of IEEE International Symposium on Information Theory.

Deciphering the splicing code

Brendan J. Frey, Weijun Gao, Ofer Shai, 2010, Nature.

A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation.

B. Frey, L. Tsui, Y. Barash, 2008, Genome research.

Convolutional Factor Graphs as Probabilistic Models pdf

Brendan J. Frey, Frank R. Kschischang, Yongyi Mao, 2004, UAI.

Joint estimation of noise and channel distortion in a generalized EM framework

Brendan J. Frey, Li Deng, Alejandro Acero, 2001, IEEE Workshop on Automatic Speech Recognition and Understanding, 2001. ASRU '01..

A Segmental HMM for Speech Waveforms

Brendan J. Frey, Kannan Achan, Sam T. Roweis, 2004 .

Embedded face and facial expression recognition

Brendan J. Frey, Thomas S. Huang, Antonio Colmenarez, 1999, Proceedings 1999 International Conference on Image Processing (Cat. 99CH36348).

Min-Max Problems on Factor Graphs

Brendan J. Frey, Russell Greiner, Siamak Ravanbakhsh, 2014, ICML.

Classifying and segmenting microscopy images with deep multiple instance learning

Brendan J. Frey, Jimmy Ba, Oren Z. Kraus, 2015, Bioinform..

Computer vision for high content screening

Oren Z. Kraus, B. Frey, 2016, Critical reviews in biochemistry and molecular biology.

Inferring global levels of alternative splicing isoforms using a generative model of microarray data

Brendan J. Frey, Quaid Morris, Ofer Shai, 2006, Bioinform..

Alternative splicing of conserved exons is frequently species-specific in human and mouse.

B. Frey, T. Hughes, Q. Morris, 2005, Trends in genetics : TIG.

Mixtures of local linear subspaces for face recognition

Brendan J. Frey, Thomas S. Huang, Antonio Colmenarez, 1998, Proceedings. 1998 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Cat. No.98CB36231).

"Codes" on images and iterative phase unwrapping

Brendan J. Frey, Ralf Koetter, Nemanja Petrovic, 2001, Proceedings 2001 IEEE Information Theory Workshop (Cat. No.01EX494).

FLoSS: Facility location for subspace segmentation

Brendan J. Frey, Parham Aarabi, Nevena Lazic, 2009, 2009 IEEE 12th International Conference on Computer Vision.

Signal-space characterization of iterative decoding

Brendan J. Frey, Alexander Vardy, Ralf Koetter, 2001, IEEE Trans. Inf. Theory.

Skewness and pseudocodewords in iterative decoding

B. Frey, A. Vardy, R. Kotter, 1998, Proceedings. 1998 IEEE International Symposium on Information Theory (Cat. No.98CH36252).

Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast

Inmar E. Givoni, B. Frey, T. Hughes, 2006, Cell.

Adaptive dropout for training deep neural networks

Brendan J. Frey, Jimmy Ba, Jimmy Ba, 2013, NIPS.

Learning structural element patch models with hierarchical palettes

Brendan J. Frey, Ryan P. Adams, Inmar E. Givoni, 2012, 2012 IEEE Conference on Computer Vision and Pattern Recognition.

A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements

Brendan J. Frey, Anitha Kannan, Andrew Emili, 2007, RECOMB.

Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling

Michelle S. Scott, B. Frey, T. Hughes, 2006, Cell.

The functional landscape of mouse gene expression

B. Frey, T. Hughes, Q. Morris, 2004, Journal of biology.

Transformation-Invariant Clustering and Dimensionality Reduction Using EM

Brendan J. Frey, Nebojsa Jojic, B. Frey, 2001 .

Transformation-invariant filtering using expectation maximization

B. Frey, N. Jojic, 2000, Proceedings of the IEEE 2000 Adaptive Systems for Signal Processing, Communications, and Control Symposium (Cat. No.00EX373).

Generating and designing DNA with deep generative models pdf

Brendan J. Frey, Nathan Killoran, David Duvenaud, 2017, ArXiv.

A simple algorithm that discovers efficient perceptual codes

Peter Dayan, Brendan J. Frey, Geoffrey E. Hinton, 1997 .

A comparison of algorithms for inference and learning in probabilistic graphical models

Brendan J. Frey, Nebojsa Jojic, B. Frey, 2005, IEEE Transactions on Pattern Analysis and Machine Intelligence.

Fast Exact Inference for Recursive Cardinality Models

Brendan J. Frey, Ryan P. Adams, Richard S. Zemel, 2012, UAI.

Shining Bright: The Golden Era of Signal Processing

Vikram Krishnamurthy, Brendan J. Frey, Holger Boche, 2011 .

A segment based probabilistic generative model of speech

Brendan J. Frey, Aaron Hertzmann, Kannan Achan, 2005, Proceedings. (ICASSP '05). IEEE International Conference on Acoustics, Speech, and Signal Processing, 2005..

Winner-Take-All Autoencoders

Brendan J. Frey, Alireza Makhzani, B. Frey, 2014, NIPS.

Advances in Algorithms for Inference and Learning in Complex Probability Models

Brendan J. Frey, Nebojsa Jojic, B. Frey, 2003 .

Markovian inference in belief networks

Charles M. Bishop, B. Frey, N. Lawrence, 1998 .

Stel component analysis: Modeling spatial correlations in image class structure

Brendan J. Frey, Nebojsa Jojic, Alessandro Perina, 2009, 2009 IEEE Conference on Computer Vision and Pattern Recognition.

Does the Wake-sleep Algorithm Produce Good Density Estimators?

Brendan J. Frey, Geoffrey E. Hinton, Peter Dayan, 1995, NIPS.

Bayesian networks for pattern classification, data compression, and channel coding

Brendan J. Frey, Geoffrey E. Hinton, B. Frey, 1997 .

Transformation-Invariant Clustering Using the EM Algorithm

B. Frey, N. Jojic, 2003, IEEE Trans. Pattern Anal. Mach. Intell..

cDeepbind: A context sensitive deep learning model of RNA-protein binding

Brendan J. Frey, David Duvenaud, Leo J. Lee, 2018, bioRxiv.

Free energy coding

Brendan J. Frey, Geoffrey E. Hinton, B. Frey, 1996, Proceedings of Data Compression Conference - DCC '96.

Efficient Stochastic Source Coding and an Application to a Bayesian Network Source Model

Brendan J. Frey, Geoffrey E. Hinton, B. Frey, 1997, Comput. J..

Iterative Decoding of Compound Codes by Probability Propagation in Graphical Models

Brendan J. Frey, Frank R. Kschischang, B. Frey, 1998, IEEE J. Sel. Areas Commun..

Automated analysis of high‐content microscopy data with deep learning

Yolanda T. Chong, Oren Z. Kraus, Jimmy Ba, 2017, Molecular systems biology.

Video Epitomes

Brendan J. Frey, Nebojsa Jojic, Vincent Cheung, 2005, CVPR.

Solving the Uncapacitated Facility Location Problem Using Message Passing Algorithms

Brendan J. Frey, Parham Aarabi, Nevena Lazic, 2010, AISTATS.

Time-series classification using mixed-state dynamic Bayesian networks

Vladimir Pavlovic, Brendan J. Frey, Thomas S. Huang, 1999, Proceedings. 1999 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Cat. No PR00149).

ALGONQUIN: iterating laplace's method to remove multiple types of acoustic distortion for robust speech recognition

Brendan J. Frey, Li Deng, Alex Acero, 2001, INTERSPEECH.

A Revolution: Belief Propagation in Graphs with Cycles

Brendan J. Frey, David J. C. MacKay, B. Frey, 1997, NIPS.

Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis

B. Frey, B. Andrews, Zhijian Li, 2010, The Journal of cell biology.

Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression.

B. Frey, B. Blencowe, C. Misquitta, 2006, Genes & development.

Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder

Daniele Merico, Pingzhao Hu, Christian R Marshall, 2014, Nature Genetics.

Genome-wide characteristics of de novo mutations in autism

Samuel S. Gross, B. Frey, J. R. MacDonald, 2016, npj Genomic Medicine.

A Computational High-Throughput Method for Detecting miRNA Targets

B. Frey, Q. Morris, Jim C. Huang, 2005 .

Machine Learning Approaches to Refining Post-translational Modification Predictions and Protein Identifications from Tandem Mass Spectrometry

B. Frey, C. Chung, 2012 .

Does conservation account for splicing patterns?

B. Frey, B. Alipanahi, M. Wainberg, 2016, BMC Genomics.

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Michael D. Wilson, Philip M. Kim, B. Frey, 2012, Science.

Allele-specific transcription factor binding as a benchmark for assessing variant impact predictors

B. Frey, D. Merico, Andrew Delong, 2018, bioRxiv.

ACCOUNTING FOR UNCERTAINTY IN OBSERVATIONS : A NEW PARADIGM FOR ROBUST AUTOMATIC SPEECH RECOGNITION

B. Frey, T. Kristjansson, 2022 .

Inference of the human polyadenylation code

B. Frey, Andrew Delong, M. Leung, 2017, bioRxiv.

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

B. Frey, J. R. MacDonald, John Wei, 2017, Nature Neuroscience.

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes

Igor Jurisica, Andrew Emili, Anitha Kannan, 2022 .

IMA Seminar Series 2008 / 2009

B. Frey, D. Dueck, 2009 .

Probability Propagation and Iterative Decoding

Brendan J. Frey, Frank R. Kschischang, B. Frey, 1996 .

Early Detection and Trellis Splicing Reduced Complexity Soft Iterative Decoding

B. Frey, F. Kschischang, 1998 .

Comparative Proteomics Profiling of a Phospholamban Mutant Mouse Model of Dilated Cardiomyopathy Reveals Progressive Intracellular Stress Responses*S

Andrew Emili, Anitha Kannan, Thomas Kislinger, 2008, Molecular & Cellular Proteomics.

Network cleanup

B. Frey, B. Alipanahi, 2013, Nature Biotechnology.

Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine

Michael Brudno, Daniele Merico, Christian R Marshall, 2016, npj Genomic Medicine.

ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping

B. Frey, D. Merico, E. Wienholds, 2019, npj Genomic Medicine.

ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping

B. Frey, D. Merico, E. Wienholds, 2019, npj Genomic Medicine.

Bayesian Inference of MicroRNA Targets from Sequence and Expression Data

Brendan J. Frey, Quaid Morris, Jim C. Huang, 2007, J. Comput. Biol..

GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data

Brendan J. Frey, Wen Zhang, Quaid Morris, 2004, Pacific Symposium on Biocomputing.

Probabilistic estimation of short sequence expression using RNA-Seq data and the “positional bootstrap”

B. Frey, H. Y. Xiong, Leo J. Lee, 2016, bioRxiv.

MBNL proteins repress embryonic stem cell-specific alternative splicing and reprogramming

Eric T. Wang, B. Frey, B. Alipanahi, 2014 .

Inference of the human polyadenylation code

B. Frey, Andrew Delong, M. Leung, 2017, bioRxiv.

Genome analysis Inference of the human polyadenylation code

B. Frey, Andrew Delong, M. Leung, 2018 .

Addendum: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

B. Frey, Leo J. Lee, B. Blencowe, 2009, Nature Genetics.

Impacto Global da Signal Processing Magazine

Ghassan AlRegib, Mihaela van der Schaar, Brendan J. Frey, 2011 .

Factorgrams: A tool for visualizing multi-way associations in biological data

Inmar E. Givoni, B. Frey, D. Dueck, 2006 .

Using epitomes to model genetic diversity: Rational design of HIV vaccines

Brendan J. Frey, Nebojsa Jojic, David Heckerman, 2005, NIPS.

How Many New Genes Are There?

B. Frey, Leo J. Lee, T. Hughes, 2006, Science.

Probabilistic Inference in Graphical Models

Brendan J. Frey, B. Frey, 1998 .

Points Clustering by Passing Messages Between Data

Brendan J. Frey, B. Frey, 2007 .

Inferring Alternative Splicing Combinations from Comprehensive Putative-Junction Microarray Data

B. Frey, Leo J. Lee, C. Misquitta, 2008 .

Bayesian n-Choose-k Models for Classification and Ranking

Brendan J. Frey, B. Frey, 2012, NIPS 2012.

Additional file 3 of Does conservation account for splicing patterns

Brendan J. Frey, Michael Wainberg, Babak Alipanahi, 2016 .

Manuscript Word Count: Abstract: 193; Text, with citations, without references: 3921 Number of Tables: 2; Supplemental Files: Yes Whole-genome sequencing suggests schizophrenia risk mechanisms in humans with 22q11.2 deletion syndrome

Brendan J. Frey, Daniele Merico, Babak Alipanahi, 2015 .

Additional file 2 of Does conservation account for splicing patterns

Brendan J. Frey, Michael Wainberg, Babak Alipanahi, 2016 .

Iterated Conditional Modes for Cross-Hybridization Compensation in DNA Microarray Data

Brendan J. Frey, Quaid Morris, Jim C. Huang, 2004 .

Information for : “ C 2 H 2 zinc finger proteins greatly expand the human regulatory lexicon ”

Philip M. Kim, B. Frey, H. Najafabadi, 2014 .

RTfold: RNA secondary structure prediction using deep learning with domain inductive bias

B. Frey, Leo J. Lee, A. Jung, 2022 .

Non-metric affinity propagation for unsupervised image categorization

Brendan J. Frey, Delbert Dueck, B. Frey, 2007, 2007 IEEE 11th International Conference on Computer Vision.

Learning Montages of Transformed Latent Images as Representations of Objects That Change in Appearance

Brendan J. Frey, Nebojsa Jojic, Christopher Joseph Pal, 2002, ECCV.

Cumulative Distribution Networks and the Derivative-sum-product Algorithm: Models and Inference for Cumulative Distribution Functions on Graphs

Brendan J. Frey, Jim C. Huang, B. Frey, 2008, J. Mach. Learn. Res..

Learning Graphical Models of Images, Videos and Their Spatial Transformations

Brendan J. Frey, Nebojsa Jojic, B. Frey, 2000, UAI.

Variational Learning in Mixed-State Dynamic Graphical Models

Vladimir Pavlovic, Brendan J. Frey, Thomas S. Huang, 1999, UAI.

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

Eric T. Wang, Christopher B. Burge, Brendan J. Frey, 2013, Nature.

A Panoramic View of Yeast Noncoding RNA Processing

Brendan J. Frey, Mark D. Robinson, Nevan J. Krogan, 2003, Cell.

Widespread intron retention in mammals functionally tunes transcriptomes

B. Frey, B. Alipanahi, B. Blencowe, 2014, Genome research.

nonsense-mediated mRNA decay to control gene expression widespread coupling of alternative splicing with Quantitative microarray profiling provides evidence against Material Supplemental

B. Frey, B. Blencowe, C. Misquitta, 2006 .

transcriptomes Widespread intron retention in mammals functionally tunes Material

B. Frey, B. Alipanahi, B. Blencowe, 2014 .

A graph neural network approach for molecule carcinogenicity prediction

B. Frey, Leo J. Lee, Lazar Atanackovic, 2021, bioRxiv.

A compendium of RNA-binding motifs for decoding gene regulation

Brendan J. Frey, Xiao Li, Hong Zheng, 2013, Nature.

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

Brendan J. Frey, Babak Alipanahi, Andrew Delong, 2016, Proceedings of the IEEE.

COSSMO: predicting competitive alternative splice site selection using deep learning

Brendan J. Frey, Hannes Bretschneider, Khalid Zuberi, 2018, bioRxiv.

Deep learning of the tissue-regulated splicing code

Brendan J. Frey, Hui Yuan Xiong, Leo J. Lee, 2014, Bioinform..

STORMSeq: A Method for Ranking Regulatory Sequences by Integrating Experimental Datasets with Diverse Computational Predictions

Brendan J. Frey, Jim C. Huang, B. Frey, 2011, Handbook of Statistical Bioinformatics.

Matrix Tile Analysis pdf

Brendan J. Frey, Inmar E. Givoni, Vincent Cheung, 2006, UAI.

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Michael D. Wilson, Philip M. Kim, B. Frey, 2013 .

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

Mihai Albu, Philip M. Kim, Philip M Kim, 2015, Nature Biotechnology.

Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome

Daniele Merico, Christian R Marshall, Babak Alipanahi, 2015, G3: Genes, Genomes, Genetics.

AVISPA: a web tool for the prediction and analysis of alternative splicing

Weijun Gao, Juan González-Vallinas, Hui Yuan Xiong, 2013, Genome Biology.

HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps

Brendan J. Frey, Leo J. Lee, Michael C Dimmick, 2020, bioRxiv.

Deep learning in biomedicine

Michael Wainberg, Daniele Merico, Andrew Delong, 2018, Nature Biotechnology.

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause Microcephaly-Capillary Malformation syndrome

B. Frey, Leo J. Lee, Soma Das, 2013, Nature Genetics.

Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data

Brendan J. Frey, Quaid Morris, Jim C. Huang, 2006, RECOMB.

Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models

Brendan J. Frey, B. Frey, 2002, UAI.

Bayesian Learning of MicroRNA Targets from Sequence and Expression Data

B. Frey, Q. Morris, Jim C. Huang, 2006 .

Hierarchical Affinity Propagation pdf

Brendan J. Frey, Clement Chung, Inmar E. Givoni, 2011, UAI.

Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism

Daniele Merico, Michael D. Wilson, Eleonora Maino, 2017, Nature Medicine.

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data

Brendan J. Frey, Quaid Morris, Timothy R. Hughes, 2006, J. Comput. Biol..

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model

Brendan J. Frey, Mark D. Robinson, Quaid Morris, 2005, RECOMB.

Probabilistic Inference of Alternative Splicing Events in Microarray Data

Brendan J. Frey, Quaid Morris, Ofer Shai, 2004, NIPS.

ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping.

B. Frey, D. Merico, J. Dowling, 2020, NPJ genomic medicine.

Multi-way clustering of microarray data using probabilistic sparse matrix factorization

Brendan J. Frey, Delbert Dueck, Quaid Morris, 2005, ISMB.

Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis

B. Frey, B. Andrews, Zhijian Li, 2010, Journal of Cell Biology.

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data

Brendan J. Frey, Nebojsa Jojic, Boyko Kakaradov, 2012, BMC Bioinformatics.

Identifying transcription factor functions and targets by phenotypic activation

Charles Boone, Timothy R Hughes, Quaid D Morris, 2006, Proceedings of the National Academy of Sciences.

Probabilistic n-Choose-k Models for Classification and Ranking

Brendan J. Frey, Ryan P. Adams, Richard S. Zemel, 2012, NIPS.

Variational Probabilistic Speech Separation Using Microphone Arrays

Brendan J. Frey, Parham Aarabi, Steven J. Rennie, 2007, IEEE Transactions on Audio, Speech, and Language Processing.

Probabilistic multimedia objects (multijects): a novel approach to video indexing and retrieval in multimedia systems

Brendan J. Frey, Milind R. Naphade, Thomas S. Huang, 1998, Proceedings 1998 International Conference on Image Processing. ICIP98 (Cat. No.98CB36269).

Towards non-stationary model-based noise adaptation for large vocabulary speech recognition

Brendan J. Frey, Li Deng, Alex Acero, 2001, 2001 IEEE International Conference on Acoustics, Speech, and Signal Processing. Proceedings (Cat. No.01CH37221).

Real-time On-line Learning of Transformed Hidden Markov Models from Video

Brendan J. Frey, Nebojsa Jojic, Thomas S. Huang, 2003, AISTATS.

Structured ranking learning using cumulative distribution networks

Brendan J. Frey, Jim C. Huang, B. Frey, 2008, NIPS.

Computational refinement of post-translational modifications predicted from tandem mass spectrometry

Jian Liu, Brendan J. Frey, Clement Chung, 2011, Bioinform..

Machine Learning Approaches for RNA Editing Prediction

B. Frey, Leo J. Lee, A. Jung, 2020 .

Transformed hidden Markov models: estimating mixture models of images and inferring spatial transformations in video sequences

Brendan J. Frey, Nebojsa Jojic, Thomas S. Huang, 2000, Proceedings IEEE Conference on Computer Vision and Pattern Recognition. CVPR 2000 (Cat. No.PR00662).

A generalizable pre-clinical research approach for orphan disease therapy

Sean Ekins, Kym M Boycott, Mark E Samuels, 2012, Orphanet Journal of Rare Diseases.

Unwrapping of MR phase images using a Markov random field model

Brendan J. Frey, Zhi-Pei Liang, Lei Ying, 2006, IEEE Transactions on Medical Imaging.

Are Random Forests Truly the Best Classifiers?

Brendan J. Frey, Michael Wainberg, Babak Alipanahi, 2016, J. Mach. Learn. Res..

Translating images by unsupervised estimation of switching filters

Brendan J. Frey, Kannan Achan, Romer Rosales, 2004, IEEE Workshop on Statistical Signal Processing, 2003.

Unsupervised image translation

Brendan J. Frey, Rómer Rosales, Kannan Achan, 2003, Proceedings Ninth IEEE International Conference on Computer Vision.

Response to Comment on "Clustering by Passing Messages Between Data Points"

Brendan J. Frey, Delbert Dueck, B. Frey, 2008, Science.

Generative Model for Layers of Appearance and Deformation

Brendan J. Frey, Nebojsa Jojic, Anitha Kannan, 2005, AISTATS.

Enforcing integrability for surface reconstruction algorithms using belief propagation in graphical models

Brendan J. Frey, Thomas S. Huang, Ralf Koetter, 2001, Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001.

Video Epitomes

Brendan J. Frey, Nebojsa Jojic, Vincent Cheung, 2005, 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05).

Semi-Supervised Affinity Propagation with Instance-Level Constraints

Brendan J. Frey, Inmar E. Givoni, B. Frey, 2009, AISTATS.

Variational inference for continuous sigmoidal Bayesian networks

B. Frey, 1996, Proceedings of the Sixth International Workshop on Artificial Intelligence and Statistics.

A Binary Variable Model for Affinity Propagation

Brendan J. Frey, Inmar E. Givoni, B. Frey, 2009, Neural Computation.

Event-coupled hidden Markov models

Brendan J. Frey, Thomas S. Huang, Trausti T. Kristjansson, 2000, 2000 IEEE International Conference on Multimedia and Expo. ICME2000. Proceedings. Latest Advances in the Fast Changing World of Multimedia (Cat. No.00TH8532).

collagen and mechanical forces Biomechanics of the lung parenchyma: critical roles of

B. Frey, D. Stamenović, A. Emili, 2005 .

Factor graphs and the sum-product algorithm

B. Frey, F. Kschischang, H. Loeliger, 2001, IEEE Trans. Inf. Theory.

Estimating mixture models of images and inferring spatial transformations using the EM algorithm

Brendan J. Frey, Nebojsa Jojic, B. Frey, 1999, Proceedings. 1999 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Cat. No PR00149).

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes

B. Frey, A. Kannan, A. Emili, 2007, Molecular Systems Biology.

Transcriptional Profiling of Endocrine Cerebro-Osteodysplasia Using Microarray and Next-Generation Sequencing

Brendan J. Frey, Benjamin J. Blencowe, Robert A. Hegele, 2011, PloS one.

Early Detection and Trellis Splicing: Reduced-Complexity Iterative Decoding

Brendan J. Frey, Frank R. Kschischang, B. Frey, 1998, IEEE J. Sel. Areas Commun..

Comparison of GenASAP with supervised methods

B. Frey, Q. Morris, B. Blencowe, 2005 .

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry

Brendan J. Frey, Clement Chung, Andrew Emili, 2013, Bioinform..

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass

Brendan J. Frey, Clement Chung, B. Frey, 2013 .

Nonparametric Bayesian Approach to Post-translational Modification Refinement of Predictions from Tandem Mass Spectrometry

Clement Chung, Andrew Emili, B. Frey, 2012 .

ALGONQUIN - Learning Dynamic Noise Models From Noisy Speech for Robust Speech Recognition

Brendan J. Frey, Li Deng, Alex Acero, 2001, NIPS.

Robust variational speech separation using fewer microphones than speakers

Steven J. Rennie, B. Frey, Kannan Achan, 2003, 2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698).

Factorizing appearance using epitomic flobject analysis

Brendan J. Frey, Patrick S. Li, B. Frey, 2012, 2012 IEEE Conference on Computer Vision and Pattern Recognition.

Inference of the human polyadenylation code

B. Frey, Andrew Delong, M. Leung, 2017, bioRxiv.

Transformed component analysis: joint estimation of spatial transformations and image components

Brendan J. Frey, Nebojsa Jojic, B. Frey, 1999, Proceedings of the Seventh IEEE International Conference on Computer Vision.

Spatial Bias Removal in Microarray Images

Brendan J. Frey, Ofer Shai, Quaid D. Morris, 2003 .

Denoising and Untangling Graphs Using Degree Priors

Brendan J. Frey, Quaid Morris, B. Frey, 2003, NIPS.

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

B. Frey, B. Alipanahi, Andrew Delong, 2015, Nature Biotechnology.

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Philip M. Kim, B. Frey, Leo J. Lee, 2012, Science.

Alternative splicing of conserved exons is frequently species-specific in human and mouse.

B. Frey, T. Hughes, B. Blencowe, 2005, Trends in genetics : TIG.

Bioinformatics Original Paper Inferring Global Levels of Alternative Splicing Isoforms Using a Generative Model of Microarray Data

B. Frey, B. Blencowe, O. Shai, 2022 .

A Factorized Variational Technique for Phase Unwrapping in Markov Random Field pdf

Brendan J. Frey, Ralf Koetter, Kannan Achan, 2001, UAI.

Unwrapping phase images by propagating probabilities across graphs

Brendan J. Frey, Ralf Koetter, David C. Munson, 2001, 2001 IEEE International Conference on Acoustics, Speech, and Signal Processing. Proceedings (Cat. No.01CH37221).

Unwrapping phases by relaxed mean field inference

Brendan J. Frey, Ralf Koetter, David C. Munson, 2001, 2001 IEEE International Conference on Acoustics, Speech, and Signal Processing. Proceedings (Cat. No.01CH37221).

A Revolution: Belief Propagation Graphs with Cycles

B. Frey, D. MacKay, 1998 .

Fast, Large-Scale Transformation-Invariant Clustering

Brendan J. Frey, Nebojsa Jojic, B. Frey, 2001, NIPS.

Keeping Flexible Active Contours on Track using Metropolis Updates

Brendan J. Frey, Trausti T. Kristjansson, B. Frey, 2000, NIPS.

Min-Max Propagation

Brendan J. Frey, Siamak Ravanbakhsh, Inmar E. Givoni, 2017, NIPS.

Rateless Coding for Arbitrary Channel Mixtures With Decoder Channel State Information

Brendan J. Frey, Frank R. Kschischang, Stark C. Draper, 2009, IEEE Transactions on Information Theory.

Probabilistic Inference of Speech Signals from Phaseless Spectrograms

Brendan J. Frey, Kannan Achan, Sam T. Roweis, 2003, NIPS.

Noise robust speech recognition using Gaussian basis functions for non-linear likelihood function approximation

Brendan J. Frey, Christopher Joseph Pal, Trausti T. Kristjansson, 2002, 2002 IEEE International Conference on Acoustics, Speech, and Signal Processing.

Variational Speech Separation of More Sources than Mixtures

Brendan J. Frey, Parham Aarabi, Kannan Achan, 2005, AISTATS.

Speech recognition in adverse environments: a probabilistic approach

Brendan J. Frey, Trausti T. Kristjansson, B. Frey, 2002 .

Learning the "Epitome" of an Image

Brendan J. Frey, Nebojsa Jojic, B. Frey, 2002 .