List of works - Brendan J. Frey

A Revolution: Belief Propagation in Graphs with Cycles ⬇️

A binary variable model for affinity propagation

scientific article published in June 2009

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

scientific article

A compendium of RNA-binding motifs for decoding gene regulation.

scientific article

A generalizable pre-clinical research approach for orphan disease therapy

scientific article published on 15 June 2012

A panoramic view of yeast noncoding RNA processing

scientific article

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

scientific article

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

scholarly article by Brendan J. Frey et al published 2002 in Advances in Neural Information Processing Systems 14

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

scientific article published on 08 April 2020

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

scientific article

Accumulator Networks: Suitors of Local Probability Propagation ⬇️

Adaptive dropout for training deep neural networks ⬇️

scholarly article by Jimmy Ba & Brendan Frey published 2013 in Advances in Neural Information Processing Systems 26

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

scientific article published on 01 February 2005

Are Random Forests Truly the Best Classifiers? ⬇️

scientific article (publication date: 2016)

Automated analysis of high-content microscopy data with deep learning

scientific article

Bayesian inference of MicroRNA targets from sequence and expression data

scientific article

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context ⬇️

scientific article published on July 29, 2011

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

scientific article

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

scientific article published on 18 February 2015

COSSMO: predicting competitive alternative splice site selection using deep learning.

scientific article published in July 2018

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

scientific article

Classifying and segmenting microscopy images with deep multiple instance learning

scientific article

Clustering by passing messages between data points

scientific article

Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses

scientific article

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

scientific article published on January 22, 2011

Computer vision for high content screening

scientific article

Continuous Sigmoidal Belief Networks Trained using Slice Sampling ⬇️

scientific article published in January 1997

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

scientific article

Deciphering the splicing code

scientific article

Deep learning in biomedicine

scientific article published on 06 September 2018

Deep learning of the tissue-regulated splicing code

scientific article published on June 2014

Denoising and Untangling Graphs Using Degree Priors ⬇️

scientific article published in January 2004

Does conservation account for splicing patterns?

scientific article

Does the Wake-sleep Algorithm Produce Good Density Estimators? ⬇️

scientific article published in January 1996

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

article by Ainslie B. Parsons et al published August 2006 in Cell

Fast Transformation-Invariant Factor Analysis ⬇️

scientific article published in January 2003

Fast, Large-Scale Transformation-Invariant Clustering ⬇️

Functional coordination of alternative splicing in the mammalian central nervous system

scientific article published on January 2007

GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data

scientific article

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data

scientific article

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs

scientific article published on 28 August 2005

Genome-wide characteristics of de novo mutations in autism

scientific article published on August 2016

Genrate: a generative model that finds and scores new genes and exons in genomic microarray data

scientific article

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling

scientific journal article

How many new genes are there?

scientific article published on 01 March 2006

Identifying transcription factor functions and targets by phenotypic activation

scientific article

Inference of the Human Polyadenylation Code

scientific article published on 10 April 2018

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

scientific article published on 10 January 2006

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

scientific article published on 08 May 2007

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

scientific article published on January 2010

Keeping Flexible Active Contours on Track using Metropolis Updates ⬇️

Learning Wake-Sleep Recurrent Attention Models ⬇️

Local Probability Propagation for Factor Analysis ⬇️

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

scientific article published on 05 June 2013

Min-Max Propagation ⬇️

scientific article published in January 2017

Mixture Modeling by Affinity Propagation ⬇️

scientific article published in January 2006

Model-based detection of alternative splicing signals

scientific article

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

scientific article

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome

scientific article

Network cleanup

scientific article published in August 2013

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

scientific article

PixelGAN Autoencoders ⬇️

scientific article published in January 2017

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

scientific article

Probabilistic Inference of Alternative Splicing Events in Microarray Data ⬇️

scientific article published in January 2005

Probabilistic Inference of Speech Signals from Phaseless Spectrograms ⬇️

scientific article published in January 2004

Probabilistic n-Choose-k Models for Classification and Ranking ⬇️

scientific article published in January 2012

Product Analysis: Learning to Model Observations as Products of Hidden Variables ⬇️

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

scientific article

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease

scientific article published on 18 December 2014

Rateless Coding for Arbitrary Channel Mixtures With Decoder Channel State Information

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

scientific article

Sequentially Fitting ``Inclusive'' Trees for Inference in Noisy-OR Networks ⬇️

Structured ranking learning using cumulative distribution networks ⬇️

The evolutionary landscape of alternative splicing in vertebrate species

scientific article

The functional landscape of mouse gene expression

scientific article

Topographic Transformation as a Discrete Latent Variable ⬇️

scientific article published in January 2000

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

scientific article published on September 27, 2011

Unwrapping of MR phase images using a Markov random field model

scientific article published in January 2006

Using "epitomes" to model genetic diversity: Rational design of HIV vaccine cocktails ⬇️

scientific article published in January 2006

Using expression profiling data to identify human microRNA targets

scientific article

Very loopy belief propagation for unwrapping phase images ⬇️

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine

scientific article

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

scientific article published on 6 March 2017

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

scientific article

Widespread intron retention in mammals functionally tunes transcriptomes

scientific article

List of works by Brendan J. Frey

A Revolution: Belief Propagation in Graphs with Cycles ⬇️

A binary variable model for affinity propagation

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

A compendium of RNA-binding motifs for decoding gene regulation.

A generalizable pre-clinical research approach for orphan disease therapy

A panoramic view of yeast noncoding RNA processing

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

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

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

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

Accumulator Networks: Suitors of Local Probability Propagation ⬇️

Adaptive dropout for training deep neural networks ⬇️

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

Are Random Forests Truly the Best Classifiers? ⬇️

Automated analysis of high-content microscopy data with deep learning

Bayesian inference of MicroRNA targets from sequence and expression data

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context ⬇️

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

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

COSSMO: predicting competitive alternative splice site selection using deep learning.

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

Classifying and segmenting microscopy images with deep multiple instance learning

Clustering by passing messages between data points

Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses

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

Computer vision for high content screening

Continuous Sigmoidal Belief Networks Trained using Slice Sampling ⬇️

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

Deciphering the splicing code

Deep learning in biomedicine

Deep learning of the tissue-regulated splicing code

Denoising and Untangling Graphs Using Degree Priors ⬇️

Does conservation account for splicing patterns?

Does the Wake-sleep Algorithm Produce Good Density Estimators? ⬇️

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

Fast Transformation-Invariant Factor Analysis ⬇️

Fast, Large-Scale Transformation-Invariant Clustering ⬇️

Functional coordination of alternative splicing in the mammalian central nervous system

GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs

Genome-wide characteristics of de novo mutations in autism

Genrate: a generative model that finds and scores new genes and exons in genomic microarray data

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling

How many new genes are there?

Identifying transcription factor functions and targets by phenotypic activation

Inference of the Human Polyadenylation Code

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

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

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

Keeping Flexible Active Contours on Track using Metropolis Updates ⬇️

Learning Wake-Sleep Recurrent Attention Models ⬇️

Local Probability Propagation for Factor Analysis ⬇️

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

Min-Max Propagation ⬇️

Mixture Modeling by Affinity Propagation ⬇️

Model-based detection of alternative splicing signals

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

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome

Network cleanup

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

PixelGAN Autoencoders ⬇️

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

Probabilistic Inference of Alternative Splicing Events in Microarray Data ⬇️

Probabilistic Inference of Speech Signals from Phaseless Spectrograms ⬇️

Probabilistic n-Choose-k Models for Classification and Ranking ⬇️

Product Analysis: Learning to Model Observations as Products of Hidden Variables ⬇️

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

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease

Rateless Coding for Arbitrary Channel Mixtures With Decoder Channel State Information

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

Sequentially Fitting ``Inclusive'' Trees for Inference in Noisy-OR Networks ⬇️

Structured ranking learning using cumulative distribution networks ⬇️

The evolutionary landscape of alternative splicing in vertebrate species

The functional landscape of mouse gene expression

Topographic Transformation as a Discrete Latent Variable ⬇️

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

Unwrapping of MR phase images using a Markov random field model

Using "epitomes" to model genetic diversity: Rational design of HIV vaccine cocktails ⬇️