Author details

Full Name

Brendan J Frey

Affiliation

University of Toronto

ORCID

Career Start Year

1995

Papers

H Index

Expertise

CM4AI Collaborator

Nevan J Krogan (CM4AI)

PMID	Paper Title	Journal Title	Published Year
35758812	A graph neural network approach for molecule carcinogenicity prediction.	Bioinformatics	2022
32284880	<i>ATP7B</i> variant c.1934Tâ¿¿>â¿¿G p.Met645Arg causes Wilson disease by promoting exon 6 skipping.	NPJ Genom Med	2020
29648582	Inference of the human polyadenylation code.	Bioinformatics	2018
30188539	Deep learning in biomedicine.	Nat Biotechnol	2018
29949959	COSSMO: predicting competitive alternative splice site selection using deep learning.	Bioinformatics	2018
28714989	Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism.	Nat Med	2017
28420678	Automated analysis of high-content microscopy data with deep learning.	Mol Syst Biol	2017
28263302	Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.	Nat Neurosci	2017
26806341	Computer vision for high content screening.	Crit Rev Biochem Mol Biol	2016
28567303	Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.	NPJ Genom Med	2016
27717327	Does conservation account for splicing patterns?	BMC Genomics	2016
27525107	Genome-wide characteristics of <i>de novo</i> mutations in autism.	NPJ Genom Med	2016
27307644	Classifying and segmenting microscopy images with deep multiple instance learning.	Bioinformatics	2016
25525159	RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.	Science	2015
26384369	Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome.	G3 (Bethesda)	2015
26213851	Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.	Nat Biotechnol	2015
25690854	C2H2 zinc finger proteins greatly expand the human regulatory lexicon.	Nat Biotechnol	2015
24931975	Deep learning of the tissue-regulated splicing code.	Bioinformatics	2014
25258385	Widespread intron retention in mammals functionally tunes transcriptomes.	Genome Res	2014
24859339	Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder.	Nat Genet	2014
23542699	Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome.	Nat Genet	2013
24156756	AVISPA: a web tool for the prediction and analysis of alternative splicing.	Genome Biol	2013
23846655	A compendium of RNA-binding motifs for decoding gene regulation.	Nature	2013
23929347	Network cleanup.	Nat Biotechnol	2013
23739326	MBNL proteins repress ES-cell-specific alternative splicing and reprogramming.	Nature	2013
23419374	Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry.	Bioinformatics	2013
22537040	Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data.	BMC Bioinformatics	2012
23258890	The evolutionary landscape of alternative splicing in vertebrate species.	Science	2012
22704758	A generalizable pre-clinical research approach for orphan disease therapy.	Orphanet J Rare Dis	2012
21258065	Computational refinement of post-translational modifications predicted from tandem mass spectrometry.	Bioinformatics	2011
21803804	Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.	Bioinformatics	2011
21980446	Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing.	PLoS One	2011
20065090	Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis.	J Cell Biol	2010
20445623	Deciphering the splicing code.	Nature	2010
20529924	Model-based detection of alternative splicing signals.	Bioinformatics	2010
19191593	A binary variable model for affinity propagation.	Neural Comput	2009
18056057	Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses.	Mol Cell Proteomics	2008
18978789	Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.	Nat Genet	2008
18456862	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.	Genome Res	2008
18229676	Comparing sequence and expression for predicting microRNA targets using GenMiR3.	Pac Symp Biocomput	2008
17218491	Clustering by passing messages between data points.	Science	2007
18026111	Using expression profiling data to identify human microRNA targets.	Nat Methods	2007
17565696	Functional coordination of alternative splicing in the mammalian central nervous system.	Genome Biol	2007
17683260	Bayesian inference of MicroRNA targets from sequence and expression data.	J Comput Biol	2007
17486137	Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.	Mol Syst Biol	2007
16615898	Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.	Cell	2006
16901791	Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast.	Cell	2006
16880382	Identifying transcription factor functions and targets by phenotypic activation.	Proc Natl Acad Sci U S A	2006
16403798	Inferring global levels of alternative splicing isoforms using a generative model of microarray data.	Bioinformatics	2006
16398421	Unwrapping of MR phase images using a Markov random field model.	IEEE Trans Med Imaging	2006

1 - 50 of 64

Guy Karlebach

Max Planck Institute for Psycholinguistics

Career Start Year 2008

Number of shared co-authors 0

Oliver Stegle

Wellcome Sanger Institute

Career Start Year 2008

Number of shared co-authors 4

Yuanfang Guan

University of Michigan ann arbor

Career Start Year 2007

Number of shared co-authors 2

Joshua W K Ho

The University of Hong Kong

Career Start Year 2006

Number of shared co-authors 1

Jun S Song

University of Illinois at Urbana-Champaign

Career Start Year 2005

Number of shared co-authors 2

Dongxiao Zhu

Wayne State University

Career Start Year 2005

Number of shared co-authors 0

Anshul Kundaje

Stanford University.

Career Start Year 2004

Number of shared co-authors 2

Stephen A Ramsey

Oregon State University

Career Start Year 2004

Number of shared co-authors 0

Manolis Kellis

Massachusetts Institute of Technology

Career Start Year 2003

Number of shared co-authors 4

Gerald Quon

University of California davis

Career Start Year 2003

Number of shared co-authors 8

Zhandong Liu

Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital

Career Start Year 2003

Number of shared co-authors 3

Su-In Lee

University of Washington

Career Start Year 2003

Number of shared co-authors 2

Mikael Huss

Stockholm University

Career Start Year 2003

Number of shared co-authors 3

Zhaohui S Qin

Emory University

Career Start Year 2002

Number of shared co-authors 4

Ziv Bar-Joseph

Carnegie Mellon University

Career Start Year 2001

Number of shared co-authors 5

Olga G Troyanskaya

Lewis-Sigler Institute for Integrative Genomics, Princeton University

Career Start Year 2001

Number of shared co-authors 12

Daphne Koller

Stanford University

Career Start Year 2001

Number of shared co-authors 4

Uwe Ohler

Humboldt University

Career Start Year 1999

Number of shared co-authors 2

Wei Wang

IBM Thomas J Watson Research Center, University of California Los Angeles, University of North Carolina at Chapel Hill

Career Start Year 1999

Number of shared co-authors 0

Gunnar R??tsch

ETH Zurich

Career Start Year 1999

Number of shared co-authors 8

Melissa S Cline

Genomics Institute, University of California Santa Cruz

Career Start Year 1997

Number of shared co-authors 4

Panayiotis V Benos

University of Florida

Career Start Year 1996

Number of shared co-authors 1

Ron Shamir

Tel Aviv University

Career Start Year 1995

Number of shared co-authors 1

David Kulp

Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard

Career Start Year 1994

Number of shared co-authors 2

Mark Gerstein

Yale University

Career Start Year 1991

Number of shared co-authors 20

Wing Hung Wong

Stanford University

Career Start Year 1991

Number of shared co-authors 1

Roderic Guig??

Barcelona Institute of Science and Technology

Career Start Year 1990

Number of shared co-authors 5

David Haussler

Genomics Institute, University of California Santa Cruz

Career Start Year 1986

Number of shared co-authors 9

Donald Geman

Johns Hopkins University

Career Start Year 1984

Number of shared co-authors 0

Stuart Aitken

Queensland Children's Hospital

Career Start Year 1982

Number of shared co-authors 1

row(s) 1 - 30 of 30

Benjamin J Blencowe

University of Toronto

Co-authored papers 19

Timothy R Hughes

University of Toronto

Co-authored papers 17

Quaid Morris

Sloan Kettering Institute

Co-authored papers 17

Qun Pan

University of Toronto

Co-authored papers 10

Ofer Shai

University of Toronto

Co-authored papers 8

Wen Zhang

Nanjing Agricultural University

Co-authored papers 7

Andrew Emili

Boston University School of Medicine, Boston University

Co-authored papers 6

Stephen W Scherer

The Hospital for Sick Children

Co-authored papers 6

Naveed Mohammad

Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital

Co-authored papers 5

Ryan K C Yuen

Co-authored papers 5

Christian R Marshall

Co-authored papers 5

Charles Boone

University of Toronto

Co-authored papers 4

Janet Rossant

The Hospital for Sick Children

Co-authored papers 4

Mark D Robinson

University of Zurich

Co-authored papers 4

Brenda J Andrews

University of Toronto

Co-authored papers 4

Oren Z Kraus

University of Toronto

Co-authored papers 3

Gordon Chua

University of Calgary

Co-authored papers 3

Amit G Deshwar

University of Toronto

Co-authored papers 3

Jack F Greenblatt

College Street, University of Toronto

Co-authored papers 3

Sanie Mnaimneh

University of Toronto

Co-authored papers 3

Thomas Kislinger

Princess Margaret Cancer Centre, University Health Network, University of Toronto

Co-authored papers 3

Tomas Babak

Queen's University

Co-authored papers 3

Matthew T Weirauch

University of Cincinnati College of Medicine

Co-authored papers 3

Mehdi Zarrei

Co-authored papers 3

J??rg Grigull

York University

Co-authored papers 2

Nevan J Krogan (CM4AI)

University of California San Francisco

Co-authored papers 2

Eric Sat

The University of Hong Kong

Co-authored papers 2

Wen-Tao Peng

West China Second University Hospital, Sichuan University

Co-authored papers 2

David Glazer

Verily Life Sciences LLC

Co-authored papers 2

Owen Ryan

University of California berkeley

Co-authored papers 2

1 - 30

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