B. Frey

Most-cited papers

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
Q. Pan, O. Shai, Leo J. Lee, B. Frey +1 more
2008Nature Genetics3,944 citations Open access
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Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Babak Alipanahi, A. Delong, M. Weirauch, B. Frey
2015Nature Biotechnology2,758 citations Open access
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A compendium of RNA-binding motifs for decoding gene regulation
Debashish Ray, Hilal Kazan, Kate B. Cook, M. Weirauch +31 more
2013Nature1,479 citations Open access
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The human splicing code reveals new insights into the genetic determinants of disease
Hui Y. Xiong, Babak Alipanahi, Leo J. Lee, Hannes Bretschneider +13 more
2014Science1,229 citations Open access
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Deciphering the splicing code
Yoseph Barash, John A. Calarco, Wei-Jun Gao, Q. Pan +4 more
2010Nature890 citations
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The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
N. Barbosa-Morais, M. Irimia, Q. Pan, Hui Y. Xiong +13 more
2012Science813 citations
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Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
Ryan K. C. Yuen, D. Merico, M. Bookman, J. Howe +79 more
2017Nature Neuroscience759 citations Open access
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Widespread intron retention in mammals functionally tunes transcriptomes
Ulrich Braunschweig, N. Barbosa-Morais, Q. Pan, Emil N. Nachman +5 more
2014Genome Research643 citations Open access
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k-Sparse Autoencoders
Alireza Makhzani, B. Frey
2013International Conference on Learning Representations627 citations
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Deep learning in biomedicine
Michael Wainberg, D. Merico, A. Delong, B. Frey
2018Nature Biotechnology530 citations
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Deep learning of the tissue-regulated splicing code
M. Leung, Hui Y. Xiong, Leo J. Lee, B. Frey
2014Bioinform.458 citations Open access
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Classifying and segmenting microscopy images with deep multiple instance learning
O. Kraus, Jimmy Ba, B. Frey
2015Bioinform.425 citations Open access
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Adaptive dropout for training deep neural networks
Jimmy Ba, B. Frey
2013Neural Information Processing Systems398 citations
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C2H2 zinc finger proteins greatly expand the human regulatory lexicon
H. Najafabadi, S. Mnaimneh, F. Schmitges, Michael Garton +9 more
2015Nature Biotechnology347 citations
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Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine
D. Stavropoulos, D. Merico, R. Jobling, S. Bowdin +59 more
2016npj Genomic Medicine314 citations Open access
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MBNL proteins repress embryonic stem cell-specific alternative splicing and reprogramming
Hong Han, M. Irimia, P. Ross, H. Sung +23 more
2014301 citations
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Winner-Take-All Autoencoders
Alireza Makhzani, B. Frey
2014Neural Information Processing Systems257 citations
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Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets
M. Leung, A. Delong, Babak Alipanahi, B. Frey
2016Proceedings of the IEEE251 citations Open access
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Genome-wide characteristics of de novo mutations in autism
Ryan K. C. Yuen, D. Merico, Hong-Zhi Cao, G. Pellecchia +44 more
2016npj Genomic Medicine225 citations Open access
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Are Random Forests Truly the Best Classifiers?
Michael Wainberg, Babak Alipanahi, B. Frey
2016Journal of machine learning research178 citations
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Generating and designing DNA with deep generative models
N. Killoran, Leo J. Lee, A. Delong, D. Duvenaud +1 more
2017arXiv.org170 citations
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Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder
M. Uddin, K. Tammimies, G. Pellecchia, Babak Alipanahi +11 more
2014Nature Genetics161 citations
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A Binary Variable Model for Affinity Propagation
Inmar E. Givoni, B. Frey
2009Neural Computation154 citations Open access
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Factor Graphs and Algorithms
B. Frey, F. Kschischang, Hans-Andrea Loeliger
2008125 citations
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Mutations in STAMBP, encoding a deubiquitinating enzyme, cause Microcephaly-Capillary Malformation syndrome
Laura M McDonell, G. Mirzaa, Diana Alcantara, J. Schwartzentruber +26 more
2013Nature Genetics116 citations Open access
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Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis
F. Vizeacoumar, N. van Dyk, Frederick S.Vizeacoumar, V. Cheung +12 more
2010Journal of Cell Biology116 citations Open access
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Stel component analysis: Modeling spatial correlations in image class structure
N. Jojic, A. Perina, M. Cristani, Vittorio Murino +1 more
20092009 IEEE Conference on Computer Vision and Pattern Recognition116 citations
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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.
I. Aznarez, Yoseph Barash, O. Shai, David He +6 more
2008Genome Research104 citations Open access
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FLoSS: Facility location for subspace segmentation
Nevena Lazic, Inmar E. Givoni, B. Frey, Parham Aarabi
2009IEEE International Conference on Computer Vision90 citations
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Hierarchical Affinity Propagation
Inmar E. Givoni, C. Chung, B. Frey
2011Conference on Uncertainty in Artificial Intelligence88 citations
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Response to Comment on "Clustering by Passing Messages Between Data Points"
B. Frey, D. Dueck
2008Science81 citations
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Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism
D. Kemaladewi, E. Maino, Elzbieta Hyatt, Hua-Yun Hou +12 more
2017Nature Medicine80 citations
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Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
Boyko Kakaradov, Hui Y. Xiong, Leo J. Lee, N. Jojic +1 more
2012BMC Bioinformatics68 citations Open access
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Learning Wake-Sleep Recurrent Attention Models
Jimmy Ba, R. Grosse, R. Salakhutdinov, B. Frey
2015Neural Information Processing Systems65 citations
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Fast Exact Inference for Recursive Cardinality Models
Daniel Tarlow, Kevin Swersky, R. Zemel, Ryan P. Adams +1 more
2012Conference on Uncertainty in Artificial Intelligence62 citations
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Semi-Supervised Affinity Propagation with Instance-Level Constraints
Inmar E. Givoni, B. Frey
2009International Conference on Artificial Intelligence and Statistics62 citations
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Solving the Uncapacitated Facility Location Problem Using Message Passing Algorithms
Nevena Lazic, B. Frey, Parham Aarabi
2010International Conference on Artificial Intelligence and Statistics59 citations
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Computer vision for high content screening
O. Kraus, B. Frey
2016Critical reviews in biochemistry and molecular biology52 citations
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COSSMO: predicting competitive alternative splice site selection using deep learning
Hannes Bretschneider, Shreshth Gandhi, A. Deshwar, Khalid Zuberi +1 more
2018bioRxiv51 citations Open access
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Constructing Treatment Portfolios Using Affinity Propagation
D. Dueck, B. Frey, N. Jojic, V. Jojic +4 more
2008Annual International Conference on Research in Computational Molecular Biology51 citations
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Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome
D. Merico, M. Zarrei, G. Costain, L. Ogura +11 more
2015G3: Genes, Genomes, Genetics47 citations Open access
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AVISPA: a web tool for the prediction and analysis of alternative splicing
Yoseph Barash, Jorge Vaquero-Garcia, Juan González-Vallinas, Hui Y. Xiong +3 more
2013Genome Biology45 citations Open access
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Cumulative Distribution Networks and the Derivative-sum-product Algorithm: Models and Inference for Cumulative Distribution Functions on Graphs
Jim C. Huang, B. Frey
2008Journal of machine learning research40 citations
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Information for : “ C 2 H 2 zinc finger proteins greatly expand the human regulatory lexicon ”
H. Najafabadi, S. Mnaimneh, F. Schmitges, Michael Garton +9 more
201439 citations
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Inference of the human polyadenylation code
M. Leung, A. Delong, B. Frey
2017bioRxiv38 citations Open access
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A generalizable pre-clinical research approach for orphan disease therapy
C. Beaulieu, M. Samuels, S. Ekins, C. McMaster +6 more
2012Orphanet Journal of Rare Diseases35 citations Open access
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A Winner-Take-All Method for Training Sparse Convolutional Autoencoders
Alireza Makhzani, B. Frey
2014arXiv.org33 citations
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A graph neural network approach for molecule carcinogenicity prediction
Phil Fradkin, A. Young, Lazar Atanackovic, B. Frey +2 more
2022Bioinform.27 citations Open access
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Network cleanup
Babak Alipanahi, B. Frey
2013Nature Biotechnology26 citations
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HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps
Michael C Dimmick, Leo J. Lee, B. Frey
2020bioRxiv25 citations Open access
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