Frey, Brendan J

Factor graphs and the sum-product algorithm

Kschischang, F. R., Frey, B. J., & Loeliger, H.-A. (2001) · IEEE Transactions on Information Theory

Bayesian Modeling and Causal InferenceError Correcting Code Techniques

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

Pan, Q., Shai, O., Lee, L. J., Frey, B. J., & Blencowe, B. J. (2008) · Nature Genetics

RNA Research and SplicingGenomics and Phylogenetic Studies

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

Alipanahi, B., Delong, A., Weirauch, M. T., & Frey, B. J. (2015) · Nature Biotechnology

Genomics and Chromatin DynamicsMachine Learning in Bioinformatics

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Adversarial Autoencoders

Makhzani, A., Shlens, J., Jaitly, N., Goodfellow, I., & Frey, B. (2015) · arXiv

Generative Adversarial Networks and Image SynthesisAdversarial Robustness in Machine Learning

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A compendium of RNA-binding motifs for decoding gene regulation

Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature

RNA Research and SplicingRNA and protein synthesis mechanisms

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The "Wake-Sleep" Algorithm for Unsupervised Neural Networks

Hinton, G. E., Dayan, P., Frey, B. J., & Neal, R. M. (1995) · Science

Neural Networks and ApplicationsNeural dynamics and brain function

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The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Barbosa-Morais, N. L., Irimia, M., Pan, Q., Xiong, H. Y., Gueroussov, S., Lee, L. J., Slobodeniuc, V., Kutter, C., Watt, S., Çolak, R., et al. (2012) · Science

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 1,063

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

C Yuen, R. K., Merico, D., Bookman, M., L Howe, J., Thiruvahindrapuram, B., Patel, R. V., Whitney, J., Deflaux, N., Bingham, J., Wang, Z., et al. (2017) · Nature Neuroscience

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

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Widespread intron retention in mammals functionally tunes transcriptomes

Braunschweig, U., Barbosa-Morais, N. L., Pan, Q., Nachman, E. N., Alipanahi, B., Gonatopoulos-Pournatzis, T., Frey, B., Irimia, M., & Blencowe, B. J. (2014) · Genome Research

RNA Research and SplicingCancer-related molecular mechanisms research

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

Kislinger, T., Cox, B., Kannan, A., Chung, C., Hu, P., Ignatchenko, A., Scott, M. S., Gramolini, A. O., Morris, Q., Hallett, M. T., et al. (2006) · Cell

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

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Deep learning of the tissue-regulated splicing code

Leung, M. K. K., Xiong, H. Y., Lee, L. J., & Frey, B. J. (2014) · Bioinformatics

RNA Research and SplicingGenomics and Phylogenetic Studies

Cited by 459

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

Najafabadi, H. S., Mnaimneh, S., Schmitges, F. W., Garton, M., Lam, K. N., Yang, A., Albu, M., Weirauch, M. T., Radovani, E., Kim, P. M., et al. (2015) · Nature Biotechnology

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

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

Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A. L., Mohammad, N., Babak, T., Siu, H., Hughes, T. R., Morris, Q. D., et al. (2004) · Molecular Cell

RNA Research and SplicingCancer-related molecular mechanisms research

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Genome-wide characteristics of de novo mutations in autism

Yuen, R. K., Merico, D., Cao, H., Pellecchia, G., Alipanahi, B., Thiruvahindrapuram, B., Tong, X., Sun, Y., Cao, D., Zhang, T., et al. (2016) · npj Genomic Medicine

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

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

Uddin, M., Tammimies, K., Pellecchia, G., Alipanahi, B., Hu, P., Wang, Z., Pinto, D., Lau, L., Nalpathamkalam, T., Marshall, C. R., et al. (2014) · Nature Genetics

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

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Functional coordination of alternative splicing in the mammalian central nervous system

Fagnani, M., Barash, Y., Ip, J. Y., Misquitta, C., Pan, Q., Saltzman, A. L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., et al. (2007) · Genome Biology

RNA Research and SplicingRNA regulation and disease

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Inference of the human polyadenylation code

Leung, M. K. K., Delong, A., & Frey, B. J. (2018) · Bioinformatics

RNA Research and SplicingGenomics and Phylogenetic Studies

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Orthrus: toward evolutionary and functional RNA foundation models

Fradkin, P., Shi, R. “., Dalal, T., Isaev, K., Frey, B. J., Lee, L. J., Morris, Q., & Wang, B. (2026) · Nature Methods

Genomics and Phylogenetic StudiesRNA Research and Splicing

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Orthrus: Towards Evolutionary and Functional RNA Foundation Models

Fradkin, P., Shi, R., Dalal, T., Isaev, K., Frey, B. J., Lee, L. J., Morris, Q., & Wang, B. (2024) · Nature Methods

Genomics and Phylogenetic StudiesRNA Research and Splicing

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