Brendan J. Frey - Publications

1997 Computer Science University of Toronto, Toronto, ON, Canada 

74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Merico D, Spickett C, O'Hara M, Kakaradov B, Deshwar AG, Fradkin P, Gandhi S, Gao J, Grant S, Kron K, Schmitges FW, Shalev Z, Sun M, Verby M, Cahill M, ... ... Frey BJ, et al. ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping. Npj Genomic Medicine. 5: 16. PMID 33579975 DOI: 10.1038/s41525-020-0123-6  0.44
2020 Merico D, Spickett C, O'Hara M, Kakaradov B, Deshwar AG, Fradkin P, Gandhi S, Gao J, Grant S, Kron K, Schmitges FW, Shalev Z, Sun M, Verby M, Cahill M, ... ... Frey BJ, et al. variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping. Npj Genomic Medicine. 5: 16. PMID 32284880 DOI: 10.1038/S41525-020-0123-6  0.44
2018 Bretschneider H, Gandhi S, Deshwar AG, Zuberi K, Frey BJ. COSSMO: predicting competitive alternative splice site selection using deep learning. Bioinformatics (Oxford, England). 34: i429-i437. PMID 29949959 DOI: 10.1093/bioinformatics/bty244  0.44
2017 Kemaladewi DU, Maino E, Hyatt E, Hou H, Ding M, Place KM, Zhu X, Bassi P, Baghestani Z, Deshwar AG, Merico D, Xiong HY, Frey BJ, Wilson MD, Ivakine EA, et al. Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism. Nature Medicine. PMID 28714989 DOI: 10.1038/Nm.4367  0.44
2017 Kraus OZ, Grys BT, Ba J, Chong Y, Frey BJ, Boone C, Andrews BJ. Automated analysis of high-content microscopy data with deep learning. Molecular Systems Biology. 13: 924. PMID 28420678 DOI: 10.15252/Msb.20177551  0.76
2016 Kraus OZ, Ba JL, Frey BJ. Classifying and segmenting microscopy images with deep multiple instance learning. Bioinformatics (Oxford, England). 32: i52-i59. PMID 27307644 DOI: 10.1093/Bioinformatics/Btw252  0.76
2016 Kraus OZ, Frey BJ. Computer vision for high content screening. Critical Reviews in Biochemistry and Molecular Biology. 51: 102-9. PMID 26806341 DOI: 10.3109/10409238.2015.1135868  0.76
2015 Merico D, Zarrei M, Costain G, Ogura L, Alipanahi B, Gazzellone MJ, Butcher NJ, Thiruvahindrapuram B, Nalpathamkalam T, Chow EW, Andrade DM, Frey BJ, Marshall CR, Scherer SW, Bassett AS. Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome. G3 (Bethesda, Md.). 5: 2453-61. PMID 26384369 DOI: 10.1534/G3.115.021345  1
2015 Alipanahi B, Delong A, Weirauch MT, Frey BJ. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology. 33: 831-8. PMID 26213851 DOI: 10.1038/Nbt.3300  1
2015 Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nature Biotechnology. 33: 555-62. PMID 25690854 DOI: 10.1038/Nbt.3128  1
2015 Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, ... ... Frey BJ, et al. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science (New York, N.Y.). 347: 1254806. PMID 25525159 DOI: 10.1126/Science.1254806  1
2014 Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, Frey B, Irimia M, Blencowe BJ. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Research. 24: 1774-86. PMID 25258385 DOI: 10.1101/Gr.177790.114  1
2014 Uddin M, Tammimies K, Pellecchia G, Alipanahi B, Hu P, Wang Z, Pinto D, Lau L, Nalpathamkalam T, Marshall CR, Blencowe BJ, Frey BJ, Merico D, Yuen RK, Scherer SW. Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. Nature Genetics. 46: 742-7. PMID 24859339 DOI: 10.1038/Ng.2980  1
2013 Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, ... ... Frey BJ, et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 499: 172-7. PMID 23846655 DOI: 10.1038/Nature12311  1
2013 Han H, Irimia M, Ross PJ, Sung HK, Alipanahi B, David L, Golipour A, Gabut M, Michael IP, Nachman EN, Wang E, Trcka D, Thompson T, O'Hanlon D, Slobodeniuc V, ... ... Frey BJ, et al. MBNL proteins repress ES-cell-specific alternative splicing and reprogramming. Nature. 498: 241-5. PMID 23739326 DOI: 10.1038/Nature12270  1
2013 McDonell LM, Mirzaa GM, Alcantara D, Schwartzentruber J, Carter MT, Lee LJ, Clericuzio CL, Graham JM, Morris-Rosendahl DJ, Polster T, Acsadi G, Townshend S, Williams S, Halbert A, Isidor B, ... ... Frey BJ, et al. Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly-capillary malformation syndrome. Nature Genetics. 45: 556-62. PMID 23542699 DOI: 10.1038/Ng.2602  1
2013 Chua JC, Givoni IE, Adams RP, Frey BJ. Bayesian painting by numbers: Flexible priors for colour-invariant object recognition Studies in Computational Intelligence. 411: 89-117. DOI: 10.1007/978-3-642-28661-2-4  1
2012 Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, ... Frey BJ, et al. The evolutionary landscape of alternative splicing in vertebrate species. Science (New York, N.Y.). 338: 1587-93. PMID 23258890 DOI: 10.1126/Science.1230612  1
2012 Beaulieu CL, Samuels ME, Ekins S, McMaster CR, Edwards AM, Krainer AR, Hicks GG, Frey BJ, Boycott KM, Mackenzie AE. A generalizable pre-clinical research approach for orphan disease therapy. Orphanet Journal of Rare Diseases. 7: 39. PMID 22704758 DOI: 10.1186/1750-1172-7-39  1
2012 Kakaradov B, Xiong HY, Lee LJ, Jojic N, Frey BJ. Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. Bmc Bioinformatics. 13: S11. PMID 22537040 DOI: 10.1186/1471-2105-13-S6-S11  1
2012 Chua J, Givoni I, Adams R, Frey B. Learning structural element patch models with hierarchical palettes Proceedings of the Ieee Computer Society Conference On Computer Vision and Pattern Recognition. 2416-2423. DOI: 10.1109/CVPR.2012.6247955  1
2011 Lahiry P, Lee LJ, Frey BJ, Rupar CA, Siu VM, Blencowe BJ, Hegele RA. Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing. Plos One. 6: e25400. PMID 21980446 DOI: 10.1371/Journal.Pone.0025400  1
2011 Li PS, Givoni IE, Frey BJ. Learning better image representations using 'flobject analysis' Proceedings of the Ieee Computer Society Conference On Computer Vision and Pattern Recognition. 2721-2728. DOI: 10.1109/CVPR.2011.5995649  1
2010 Barash Y, Blencowe BJ, Frey BJ. Model-based detection of alternative splicing signals. Bioinformatics (Oxford, England). 26: i325-33. PMID 20529924 DOI: 10.1093/Bioinformatics/Btq200  1
2010 Barash Y, Calarco JA, Gao W, Pan Q, Wang X, Shai O, Blencowe BJ, Frey BJ. Deciphering the splicing code. Nature. 465: 53-9. PMID 20445623 DOI: 10.1038/Nature09000  1
2010 Vizeacoumar FJ, van Dyk N, S Vizeacoumar F, Cheung V, Li J, Sydorskyy Y, Case N, Li Z, Datti A, Nislow C, Raught B, Zhang Z, Frey B, Bloom K, Boone C, et al. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. The Journal of Cell Biology. 188: 69-81. PMID 20065090 DOI: 10.1083/Jcb.200909013  1
2009 Givoni IE, Frey BJ. A binary variable model for affinity propagation. Neural Computation. 21: 1589-600. PMID 19191593 DOI: 10.1162/Neco.2009.05-08-785  1
2009 Draper SC, Kschischang FR, Frey B. Rateless coding for arbitrary channel mixtures with decoder channel state information Ieee Transactions On Information Theory. 55: 4119-4133. DOI: 10.1109/Tit.2009.2025577  1
2009 Lazic N, Givoni I, Frey B, Aarabi P. FLoSS: Facility location for subspace segmentation Proceedings of the Ieee International Conference On Computer Vision. 825-832. DOI: 10.1109/ICCV.2009.5459302  1
2009 Jojic N, Perina A, Cristani M, Murino V, Frey B. Stel component analysis: Modeling spatial correlations in image class structure 2009 Ieee Computer Society Conference On Computer Vision and Pattern Recognition Workshops, Cvpr Workshops 2009. 2044-2051. DOI: 10.1109/CVPRW.2009.5206581  1
2008 Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics. 40: 1413-5. PMID 18978789 DOI: 10.1038/Ng.259  1
2008 Aznarez I, Barash Y, Shai O, He D, Zielenski J, Tsui LC, Parkinson J, Frey BJ, Rommens JM, Blencowe BJ. 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 Research. 18: 1247-58. PMID 18456862 DOI: 10.1101/Gr.073155.107  1
2008 Huang JC, Frey BJ, Morris QD. Comparing sequence and expression for predicting microRNA targets using GenMiR3. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 52-63. PMID 18229676 DOI: 10.1142/9789812776136_0007  1
2008 Gramolini AO, Kislinger T, Alikhani-Koopaei R, Fong V, Thompson NJ, Isserlin R, Sharma P, Oudit GY, Trivieri MG, Fagan A, Kannan A, Higgins DG, Huedig H, Hess G, Arab S, ... ... Frey B, et al. Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses. Molecular & Cellular Proteomics : McP. 7: 519-33. PMID 18056057 DOI: 10.1074/Mcp.M700245-Mcp200  1
2008 Kannan A, Jojic N, Frey BJ. Fast transformation-invariant component analysis International Journal of Computer Vision. 77: 87-101. DOI: 10.1007/S11263-007-0094-4  1
2008 Cheung V, Frey BJ, Jojic N. Video epitomes International Journal of Computer Vision. 76: 141-152. DOI: 10.1007/S11263-006-0001-4  1
2008 Dueck D, Frey BJ, Jojic N, Jojic V, Giaever G, Emili A, Musso G, Hegele R. Constructing treatment portfolios using affinity propagation Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 360-371. DOI: 10.1007/978-3-540-78839-3_31  1
2007 Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL, Hughes TR, Blencowe BJ, Frey BJ, Morris QD. Using expression profiling data to identify human microRNA targets. Nature Methods. 4: 1045-9. PMID 18026111 DOI: 10.1038/Nmeth1130  1
2007 Huang JC, Morris QD, Frey BJ. Bayesian inference of MicroRNA targets from sequence and expression data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 550-63. PMID 17683260 DOI: 10.1089/Cmb.2007.R002  1
2007 Fagnani M, Barash Y, Ip JY, Misquitta C, Pan Q, Saltzman AL, Shai O, Lee L, Rozenhek A, Mohammad N, Willaime-Morawek S, Babak T, Zhang W, Hughes TR, van der Kooy D, ... Frey BJ, et al. Functional coordination of alternative splicing in the mammalian central nervous system. Genome Biology. 8: R108. PMID 17565696 DOI: 10.1186/Gb-2007-8-6-R108  1
2007 Cox B, Kislinger T, Wigle DA, Kannan A, Brown K, Okubo T, Hogan B, Jurisica I, Frey B, Rossant J, Emili A. Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes. Molecular Systems Biology. 3: 109. PMID 17486137 DOI: 10.1038/Msb4100151  1
2007 Rennie SJ, Aarabi P, Frey BJ. Variational probabilistic speech separation using microphone arrays Ieee Transactions On Audio, Speech and Language Processing. 15: 135-149. DOI: 10.1109/Tasl.2006.876865  1
2006 Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, Porter J, Chua G, Sopko R, Brost RL, Ho CH, Wang J, Ketela T, Brenner C, Brill JA, Fernandez GE, ... ... Frey BJ, et al. Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell. 126: 611-25. PMID 16901791 DOI: 10.1016/J.Cell.2006.06.040  1
2006 Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, Hughes TR. Identifying transcription factor functions and targets by phenotypic activation. Proceedings of the National Academy of Sciences of the United States of America. 103: 12045-50. PMID 16880382 DOI: 10.1073/Pnas.0605140103  1
2006 Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey B, Emili A. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell. 125: 173-86. PMID 16615898 DOI: 10.1016/J.Cell.2006.01.044  1
2006 Frey BJ, Morris QD, Hughes TR. GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 200-14. PMID 16597235 DOI: 10.1089/Cmb.2006.13.200  1
2006 Pan Q, Saltzman AL, Kim YK, Misquitta C, Shai O, Maquat LE, Frey BJ, Blencowe BJ. Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes & Development. 20: 153-8. PMID 16418482 DOI: 10.1101/Gad.1382806  1
2006 Shai O, Morris QD, Blencowe BJ, Frey BJ. Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinformatics (Oxford, England). 22: 606-13. PMID 16403798 DOI: 10.1093/Bioinformatics/Btk028  1
2006 Ying L, Liang ZP, Munson DC, Koetter R, Frey BJ. Unwrapping of MR phase images using a Markov random field model. Ieee Transactions On Medical Imaging. 25: 128-36. PMID 16398421 DOI: 10.1109/Tmi.2005.861021  1
2006 Kannan A, Frey B, Jojic N. A generative model of dense optical flow in layers Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3667: 104-114. DOI: 10.1007/11676959_9  1
2005 Frey BJ, Jojic N. A comparison of algorithms for inference and learning in probabilistic graphical models. Ieee Transactions On Pattern Analysis and Machine Intelligence. 27: 1392-416. PMID 16173184 DOI: 10.1109/Tpami.2005.169  1
2005 Frey BJ, Mohammad N, Morris QD, Zhang W, Robinson MD, Mnaimneh S, Chang R, Pan Q, Sat E, Rossant J, Bruneau BG, Aubin JE, Blencowe BJ, Hughes TR. Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs. Nature Genetics. 37: 991-6. PMID 16127451 DOI: 10.1038/Ng1630  1
2005 Huang JC, Morris QD, Hughes TR, Frey BJ. GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. Bioinformatics (Oxford, England). 21: i222-31. PMID 15961461 DOI: 10.1093/Bioinformatics/Bti1045  1
2005 Dueck D, Morris QD, Frey BJ. Multi-way clustering of microarray data using probabilistic sparse matrix factorization. Bioinformatics (Oxford, England). 21: i144-51. PMID 15961451 DOI: 10.1093/Bioinformatics/Bti1041  1
2005 Frey BJ, Morris QD, Zhang W, Mohammad N, Hughes TR. Genrate: a generative model that finds and scores new genes and exons in genomic microarray data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 495-506. PMID 15759654  1
2005 Pan Q, Bakowski MA, Morris Q, Zhang W, Frey BJ, Hughes TR, Blencowe BJ. Alternative splicing of conserved exons is frequently species-specific in human and mouse. Trends in Genetics : Tig. 21: 73-7. PMID 15661351 DOI: 10.1016/J.Tig.2004.12.004  1
2005 Achan K, Roweis S, Hertzmann A, Frey B. A segment-based probabilistic generative model of speech Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. V221-V224. DOI: 10.1109/ICASSP.2005.1416280  1
2004 Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Molecular Cell. 16: 929-41. PMID 15610736 DOI: 10.1016/J.Molcel.2004.12.004  1
2004 Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, ... ... Frey BJ, et al. The functional landscape of mouse gene expression. Journal of Biology. 3: 21. PMID 15588312 DOI: 10.1186/Jbiol16  1
2004 Draper SC, Frey BJ, Kschischang FR. Efficient variable length channel coding for unknown DMCs Ieee International Symposium On Information Theory - Proceedings. 377.  1
2003 Frey BJ, Jojic N. Transformation-invariant clustering using the EM algorithm Ieee Transactions On Pattern Analysis and Machine Intelligence. 25: 1-17. DOI: 10.1109/Tpami.2003.1159942  1
2003 Rennie S, Aarabi P, Kristjansson T, Frey BJ, Achan K. Robust variational speech separation using fewer microphones than speakers Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. 1: 88-91. DOI: 10.1109/ICME.2003.1221723  1
2003 Ying L, Munson DC, Koetter R, Frey BJ. Multibaseline insar terrain elevation estimation: A dynamic programming approach Ieee International Conference On Image Processing. 3: 157-160. DOI: 10.1021/Bm025676W  1
2002 Ying L, Frey BJ, Koetter R, Munson DC. An iterative dynamic programming approach to 2-D phase unwrapping International Geoscience and Remote Sensing Symposium (Igarss). 1: 469-471.  1
2001 Frey BJ, Koetter R, Forney J, Kschischang FR, McEliece RJ, Spielman DA. Introduction to the special issue on codes on graphs and iterative algorithms Ieee Transactions On Information Theory. 47: 493-497. DOI: 10.1109/Tit.2001.910571  1
2001 Frey BJ, Koetter R, Vardy A. Signal-space characterization of iterative decoding Ieee Transactions On Information Theory. 47: 766-781. DOI: 10.1109/18.910587  1
2001 Kschischang FR, Frey BJ, Loeliger HA. Factor graphs and the sum-product algorithm Ieee Transactions On Information Theory. 47: 498-519. DOI: 10.1109/18.910572  1
2000 Frey BJ, Jojic N. Transformation-invariant filtering using expectation maximization Ieee 2000 Adaptive Systems For Signal Processing, Communications, and Control Symposium, as-Spcc 2000. 19-24. DOI: 10.1109/ASSPCC.2000.882440  1
1999 Frey BJ, Hinton GE. Variational learning in nonlinear gaussian belief networks. Neural Computation. 11: 193-213. PMID 9950729 DOI: 10.1162/089976699300016872  1
1998 Kschischang FR, Frey BJ. Iterative decoding of compound codes by probability propagation in graphical models Ieee Journal On Selected Areas in Communications. 16: 219-230. DOI: 10.1109/49.661110  1
1998 Frey BJ, Kschischang FR. Early detection and trellis splicing: Reduced-complexity iterative decoding Ieee Journal On Selected Areas in Communications. 16: 153-159. DOI: 10.1109/49.661104  1
1998 Naphade MR, Kristjansson T, Frey B, Huang TS. Probabilistic multimedia objects (multijects): a novel approach to video indexing and retrieval in multimedia systems Ieee International Conference On Image Processing. 3: 536-540.  1
1997 Frey BJ, Hinton GE. Efficient Stochastic Source Coding and an Application to a Bayesian Network Source Model Computer Journal. 40: x9-165. DOI: 10.1093/Comjnl/40.2_And_3.157  1
1995 Hinton GE, Dayan P, Frey BJ, Neal RM. The "wake-sleep" algorithm for unsupervised neural networks. Science (New York, N.Y.). 268: 1158-61. PMID 7761831 DOI: 10.1126/Science.7761831  1
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