DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
暂无分享,去创建一个
Maxat Kulmanov | Robert Hoehndorf | Mohammed Asif Khan | R. Hoehndorf | Maxat Kulmanov | Mohammed Asif Khan
[1] John D. Osborne,et al. Annotating the human genome with Disease , 2009 .
[2] O. Troyanskaya,et al. Predicting effects of noncoding variants with deep learning–based sequence model , 2015, Nature Methods.
[3] Davide Heller,et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences , 2015, Nucleic Acids Res..
[4] Krzysztof J. Cios,et al. Protein annotation from protein interaction networks and Gene Ontology , 2011, J. Biomed. Informatics.
[5] Predrag Radivojac,et al. Information-theoretic evaluation of predicted ontological annotations , 2013, Bioinform..
[6] B. Frey,et al. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning , 2015, Nature Biotechnology.
[7] Jingyu Hou. Protein Function Prediction from Functional Connectivity , 2017 .
[8] Silvio C. E. Tosatto,et al. InterPro in 2017—beyond protein family and domain annotations , 2016, Nucleic Acids Res..
[9] Adam P. Rosebrock,et al. A global genetic interaction network maps a wiring diagram of cellular function , 2016, Science.
[10] David A. Lee,et al. Functional classification of CATH superfamilies: a domain-based approach for protein function annotation , 2015, Bioinform..
[11] Q JiangJonathan,et al. Predicting Protein Function by Multi-Label Correlated Semi-Supervised Learning , 2012 .
[12] Michael J. E. Sternberg,et al. CombFunc: predicting protein function using heterogeneous data sources , 2012, Nucleic Acids Res..
[13] Geoffrey E. Hinton,et al. Learning distributed representations of concepts. , 1989 .
[14] W. Kibbe,et al. Annotating the human genome with Disease Ontology , 2009, BMC Genomics.
[15] N. Blackstone,et al. Molecular Biology of the Cell.Fourth Edition.ByBruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and, Peter Walter.New York: Garland Science.$102.00. xxxiv + 1463 p; ill.; glossary (G:1–G:36); index (I:1–I:49); tables (T:1). ISBN: 0–8153–3218–1. [CD‐ROM included.] 2002. , 2003 .
[16] Philip Resnik,et al. Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language , 1999, J. Artif. Intell. Res..
[17] Yoshua Bengio,et al. Understanding the difficulty of training deep feedforward neural networks , 2010, AISTATS.
[18] Gultekin Özsoyoglu,et al. Protein Function Prediction Based on Patterns in Biological Networks , 2008, RECOMB.
[19] Karin M. Verspoor,et al. Roles for text mining in protein function prediction. , 2014, Methods in molecular biology.
[20] R. Sharan,et al. Network-based prediction of protein function , 2007, Molecular systems biology.
[21] Dusanka Janezic,et al. Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison , 2013, PLoS Comput. Biol..
[22] Anna Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP) — round x , 2014, Proteins.
[23] Yuan Yu,et al. TensorFlow: A system for large-scale machine learning , 2016, OSDI.
[24] Michael I. Jordan,et al. Genome-scale phylogenetic function annotation of large and diverse protein families. , 2011, Genome research.
[25] Suzanna Lewis,et al. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium , 2011, Briefings Bioinform..
[26] Weidong Tian,et al. GoFDR: A sequence alignment based method for predicting protein functions. , 2016, Methods.
[27] Jingyu Hou,et al. New Approaches of Protein Function Prediction from Protein Interaction Networks , 2017 .
[28] Jason Weston,et al. Natural Language Processing (Almost) from Scratch , 2011, J. Mach. Learn. Res..
[29] Yoshua Bengio,et al. Convolutional networks for images, speech, and time series , 1998 .
[30] Akira R. Kinjo,et al. Neuro-symbolic representation learning on biological knowledge graphs , 2016, Bioinform..
[31] Daniel W. A. Buchan,et al. A large-scale evaluation of computational protein function prediction , 2013, Nature Methods.
[32] Paul N. Schofield,et al. The anatomy of phenotype ontologies: principles, properties and applications , 2017, Briefings Bioinform..
[33] Yoshua Bengio,et al. A Neural Probabilistic Language Model , 2003, J. Mach. Learn. Res..
[34] Jonathan Qiang Jiang,et al. Predicting Protein Function by Multi-Label Correlated Semi-Supervised Learning , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[35] Zhen Li,et al. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model , 2016, bioRxiv.
[36] Mariano Sigman,et al. The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers , 2017, PLoS Comput. Biol..
[37] Hannah Currant,et al. FFPred 3: feature-based function prediction for all Gene Ontology domains , 2016, Scientific Reports.
[38] Asa Ben-Hur,et al. Hierarchical Classification of Gene Ontology Terms Using the Gostruct Method , 2010, J. Bioinform. Comput. Biol..
[39] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[40] I. Xenarios,et al. UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. , 2016, Methods in molecular biology.
[41] Davide Heller,et al. STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..