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References from Representation learning applications in biological sequence analysis. Local targets link to admitted publications; unresolved targets remain external evidence.
Ensembl 2019
2019 · External reference
Deep learning for computational biology
10.15252/msb.20156651 · 2016 · External reference
10.1038/s41588-018-0295-5
10.1038/s41588-018-0295-5 · External reference
Natural language processing
10.1002/aris.1440370103 · 2005 · External reference
10.1073/pnas.1814684116
10.1073/pnas.1814684116 · External reference
10.1109/tpami.2013.50
10.1109/tpami.2013.50 · External reference
10.1101/2020.12.15.422761
10.1101/2020.12.15.422761 · External reference
Embeddings from deep learning transfer GO annotations beyond homology
10.1038/s41598-020-80786-0 · 2021 · External reference
10.1080/00437956.1954.11659520
10.1080/00437956.1954.11659520 · External reference
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2013 · External reference
A neural probabilistic language model
2003 · External reference
10.1145/1390156.1390177
10.1145/1390156.1390177 · 2008 · External reference
10.3115/v1/d14-1162
10.3115/v1/d14-1162 · External reference
10.1162/tacl_a_00051
10.1162/tacl_a_00051 · External reference
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Translation
1955 · External reference
10.1162/neco.1997.9.8.1735
10.1162/neco.1997.9.8.1735 · External reference
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2010 · External reference
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2014 · External reference
10.18653/v1/n18-1202
10.18653/v1/n18-1202 · External reference
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2017 · External reference
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10.18653/v1/d16-1147
10.18653/v1/d16-1147 · External reference
Attention Is All You Need
2017 · External reference
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10.18653/v1/d15-1166
10.18653/v1/d15-1166 · External reference
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10.18653/v1/p18-1031
10.18653/v1/p18-1031 · External reference
10.1609/aaai.v32i1.11996
10.1609/aaai.v32i1.11996 · External reference
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10.1371/journal.pone.0141287
10.1371/journal.pone.0141287 · External reference
HLA class I binding prediction via convolutional neural networks
10.1093/bioinformatics/btx264 · 2017 · External reference
Protein classification using modified n-grams and skip-grams
10.1093/bioinformatics/btx823 · 2018 · External reference
10.1261/rna.069112.118
10.1261/rna.069112.118 · External reference
A k-mer grammar analysis to uncover maize regulatory architecture
10.1186/s12870-019-1693-2 · 2019 · External reference
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)
10.1038/s41598-019-38746-w · 2019 · External reference
MHCSeqNet: a deep neural network model for universal MHC binding prediction
10.1186/s12859-019-2892-4 · 2019 · External reference
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses., PLoS Comput
2019 · External reference
Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics
10.1089/cmb.2018.0174 · 2019 · External reference
Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network
10.1177/1176934318821072 · 2019 · External reference
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences
10.1093/bioinformatics/bty535 · 2019 · External reference
Using word embedding technique to efficiently represent protein sequences for identifying substrate specificities of transporters
10.1016/j.ab.2019.04.011 · 2019 · External reference
Discovering nuclear targeting signal sequence through protein language learning and multivariate analysis
10.1016/j.ab.2019.113565 · 2020 · External reference
Learning a functional grammar of protein domains using natural language word embedding techniques
10.1002/prot.25842 · 2020 · External reference
Its2vec: Fungal Species Identification Using Sequence Embedding and Random Forest Classification
10.1155/2020/2468789 · 2020 · External reference
DNA sequences performs as natural language processing by exploiting deep learning algorithm for the identification of N4-methylcytosine
10.1038/s41598-020-80430-x · 2021 · External reference
Learned protein embeddings for machine learning
2018 · External reference
Prediction of enhancer-promoter interactions via natural language processing
10.1186/s12864-018-4459-6 · 2018 · External reference
IDP-Seq2Seq: Identification of Intrinsically Disordered Regions based on Sequence to Sequence Learning
2020 · External reference
10.1093/bioinformatics/btx234
10.1093/bioinformatics/btx234 · External reference
CircSLNN: Identifying RBP-Binding Sites on circRNAs via Sequence Labeling Neural Networks
10.3389/fgene.2019.01184 · 2019 · External reference
Classifying Promoters by Interpreting the Hidden Information of DNA Sequences via Deep Learning and Combination of Continuous FastText N-Grams
2019 · External reference
10.1016/j.ab.2019.02.017
10.1016/j.ab.2019.02.017 · External reference
TNFPred: identifying tumor necrosis factors using hybrid features based on word embeddings., BMC Med
2020 · External reference
A Computational Framework Based on Ensemble Deep Neural Networks for Essential Genes Identification
2020 · External reference
ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins
10.1093/bioinformatics/btaa580 · 2020 · External reference
10.1126/science.abd7331
10.1126/science.abd7331 · External reference
10.1038/s41592-019-0598-1
10.1038/s41592-019-0598-1 · External reference
UDSMProt: universal deep sequence models for protein classification
10.1093/bioinformatics/btaa003 · 2020 · External reference
USMPep: universal sequence models for major histocompatibility complex binding affinity prediction
10.1186/s12859-020-03631-1 · 2020 · External reference
BindSpace decodes transcription factor binding signals by large-scale sequence embedding
10.1038/s41592-019-0511-y · 2019 · External reference
10.1093/bioinformatics/btaa433
10.1093/bioinformatics/btaa433 · External reference
Modeling aspects of the language of life through transfer-learning protein sequences
10.1186/s12859-019-3220-8 · 2019 · External reference
Sequence-to-function deep learning frameworks for engineered riboregulators
10.1038/s41467-020-18676-2 · 2020 · External reference
Novel transformer networks for improved sequence labeling in genomics
2020 · External reference
Evaluating protein transfer learning with tape
2019 · External reference
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
2020 · External reference
10.1101/2020.07.12.199554
10.1101/2020.07.12.199554 · External reference
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
10.1093/bioinformatics/btab083 · 2021 · External reference
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides
10.1093/bioinformatics/btab133 · 2021 · External reference
A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information
2021 · External reference
10.1101/2021.04.27.441365
10.1101/2021.04.27.441365 · External reference
10.1093/bioinformatics/btaa013
10.1093/bioinformatics/btaa013 · External reference
SDN2GO: An integrated deep learning model for protein function prediction
10.3389/fbioe.2020.00391 · 2020 · External reference
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Netsurfp-2.0: Improved prediction of protein structural features by integrated deep learning
10.1002/prot.25674 · 2019 · External reference
10.1093/bioinformatics/btx431
10.1093/bioinformatics/btx431 · External reference
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function
10.1101/2020.04.07.028373 · 2020 · External reference
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10.1101/2021.02.12.430858
10.1101/2021.02.12.430858 · External reference
10.1101/2020.06.26.174417
10.1101/2020.06.26.174417 · External reference
10.1093/bioinformatics/btv256
10.1093/bioinformatics/btv256 · External reference
10.1021/jm300687e
10.1021/jm300687e · External reference
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10.1093/nar/gkaa1100
10.1093/nar/gkaa1100 · External reference
10.1038/nature12311
10.1038/nature12311 · External reference
10.1016/j.cell.2014.08.009
10.1016/j.cell.2014.08.009 · External reference
Affinity regression predicts the recognition code of nucleic acid–binding proteins
10.1038/nbt.3343 · 2015 · External reference
Inferring rna sequence preferences for poorly studied rna-binding proteins based on co-evolution
10.1186/s12859-018-2091-8 · 2018 · External reference
Sequence-to-function deep learning frameworks for engineered riboregulators
10.1038/s41467-020-18676-2 · 2020 · External reference
A deep learning approach to programmable rna switches
2020 · External reference
10.1016/j.cell.2014.10.002
10.1016/j.cell.2014.10.002 · External reference
10.1016/j.cell.2016.04.059
10.1016/j.cell.2016.04.059 · External reference
10.1038/s41592-019-0598-1
10.1038/s41592-019-0598-1 · External reference
10.1093/bioinformatics/btu739
10.1093/bioinformatics/btu739 · External reference
10.1038/nature17995
10.1038/nature17995 · External reference
Learning mutational semantics
2020 · External reference
10.1128/aem.03006-05
10.1128/aem.03006-05 · External reference
Keggrest: Client-side rest access to kegg
2016 · External reference
American Gut: an Open Platform for Citizen Science Microbiome Research
10.1128/msystems.00031-18 · 2018 · External reference
Characteristics of Sentence Length in Running Text
10.1093/llc/8.1.20 · 1993 · External reference
10.1101/2021.02.17.431338
10.1101/2021.02.17.431338 · External reference
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10.1101/2020.10.09.334243
10.1101/2020.10.09.334243 · External reference
Poincaré maps for analyzing complex hierarchies in single-cell data
10.1038/s41467-020-16822-4 · 2020 · External reference
Evaluating representations for gene ontology terms
2020 · External reference
Evaluation of methods for protein representation learning: a quantitative
2020 · External reference
