Deepro-Glu: combination of convolutional neural network and Bi-LSTM models using ProtBert and handcrafted features to identify lysine glutarylation sites

Adapt-Kcr: a novel deep learning framework for accurate prediction of lysine crotonylation sites based on learning embedding features and attention architecture

(2022) Zutan Li et al.   BRIEFINGS IN BIOINFORMATICS

An analysis of protein language model embeddings for fold prediction

(2022) Amelia Villegas-Morcillo et al.   BRIEFINGS IN BIOINFORMATICS

PepNN: a deep attention model for the identification of peptide binding sites

(2022) Osama Abdin et al.   Communications Biology

ACP-2DCNN: Deep learning-based model for improving prediction of anticancer peptides using two-dimensional convolutional neural network

(2022) Ali Ghulam et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Deep Neural Network Framework Based on Word Embedding for Protein Glutarylation Sites Prediction

(2022) Chuan-Ming Liu et al.   Life-Basel

Post-translational modifications: Regulators of neurodegenerative proteinopathies

(2021) Rohan Gupta et al.   AGEING RESEARCH REVIEWS

PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein–protein interaction information

(2021) Hangyuan Yang et al.   BIOINFORMATICS

STALLION: a stacking-based ensemble learning framework for prokaryotic lysine acetylation site prediction

(2021) Shaherin Basith et al.   BRIEFINGS IN BIOINFORMATICS

iAnt: Combination of Convolutional Neural Network and Random Forest Models using PSSM and BERT Features to Identify Antioxidant Proteins

(2021) Hoang V. Tran et al.   Current Bioinformatics

MDCAN-Lys: A Model for Predicting Succinylation Sites Based on Multilane Dense Convolutional Attention Network

(2021) Huiqing Wang et al.   Biomolecules

predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

(2021) Md Khaled Ben Islam et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation

(2020) Davide Chicco et al.   BMC GENOMICS

Fundamentals of Recurrent Neural Network (RNN) and Long Short-Term Memory (LSTM) network

(2020) Alex Sherstinsky   PHYSICA D-NONLINEAR PHENOMENA

Computational identification of lysine glutarylation sites using positive-unlabeled learning

(2020) Zhe Ju et al.   CURRENT GENOMICS

DeepPred-SubMito: A Novel Submitochondrial Localization Predictor Based on Multi-Channel Convolutional Neural Network and Dataset Balancing Treatment

(2020) Xiao Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

iGlu_AdaBoost: Identification of Lysine Glutarylation Using the AdaBoost Classifier

(2020) Lijun Dou et al.   JOURNAL OF PROTEOME RESEARCH

Accurately Predicting Glutarylation Sites Using Sequential Bi-Peptide-Based Evolutionary Features

(2020) Md. Easin Arafat et al.   Genes

SSKM_Succ: A Novel Succinylation Sites Prediction Method Incorporating K-Means Clustering With a New Semi-Supervised Learning Algorithm

(2020) Qiao Ning et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

mlDEEPre: Multi-Functional Enzyme Function Prediction With Hierarchical Multi-Label Deep Learning

(2019) Zhenzhen Zou et al.   Frontiers in Genetics

Prediction of lysine formylation sites using the composition of k-spaced amino acid pairs via Chou's 5-steps rule and general pseudo components

(2019) Zhe Ju et al.   GENOMICS

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

(2019) Martin Steinegger et al.   NATURE METHODS

An attention-gated convolutional neural network for sentence classification

(2019) Yang Liu et al.   Intelligent Data Analysis

Modeling aspects of the language of life through transfer-learning protein sequences

(2019) Michael Heinzinger et al.   BMC BIOINFORMATICS

Proteomic approaches beyond expression profiling and PTM analysis

(2018) Jiaqi Fu et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Prediction of lysine glutarylation sites by maximum relevance minimum redundancy feature selection

(2018) Zhe Ju et al.   ANALYTICAL BIOCHEMISTRY

Object-Part Attention Model for Fine-Grained Image Classification

(2018) Yuxin Peng et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

iGlu-Lys: A Predictor for Lysine Glutarylation through Amino Acid Pair Order Features

(2018) Yan Xu et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Recent advances in convolutional neural networks

(2018) Jiuxiang Gu et al.   PATTERN RECOGNITION

Identification of the YEATS domain of GAS41 as a pH-dependent reader of histone succinylation

(2018) Yi Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework

(2018) Yanju Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Lysine benzoylation is a histone mark regulated by SIRT2

(2018) He Huang et al.   Nature Communications

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

iKcr-PseEns: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier

(2017) Wang-Ren Qiu et al.   GENOMICS

CIPPN: computational identification of protein pupylation sites by using neural network

(2017) Wenzheng Bao et al.   Oncotarget

Proteome-wide Lysine Glutarylation Profiling of the Mycobacterium tuberculosis H37Rv

(2016) Longxiang Xie et al.   JOURNAL OF PROTEOME RESEARCH

Harnessing Computational Biology for Exact Linear B-Cell Epitope Prediction: A Novel Amino Acid Composition-Based Feature Descriptor

(2015) Vijayakumar Saravanan et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Lysine Glutarylation Is a Protein Posttranslational Modification Regulated by SIRT5

(2014) Minjia Tan et al.   Cell Metabolism