Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery

FCNN-based axon segmentation for convection-enhanced delivery optimization

(2019) Marco Vidotto et al.   International Journal of Computer Assisted Radiology and Surgery

A deep learning method to more accurately recall known lysine acetylation sites

(2019) Meiqi Wu et al.   BMC BIOINFORMATICS

Deep learning for liver tumor diagnosis part I: development of a convolutional neural network classifier for multi-phasic MRI

(2019) Charlie A. Hamm et al.   EUROPEAN RADIOLOGY

Over-fitting and Use of Mismatched Cohorts in Deep Learning Models: Preventable Design Limitations

(2018) Srinivas R Mummadi et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

DeepFam: deep learning based alignment-free method for protein family modeling and prediction

(2018) Seokjun Seo et al.   BIOINFORMATICS

BNPMDA: Bipartite Network Projection for MiRNA–Disease Association prediction

(2018) Xing Chen et al.   BIOINFORMATICS

Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks

(2018) Xiaoyong Pan et al.   BMC GENOMICS

Drug and Nondrug Classification Based on Deep Learning with Various Feature Selection Strategies

(2018) Long Yu et al.   Current Bioinformatics

The Advances and Challenges of Deep Learning Application in Biological Big Data Processing

(2018) Li Peng et al.   Current Bioinformatics

Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate

(2018) Chun Yu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Type IV secretion in Gram-negative and Gram-positive bacteria

(2018) Elisabeth Grohmann et al.   MOLECULAR MICROBIOLOGY

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

Deep neural network for traffic sign recognition systems: An analysis of spatial transformers and stochastic optimisation methods

(2018) Álvaro Arcos-García et al.   NEURAL NETWORKS

Facial expression recognition via learning deep sparse autoencoders

(2018) Nianyin Zeng et al.   NEUROCOMPUTING

Integration of deep feature representations and handcrafted features to improve the prediction of N 6 -methyladenosine sites

(2018) Leyi Wei et al.   NEUROCOMPUTING

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Predicting human protein function with multi-task deep neural networks

(2018) Rui Fa et al.   PLoS One

Deep learning in omics: a survey and guideline

(2018) Zhiqiang Zhang et al.   Briefings in Functional Genomics

A Hybrid Deep Learning Model for Predicting Protein Hydroxylation Sites

(2018) Haixia Long et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction

(2018) Xing Chen et al.   PLoS Computational Biology

Development of a Prediction Model for Colorectal Cancer among Patients with Type 2 Diabetes Mellitus Using a Deep Neural Network

(2018) Meng-Hsuen Hsieh et al.   Journal of Clinical Medicine

Bartonella quintana type IV secretion effector BepE ‐induced selective autophagy by conjugation with K63 polyubiquitin chain

(2018) Chunyan Wang et al.   CELLULAR MICROBIOLOGY

Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA

(2018) Quan Zou et al.   RNA

PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method

(2018) Yi Xiong et al.   Frontiers in Microbiology

Effective prediction of bacterial type IV secreted effectors by combined features of both C-termini and N-termini

(2017) Yu Wang et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Bordetella Pertussis virulence factors in the continuing evolution of whooping cough vaccines for improved performance

(2017) Dorji Dorji et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

Ensemble Architecture for Prediction of Enzyme-ligand Binding Residues Using Evolutionary Information

(2017) Priyadarshini P. Pai et al.   Molecular Informatics

Bacterial pathogenesis: Activating Helicobacter effector delivery

(2017) Irene Vacca   NATURE REVIEWS MICROBIOLOGY

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

Effectors from Wheat Rust Fungi Suppress Multiple Plant Defense Responses

(2017) Sowmya R. Ramachandran et al.   PHYTOPATHOLOGY

MultipleLegionella pneumophilaeffector virulence phenotypes revealed through high-throughput analysis of targeted mutant libraries

(2017) Stephanie R. Shames et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction

(2017) Xing Chen et al.   PLoS Computational Biology

Computational prediction of secretion systems and secretomes of Brucella: identification of novel type IV effectors and their interaction with the host

(2016) Jagadesan Sankarasubramanian et al.   Molecular BioSystems

Deep neural network with weight sparsity control and pre-training extracts hierarchical features and enhances classification performance: Evidence from whole-brain resting-state functional connectivity patterns of schizophrenia

(2016) Junghoe Kim et al.   NEUROIMAGE

RaptorX-Property: a web server for protein structure property prediction

(2016) Sheng Wang et al.   NUCLEIC ACIDS RESEARCH

Interaction of Mycobacterium tuberculosis Virulence Factor RipA with Chaperone MoxR1 Is Required for Transport through the TAT Secretion System

(2016) Manish Bhuwan et al.   mBio

Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges

(2016) Humira Sonah et al.   Frontiers in Plant Science

Identification of novel X anthomonas euvesicatoria type III effector proteins by a machine-learning approach

(2015) Doron Teper et al.   MOLECULAR PLANT PATHOLOGY

Secretion systems in Gram-negative bacteria: structural and mechanistic insights

(2015) Tiago R. D. Costa et al.   NATURE REVIEWS MICROBIOLOGY

Inhibition of inflammasome activation by Coxiella burnetii type IV secretion system effector IcaA

(2015) Larissa D. Cunha et al.   Nature Communications

Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi

(2015) Karine de Guillen et al.   PLoS Pathogens

Effector-Mining in the Poplar Rust Fungus Melampsora larici-populina Secretome

(2015) Cécile Lorrain et al.   Frontiers in Plant Science

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

DISOPRED3: precise disordered region predictions with annotated protein-binding activity

(2014) David T. Jones et al.   BIOINFORMATICS

Prediction of bacterial type IV secreted effectors by C-terminal features

(2014) Yejun Wang et al.   BMC GENOMICS

Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles

(2013) Lingyun Zou et al.   BIOINFORMATICS

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Molecular evolution of key genes for type II secretion in Legionella pneumophila

(2011) Joana Costa et al.   ENVIRONMENTAL MICROBIOLOGY

Introduction to machine learning for brain imaging

(2010) Steven Lemm et al.   NEUROIMAGE

What Are Next Generation Innovative Therapeutic Targets? Clues from Genetic, Structural, Physicochemical, and Systems Profiles of Successful Targets

(2009) F. Zhu et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

Genome-Scale Identification of Legionella pneumophila Effectors Using a Machine Learning Approach

(2009) David Burstein et al.   PLoS Pathogens

Predicting RNA-binding sites of proteins using support vector machines and evolutionary information

(2008) Cheng-Wei Cheng et al.   BMC BIOINFORMATICS