T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model

Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

(2021) Alexander Rives et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping bacterial effector arsenals: in vivo and in silico approaches to defining the protein features dictating effector secretion by bacteria

(2020) Yi Wei Lee et al.   CURRENT OPINION IN MICROBIOLOGY

T4SE-XGB: Interpretable Sequence-Based Prediction of Type IV Secreted Effectors Using eXtreme Gradient Boosting Algorithm

(2020) Tianhang Chen et al.   Frontiers in Microbiology

Protein Function Prediction: From Traditional Classifier to Deep Learning

(2019) Zhibin Lv et al.   PROTEOMICS

Prediction of T4SS Effector Proteins for Anaplasma phagocytophilum Using OPT4e, A New Software Tool

(2019) Zhila Esna Ashari et al.   Frontiers in Microbiology

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

(2019) Jiajun Hong et al.   BRIEFINGS IN BIOINFORMATICS

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

(2018) Elisabeth Grohmann et al.   MOLECULAR MICROBIOLOGY

A deep learning framework for sequence-based bacteria type IV secreted effectors prediction

(2018) Li Xue et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

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

Autophagy Evasion and Endoplasmic Reticulum Subversion: The Yin and Yang ofLegionellaIntracellular Infection

(2016) Racquel Kim Sherwood et al.   Annual Review of Microbiology

Subversion of Retrograde Trafficking by Translocated Pathogen Effectors

(2016) Nicolas Personnic et al.   TRENDS IN MICROBIOLOGY

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

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

Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context

(2013) Damien F. Meyer et al.   NUCLEIC ACIDS RESEARCH

Brucella Modulates Secretory Trafficking via Multiple Type IV Secretion Effector Proteins

(2013) Sebenzile Myeni et al.   PLoS Pathogens

SecReT4: a web-based bacterial type IV secretion system resource

(2012) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

Dot/Icm Type IVB Secretion System Requirements for Coxiella burnetii Growth in Human Macrophages

(2011) P. A. Beare et al.   mBio

Microreview: Type IV secretion systems: versatility and diversity in function

(2010) Karin Wallden et al.   CELLULAR MICROBIOLOGY

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

Biological Diversity of Prokaryotic Type IV Secretion Systems

(2009) C. E. Alvarez-Martinez et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A Legionella pneumophila Effector Protein Encoded in a Region of Genomic Plasticity Binds to Dot/Icm-Modified Vacuoles

(2009) Shira Ninio et al.   PLoS Pathogens

The CGView Server: a comparative genomics tool for circular genomes

(2008) J. R. Grant et al.   NUCLEIC ACIDS RESEARCH