An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features

Gene essentiality prediction based on fractal features and machine learning

(2017) Yongming Yu et al.   Molecular BioSystems

Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments

(2016) Tong Ding et al.   PLoS One

Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy

(2016) Osher Cohen et al.   PLoS One

Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea

(2015) Ana Laura Grazziotin et al.   FEBS Journal

Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions

(2015) Abhishek Subramanian et al.   GENOMICS

Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media

(2015) Oren Ish-Am et al.   PLoS One

Predicting bacterial essential genes using only sequence composition information

(2014) L.W. Ning et al.   GENETICS AND MOLECULAR RESEARCH

Predicting essential genes in prokaryotic genomes using a linear method: ZUPLS

(2014) Kai Song et al.   Integrative Biology

Antibiotic-free segregational plasmid stabilization in Escherichia coli owing to the knockout of triosephosphate isomerase (tpiA)

(2014) Ram Velur Selvamani et al.   Microbial Cell Factories

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

A new computational strategy for predicting essential genes

(2013) Jian Cheng et al.   BMC GENOMICS

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements: Table 1.

(2013) Hao Luo et al.   NUCLEIC ACIDS RESEARCH

F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks

(2012) Abdelhalim Larhlimi et al.   BMC BIOINFORMATICS

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Essential genes as antimicrobial targets and cornerstones of synthetic biology

(2012) Mario Juhas et al.   TRENDS IN BIOTECHNOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Systems-biology approaches for predicting genomic evolution

(2011) Balázs Papp et al.   NATURE REVIEWS GENETICS

Essence of life: essential genes of minimal genomes

(2011) Mario Juhas et al.   TRENDS IN CELL BIOLOGY

Identifying essential genes in bacterial metabolic networks with machine learning methods

(2010) Kitiporn Plaimas et al.   BMC Systems Biology

Robust weighted kernel logistic regression in imbalanced and rare events data

(2010) Maher Maalouf et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

It's the machine that matters: Predicting gene function and phenotype from protein networks

(2010) Peggy I. Wang et al.   Journal of Proteomics

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Investigating the predictability of essential genes across distantly related organisms using an integrative approach

(2010) Jingyuan Deng et al.   NUCLEIC ACIDS RESEARCH

How to identify essential genes from molecular networks?

(2009) Gabriel del Rio et al.   BMC Systems Biology

Bacterial genomic G+C composition-eliciting environmental adaptation

(2009) Scott Mann et al.   GENOMICS

Predicting essential genes based on network and sequence analysis

(2009) Yih-Chii Hwang et al.   Molecular BioSystems

Update on the Keio collection of Escherichia coli single-gene deletion mutants

(2009) Natsuko Yamamoto et al.   Molecular Systems Biology

Removal of a ribosome small subunit-dependent GTPase confers salt resistance on Escherichia coli cells

(2009) Y. Hase et al.   RNA

Machine learning based analyses on metabolic networks supports high-throughput knockout screens

(2008) Kitiporn Plaimas et al.   BMC Systems Biology

In silico network topology-based prediction of gene essentiality

(2007) João Paulo Müller da Silva et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS