Integration of bioinformatics to biodegradation

Bacterial degradation of chlorophenols and their derivatives

(2014) Pankaj Arora et al.   Microbial Cell Factories

Complete genome sequence of Pseudomonas sp. strain VLB120 a solvent tolerant, styrene degrading bacterium, isolated from forest soil

(2013) Kirsten A.K. Köhler et al.   JOURNAL OF BIOTECHNOLOGY

Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways

(2013) Kent McClymont et al.   NUCLEIC ACIDS RESEARCH

Genomic and Functional Analyses of the Gentisate and Protocatechuate Ring-Cleavage Pathways and Related 3-Hydroxybenzoate and 4-Hydroxybenzoate Peripheral Pathways in Burkholderia xenovorans LB400

(2013) María José Romero-Silva et al.   PLoS One

Predicting Chemical Toxicity Effects Based on Chemical-Chemical Interactions

(2013) Lei Chen et al.   PLoS One

Degradation of chlorinated nitroaromatic compounds

(2012) Pankaj Kumar Arora et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The automatic annotation of bacterial genomes

(2012) E. J. Richardson et al.   BRIEFINGS IN BIOINFORMATICS

Genome Sequence of the Nitroaromatic Compound-Degrading Bacterium Burkholderia sp. Strain SJ98

(2012) S. Kumar et al.   JOURNAL OF BACTERIOLOGY

Estimation of Carcinogenicity Using Molecular Fragments Tree

(2012) Yong Wang et al.   Journal of Chemical Information and Modeling

Computational tools for the synthetic design of biochemical pathways

(2012) Marnix H. Medema et al.   NATURE REVIEWS MICROBIOLOGY

Computational modeling of P450s for toxicity prediction

(2011) Nitish Kumar Mishra   Expert Opinion on Drug Metabolism & Toxicology

Complete Genome Sequence of the BTEX-Degrading Bacterium Pseudoxanthomonas spadix BD-a59

(2011) S. H. Lee et al.   JOURNAL OF BACTERIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

AGeS: A Software System for Microbial Genome Sequence Annotation

(2011) Kamal Kumar et al.   PLoS One

Finding metabolic pathways using atom tracking

(2010) Allison P. Heath et al.   BIOINFORMATICS

Machine learning methods for metabolic pathway prediction

(2010) Joseph M Dale et al.   BMC BIOINFORMATICS

CAESAR models for developmental toxicity

(2010) Antonio Cassano et al.   Chemistry Central Journal

Metabolic networks, microbial ecology and ‘omics’ technologies: towards understanding in situ biodegradation processes

(2010) Ramiro Vilchez-Vargas et al.   ENVIRONMENTAL MICROBIOLOGY

PathPred: an enzyme-catalyzed metabolic pathway prediction server

(2010) Y. Moriya et al.   NUCLEIC ACIDS RESEARCH

The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader

(2010) Athanasios Lykidis et al.   PLoS One

DREAMS of metabolism

(2010) Keng Cher Soh et al.   TRENDS IN BIOTECHNOLOGY

MetNetAligner: a web service tool for metabolic network alignments

(2009) Qiong Cheng et al.   BIOINFORMATICS

DIYA: a bacterial annotation pipeline for any genomics lab

(2009) Andrew C. Stewart et al.   BIOINFORMATICS

WeGAS: A Web-Based Microbial Genome Annotation System

(2009) Daesang LEE et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Computational framework for predictive biodegradation

(2009) Stacey D. Finley et al.   BIOTECHNOLOGY AND BIOENGINEERING

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

FMM: a web server for metabolic pathway reconstruction and comparative analysis

(2009) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

DESHARKY: automatic design of metabolic pathways for optimal cell growth

(2008) Guillermo Rodrigo et al.   BIOINFORMATICS

The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

(2008) Chenggang Yu et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Resources for global risk assessment: The International Toxicity Estimates for Risk (ITER) and Risk Information Exchange (RiskIE) databases

(2008) Andrea Wullenweber et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Acutoxbase, an innovative database for in vitro acute toxicity studies

(2008) Agnieszka Kinsner-Ovaskainen et al.   TOXICOLOGY IN VITRO