Simultaneous prediction of enzyme orthologs from chemical transformation patterns forde novometabolic pathway reconstruction

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Metabolome-scalede novopathway reconstruction using regioisomer-sensitive graph alignments

(2015) Yoshihiro Yamanishi et al.   BIOINFORMATICS

Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics

(2015) Pierre-Yves Colin et al.   Nature Communications

Insect host plant selection in complex environments

(2015) David Carrasco et al.   Current Opinion in Insect Science

Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach

(2014) Masaaki Kotera et al.   BIOINFORMATICS

EC-BLAST: a tool to automatically search and compare enzyme reactions

(2014) Syed Asad Rahman et al.   NATURE METHODS

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list

(2014) Masaaki Kotera et al.   Journal of Bioinformatics and Computational Biology

Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets

(2013) M. Kotera et al.   BIOINFORMATICS

Fifty-five years of enzyme classification: advances and difficulties

(2013) Andrew G. McDonald et al.   FEBS Journal

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine

(2012) Yoshihiko Matsuta et al.   BIOINFORMATICS

Is EC class predictable from reaction mechanism?

(2012) Neetika Nath et al.   BMC BIOINFORMATICS

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Evaluation method for the potential functionome harbored in the genome and metagenome

(2012) Hideto Takami et al.   BMC GENOMICS

Natural Products As Sources of New Drugs over the 30 Years from 1981 to 2010

(2012) David J. Newman et al.   JOURNAL OF NATURAL PRODUCTS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

KNApSAcK Family Databases: Integrated Metabolite–Plant Species Databases for Multifaceted Plant Research

(2011) Farit Mochamad Afendi et al.   PLANT AND CELL PHYSIOLOGY

Similarity Perception of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Different Classification Methods

(2010) Xiaoying Hu et al.   Journal of Chemical Information and Modeling

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

PathPred: an enzyme-catalyzed metabolic pathway prediction server

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

Automatic Assignment of EC Numbers

(2010) Volker Egelhofer et al.   PLoS Computational Biology

E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs

(2009) Y. Yamanishi et al.   BIOINFORMATICS

Assignment of EC Numbers to Enzymatic Reactions with MOLMAP Reaction Descriptors and Random Forests

(2009) Diogo A. R. S. Latino et al.   Journal of Chemical Information and Modeling

First evidence of a membrane-bound, tyramine and β-phenylethylamine producing, tyrosine decarboxylase inEnterococcus faecalis: A two-dimensional electrophoresis proteomic study

(2009) Enrica Pessione et al.   PROTEOMICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Eliciting Possible Reaction Equations and Metabolic Pathways Involving Orphan Metabolites

(2008) Masaaki Kotera et al.   Journal of Chemical Information and Modeling

The University of Minnesota pathway prediction system: predicting metabolic logic

(2008) Lynda B.M. Ellis et al.   NUCLEIC ACIDS RESEARCH