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Gi Bae Kim et al.
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Martin Mascher et al.
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Celine Brouard et al.
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CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification
Yannick Djoumbou-Feunang et al.
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New approach for understanding genome variations in KEGG
Minoru Kanehisa et al.
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BRENDA in 2019: a European ELIXIR core data resource
Lisa Jeske et al.
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Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways
Anika Kueken et al.
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The BioCyc collection of microbial genomes and metabolic pathways
Peter D. Karp et al.
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The MetaCyc database of metabolic pathways and enzymes
Ron Caspi et al.
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Spectroscopic methods to analyze drug metabolites
Jong-Jae Yi et al.
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A graph-based approach to analyze flux-balanced pathways in metabolic networks
Mona Arabzadeh et al.
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Feature extraction method for proteins based on Markov tripeptide by compressive sensing
C. F. Gao et al.
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RetroPath2.0: A retrosynthesis workflow for metabolic engineers
Baudoin Delepine et al.
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UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences
Pu-Feng Du et al.
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Pse-Analysis: a python package for DNA/RNA and protein/peptide sequence analysis based on pseudo components and kernel methods
Bin Liu et al.
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Automatic single- and multi-label enzymatic function prediction by machine learning
Shervine Amidi et al.
PEERJ (2017)
Computer-Assisted Retrosynthesis Based on Molecular Similarity
Connor W. Coley et al.
ACS CENTRAL SCIENCE (2017)
Application of K-Means Clustering Algorithm in Grouping the DNA Sequences of Hepatitis B Virus (HBV)
A. Bustamam et al.
INTERNATIONAL SYMPOSIUM ON CURRENT PROGRESS IN MATHEMATICS AND SCIENCES 2016 (ISCPMS 2016) (2017)
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Lin Wang et al.
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Celine Brouard et al.
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Minoru Kanehisa et al.
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Jennifer N. Wei et al.
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Implementation and comparison of kernel-based learning methods to predict metabolic networks
Abiel Roche-Lima
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Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences
Bin Liu et al.
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Kai Duehrkop et al.
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Nives Skunca et al.
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Huibin Shen et al.
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Luna De Ferrari et al.
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Felicity Allen et al.
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Franziska Hufsky et al.
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Masaaki Kotera et al.
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Bing Niu et al.
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Lars J. Kangas et al.
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Fangping Mu et al.
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Michael D. Schmidt et al.
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Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
Lei Chen et al.
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Sequence feature-based prediction of protein stability changes upon amino acid substitutions
Shaolei Teng et al.
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Pathway identification by network pruning in the metabolic network of Escherichia coli
P. Gerlee et al.
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An optimization model for metabolic pathways
F. J. Planes et al.
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The FEATURE framework for protein function annotation: modelling new functions, improving performance, and extending to novel applications
Inbal Halperin et al.
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The RAST server: Rapid annotations using subsystems technology
Ramy K. Aziz et al.
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Masaaki Kotera et al.
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KEGG Atlas mapping for global analysis of metabolic pathways
Shujiro Okuda et al.
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Getting Started in Biological Pathway Construction and Analysis
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KAAS: an automatic genome annotation and pathway reconstruction server
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CA Smith et al.
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W Zhong et al.
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N Friedman
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ML Green et al.
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A Bayesian networks approach for predicting protein-protein interactions from genomic data
R Jansen et al.
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SM Paley et al.
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I Schomburg et al.
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The EcoCyc database
PD Karp et al.
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The MetaCyc database
PD Karp et al.
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GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
J Besemer et al.
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O Ebenhoh et al.
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R Overbeek et al.
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