The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana

(2013) Federico M. Giorgi et al.   BIOINFORMATICS

A systematic comparison of the MetaCyc and KEGG pathway databases

(2013) Tomer Altman et al.   BMC BIOINFORMATICS

Members of the Sinorhizobium meliloti ChvI regulon identified by a DNA binding screen

(2013) Louise Bélanger et al.   BMC MICROBIOLOGY

Inactivation of the Pta-AckA Pathway Causes Cell Death in Staphylococcus aureus

(2013) M. R. Sadykov et al.   JOURNAL OF BACTERIOLOGY

Activation of CpxRA in Haemophilus ducreyi Primarily Inhibits the Expression of Its Targets, Including Major Virulence Determinants

(2013) D. Gangaiah et al.   JOURNAL OF BACTERIOLOGY

Role of Central Metabolism in the Osmoadaptation of the Halophilic BacteriumChromohalobacter salexigens

(2013) José M. Pastor et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Adaptation of Cupriavidus necator to conditions favoring polyhydroxyalkanoate production

(2013) João M.B.T. Cavalheiro et al.   JOURNAL OF BIOTECHNOLOGY

Biotechnological potential of respiring Zymomonas mobilis: A stoichiometric analysis of its central metabolism

(2013) Agris Pentjuss et al.   JOURNAL OF BIOTECHNOLOGY

Reconstruction and analysis of the industrial strain Bacillus megaterium WSH002 genome-scale in silico metabolic model

(2013) Wei Zou et al.   JOURNAL OF BIOTECHNOLOGY

Genome-scale reconstruction and in silico analysis of Klebsiella oxytoca for 2,3-butanediol production

(2013) Jong Myoung Park et al.   Microbial Cell Factories

An updated metabolic view of the Bacillus subtilis 168 genome

(2013) E. Belda et al.   MICROBIOLOGY-SGM

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

(2013) Christopher A Desjardins et al.   NATURE GENETICS

Regulation of reductive dehalogenase gene transcription in Dehalococcoides mccartyi

(2013) A. Wagner et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

CathaCyc, a Metabolic Pathway Database Built from Catharanthus roseus RNA-Seq Data

(2013) Alex Van Moerkercke et al.   PLANT AND CELL PHYSIOLOGY

The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii

(2013) Daniel N. Farrugia et al.   PLoS One

Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

(2013) D. P. R. Herlemann et al.   mBio

The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments

(2012) David Damerell et al.   BIOLOGICAL CHEMISTRY

Genome-scale metabolic representation of Amycolatopsis balhimycina

(2012) Wanwipa Vongsangnak et al.   BIOTECHNOLOGY AND BIOENGINEERING

A constraint-based model of Scheffersomyces stipitis for improved ethanol production

(2012) Ting Liu et al.   Biotechnology for Biofuels

Prediction of dynamic metabolic behavior of Pediococcus pentosaceus producing lactic acid from lignocellulosic sugars

(2012) Philipp Adler et al.   BIOTECHNOLOGY PROGRESS

The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features

(2012) Muktak Aklujkar et al.   BMC GENOMICS

A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens)

(2012) Falk Hildebrand et al.   BMC GENOMICS

Role of trehalose in heat and desiccation tolerance in the soil bacterium Rhizobium etli

(2012) Mercedes Reina-Bueno et al.   BMC MICROBIOLOGY

The gpsX gene encoding a glycosyltransferase is important for polysaccharide production and required for full virulence in Xanthomonas citri subsp. citri

(2012) Jinyun Li et al.   BMC MICROBIOLOGY

Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction

(2012) Sang-Hoon Kim et al.   BMC MICROBIOLOGY

iAK692: A genome-scale metabolic model of Spirulina platensis C1

(2012) Amornpan Klanchui et al.   BMC Systems Biology

Computational systems biology and in silico modeling of the human microbiome

(2012) E. Borenstein   BRIEFINGS IN BIOINFORMATICS

Metaproteome analysis to determine the metabolically active part of a thermophilic microbial community producing biogas from agricultural biomass

(2012) Angelika Hanreich et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Vitamin B12 Synthesis and Salvage Pathways Were Acquired by Horizontal Gene Transfer to the Thermotogales

(2012) Kristen S. Swithers et al.   Genome Biology and Evolution

The chemical interactome space between the human host and the genetically defined gut metabotypes

(2012) Ulrik Plesner Jacobsen et al.   ISME Journal

Reconstruction and analysis of a genome-scale metabolic model of the vitamin C producing industrial strain Ketogulonicigenium vulgare WSH-001

(2012) Wei Zou et al.   JOURNAL OF BIOTECHNOLOGY

Accurate Atom-Mapping Computation for Biochemical Reactions

(2012) Mario Latendresse et al.   Journal of Chemical Information and Modeling

Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

(2012) Balaji Balagurunathan et al.   Microbial Cell Factories

Identification of triclosan-degrading bacteria using stable isotope probing, fluorescence in situ hybridization and microautoradiography

(2012) I. B. Lolas et al.   MICROBIOLOGY-SGM

Reconstruction and analysis of the genome-scale metabolic network of Candida glabrata

(2012) Nan Xu et al.   Molecular BioSystems

Identification of drug targets by chemogenomic and metabolomic profiling in yeast

(2012) Manhong Wu et al.   Pharmacogenetics and Genomics

The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway

(2012) Michele Fabris et al.   PLANT JOURNAL

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

(2012) Hideto Takami et al.   PLoS One

Fatty Acid Composition of Developing Sea Buckthorn (Hippophae rhamnoides L.) Berry and the Transcriptome of the Mature Seed

(2012) Tahira Fatima et al.   PLoS One

Phenotypic and Transcriptomic Response of Auxotrophic Mycobacterium avium Subsp. paratuberculosis leuD Mutant under Environmental Stress

(2012) Jenn-Wei Chen et al.   PLoS One

Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

(2012) Thomas Ulas et al.   PLoS One

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus

(2012) J. I. Khudyakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bioinformatics for the Human Microbiome Project

(2012) Dirk Gevers et al.   PLoS Computational Biology

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Chapter 12: Human Microbiome Analysis

(2012) Xochitl C. Morgan et al.   PLoS Computational Biology

Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides

(2012) Tara A. Gianoulis et al.   PLoS Genetics

Quantitative Proteomics of Intracellular Campylobacter jejuni Reveals Metabolic Reprogramming

(2012) Xiaoyun Liu et al.   PLoS Pathogens

CcpA Regulates Arginine Biosynthesis in Staphylococcus aureus through Repression of Proline Catabolism

(2012) Austin S. Nuxoll et al.   PLoS Pathogens

Engineered Corynebacterium glutamicum as an endotoxin-free platform strain for lactate-based polyester production

(2011) Yuyang Song et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A survey of metabolic databases emphasizing the MetaCyc family

(2011) Peter D. Karp et al.   ARCHIVES OF TOXICOLOGY

Construction and elementary mode analysis of a metabolic model for Shewanella oneidensis MR-1

(2011) C.M. Flynn et al.   BIOSYSTEMS

The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions

(2011) Stefano Ghignone et al.   ISME Journal

Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A

(2011) M. N. Benedict et al.   JOURNAL OF BACTERIOLOGY

Pathway-Based Functional Analysis of Metagenomes

(2011) Itai Sharon et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Metabolomic analysis of trypanosomatid protozoa

(2011) Darren J. Creek et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

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

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

Machine learning methods for metabolic pathway prediction

(2010) Joseph M Dale et al.   BMC BIOINFORMATICS

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

(2010) A. Bombarely et al.   NUCLEIC ACIDS RESEARCH

Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants

(2010) P. Zhang et al.   PLANT PHYSIOLOGY

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

(2009) Patrick May et al.   BMC GENOMICS

Reconstruction of metabolic pathways for the cattle genome

(2009) Seongwon Seo et al.   BMC Systems Biology

LeishCyc: a biochemical pathways database for Leishmania major

(2009) Maria A Doyle et al.   BMC Systems Biology

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

MouseCyc: a curated biochemical pathways database for the laboratory mouse

(2009) Alexei V Evsikov et al.   GENOME BIOLOGY

dictyBase—a Dictyostelium bioinformatics resource update

(2008) Petra Fey et al.   NUCLEIC ACIDS RESEARCH

ExplorEnz: the primary source of the IUBMB enzyme list

(2008) A. G. McDonald et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH