Published in Nucleic Acids Res on November 05, 2009
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res (2010) 2.22
A tuberous sclerosis complex signalling node at the peroxisome regulates mTORC1 and autophagy in response to ROS. Nat Cell Biol (2013) 1.96
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans. Database (Oxford) (2013) 1.48
Identification of novel plant peroxisomal targeting signals by a combination of machine learning methods and in vivo subcellular targeting analyses. Plant Cell (2011) 1.09
VAPs and ACBD5 tether peroxisomes to the ER for peroxisome maintenance and lipid homeostasis. J Cell Biol (2017) 1.04
Response of the mitochondrial proteome of rat renal proximal convoluted tubules to chronic metabolic acidosis. Am J Physiol Renal Physiol (2012) 0.98
Metabolomics and malaria biology. Mol Biochem Parasitol (2010) 0.95
Integration of peroxisomes into an endomembrane system that governs cellular aging. Front Physiol (2012) 0.93
The PEX7-mediated peroxisomal import system is required for fungal development and pathogenicity in Magnaporthe oryzae. PLoS One (2011) 0.90
Import of proteins into the peroxisomal matrix. Front Physiol (2013) 0.90
PredPlantPTS1: A Web Server for the Prediction of Plant Peroxisomal Proteins. Front Plant Sci (2012) 0.89
Classification of subcellular location by comparative proteomic analysis of native and density-shifted lysosomes. Mol Cell Proteomics (2011) 0.87
An inventory of peroxisomal proteins and pathways in Drosophila melanogaster. Traffic (2012) 0.83
One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy. Nat Methods (2016) 0.81
Short-read sequencing for genomic analysis of the brown rot fungus Fibroporia radiculosa. Appl Environ Microbiol (2012) 0.80
Peroxisomal biogenesis in ischemic brain. Antioxid Redox Signal (2015) 0.79
Intracellular targeting of ascomycetous catalase-peroxidases (KatG1s). Arch Microbiol (2013) 0.79
Targeting a heterologous protein to multiple plant organelles via rationally designed 5' mRNA tags. J Biol Eng (2013) 0.79
One of Three Pex11 Family Members Is Required for Peroxisomal Proliferation and Full Virulence of the Rice Blast Fungus Magnaporthe oryzae. PLoS One (2015) 0.77
hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms. Autophagy (2016) 0.76
The cytosolic domain of Pex22p stimulates the Pex4p-dependent ubiquitination of the PTS1-receptor. PLoS One (2014) 0.76
Accounting for protein subcellular localization: A compartmental map of the rat liver proteome. Mol Cell Proteomics (2016) 0.76
Peroxisomal Import Reduces the Proapoptotic Activity of Deubiquitinating Enzyme USP2. PLoS One (2015) 0.75
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Arginine and Lysine Transporters Are Essential for Trypanosoma brucei. PLoS One (2017) 0.75
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Ensembl 2007. Nucleic Acids Res (2006) 20.10
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol (2006) 12.96
ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics (2001) 11.54
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics (2009) 9.81
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Contribution of the endoplasmic reticulum to peroxisome formation. Cell (2005) 5.28
Pre- and postinvasion defenses both contribute to nonhost resistance in Arabidopsis. Science (2005) 3.81
Biochemistry of mammalian peroxisomes revisited. Annu Rev Biochem (2006) 3.59
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Blocks-based methods for detecting protein homology. Electrophoresis (2000) 2.19
AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes. Plant Physiol (2004) 2.11
Metabolic functions of glycosomes in trypanosomatids. Biochim Biophys Acta (2006) 1.80
Plant peroxisomes respire in the light: some gaps of the photorespiratory C2 cycle have become filled--others remain. Biochim Biophys Acta (2006) 1.57
Origin and evolution of the peroxisomal proteome. Biol Direct (2006) 1.55
The peroxisome: still a mysterious organelle. Histochem Cell Biol (2008) 1.41
The evolutionary origin of peroxisomes: an ER-peroxisome connection. Mol Biol Evol (2006) 1.39
Metabolic and molecular basis of peroxisomal disorders: a review. Am J Med Genet A (2004) 1.39
In silico prediction of the glycosomal enzymes of Leishmania major and trypanosomes. Mol Biochem Parasitol (2006) 1.36
Arabidopsis peroxisomal citrate synthase is required for fatty acid respiration and seed germination. Plant Cell (2005) 1.35
Mitochondria and peroxisomes: are the 'big brother' and the 'little sister' closer than assumed? Bioessays (2007) 1.30
Reactive oxygen species and peroxisomes: struggling for balance. Biofactors (2009) 1.21
The mouse Nudt7 gene encodes a peroxisomal nudix hydrolase specific for coenzyme A and its derivatives. Biochem J (2001) 1.19
A central role for the peroxisomal membrane in glyoxylate cycle function. Biochim Biophys Acta (2006) 1.18
Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer. Eur J Biochem (2002) 1.12
Distinct intracellular localization of Gpd1p and Gpd2p, the two yeast isoforms of NAD+-dependent glycerol-3-phosphate dehydrogenase, explains their different contributions to redox-driven glycerol production. J Biol Chem (2004) 1.11
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. Nucleic Acids Res (2006) 1.08
Toxoplasma gondii catalase: are there peroxisomes in toxoplasma? J Cell Sci (2000) 1.02
Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling. Bioinformatics (2009) 1.00
Differential cellular and subcellular localization of heme-binding protein 23/peroxiredoxin I and heme oxygenase-1 in rat liver. J Histochem Cytochem (2003) 0.93
Dehydrogenases of the pentose phosphate pathway in rat liver peroxisomes. Eur J Biochem (1989) 0.87
Disruption of the peroxisomal citrate synthase CshA affects cell growth and multicellular development in Dictyostelium discoideum. Mol Microbiol (2004) 0.80
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics (2009) 9.81
ETE: a python Environment for Tree Exploration. BMC Bioinformatics (2010) 4.17
The human phylome. Genome Biol (2007) 3.81
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res (2013) 3.77
PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res (2007) 3.30
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res (2007) 3.09
The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A (2012) 2.24
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res (2010) 2.22
Immunity and other defenses in pea aphids, Acyrthosiphon pisum. Genome Biol (2010) 2.09
Joining forces in the quest for orthologs. Genome Biol (2009) 1.96
Monocyte chemoattractant protein-1: a key mediator in inflammatory processes. Int J Biochem Cell Biol (2008) 1.72
Acquisition of prokaryotic genes by fungal genomes. Trends Genet (2009) 1.72
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res (2013) 1.69
An anaerobic mitochondrion that produces hydrogen. Nature (2005) 1.64
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res (2010) 1.59
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res (2011) 1.53
The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PLoS One (2009) 1.53
2x genomes--depth does matter. Genome Biol (2010) 1.47
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi. BMC Biol (2012) 1.45
General aspects and neuropathology of X-linked adrenoleukodystrophy. Brain Pathol (2010) 1.41
The evolutionary origin of peroxisomes: an ER-peroxisome connection. Mol Biol Evol (2006) 1.39
Toward community standards in the quest for orthologs. Bioinformatics (2012) 1.36
Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc Natl Acad Sci U S A (2013) 1.36
Antioxidants halt axonal degeneration in a mouse model of X-adrenoleukodystrophy. Ann Neurol (2011) 1.31
Early oxidative damage underlying neurodegeneration in X-adrenoleukodystrophy. Hum Mol Genet (2008) 1.27
Current and future pharmacological treatment strategies in X-linked adrenoleukodystrophy. Brain Pathol (2010) 1.27
Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin. FEBS Lett (2005) 1.21
Pathomechanisms underlying X-adrenoleukodystrophy: a three-hit hypothesis. Brain Pathol (2010) 1.20
A midzone-based ruler adjusts chromosome compaction to anaphase spindle length. Science (2011) 1.19
Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes. Genome Biol (2013) 1.18
Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains. ISME J (2010) 1.17
Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest. PLoS One (2013) 1.15
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief Bioinform (2011) 1.15
Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus. BMC Genomics (2012) 1.14
Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression. Bioessays (2010) 1.10
Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics (2010) 1.09
From Saccharomyces cerevisiae to Candida glabratain a few easy steps: important adaptations for an opportunistic pathogen. FEMS Microbiol Lett (2010) 1.08
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. Nucleic Acids Res (2006) 1.08
A key role for the peroxisomal ABCD2 transporter in fatty acid homeostasis. Am J Physiol Endocrinol Metab (2008) 1.07
Biogenic amines and polyamines: similar biochemistry for different physiological missions and biomedical applications. Crit Rev Biochem Mol Biol (2003) 1.07
Inactivation of the peroxisomal ABCD2 transporter in the mouse leads to late-onset ataxia involving mitochondria, Golgi and endoplasmic reticulum damage. Hum Mol Genet (2005) 1.06
The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties. Int J Food Microbiol (2012) 1.04
Valproic acid induces antioxidant effects in X-linked adrenoleukodystrophy. Hum Mol Genet (2010) 1.03
TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees. Nucleic Acids Res (2011) 1.02
Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling. Bioinformatics (2009) 1.00
YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA (2010) 0.99
Oxidative stress underlying axonal degeneration in adrenoleukodystrophy: a paradigm for multifactorial neurodegenerative diseases? Biochim Biophys Acta (2012) 0.99
Comparative transcriptomics of early dipteran development. BMC Genomics (2013) 0.99
Mouse liver PMP70 and ALDP: homomeric interactions prevail in vivo. Biochim Biophys Acta (2004) 0.98
ABCD2 is abundant in adipose tissue and opposes the accumulation of dietary erucic acid (C22:1) in fat. J Lipid Res (2010) 0.96
Variation and evolution of biomolecular systems: searching for functional relevance. FEBS Lett (2005) 0.96
The kinomes of apicomplexan parasites. Microbes Infect (2012) 0.96
AMMO-Prot: amine system project 3D-model finder. BMC Bioinformatics (2008) 0.94
Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies. Genome Biol Evol (2014) 0.93
Spectroscopic analysis of recombinant rat histidine decarboxylase. J Biochem (2002) 0.93
Oxidative stress modulates mitochondrial failure and cyclophilin D function in X-linked adrenoleukodystrophy. Brain (2012) 0.92
Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis. Genome Biol Evol (2013) 0.91
Functional genomic analysis unravels a metabolic-inflammatory interplay in adrenoleukodystrophy. Hum Mol Genet (2011) 0.91
Mammalian histidine decarboxylase: from structure to function. Bioessays (2005) 0.91
Inferring gene function from evolutionary change in signatures of translation efficiency. Genome Biol (2014) 0.91
Genome, Transcriptome, and Functional Analyses of Penicillium expansum Provide New Insights Into Secondary Metabolism and Pathogenicity. Mol Plant Microbe Interact (2015) 0.91
Neuroinflammatory signals in Alzheimer disease and APP/PS1 transgenic mice: correlations with plaques, tangles, and oligomeric species. J Neuropathol Exp Neurol (2015) 0.90
Oxidative damage compromises energy metabolism in the axonal degeneration mouse model of X-adrenoleukodystrophy. Antioxid Redox Signal (2011) 0.90
Steroid hormones control circadian Elovl3 expression in mouse liver. Endocrinology (2008) 0.90
The Schistosoma mansoni phylome: using evolutionary genomics to gain insight into a parasite's biology. BMC Genomics (2012) 0.89
Epigallocatechin gallate reduces human monocyte mobility and adhesion in vitro. Br J Pharmacol (2009) 0.89
Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence. BMC Evol Biol (2009) 0.89
Pioglitazone halts axonal degeneration in a mouse model of X-linked adrenoleukodystrophy. Brain (2013) 0.89
Amyloid generation and dysfunctional immunoproteasome activation with disease progression in animal model of familial Alzheimer's disease. Brain Pathol (2012) 0.89
Polyamines are present in mast cell secretory granules and are important for granule homeostasis. PLoS One (2010) 0.89
High variability of mitochondrial gene order among fungi. Genome Biol Evol (2014) 0.88
The role of peroxisomal ABC transporters in the mouse adrenal gland: the loss of Abcd2 (ALDR), Not Abcd1 (ALD), causes oxidative damage. Lab Invest (2007) 0.88
Mitochondrial genome variability within the Candida parapsilosis species complex. Mitochondrion (2012) 0.87
The functional interaction of 14-3-3 proteins with the ERK1/2 scaffold KSR1 occurs in an isoform-specific manner. J Biol Chem (2008) 0.87
Measuring guide-tree dependency of inferred gaps in progressive aligners. Bioinformatics (2013) 0.87
Functional genomics reveals dysregulation of cortical olfactory receptors in Parkinson disease: novel putative chemoreceptors in the human brain. J Neuropathol Exp Neurol (2013) 0.87
Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinformatics (2010) 0.87
Regulation of Candida glabrata oxidative stress resistance is adapted to host environment. FEBS Lett (2010) 0.87
Mitochondrial dysfunction in central nervous system white matter disorders. Glia (2014) 0.87
PGC-1α overexpression exacerbates β-amyloid and tau deposition in a transgenic mouse model of Alzheimer's disease. FASEB J (2014) 0.86
A phylogenomics approach for selecting robust sets of phylogenetic markers. Nucleic Acids Res (2014) 0.86
Bezafibrate administration improves behavioral deficits and tau pathology in P301S mice. Hum Mol Genet (2012) 0.86
Bezafibrate lowers very long-chain fatty acids in X-linked adrenoleukodystrophy fibroblasts by inhibiting fatty acid elongation. J Inherit Metab Dis (2012) 0.86
Local changes in the catalytic site of mammalian histidine decarboxylase can affect its global conformation and stability. Eur J Biochem (2003) 0.86
Mathematical modeling of polyamine metabolism in mammals. J Biol Chem (2006) 0.85
TACC3-TSC2 maintains nuclear envelope structure and controls cell division. Cell Cycle (2010) 0.85
Evolutionary expansion of the Ras switch regulatory module in eukaryotes. Nucleic Acids Res (2011) 0.85
Anti-angiogenic effects of homocysteine on cultured endothelial cells. Biochem Biophys Res Commun (2002) 0.85
Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes. Gene (2010) 0.84
Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency. Mitochondrion (2009) 0.84
H3 autoreceptors modulate histamine synthesis through calcium/calmodulin- and cAMP-dependent protein kinase pathways. Mol Pharmacol (2004) 0.83
Histone deacetylase inhibitor upregulates peroxisomal fatty acid oxidation and inhibits apoptotic cell death in abcd1-deficient glial cells. PLoS One (2013) 0.83
Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. BMC Genomics (2014) 0.83
Insulin-like growth factor-1 and neurotrophin-3 gene therapy prevents motor decline in an X-linked adrenoleukodystrophy mouse model. Ann Neurol (2009) 0.83
The absence of ABCD2 sensitizes mice to disruptions in lipid metabolism by dietary erucic acid. J Lipid Res (2012) 0.82
Glutathione imbalance in patients with X-linked adrenoleukodystrophy. Mol Genet Metab (2013) 0.81
Homocysteine is a potent inhibitor of human tumor cell gelatinases. Biochem Biophys Res Commun (2003) 0.81
Evolution of spliceosomal introns following endosymbiotic gene transfer. BMC Evol Biol (2010) 0.81
CycADS: an annotation database system to ease the development and update of BioCyc databases. Database (Oxford) (2011) 0.81