Published in Proteomics on March 22, 2011
Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog (2013) 1.72
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol (2012) 1.27
Peppy: proteogenomic search software. J Proteome Res (2013) 1.07
Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes Dev (2013) 1.04
Systemic cold stress adaptation of Chlamydomonas reinhardtii. Mol Cell Proteomics (2013) 0.95
xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud. Plant Cell (2016) 0.76
Dual use of peptide mass spectra: Protein atlas and genome annotation. Curr Plant Biol (2015) 0.75
Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis (1999) 45.01
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods (2007) 25.29
TANDEM: matching proteins with tandem mass spectra. Bioinformatics (2004) 17.41
Open mass spectrometry search algorithm. J Proteome Res (2004) 15.25
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
Mass spectrometry and protein analysis. Science (2006) 8.05
C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet (2003) 7.25
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res (2004) 5.53
Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics (2008) 5.46
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom (2003) 4.56
Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A (2008) 3.45
Improving gene annotation using peptide mass spectrometry. Genome Res (2006) 2.69
Recent advances in gene structure prediction. Curr Opin Struct Biol (2004) 1.90
EGASP: collaboration through competition to find human genes. Nat Methods (2005) 1.72
Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics (2010) 1.71
Characterizing the anaerobic response of Chlamydomonas reinhardtii by quantitative proteomics. Mol Cell Proteomics (2010) 1.43
Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii. Proteomics (2006) 1.10
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA. Genome Biol (2006) 1.06
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics (2010) 1.05
Competition boosts bid to find human genes. Nature (2005) 0.93
A new approach that allows identification of intron-split peptides from mass spectrometric data in genomic databases. FEBS Lett (2004) 0.82
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (2010) 5.56
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
The Amphimedon queenslandica genome and the evolution of animal complexity. Nature (2010) 5.11
Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A (2008) 3.45
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18
Draft genome sequence of the oilseed species Ricinus communis. Nat Biotechnol (2010) 2.52
Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science (2013) 2.51
An ancient light-harvesting protein is critical for the regulation of algal photosynthesis. Nature (2009) 2.47
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol Syst Biol (2011) 2.44
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A (2010) 2.30
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. BMC Bioinformatics (2006) 2.25
Successful herbivore attack due to metabolic diversion of a plant chemical defense. Proc Natl Acad Sci U S A (2004) 2.13
WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Res (2013) 1.95
Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci U S A (2011) 1.85
Adaptation to Fe-deficiency requires remodeling of the photosynthetic apparatus. EMBO J (2002) 1.83
A plastid protein crucial for Ca2+-regulated stomatal responses. New Phytol (2008) 1.81
Reciprocal expression of two candidate di-iron enzymes affecting photosystem I and light-harvesting complex accumulation. Plant Cell (2002) 1.74
Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog (2013) 1.72
The role of recombination in the emergence of a complex and dynamic HIV epidemic. Retrovirology (2010) 1.69
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. BMC Bioinformatics (2008) 1.63
jpHMM: improving the reliability of recombination prediction in HIV-1. Nucleic Acids Res (2009) 1.61
A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics (2011) 1.60
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. Nucleic Acids Res (2006) 1.58
Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii. Proteomics (2007) 1.56
Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiol (2006) 1.51
Inhibiting the expression of DNA replication-initiation proteins induces apoptosis in human cancer cells. Cancer Res (2003) 1.46
Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics (2014) 1.46
Noc3p, a bHLH protein, plays an integral role in the initiation of DNA replication in budding yeast. Cell (2002) 1.44
Identification of novel factors involved in or regulating initiation of DNA replication by a genome-wide phenotypic screen in Saccharomyces cerevisiae. Cell Cycle (2010) 1.43
Characterizing the anaerobic response of Chlamydomonas reinhardtii by quantitative proteomics. Mol Cell Proteomics (2010) 1.43
Elevated matrix metalloproteinase expression after stent implantation is associated with restenosis. Int J Cardiol (2005) 1.43
Proteomics of Chlamydomonas reinhardtii light-harvesting proteins. Eukaryot Cell (2003) 1.38
N-terminal processing of Lhca3 Is a key step in remodeling of the photosystem I-light-harvesting complex under iron deficiency in Chlamydomonas reinhardtii. J Biol Chem (2005) 1.36
PredAlgo: a new subcellular localization prediction tool dedicated to green algae. Mol Biol Evol (2012) 1.33
Subunit composition of NDH-1 complexes of Synechocystis sp. PCC 6803: identification of two new ndh gene products with nuclear-encoded homologues in the chloroplast Ndh complex. J Biol Chem (2004) 1.32
Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol (2012) 1.27
Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species. Nucleic Acids Res (2011) 1.23
Control of hydrogen photoproduction by the proton gradient generated by cyclic electron flow in Chlamydomonas reinhardtii. Plant Cell (2011) 1.22
NAB1 is an RNA binding protein involved in the light-regulated differential expression of the light-harvesting antenna of Chlamydomonas reinhardtii. Plant Cell (2005) 1.21
Metabolic network analysis integrated with transcript verification for sequenced genomes. Nat Methods (2009) 1.21
Cdc48p is required for the cell cycle commitment point at Start via degradation of the G1-CDK inhibitor Far1p. J Cell Biol (2003) 1.15
The chloroplast calcium sensor CAS is required for photoacclimation in Chlamydomonas reinhardtii. Plant Cell (2011) 1.15
Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics (2008) 1.15
Calcium-dependent regulation of cyclic photosynthetic electron transfer by a CAS, ANR1, and PGRL1 complex. Proc Natl Acad Sci U S A (2012) 1.11
Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii. Proteomics (2006) 1.10
Advanced glycation end products depress function of endothelial progenitor cells via p38 and ERK 1/2 mitogen-activated protein kinase pathways. Basic Res Cardiol (2008) 1.07
Biochemical and structural studies of the large Ycf4-photosystem I assembly complex of the green alga Chlamydomonas reinhardtii. Plant Cell (2009) 1.06
Advanced glycosylation end products might promote atherosclerosis through inducing the immune maturation of dendritic cells. Arterioscler Thromb Vasc Biol (2005) 1.06
The chloroplast proteome: a survey from the Chlamydomonas reinhardtii perspective with a focus on distinctive features. Curr Genet (2011) 1.05
The structure and function of eukaryotic photosystem I. Biochim Biophys Acta (2010) 1.04
pymzML--Python module for high-throughput bioinformatics on mass spectrometry data. Bioinformatics (2012) 1.03
Modifications of the lipoamide-containing mitochondrial subproteome in a yeast mutant defective in cysteine desulfurase. Mol Cell Proteomics (2006) 1.03
Sequence analysis of bacterial artificial chromosome clones from the apospory-specific genomic region of Pennisetum and Cenchrus. Plant Physiol (2008) 1.03
WD60/FAP163 is a dynein intermediate chain required for retrograde intraflagellar transport in cilia. Mol Biol Cell (2013) 1.02
PGRL1 participates in iron-induced remodeling of the photosynthetic apparatus and in energy metabolism in Chlamydomonas reinhardtii. J Biol Chem (2009) 1.02
Pairwise interactions of the six human MCM protein subunits. J Mol Biol (2004) 1.01
An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genet (2011) 1.01
Comparison of the subunit compositions of the PSI-LHCI supercomplex and the LHCI in the green alga Chlamydomonas reinhardtii. Biochemistry (2004) 1.01
Phosphorylation of calcineurin B-like (CBL) calcium sensor proteins by their CBL-interacting protein kinases (CIPKs) is required for full activity of CBL-CIPK complexes toward their target proteins. J Biol Chem (2012) 1.01
Active cochlear amplification is dependent on supporting cell gap junctions. Nat Commun (2013) 1.00
Reversible gas uptake by a nonporous crystalline solid involving multiple changes in covalent bonding. J Am Chem Soc (2007) 0.99
Ferritin is required for rapid remodeling of the photosynthetic apparatus and minimizes photo-oxidative stress in response to iron availability in Chlamydomonas reinhardtii. Plant J (2008) 0.99
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. Nucleic Acids Res (2012) 0.99
Analysis of the vacuolar luminal proteome of Saccharomyces cerevisiae. FEBS J (2007) 0.99
Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts. Plant Physiol (2005) 0.98
Risk of cardiac dysfunction with trastuzumab in breast cancer patients: a meta-analysis. Cancer Treat Rev (2010) 0.98
Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots. New Phytol (2014) 0.98
Autographa californica multiple nucleopolyhedrovirus 38K is a novel nucleocapsid protein that interacts with VP1054, VP39, VP80, and itself. J Virol (2008) 0.98
Proton gradient regulation 5-mediated cyclic electron flow under ATP- or redox-limited conditions: a study of ΔATpase pgr5 and ΔrbcL pgr5 mutants in the green alga Chlamydomonas reinhardtii. Plant Physiol (2014) 0.96
The role of cyclo-oxygenase 1 and 2 activity in prostaglandin E(2) secretion by cultured human adult microglia: implications for Alzheimer's disease. Brain Res (2002) 0.96
Characterization of the key step for light-driven hydrogen evolution in green algae. J Biol Chem (2009) 0.96
Characterization and structure determination of the Cdt1 binding domain of human minichromosome maintenance (Mcm) 6. J Biol Chem (2010) 0.95
Functional proteomics of circadian expressed proteins from Chlamydomonas reinhardtii. FEBS Lett (2004) 0.93
Anti-inflammatory effect of Lycium Fruit water extract in lipopolysaccharide-stimulated RAW 264.7 macrophage cells. Int Immunopharmacol (2012) 0.92
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. Bioinformatics (2012) 0.91
Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows. Bioinformatics (2011) 0.91
Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties. BMC Genomics (2012) 0.90
The interacting domains of hCdt1 and hMcm6 involved in the chromatin loading of the MCM complex in human cells. Cell Cycle (2010) 0.90
Circulating miR-214 is associated with the severity of coronary artery disease. J Geriatr Cardiol (2013) 0.90
Release of oxidized plastocyanin from photosystem I limits electron transfer between photosystem I and cytochrome b6f complex in vivo. Proc Natl Acad Sci U S A (2005) 0.90
AGEs increased migration and inflammatory responses of adventitial fibroblasts via RAGE, MAPK and NF-kappaB pathways. Atherosclerosis (2009) 0.89
Photosynthetic complex assembly in Chlamydomonas reinhardtii. Protist (2002) 0.89
Genome-wide analysis of tandem repeats in plants and green algae. G3 (Bethesda) (2014) 0.88
Cdc14p resets the competency of replication licensing by dephosphorylating multiple initiation proteins during mitotic exit in budding yeast. J Cell Sci (2010) 0.88
Protein phosphorylation is a key event of flagellar disassembly revealed by analysis of flagellar phosphoproteins during flagellar shortening in Chlamydomonas. J Proteome Res (2011) 0.88
Origin recognition complex (ORC) mediates histone 3 lysine 4 methylation through cooperation with Spp1 in Saccharomyces cerevisiae. J Biol Chem (2008) 0.88
Effectiveness of a national transitional care program in reducing acute care use. J Am Geriatr Soc (2014) 0.87
Discrimination of cinnamon bark and cinnamon twig samples sourced from various countries using HPLC-based fingerprint analysis. Food Chem (2011) 0.87
MAGIC database and interfaces: an integrated package for gene discovery and expression. Comp Funct Genomics (2004) 0.87
Structural insights into the Cdt1-mediated MCM2-7 chromatin loading. Nucleic Acids Res (2011) 0.86
Palmitic acid promotes endothelial progenitor cells apoptosis via p38 and JNK mitogen-activated protein kinase pathways. Atherosclerosis (2009) 0.85
Light induces phosphorylation of glucan water dikinase, which precedes starch degradation in turions of the duckweed Spirodela polyrhiza. Plant Physiol (2004) 0.85