Published in Nat Biotechnol on December 24, 2006
Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol (2008) 8.55
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet (2012) 8.55
Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet (2010) 5.37
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The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc (2012) 4.41
Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol (2008) 4.34
Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature (2009) 4.07
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Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol (2010) 3.65
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Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A (2010) 3.40
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Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proc Natl Acad Sci U S A (2009) 2.39
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Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. Genome Res (2009) 1.83
Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol (2013) 1.81
Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol (2009) 1.81
Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics (2010) 1.71
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Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol (2009) 1.64
Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages. Nucleic Acids Res (2014) 1.63
Direct link between RACK1 function and localization at the ribosome in vivo. Mol Cell Biol (2008) 1.61
Composite effects of gene determinants on the translation speed and density of ribosomes. Genome Biol (2011) 1.61
Determinants of protein abundance and translation efficiency in S. cerevisiae. PLoS Comput Biol (2007) 1.60
Structural and metabolic transitions of C4 leaf development and differentiation defined by microscopy and quantitative proteomics in maize. Plant Cell (2010) 1.58
Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent. PLoS Biol (2012) 1.58
Proteomics of photoreceptor outer segments identifies a subset of SNARE and Rab proteins implicated in membrane vesicle trafficking and fusion. Mol Cell Proteomics (2008) 1.56
Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol Syst Biol (2010) 1.56
The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics (2008) 1.54
Deletion of the Cel48S cellulase from Clostridium thermocellum. Proc Natl Acad Sci U S A (2010) 1.54
Optimized protein extraction for quantitative proteomics of yeasts. PLoS One (2007) 1.53
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. J Proteome Res (2013) 1.52
Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Mol Cell Proteomics (2011) 1.51
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics (2008) 1.51
Bacterial fatty acid synthesis and its relationships with polyketide synthetic pathways. Methods Enzymol (2009) 1.50
Megadalton complexes in the chloroplast stroma of Arabidopsis thaliana characterized by size exclusion chromatography, mass spectrometry, and hierarchical clustering. Mol Cell Proteomics (2010) 1.50
Uncovering genes with divergent mRNA-protein dynamics in Streptomyces coelicolor. PLoS One (2008) 1.46
Protein synthesis rate is the predominant regulator of protein expression during differentiation. Mol Syst Biol (2013) 1.46
Translational selection is ubiquitous in prokaryotes. PLoS Genet (2010) 1.45
Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs. Mol Syst Biol (2011) 1.45
Perspectives of targeted mass spectrometry for protein biomarker verification. Curr Opin Chem Biol (2009) 1.45
Inference of quantitative models of bacterial promoters from time-series reporter gene data. PLoS Comput Biol (2015) 1.44
The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli. PLoS One (2014) 1.44
Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics. Nucleic Acids Res (2012) 1.43
Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast. Genome Biol (2012) 1.40
You're one in a googol: optimizing genes for protein expression. J R Soc Interface (2009) 1.39
Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics (2007) 1.39
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. J Proteome Res (2012) 1.39
Comparative proteomics of chloroplast envelopes from C3 and C4 plants reveals specific adaptations of the plastid envelope to C4 photosynthesis and candidate proteins required for maintaining C4 metabolite fluxes. Plant Physiol (2008) 1.38
20 years of Nature Biotechnology research tools. Nat Biotechnol (2016) 1.38
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics (2009) 1.37
Functional diversification of duplicate genes through subcellular adaptation of encoded proteins. Genome Biol (2008) 1.37
Integrating shotgun proteomics and mRNA expression data to improve protein identification. Bioinformatics (2009) 1.36
Impact of translational error-induced and error-free misfolding on the rate of protein evolution. Mol Syst Biol (2010) 1.35
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J Proteomics (2010) 1.35
The ribonome: a dominant force in co-ordinating gene expression. Biol Cell (2009) 1.35
Protein expression regulation under oxidative stress. Mol Cell Proteomics (2011) 1.34
A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol (2008) 1.32
Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry. BMC Genomics (2012) 1.31
Genome-wide annotation and quantitation of translation by ribosome profiling. Curr Protoc Mol Biol (2013) 1.30
Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics (2010) 1.29
Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes. J Biol Chem (2009) 1.29
Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol (2010) 1.29
Genome-scale analysis of translation elongation with a ribosome flow model. PLoS Comput Biol (2011) 1.29
What is the total number of protein molecules per cell volume? A call to rethink some published values. Bioessays (2013) 1.28
Tools for label-free peptide quantification. Mol Cell Proteomics (2012) 1.27
Large scale comparative proteomics of a chloroplast Clp protease mutant reveals folding stress, altered protein homeostasis, and feedback regulation of metabolism. Mol Cell Proteomics (2009) 1.27
A bayesian approach to protein inference problem in shotgun proteomics. J Comput Biol (2009) 1.26
Advances in proteomic workflows for systems biology. Curr Opin Biotechnol (2007) 1.26
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis. OMICS (2012) 1.25
Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis. Plant Cell (2009) 1.24
Identifying and quantifying proteolytic events and the natural N terminome by terminal amine isotopic labeling of substrates. Nat Protoc (2011) 1.24
Need-based up-regulation of protein levels in response to deletion of their duplicate genes. PLoS Biol (2010) 1.24
Quantitative dissection of the simple repression input-output function. Proc Natl Acad Sci U S A (2011) 1.23
Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change. Philos Trans R Soc Lond B Biol Sci (2012) 1.22
Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids. BMC Genomics (2008) 1.22
Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol (2015) 1.21
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics (2012) 1.21
The HOG pathway dictates the short-term translational response after hyperosmotic shock. Mol Biol Cell (2010) 1.21
Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol (2010) 1.20
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet (2012) 8.55
A probabilistic functional network of yeast genes. Science (2004) 8.35
Efficacy and safety of a recombinant hepatitis E vaccine in healthy adults: a large-scale, randomised, double-blind placebo-controlled, phase 3 trial. Lancet (2010) 7.11
The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res (2004) 6.72
Comparative experiments on learning information extractors for proteins and their interactions. Artif Intell Med (2005) 5.44
Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes. J Biol Chem (2004) 4.89
Characterising and predicting haploinsufficiency in the human genome. PLoS Genet (2010) 4.85
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
The need for a public proteomics repository. Nat Biotechnol (2004) 4.60
Synthetic biology: engineering Escherichia coli to see light. Nature (2005) 4.58
Clinical empathy as emotional labor in the patient-physician relationship. JAMA (2005) 4.56
Global signatures of protein and mRNA expression levels. Mol Biosyst (2009) 4.43
Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Res (2011) 4.39
Sequence and analysis of rice chromosome 4. Nature (2002) 4.39
The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res (2006) 4.27
Evolution of the protein repertoire. Science (2003) 4.24
A census of human soluble protein complexes. Cell (2012) 3.90
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79
A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet (2008) 3.62
Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line. Mol Syst Biol (2010) 3.56
PD-1 identifies the patient-specific CD8⁺ tumor-reactive repertoire infiltrating human tumors. J Clin Invest (2014) 3.54
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
Influenza virus PB1-F2 protein induces cell death through mitochondrial ANT3 and VDAC1. PLoS Pathog (2005) 3.44
A synthetic genetic edge detection program. Cell (2009) 3.20
Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci U S A (2003) 3.19
Protein interaction networks from yeast to human. Curr Opin Struct Biol (2004) 3.15
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res (2008) 3.07
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol (2010) 2.90
An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae. PLoS One (2007) 2.84
Perilipin A mediates the reversible binding of CGI-58 to lipid droplets in 3T3-L1 adipocytes. J Biol Chem (2004) 2.76
Identification of a KCNE2 gain-of-function mutation in patients with familial atrial fibrillation. Am J Hum Genet (2004) 2.66
Human formyl peptide receptor 2 senses highly pathogenic Staphylococcus aureus. Cell Host Microbe (2010) 2.64
Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A (2010) 2.61
Seminal plasma reduces the effectiveness of topical polyanionic microbicides. J Infect Dis (2007) 2.57
Endothelial FAK is essential for vascular network stability, cell survival, and lamellipodial formation. J Cell Biol (2006) 2.57
Distinct pathways of genomic progression to benign and malignant tumors of the liver. Proc Natl Acad Sci U S A (2007) 2.56
Longer forms of amyloid beta protein: implications for the mechanism of intramembrane cleavage by gamma-secretase. J Neurosci (2005) 2.48
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol (2003) 2.40
Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation. Proc Natl Acad Sci U S A (2009) 2.39
Mean age-of-onset of familial alzheimer disease caused by presenilin mutations correlates with both increased Abeta42 and decreased Abeta40. Hum Mutat (2006) 2.29
Exploiting the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol (2003) 2.24
Purification and characterization of the human gamma-secretase complex. Biochemistry (2004) 2.18
Identification of mutations in CUL7 in 3-M syndrome. Nat Genet (2005) 2.10
Sulforaphane inhibits histone deacetylase activity in BPH-1, LnCaP and PC-3 prostate epithelial cells. Carcinogenesis (2005) 2.05
Direct and potent regulation of gamma-secretase by its lipid microenvironment. J Biol Chem (2008) 2.00
A probabilistic view of gene function. Nat Genet (2004) 1.99
Caloric restriction attenuates beta-amyloid neuropathology in a mouse model of Alzheimer's disease. FASEB J (2005) 1.90
Endothelial expression of constitutively active Notch4 elicits reversible arteriovenous malformations in adult mice. Proc Natl Acad Sci U S A (2005) 1.90
The planar cell polarity effector Fuz is essential for targeted membrane trafficking, ciliogenesis and mouse embryonic development. Nat Cell Biol (2009) 1.90
Traditional Chinese medication Tongxinluo dose-dependently enhances stability of vulnerable plaques: a comparison with a high-dose simvastatin therapy. Am J Physiol Heart Circ Physiol (2009) 1.90
CUL7: A DOC domain-containing cullin selectively binds Skp1.Fbx29 to form an SCF-like complex. Proc Natl Acad Sci U S A (2002) 1.89
The relationship between alcohol use and cigarette smoking in a sample of undergraduate college students. Addict Behav (2006) 1.89
Mobile genetic element-encoded cytolysin connects virulence to methicillin resistance in MRSA. PLoS Pathog (2009) 1.89
The Bacillus subtilis spore coat protein interaction network. Mol Microbiol (2006) 1.88
Phospholipase dalpha1 and phosphatidic acid regulate NADPH oxidase activity and production of reactive oxygen species in ABA-mediated stomatal closure in Arabidopsis. Plant Cell (2009) 1.88
Immunogenicity and safety of an enterovirus 71 vaccine in healthy Chinese children and infants: a randomised, double-blind, placebo-controlled phase 2 clinical trial. Lancet (2013) 1.87
Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping. Anal Chem (2006) 1.85
Vascular development of the brain requires beta8 integrin expression in the neuroepithelium. J Neurosci (2005) 1.85
Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol (2009) 1.81
Role of the accessory gene regulator agr in community-associated methicillin-resistant Staphylococcus aureus pathogenesis. Infect Immun (2011) 1.79
Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol Cell (2010) 1.79
Senescence-associated exosome release from human prostate cancer cells. Cancer Res (2008) 1.78
The CUL7 E3 ubiquitin ligase targets insulin receptor substrate 1 for ubiquitin-dependent degradation. Mol Cell (2008) 1.73
Broad network-based predictability of Saccharomyces cerevisiae gene loss-of-function phenotypes. Genome Biol (2007) 1.73
Inhibition of notch signaling in glioblastoma targets cancer stem cells via an endothelial cell intermediate. Stem Cells (2010) 1.72
DEN1 is a dual function protease capable of processing the C terminus of Nedd8 and deconjugating hyper-neddylated CUL1. J Biol Chem (2003) 1.72
Protein abundances are more conserved than mRNA abundances across diverse taxa. Proteomics (2010) 1.71
Local injury to the endometrium in controlled ovarian hyperstimulation cycles improves implantation rates. Fertil Steril (2007) 1.65
A susceptibility locus at chromosome 3p21 linked to familial nasopharyngeal carcinoma. Cancer Res (2004) 1.65
LGL: creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol (2004) 1.65
Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data. Nat Protoc (2008) 1.62
A birth cohort analysis of the incidence of papillary thyroid cancer in the United States, 1973-2004. Thyroid (2009) 1.62
Emission factors of particulate matter and elemental carbon for crop residues and coals burned in typical household stoves in China. Environ Sci Technol (2010) 1.61
Systems approach to explore components and interactions in the presynapse. Proteomics (2009) 1.61
Staphylococcus epidermidis strategies to avoid killing by human neutrophils. PLoS Pathog (2010) 1.60
The use of hsa-miR-21, hsa-miR-181b and hsa-miR-106a as prognostic indicators of astrocytoma. Eur J Cancer (2010) 1.60
Predicting genetic modifier loci using functional gene networks. Genome Res (2010) 1.59
Evolutionarily repurposed networks reveal the well-known antifungal drug thiabendazole to be a novel vascular disrupting agent. PLoS Biol (2012) 1.58
It's the machine that matters: Predicting gene function and phenotype from protein networks. J Proteomics (2010) 1.57
Genetic background regulates beta-amyloid precursor protein processing and beta-amyloid deposition in the mouse. Hum Mol Genet (2003) 1.55
The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results. BMC Bioinformatics (2008) 1.54
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol (2008) 1.54
The cost of breast cancer screening in the Medicare population. JAMA Intern Med (2013) 1.53
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53
BDNF Val66Met polymorphism is associated with unstable angina. Clin Chim Acta (2008) 1.52
Interaction dynamics of neuronal oscillations analysed using wavelet transforms. J Neurosci Methods (2006) 1.52
Mutated PPP1R3B is recognized by T cells used to treat a melanoma patient who experienced a durable complete tumor regression. J Immunol (2013) 1.50
Understanding regional variation in Medicare expenditures for initial episodes of prostate cancer care. Med Care (2014) 1.50
Morphogenesis of bacillus spore surfaces. J Bacteriol (2003) 1.50
Identification and characterization of the constituent human serum antibodies elicited by vaccination. Proc Natl Acad Sci U S A (2014) 1.50
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Mu-calpain mediates hippocampal neuron death in rats after lithium-pilocarpine-induced status epilepticus. Brain Res Bull (2008) 1.46