Published in Proteomics on January 01, 2004
The complete genome and proteome of Mycoplasma mobile. Genome Res (2004) 3.36
AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res (2006) 2.92
The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol (2009) 2.85
Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res (2007) 2.67
Towards synthesis of a minimal cell. Mol Syst Biol (2006) 2.55
AgBase: a functional genomics resource for agriculture. BMC Genomics (2006) 2.53
Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31
A Multicomponent Animal Virus Isolated from Mosquitoes. Cell Host Microbe (2016) 2.19
Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat Methods (2011) 1.95
Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations. Genome Res (2008) 1.90
Systems biology: Functional analysis of natural microbial consortia using community proteomics. Nat Rev Microbiol (2009) 1.81
Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics (2010) 1.71
Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res (2008) 1.68
Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra. Mol Cell Proteomics (2008) 1.60
Proteogenomics: concepts, applications and computational strategies. Nat Methods (2014) 1.54
Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics (2005) 1.51
AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Res (2010) 1.48
Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol Syst Biol (2012) 1.44
Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res (2005) 1.43
Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions. BMC Genomics (2013) 1.38
Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res (2010) 1.37
Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol. Genome Res (2008) 1.36
Generating and navigating proteome maps using mass spectrometry. Nat Rev Mol Cell Biol (2010) 1.29
Complete genome and proteome of Acholeplasma laidlawii. J Bacteriol (2011) 1.24
Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. Mol Cell Proteomics (2009) 1.24
A ranking-based scoring function for peptide-spectrum matches. J Proteome Res (2009) 1.22
The speciation of the proteome. Chem Cent J (2008) 1.21
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome Res (2011) 1.20
Systematic unraveling of the unsolved pathway of nicotine degradation in Pseudomonas. PLoS Genet (2013) 1.19
Transposon mutagenesis identifies genes associated with Mycoplasma pneumoniae gliding motility. J Bacteriol (2006) 1.15
Multiple-mutation reaction: a method for simultaneous introduction of multiple mutations into the glpK gene of Mycoplasma pneumoniae. Appl Environ Microbiol (2005) 1.14
In vivo activity of enzymatic and regulatory components of the phosphoenolpyruvate:sugar phosphotransferase system in Mycoplasma pneumoniae. J Bacteriol (2004) 1.11
The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases. Mol Cell Proteomics (2010) 1.09
Analysis of the zebrafish proteome during embryonic development. Mol Cell Proteomics (2008) 1.09
Computational analysis and experimental validation of gene predictions in Toxoplasma gondii. PLoS One (2008) 1.08
Comparative proteogenomic analysis of the Leptospira interrogans virulence-attenuated strain IPAV against the pathogenic strain 56601. Cell Res (2011) 1.07
Mycoplasma pneumoniae Community Acquired Respiratory Distress Syndrome toxin expression reveals growth phase and infection-dependent regulation. Mol Microbiol (2010) 1.05
Addressing statistical biases in nucleotide-derived protein databases for proteogenomic search strategies. J Proteome Res (2012) 1.04
Experimental determination of translational starts using peptide mass mapping and tandem mass spectrometry within the proteome of Mycobacterium tuberculosis. Microbiology (2007) 1.03
The proteogenomic mapping tool. BMC Bioinformatics (2011) 1.01
Synthesis, stability, and function of cytadhesin P1 and accessory protein B/C complex of Mycoplasma pneumoniae. J Bacteriol (2006) 0.99
Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics (2009) 0.97
EPIC-DB: a proteomics database for studying Apicomplexan organisms. BMC Genomics (2009) 0.96
A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biol (2008) 0.96
Introduction to computational proteomics. PLoS Comput Biol (2007) 0.94
Comparative genome analysis of Mycoplasma pneumoniae. BMC Genomics (2015) 0.94
Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics (2013) 0.94
Lipoprotein multigene families in Mycoplasma pneumoniae. J Bacteriol (2006) 0.93
Genomic analysis reveals Mycoplasma pneumoniae repetitive element 1-mediated recombination in a clinical isolate. Infect Immun (2008) 0.92
A honey bee (Apis mellifera L.) PeptideAtlas crossing castes and tissues. BMC Genomics (2011) 0.89
Toxoplasma gondii proteomics. Expert Rev Proteomics (2009) 0.89
OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol (2011) 0.88
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum. BMC Bioinformatics (2009) 0.88
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. BMC Genomics (2011) 0.88
Proteomic analysis of acidic chaperones, and stress proteins in extreme halophile Halobacterium NRC-1: a comparative proteomic approach to study heat shock response. Proteome Sci (2006) 0.86
Accelerating string set matching in FPGA hardware for bioinformatics research. BMC Bioinformatics (2008) 0.86
The Mycoplasma pneumoniae MPN490 and Mycoplasma genitalium MG339 genes encode reca homologs that promote homologous DNA strand exchange. Infect Immun (2009) 0.84
Identification of novel immunogenic proteins from Mycoplasma bovis and establishment of an indirect ELISA based on recombinant E1 beta subunit of the pyruvate dehydrogenase complex. PLoS One (2014) 0.84
Protein profiling of human nonpigmented ciliary epithelium cell secretome: the differentiation factors characterization for retinal ganglion cell line. J Biomed Biotechnol (2011) 0.83
Proteogenomic convergence for understanding cancer pathways and networks. Clin Proteomics (2014) 0.83
JUMPg: An Integrative Proteogenomics Pipeline Identifying Unannotated Proteins in Human Brain and Cancer Cells. J Proteome Res (2016) 0.82
Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline. Mol Cell Proteomics (2014) 0.82
Proteomics characterization of cytoplasmic and lipid-associated membrane proteins of human pathogen Mycoplasma fermentans M64. PLoS One (2012) 0.80
Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances. Nucleic Acids Res (2016) 0.80
A proteogenomic analysis of Shigella flexneri using 2D LC-MALDI TOF/TOF. BMC Genomics (2011) 0.79
Comparative analysis of genomics and proteomics in Bacillus thuringiensis 4.0718. PLoS One (2015) 0.79
Probing in vivo promoter activities in Mycoplasma pneumoniae: a system for generation of single-copy reporter constructs. Appl Environ Microbiol (2006) 0.79
Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs. BMC Bioinformatics (2006) 0.78
A note on the false discovery rate of novel peptides in proteogenomics. Bioinformatics (2015) 0.78
Structural Proteomics of Herpesviruses. Viruses (2016) 0.77
Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis. Sci Rep (2016) 0.77
N-Terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography. Mol Cell Proteomics (2014) 0.77
Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232. BMC Genomics (2014) 0.76
Proteomic profiling for peritoneal dialysate: differential protein expression in diabetes mellitus. Biomed Res Int (2013) 0.76
Dual use of peptide mass spectra: Protein atlas and genome annotation. Curr Plant Biol (2015) 0.75
Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification. BMC Genomics (2016) 0.75
Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline. Mol Cell Proteomics (2016) 0.75
P40 and P90 from Mpn142 are Targets of Multiple Processing Events on the Surface of Mycoplasma pneumoniae. Proteomes (2015) 0.75
Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. Annu Rev Anal Chem (Palo Alto Calif) (2016) 0.75
Proteomics progresses in microbial physiology and clinical antimicrobial therapy. Eur J Clin Microbiol Infect Dis (2016) 0.75
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. Am J Trop Med Hyg (2016) 0.75
A proteomic view to characterize the effect of chitosan nanoparticle to hepatic cells: is chitosan nanoparticle an enhancer of PI3K/AKT1/mTOR pathway? Biomed Res Int (2014) 0.75
Pivotal Role of Computers and Software in Mass Spectrometry - SEQUEST and 20 Years of Tandem MS Database Searching. J Am Soc Mass Spectrom (2015) 0.75
GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes. Mol Cell Proteomics (2016) 0.75
RNA-guided human genome engineering via Cas9. Science (2013) 48.29
Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24
Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91
Multiplex amplification of large sets of human exons. Nat Methods (2007) 15.11
Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol (2005) 14.29
Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol (2011) 12.86
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol (2013) 11.35
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol (2009) 11.18
Clinical assessment incorporating a personal genome. Lancet (2010) 10.18
Advanced sequencing technologies: methods and goals. Nat Rev Genet (2004) 9.31
Modular epistasis in yeast metabolism. Nat Genet (2004) 8.64
Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A (2002) 8.41
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol (2005) 8.32
Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A (2003) 7.95
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res (2013) 7.77
Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol (2006) 7.64
Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science (2009) 6.96
A highly annotated whole-genome sequence of a Korean individual. Nature (2009) 6.91
Cas9 as a versatile tool for engineering biology. Nat Methods (2013) 6.87
From genetic privacy to open consent. Nat Rev Genet (2008) 5.95
Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods (2013) 5.93
Receptor sensitivity in bacterial chemotaxis. Proc Natl Acad Sci U S A (2001) 5.90
The brain activity map project and the challenge of functional connectomics. Neuron (2012) 5.52
Computational and experimental identification of C. elegans microRNAs. Mol Cell (2003) 5.22
Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science (2007) 5.19
Functional interactions between receptors in bacterial chemotaxis. Nature (2004) 5.01
A logic-gated nanorobot for targeted transport of molecular payloads. Science (2012) 4.96
Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res (2002) 4.83
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods (2013) 4.61
Genome engineering. Nat Biotechnol (2009) 4.60
Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell (2006) 4.51
Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc Natl Acad Sci U S A (2002) 4.44
Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods (2009) 4.38
Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet (2007) 4.25
Tuberculosis drug resistance mutation database. PLoS Med (2009) 4.13
Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol (2002) 4.00
Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol (2013) 3.84
Highly multiplexed subcellular RNA sequencing in situ. Science (2014) 3.77
Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature (2012) 3.74
A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A (2012) 3.72
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A (2006) 3.68
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol (2006) 3.68
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell (2011) 3.61
Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics (2009) 3.50
Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science (2011) 3.49
Bacteria subsisting on antibiotics. Science (2008) 3.47
Information access. Raw personal data: providing access. Science (2014) 3.41
Neuroscience. The brain activity map. Science (2013) 3.36
Generation of functional human hepatic endoderm from human induced pluripotent stem cells. Hepatology (2010) 3.36
The complete genome and proteome of Mycoplasma mobile. Genome Res (2004) 3.36
Computational discovery of sense-antisense transcription in the human and mouse genomes. Genome Biol (2002) 3.28
Gene synthesis by circular assembly amplification. Nat Methods (2007) 3.21
Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet (2011) 3.20
Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol (2010) 3.14
Photosynthesis genes in marine viruses yield proteins during host infection. Nature (2005) 2.99
The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell (2006) 2.99
Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res (2003) 2.97
Reprogramming of T cells from human peripheral blood. Cell Stem Cell (2010) 2.93
Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res (2009) 2.91
The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop. Genet Med (2009) 2.91
The challenges of sequencing by synthesis. Nat Biotechnol (2009) 2.89
A molecular clutch disables flagella in the Bacillus subtilis biofilm. Science (2008) 2.86
A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet (2009) 2.78
Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci U S A (2003) 2.77
Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res (2002) 2.74
Nanotools for neuroscience and brain activity mapping. ACS Nano (2013) 2.74
Genomically recoded organisms expand biological functions. Science (2013) 2.73
Fluorescent in situ sequencing on polymerase colonies. Anal Biochem (2003) 2.70
High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol (2010) 2.68
The amino-acid mutational spectrum of human genetic disease. Genome Biol (2003) 2.55
Towards synthesis of a minimal cell. Mol Syst Biol (2006) 2.55
Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet (2002) 2.52
Regulatory network of acid resistance genes in Escherichia coli. Mol Microbiol (2003) 2.42
Modeling the chemotactic response of Escherichia coli to time-varying stimuli. Proc Natl Acad Sci U S A (2008) 2.41
Moving fluid with bacterial carpets. Biophys J (2004) 2.41
Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. Proc Natl Acad Sci U S A (2002) 2.40
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res (2009) 2.38
Escherichia coli swim on the right-hand side. Nature (2005) 2.37
Hydrodynamic attraction of swimming microorganisms by surfaces. Phys Rev Lett (2008) 2.28
Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature (2007) 2.27
A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol Syst Biol (2010) 2.27
On torque and tumbling in swimming Escherichia coli. J Bacteriol (2006) 2.26
The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell (2008) 2.19
An open letter to Elias Zerhouni. Science (2005) 2.19
Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res (2011) 2.12
A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res (2003) 2.10
Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res (2012) 2.09
Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev (2005) 2.06
From systems biology to synthetic biology. Mol Syst Biol (2005) 2.05
Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res (2002) 2.04
Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol (2009) 1.99
An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A Biol Sci Med Sci (2007) 1.98
Causes and effects of N-terminal codon bias in bacterial genes. Science (2013) 1.95
Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat Genet (2006) 1.92
Force and velocity of mycoplasma mobile gliding. J Bacteriol (2002) 1.91
Autoantigen discovery with a synthetic human peptidome. Nat Biotechnol (2011) 1.90
PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics (2006) 1.90
Expression dynamics of a cellular metabolic network. Mol Syst Biol (2005) 1.85
Resurrection of the flagellar rotary motor near zero load. Proc Natl Acad Sci U S A (2008) 1.85