Published in Bioinformatics on August 04, 2004
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol (2008) 5.26
Systems approach to refining genome annotation. Proc Natl Acad Sci U S A (2006) 3.58
Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics (2007) 2.74
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57
Classification of microarray data using gene networks. BMC Bioinformatics (2007) 2.44
GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol (2009) 2.41
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Systematizing the generation of missing metabolic knowledge. Biotechnol Bioeng (2010) 1.85
Influence of metabolic network structure and function on enzyme evolution. Genome Biol (2006) 1.79
Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol (2006) 1.68
Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics (2006) 1.65
A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A (2006) 1.59
In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun (2012) 1.58
Automatic policing of biochemical annotations using genomic correlations. Nat Chem Biol (2009) 1.31
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. BMC Syst Biol (2011) 1.19
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content. J Bacteriol (2009) 1.14
Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli. J Bacteriol (2007) 1.13
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. PLoS Comput Biol (2012) 0.99
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks. Genome Biol (2012) 0.97
GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res (2012) 0.95
The MORPH algorithm: ranking candidate genes for membership in Arabidopsis and tomato pathways. Plant Cell (2012) 0.85
Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum. PLoS Comput Biol (2013) 0.84
Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis. Microb Cell Fact (2007) 0.82
Automation of gene assignments to metabolic pathways using high-throughput expression data. BMC Bioinformatics (2005) 0.82
Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network. PLoS One (2010) 0.81
Computational approaches for microalgal biofuel optimization: a review. Biomed Res Int (2014) 0.79
CINPER: an interactive web system for pathway prediction for prokaryotes. PLoS One (2012) 0.79
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. Bioinformatics (2016) 0.76
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis. Biophys Physicobiol (2016) 0.75
Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore . Metabolites (2012) 0.75
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. Front Microbiol (2016) 0.75
Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. Syst Synth Biol (2012) 0.75
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in Streptomyces coelicolor. BMC Res Notes (2011) 0.75
Missing gene identification using functional coherence scores. Sci Rep (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
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
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
Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. Neuron (2011) 4.66
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
Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci U S A (2008) 3.37
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 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
Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics (2004) 2.76
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
Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res (2009) 2.38
Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature (2007) 2.27
The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell (2008) 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
Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Nat Biotechnol (2013) 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
A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. PLoS Genet (2010) 1.81
Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods (2008) 1.77
Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. Mol Cell Proteomics (2008) 1.76
Escherichia coli gene expression responsive to levels of the response regulator EvgA. J Bacteriol (2002) 1.74
Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J Mol Biol (2002) 1.73
Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics (2013) 1.72
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res (2010) 1.72
Localization to the proteasome is sufficient for degradation. J Biol Chem (2004) 1.72