Published in PLoS One on May 14, 2010
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol (2012) 1.53
Further developments towards a genome-scale metabolic model of yeast. BMC Syst Biol (2010) 1.20
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction. PLoS Comput Biol (2015) 0.80
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
Life with 6000 genes. Science (1996) 41.51
Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science (1999) 36.25
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (2003) 32.92
KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res (2007) 29.46
Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48
The ENZYME database in 2000. Nucleic Acids Res (2000) 23.85
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2008) 21.36
Global mapping of the yeast genetic interaction network. Science (2004) 21.34
Ensembl 2007. Nucleic Acids Res (2006) 20.10
UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics (2007) 17.43
The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33
The Pathway Tools software. Bioinformatics (2002) 14.89
IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82
ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res (2007) 13.08
KEGG as a glycome informatics resource. Glycobiology (2005) 11.05
Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol (2005) 10.66
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res (2007) 10.62
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res (2006) 9.49
Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics (2007) 9.45
LIGAND: chemical database for enzyme reactions. Bioinformatics (1998) 8.36
The vertebrate genome annotation (Vega) database. Nucleic Acids Res (2007) 7.53
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res (2003) 7.22
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res (2000) 7.10
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res (2004) 6.21
What is a support vector machine? Nat Biotechnol (2006) 5.10
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol (2008) 4.55
Integrating biological databases. Nat Rev Genet (2003) 4.41
Systems biology markup language: Level 2 and beyond. Biochem Soc Trans (2003) 4.11
Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res (2004) 3.61
How complete are current yeast and human protein-interaction networks? Genome Biol (2006) 3.50
High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol (2003) 3.48
Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res (2005) 2.68
Addressing the problems with life-science databases for traditional uses and systems biology. Nat Rev Genet (2006) 1.97
Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics (2006) 1.97
Enhancement of the chemical semantic web through the use of InChI identifiers. Org Biomol Chem (2005) 1.77
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst Biol (2008) 1.73
Filling gaps in a metabolic network using expression information. Bioinformatics (2004) 1.69
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
PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways. Nucleic Acids Res (2006) 1.37
New surveyor tools for charting microbial metabolic maps. Nat Rev Microbiol (2008) 1.28
Essentiality and damage in metabolic networks. Bioinformatics (2004) 1.13
GNARE: automated system for high-throughput genome analysis with grid computational backend. J Clin Monit Comput (2005) 0.90
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Somatic STAT3 mutations in large granular lymphocytic leukemia. N Engl J Med (2012) 4.15
High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol (2010) 3.21
STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res (2009) 3.06
Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol (2011) 2.78
Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics (2004) 2.63
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature (2013) 2.61
eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol (2008) 2.45
CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics (2003) 2.28
In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinformatics (2005) 2.26
Robust detection of periodic time series measured from biological systems. BMC Bioinformatics (2005) 2.14
Posttranscriptional expression regulation: what determines translation rates? PLoS Comput Biol (2007) 2.09
Integrated assessment and prediction of transcription factor binding. PLoS Comput Biol (2006) 2.04
Gene expression dynamics in the macrophage exhibit criticality. Proc Natl Acad Sci U S A (2008) 1.95
Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov (2013) 1.93
The role of certain Post classes in Boolean network models of genetic networks. Proc Natl Acad Sci U S A (2003) 1.89
Hypusination of eukaryotic initiation factor 5A (eIF5A): a novel therapeutic target in BCR-ABL-positive leukemias identified by a proteomics approach. Blood (2006) 1.85
Full-Genome Sequences of Influenza A(H1N1)pdm09 Viruses Isolated from Finnish Patients from 2009 to 2013. Genome Announc (2014) 1.82
The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma. J Clin Invest (2013) 1.76
Software for quantification of labeled bacteria from digital microscope images by automated image analysis. Biotechniques (2005) 1.76
Computational framework for simulating fluorescence microscope images with cell populations. IEEE Trans Med Imaging (2007) 1.69
Modulation of TET2 expression and 5-methylcytosine oxidation by the CXXC domain protein IDAX. Nature (2013) 1.65
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Processing (2006) 1.61
Toxin-gene profile heterogeneity among endemic invasive European group A streptococcal isolates. J Infect Dis (2003) 1.56
Detection and interpretation of expression quantitative trait loci (eQTL). Methods (2009) 1.48
Global gene expression profile of human cord blood-derived CD133+ cells. Stem Cells (2005) 1.42
DiProDB: a database for dinucleotide properties. Nucleic Acids Res (2008) 1.41
Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans Med Imaging (2005) 1.36
Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics (2010) 1.31
Constitutive upregulation of the transforming growth factor-beta pathway in rheumatoid arthritis synovial fibroblasts. Arthritis Res Ther (2007) 1.29
Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity (2010) 1.28
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics. Bioinformatics (2009) 1.28
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity (2013) 1.27
Thymidine kinase 2 mutations in autosomal recessive progressive external ophthalmoplegia with multiple mitochondrial DNA deletions. Hum Mol Genet (2011) 1.26
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics (2007) 1.24
A novel strategy for microarray quality control using Bayesian networks. Bioinformatics (2003) 1.23
Protein networks markedly improve prediction of subcellular localization in multiple eukaryotic species. Nucleic Acids Res (2008) 1.22
Brachial plexus hypertrophy in chronic inflammatory demyelinating polyradiculoneuropathy. Neuromuscul Disord (2006) 1.20
A single-nucleotide substitution mutator phenotype revealed by exome sequencing of human colon adenomas. Cancer Res (2012) 1.19
Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. PLoS One (2009) 1.19
Predicting functionality of protein-DNA interactions by integrating diverse evidence. Bioinformatics (2009) 1.16
Gene expression profiling of potential PPARgamma target genes in mouse aorta. Physiol Genomics (2004) 1.12
Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett (2008) 1.12
Simulation of microarray data with realistic characteristics. BMC Bioinformatics (2006) 1.12
Structural robustness of metabolic networks with respect to multiple knockouts. J Theor Biol (2007) 1.11
Large-scale de novo prediction of physical protein-protein association. Mol Cell Proteomics (2011) 1.11
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images. BMC Bioinformatics (2010) 1.10
Improved triacylglycerol production in Acinetobacter baylyi ADP1 by metabolic engineering. Microb Cell Fact (2011) 1.08
Data-driven assessment of eQTL mapping methods. BMC Genomics (2010) 1.08
Effects of transcriptional pausing on gene expression dynamics. PLoS Comput Biol (2010) 1.06
Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells. Nat Struct Mol Biol (2010) 1.05
Identification and characterization of protein subcomplexes in yeast. Proteomics (2005) 1.05
Differential gene expression in adipose stem cells cultured in allogeneic human serum versus fetal bovine serum. Tissue Eng Part A (2010) 1.05
DiProGB: the dinucleotide properties genome browser. Bioinformatics (2009) 1.05
Stochastic differential equation model for cerebellar granule cell excitability. PLoS Comput Biol (2008) 1.04
Analysis of signaling pathways in 90 cancer cell lines by protein lysate array. J Proteome Res (2007) 1.04
Full-Genome Sequences of Influenza H3N2 Virus Strains Isolated from Finnish Patients during the 2012-2013 Epidemic Season. Genome Announc (2014) 1.04
The Drosophila hugin gene codes for myostimulatory and ecdysis-modifying neuropeptides. Mech Dev (2002) 1.02
Simulating fluorescent microscope images of cell populations. Conf Proc IEEE Eng Med Biol Soc (2005) 1.01
RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells (2012) 1.01
Simulation tools for biochemical networks: evaluation of performance and usability. Bioinformatics (2004) 1.01
Assessing computational methods for transcription factor target gene identification based on ChIP-seq data. PLoS Comput Biol (2013) 1.00
Identification of early gene expression changes during human Th17 cell differentiation. Blood (2012) 0.99
A linear model for transcription factor binding affinity prediction in protein binding microarrays. PLoS One (2011) 0.99
The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. BMC Genomics (2010) 0.98
In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate-limiting steps. BMC Syst Biol (2011) 0.97
Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma. J Pathol (2013) 0.96
Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music. PLoS One (2013) 0.94
Common patterns in type II restriction enzyme binding sites. Nucleic Acids Res (2005) 0.94
Impact of natural genetic variation on gene expression dynamics. PLoS Genet (2013) 0.93
Segmentation of folds in tissue section images. Conf Proc IEEE Eng Med Biol Soc (2007) 0.93
The miR-15a-miR-16-1 locus is homozygously deleted in a subset of prostate cancers. Genes Chromosomes Cancer (2011) 0.93
Draft Genome Sequence of the Hydrogen- and Ethanol-Producing Anaerobic Alkalithermophilic Bacterium Caloramator celer. Genome Announc (2013) 0.92
A data integration framework for prediction of transcription factor targets. Ann N Y Acad Sci (2009) 0.92
Extensive mass spectrometry-based analysis of the fission yeast proteome: the Schizosaccharomyces pombe PeptideAtlas. Mol Cell Proteomics (2013) 0.92
Information diversity in structure and dynamics of simulated neuronal networks. Front Comput Neurosci (2011) 0.92
Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells. Nucleic Acids Res (2012) 0.92
Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time. J Bacteriol (2012) 0.91
Leukemia prediction using sparse logistic regression. PLoS One (2013) 0.90
Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli. Mol Biosyst (2011) 0.90