Published in Annu Rev Genomics Hum Genet on January 01, 2001
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol (2006) 5.57
Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A (2002) 5.29
Systems medicine: the future of medical genomics and healthcare. Genome Med (2009) 3.85
Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol (2009) 3.60
Epistasis and its implications for personal genetics. Am J Hum Genet (2009) 3.52
Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res (2004) 3.36
Why do hubs tend to be essential in protein networks? PLoS Genet (2006) 3.29
A first version of the Caenorhabditis elegans Promoterome. Genome Res (2004) 3.29
Synthetic multivalent ligands as probes of signal transduction. Angew Chem Int Ed Engl (2006) 3.29
cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics (2006) 3.24
SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res (2009) 3.18
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A (2003) 3.15
A data integration methodology for systems biology. Proc Natl Acad Sci U S A (2005) 2.93
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues. Bioinformatics (2005) 2.82
Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell (2005) 2.82
Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep (2003) 2.51
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol Syst Biol (2011) 2.44
Chemical combination effects predict connectivity in biological systems. Mol Syst Biol (2007) 2.42
Complex systems thinking and current impasses in health disparities research. Am J Public Health (2011) 2.42
Software for systems biology: from tools to integrated platforms. Nat Rev Genet (2011) 2.42
Systems vaccinology. Immunity (2010) 2.36
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics (2009) 2.36
A decade of systems biology. Annu Rev Cell Dev Biol (2010) 2.30
Robustness: mechanisms and consequences. Trends Genet (2009) 2.27
Database development in toxicogenomics: issues and efforts. Environ Health Perspect (2004) 2.26
Can cancer be reversed by engineering the tumor microenvironment? Semin Cancer Biol (2008) 2.07
From systems biology to synthetic biology. Mol Syst Biol (2005) 2.05
Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle? Brief Bioinform (2012) 2.00
Deformation and failure of protein materials in physiologically extreme conditions and disease. Nat Mater (2009) 2.00
Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J Bacteriol (2003) 1.98
SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics (2006) 1.94
Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol (2004) 1.90
Analysis of tissue specimens by matrix-assisted laser desorption/ionization imaging mass spectrometry in biological and clinical research. Chem Rev (2013) 1.80
Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep (2003) 1.76
Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface (2009) 1.69
Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proc Natl Acad Sci U S A (2007) 1.63
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. Proc Natl Acad Sci U S A (2005) 1.63
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
Systematic quantification of gene interactions by phenotypic array analysis. Genome Biol (2004) 1.60
Nanotechnology, nanotoxicology, and neuroscience. Prog Neurobiol (2008) 1.59
A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination. PLoS One (2015) 1.58
In control: systematic assessment of microarray performance. EMBO Rep (2004) 1.55
Why are computational neuroscience and systems biology so separate? PLoS Comput Biol (2008) 1.50
Age of ovary determines remaining life expectancy in old ovariectomized mice. Aging Cell (2003) 1.50
Prediction of phenotype and gene expression for combinations of mutations. Mol Syst Biol (2007) 1.48
Mass spectrometry-based proteomics: existing capabilities and future directions. Chem Soc Rev (2012) 1.47
Maximal extraction of biological information from genetic interaction data. PLoS Comput Biol (2009) 1.42
A review of imaging techniques for systems biology. BMC Syst Biol (2008) 1.42
A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis. Plant Cell (2012) 1.42
Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. J Mol Evol (2005) 1.41
An iterative identification procedure for dynamic modeling of biochemical networks. BMC Syst Biol (2010) 1.41
Prediction of graft-versus-host disease in humans by donor gene-expression profiling. PLoS Med (2007) 1.40
A fluctuation method to quantify in vivo fluorescence data. Biophys J (2006) 1.39
Temporal transcriptional profiling of somatic and germ cells reveals biased lineage priming of sexual fate in the fetal mouse gonad. PLoS Genet (2012) 1.38
Improved prediction of prostate cancer recurrence through systems pathology. J Clin Invest (2007) 1.35
BioMediator data integration: beyond genomics to neuroscience data. AMIA Annu Symp Proc (2005) 1.34
Basic research in HIV vaccinology is hampered by reductionist thinking. Front Immunol (2012) 1.33
Construction of regulatory networks using expression time-series data of a genotyped population. Proc Natl Acad Sci U S A (2011) 1.31
Cardiovascular networks: systems-based approaches to cardiovascular disease. Circulation (2010) 1.30
The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact (2010) 1.26
Efficient characterization of high-dimensional parameter spaces for systems biology. BMC Syst Biol (2011) 1.26
Biological context networks: a mosaic view of the interactome. Mol Syst Biol (2006) 1.24
Synthetic protocell biology: from reproduction to computation. Philos Trans R Soc Lond B Biol Sci (2007) 1.23
Pleiotropy, homeostasis, and functional networks based on assays of cardiovascular traits in genetically randomized populations. Genome Res (2003) 1.22
Lessons from mathematically modeling the NF-κB pathway. Immunol Rev (2012) 1.22
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach. PLoS Comput Biol (2006) 1.21
Systems approaches to identifying gene regulatory networks in plants. Annu Rev Cell Dev Biol (2008) 1.21
Proteomic identification of multitasking proteins in unexpected locations complicates drug targeting. Nat Rev Drug Discov (2009) 1.21
Wnt signalling pathway parameters for mammalian cells. PLoS One (2012) 1.20
Systems vaccinology: learning to compute the behavior of vaccine induced immunity. Wiley Interdiscip Rev Syst Biol Med (2011) 1.19
Image-derived, three-dimensional generative models of cellular organization. Cytometry A (2011) 1.16
Bioinformatics and systems biology of the lipidome. Chem Rev (2011) 1.14
Integration of metabolomic and proteomic phenotypes: analysis of data covariance dissects starch and RFO metabolism from low and high temperature compensation response in Arabidopsis thaliana. Mol Cell Proteomics (2008) 1.13
Hybridization kinetics is different inside cells. Proc Natl Acad Sci U S A (2009) 1.13
Systems biology for the virtual plant. Plant Physiol (2005) 1.11
Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: coarse grained views of metabolic pathways. PLoS One (2008) 1.11
Normal morphogenesis of epithelial tissues and progression of epithelial tumors. Wiley Interdiscip Rev Syst Biol Med (2011) 1.10
Transcriptome and proteome exploration to model translation efficiency and protein stability in Lactococcus lactis. PLoS Comput Biol (2009) 1.10
The acute inflammatory response in trauma / hemorrhage and traumatic brain injury: current state and emerging prospects. Libyan J Med (2009) 1.08
Identification of blood biomarkers of rheumatoid arthritis by transcript profiling of peripheral blood mononuclear cells from the rat collagen-induced arthritis model. Arthritis Res Ther (2006) 1.08
Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. BMC Syst Biol (2008) 1.08
Rule-based spatial modeling with diffusing, geometrically constrained molecules. BMC Bioinformatics (2010) 1.07
Linear low-dose extrapolation for noncancer heath effects is the exception, not the rule. Crit Rev Toxicol (2011) 1.07
Genomes, phylogeny, and evolutionary systems biology. Proc Natl Acad Sci U S A (2005) 1.07
An integrated systems biology approach to the study of preterm birth using "-omic" technology--a guideline for research. BMC Pregnancy Childbirth (2011) 1.06
Advancing cancer systems biology: introducing the Center for the Development of a Virtual Tumor, CViT. Cancer Inform (2007) 1.05
Comparative analysis of multiple genome-scale data sets. Genome Res (2002) 1.05
Systems-based approaches to cardiovascular disease. Nat Rev Cardiol (2012) 1.04
Systems biology of fungal infection. Front Microbiol (2012) 1.04
The University of Washington Health Sciences Library BioCommons: an evolving Northwest biomedical research information support infrastructure. J Med Libr Assoc (2006) 1.04
Method for analyzing signaling networks in complex cellular systems. Proc Natl Acad Sci U S A (2004) 1.03
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments. Mol Syst Biol (2009) 1.03
Quantitative microscopy and systems biology: seeing the whole picture. Histochem Cell Biol (2008) 1.02
Qualitative networks: a symbolic approach to analyze biological signaling networks. BMC Syst Biol (2007) 1.02
Translational systems biology of inflammation and healing. Wound Repair Regen (2010) 1.02
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. BMC Syst Biol (2013) 1.02
Physiologically based pharmacokinetic modelling: a sound mechanistic basis is needed. Br J Clin Pharmacol (2005) 1.02
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biol (2009) 1.00
Salivary gland branching morphogenesis: a quantitative systems analysis of the Eda/Edar/NFkappaB paradigm. BMC Dev Biol (2009) 0.99
Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia. PLoS Comput Biol (2012) 0.99
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
A common language for physical mapping of the human genome. Science (1989) 17.36
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (2001) 17.11
A physical map of the human genome. Nature (2001) 12.39
An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH. Cell (1980) 10.35
Two mRNAs can be produced from a single immunoglobulin mu gene by alternative RNA processing pathways. Cell (1980) 9.86
DNA diagnostics--molecular techniques and automation. Science (1988) 8.85
Gene families: the taxonomy of protein paralogs and chimeras. Science (1997) 8.80
A ligase-mediated gene detection technique. Science (1988) 7.61
Alagille syndrome is caused by mutations in human Jagged1, which encodes a ligand for Notch1. Nat Genet (1997) 6.66
Two mRNAs with different 3' ends encode membrane-bound and secreted forms of immunoglobulin mu chain. Cell (1980) 6.32
A single VH gene segment encodes the immune response to phosphorylcholine: somatic mutation is correlated with the class of the antibody. Cell (1981) 5.87
Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A (2000) 5.87
The organization, expression, and evolution of antibody genes and other multigene families. Annu Rev Genet (1975) 5.87
A pseudogene homologous to mouse transplantation antigens: transplantation antigens are encoded by eight exons that correlate with protein domains. Cell (1981) 5.43
A molecular map of the immune response region from the major histocompatibility complex of the mouse. Nature (1982) 5.12
Three cDNA clones encoding mouse transplantation antigens: homology to immunoglobulin genes. Cell (1981) 4.95
Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics (1995) 4.83
Clusters of genes encoding mouse transplantation antigens. Cell (1982) 4.71
Antibody diversity: somatic hypermutation of rearranged VH genes. Cell (1981) 4.65
A new strategy for genome sequencing. Nature (1996) 4.61
Transgenic mice that express a myelin basic protein-specific T cell receptor develop spontaneous autoimmunity. Cell (1993) 4.59
Restricted use of T cell receptor V genes in murine autoimmune encephalomyelitis raises possibilities for antibody therapy. Cell (1988) 4.47
Genes of the major histocompatibility complex of the mouse. Annu Rev Immunol (1983) 4.44
An immunoglobulin heavy-chain gene is formed by at least two recombinational events. Nature (1980) 3.99
Striking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA. Nat Genet (1994) 3.88
IgG antibodies to phosphorylcholine exhibit more diversity than their IgM counterparts. Nature (1981) 3.86
Prostate-localized and androgen-regulated expression of the membrane-bound serine protease TMPRSS2. Cancer Res (1999) 3.79
Silkmoth chorion proteins: sequence analysis of the products of a multigene family. Proc Natl Acad Sci U S A (1978) 3.60
Structural studies of the scrapie prion protein using mass spectrometry and amino acid sequencing. Biochemistry (1993) 3.54
Introduced T cell receptor variable region gene segments recombine in pre-B cells: evidence that B and T cells use a common recombinase. Cell (1986) 3.51
Large-scale and automated DNA sequence determination. Science (1991) 3.45
Cell-type-specific cDNA probes and the murine I region: the localization and orientation of Ad alpha. Proc Natl Acad Sci U S A (1984) 3.43
The human T cell antigen receptor is encoded by variable, diversity, and joining gene segments that rearrange to generate a complete V gene. Cell (1984) 3.41
Death receptor 5, a new member of the TNFR family, and DR4 induce FADD-dependent apoptosis and activate the NF-kappaB pathway. Immunity (1997) 3.33
T cell antigen receptors and the immunoglobulin supergene family. Cell (1985) 3.23
Cell-cell interaction in prostate gene regulation and cytodifferentiation. Proc Natl Acad Sci U S A (1997) 3.22
Immunoglobulin heavy chain gene organization in mice: analysis of a myeloma genomic clone containing variable and alpha constant regions. Proc Natl Acad Sci U S A (1979) 3.19
The structure, rearrangement and expression of D beta gene segments of the murine T-cell antigen receptor. Nature (1984) 3.18
DNA sequence of a gene encoding a BALB/c mouse Ld transplantation antigen. Science (1982) 3.17
Mechanism of antibody diversity: germ line basis for variability. Science (1970) 3.05
Predominant use of a V alpha gene segment in mouse T-cell receptors for cytochrome c. Nature (1987) 2.99
Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res (2001) 2.92
Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1. Genome Res (1996) 2.91
Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay. Proc Natl Acad Sci U S A (1990) 2.88
Genes of the major histocompatibility complex in mouse and man. Science (1983) 2.88
Rearrangement of genetic information may produce immunoglobulin diversity. Nature (1979) 2.84
Mechanism of antibody synthesis: size differences between mouse kappa chains. Science (1967) 2.77
Zinc-dependent structure of a single-finger domain of yeast ADR1. Science (1988) 2.76
DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science (1993) 2.76
From hematopoiesis to neuropoiesis: evidence of overlapping genetic programs. Proc Natl Acad Sci U S A (2001) 2.66
Dynorphin-(1-13), an extraordinarily potent opioid peptide. Proc Natl Acad Sci U S A (1979) 2.66
The complete 685-kilobase DNA sequence of the human beta T cell receptor locus. Science (1996) 2.62
Mouse Cmu heavy chain immunoglobulin gene segment contains three intervening sequences separating domains. Nature (1980) 2.52
Separate elements control DJ and VDJ rearrangement in a transgenic recombination substrate. EMBO J (1990) 2.52
Identification of the class I genes of the mouse major histocompatibility complex by DNA-mediated gene transfer. Nature (1982) 2.48
Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas. Gene (1999) 2.45
Messenger RNA translation state: the second dimension of high-throughput expression screening. Proc Natl Acad Sci U S A (1999) 2.42
Mouse c-myc oncogene is located on chromosome 15 and translocated to chromosome 12 in plasmacytomas. Science (1982) 2.40
Genomic organization of the genes encoding mouse T-cell receptor alpha-chain. Nature (1985) 2.40
Cloning and characterization of two Toll/Interleukin-1 receptor-like genes TIL3 and TIL4: evidence for a multi-gene receptor family in humans. Blood (1998) 2.33
Direct evidence for chromosomal inversion during T-cell receptor beta-gene rearrangements. Nature (1986) 2.33
Rearrangement and transcription of the beta-chain genes of the T-cell antigen receptor in different types of murine lymphocytes. Nature (1985) 2.29
Expression of a myelin basic protein gene in transgenic shiverer mice: correction of the dysmyelinating phenotype. Cell (1987) 2.29
The joining of V and J gene segments creates antibody diversity. Nature (1980) 2.28
The human homolog of rat Jagged1 expressed by marrow stroma inhibits differentiation of 32D cells through interaction with Notch1. Immunity (1998) 2.23
Modulation of the NF-kappa B pathway by virally encoded death effector domains-containing proteins. Oncogene (1999) 2.21
Diversity and structure of human T-cell receptor beta-chain variable region genes. Proc Natl Acad Sci U S A (1986) 2.19
Rearranged beta T cell receptor genes in a helper T cell clone specific for lysozyme: no correlation between V beta and MHC restriction. Cell (1985) 2.14
Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. J Intern Med (2012) 2.13
Nucleotide sequence of a light chain gene of the mouse I-A subregion: A beta d. Science (1983) 2.12
Gene transfer of H-2 class II genes: antigen presentation by mouse fibroblast and hamster B-cell lines. Cell (1984) 2.12
Evidence for a rare prostate cancer-susceptibility locus at chromosome 1p36. Am J Hum Genet (1999) 2.12
Modeling the feasibility of whole genome shotgun sequencing using a pairwise end strategy. Genomics (2000) 2.05
Chromosomal mapping of mouse myelin basic protein gene and structure and transcription of the partially deleted gene in shiverer mutant mice. Cell (1985) 2.02
Pulsed field gel electrophoresis. Biotechniques (1989) 2.02
Soluble protein of the organic matrix of mollusk shells: a potential template for shell formation. Science (1975) 1.99
Cloning and characterization of the myelin basic protein gene from mouse: one gene can encode both 14 kd and 18.5 kd MBPs by alternate use of exons. Cell (1985) 1.98
Asparagine-linked glycosylation of the scrapie and cellular prion proteins. Arch Biochem Biophys (1989) 1.96
Expression of a murine polyclonal T cell receptor marker correlates with the use of specific members of the V beta 8 gene segment subfamily. J Exp Med (1987) 1.96
Genetic mapping in the major histocompatibility complex by restriction enzyme site polymorphisms: most mouse class I genes map to the Tla complex. Proc Natl Acad Sci U S A (1983) 1.96
Immunoglobulin structure: amino terminal sequences of mouse myeloma proteins that bind phosphorylcholine. Science (1974) 1.94
Amino acid sequence of homogeneous antibodies to dextran and DNA rearrangements in heavy chain V-region gene segments. Nature (1980) 1.94
Linkage and sequence homology of two human immunoglobulin gamma heavy chain constant region genes. Proc Natl Acad Sci U S A (1982) 1.93
Identification of a diversity segment of human T-cell receptor beta-chain, and comparison with the analogous murine element. Nature (1984) 1.92
Comparative genomics of the human and mouse T cell receptor loci. Immunity (2001) 1.92
The immunoglobulin mu chains of membrane-bound and secreted IgM molecules differ in their C-terminal segments. Cell (1980) 1.91
Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants. Proc Natl Acad Sci U S A (1999) 1.88
Expression and function of transplantation antigens with altered or deleted cytoplasmic domains. Cell (1983) 1.86
Regulation of gene expression by interferons: control of H-2 promoter responses. Science (1988) 1.85
Sequence-tagged connectors: a sequence approach to mapping and scanning the human genome. Proc Natl Acad Sci U S A (1999) 1.85
Mouse immunoglobulin chains. A survey of the amino-terminal sequences of kappa chains. Biochemistry (1973) 1.85
Molecular cloning of translocations involving chromosome 15 and the immunoglobulin C alpha gene from chromosome 12 in two murine plasmacytomas. Proc Natl Acad Sci U S A (1982) 1.84
Retracted Amino acid variations at a single residue in an autoimmune peptide profoundly affect its properties: T-cell activation, major histocompatibility complex binding, and ability to block experimental allergic encephalomyelitis. Proc Natl Acad Sci U S A (1990) 1.82
Rearrangement and expression of T cell antigen receptor and gamma genes during thymic development. J Exp Med (1986) 1.82
Diversity of the immunoglobulin gene superfamily. Adv Immunol (1989) 1.81
Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Res (1998) 1.81
Activation of the NF-kappaB pathway by caspase 8 and its homologs. Oncogene (2000) 1.76
Delays to thrombolysis in the treatment of myocardial infarction. J R Coll Physicians Lond (1993) 1.75