Boosting signal-to-noise in complex biology: prior knowledge is power.

PubWeight™: 1.71‹?› | Rank: Top 3%

🔗 View Article (PMC 3102020)

Published in Cell on March 18, 2011

Authors

Trey Ideker1, Janusz Dutkowski, Leroy Hood

Author Affiliations

1: Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. tideker@ucsd.edu

Articles citing this

The BioGRID interaction database: 2013 update. Nucleic Acids Res (2012) 6.09

Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine. J Intern Med (2012) 2.13

Making sense of big data in health research: Towards an EU action plan. Genome Med (2016) 1.55

Promise of personalized omics to precision medicine. Wiley Interdiscip Rev Syst Biol Med (2012) 1.53

Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages. PLoS Genet (2012) 1.37

Systems solutions by lactic acid bacteria: from paradigms to practice. Microb Cell Fact (2011) 1.34

IMMUNOLOGY. An interactive reference framework for modeling a dynamic immune system. Science (2015) 1.32

A patient tumor transplant model of squamous cell cancer identifies PI3K inhibitors as candidate therapeutics in defined molecular bins. Mol Oncol (2013) 1.28

The glucose-deprivation network counteracts lapatinib-induced toxicity in resistant ErbB2-positive breast cancer cells. Mol Syst Biol (2012) 1.23

Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol (2013) 1.20

Protein networks as logic functions in development and cancer. PLoS Comput Biol (2011) 1.19

Molecular signatures from omics data: from chaos to consensus. Biotechnol J (2012) 1.17

Data Requirements for Model-Based Cancer Prognosis Prediction. Cancer Inform (2016) 1.06

Interferon regulatory factor 7 is a major hub connecting interferon-mediated responses in virus-induced asthma exacerbations in vivo. J Allergy Clin Immunol (2011) 1.05

Systems-based approaches to cardiovascular disease. Nat Rev Cardiol (2012) 1.04

Systems biology: personalized medicine for the future? Curr Opin Pharmacol (2012) 1.04

Network analysis of GWAS data. Curr Opin Genet Dev (2013) 1.02

New technologies for 21st century plant science. Plant Cell (2012) 1.01

Genomics in 2012: challenges and opportunities in the next generation sequencing era. BMC Genomics (2012) 1.01

The cancer cell map initiative: defining the hallmark networks of cancer. Mol Cell (2015) 0.94

Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. BMC Bioinformatics (2014) 0.91

Reconceiving the hippocampal map as a topological template. Elife (2014) 0.89

When one and one gives more than two: challenges and opportunities of integrative omics. Front Genet (2012) 0.88

The choice of the filtering method in microarrays affects the inference regarding dosage compensation of the active X-chromosome. PLoS One (2011) 0.87

Network analysis of epidermal growth factor signaling using integrated genomic, proteomic and phosphorylation data. PLoS One (2012) 0.87

Identification of novel metastasis suppressor signaling pathways for breast cancer. Cell Cycle (2012) 0.86

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. Database (Oxford) (2015) 0.85

Wrangling phosphoproteomic data to elucidate cancer signaling pathways. PLoS One (2013) 0.85

White adipose tissue reference network: a knowledge resource for exploring health-relevant relations. Genes Nutr (2014) 0.83

Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. BioData Min (2013) 0.83

Network analysis identifies protein clusters of functional importance in juvenile idiopathic arthritis. Arthritis Res Ther (2014) 0.83

Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PLoS Comput Biol (2016) 0.83

Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources. PLoS One (2013) 0.81

Counting motifs in the human interactome. Nat Commun (2013) 0.81

Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome. Mol Syst Biol (2015) 0.81

Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. Orphanet J Rare Dis (2012) 0.81

How implementation of systems biology into clinical trials accelerates understanding of diseases. Front Neurol (2014) 0.81

Transcriptional landscapes of emerging autoimmunity: transient aberrations in the targeted tissue's extracellular milieu precede immune responses in Sjögren's syndrome. Arthritis Res Ther (2013) 0.80

Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion. Bioinformatics (2014) 0.79

Semi-supervised adaptive-height snipping of the hierarchical clustering tree. BMC Bioinformatics (2015) 0.78

Fostering synergy between cell biology and systems biology. Trends Cell Biol (2015) 0.77

Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks. Proteome Sci (2011) 0.77

Stochastic effects as a force to increase the complexity of signaling networks. Sci Rep (2013) 0.75

Somatic polyploidy is associated with the upregulation of c-MYC interacting genes and EMT-like signature. Oncotarget (2016) 0.75

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. BMC Bioinformatics (2011) 0.75

Autism cornered: network analyses reveal mechanisms of autism spectrum disorders. Mol Syst Biol (2014) 0.75

Metabolic systems biology: a brief primer. J Physiol (2016) 0.75

Molecular profiles to biology and pathways: a systems biology approach. Chin J Cancer (2016) 0.75

Articles cited by this

Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57

Common SNPs explain a large proportion of the heritability for human height. Nat Genet (2010) 35.02

From molecular to modular cell biology. Nature (1999) 23.51

International network of cancer genome projects. Nature (2010) 20.35

Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45

Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics (2002) 12.88

Inferring cellular networks using probabilistic graphical models. Science (2004) 9.91

A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90

A probabilistic functional network of yeast genes. Science (2004) 8.35

Analysing biological pathways in genome-wide association studies. Nat Rev Genet (2010) 6.63

A global protein kinase and phosphatase interaction network in yeast. Science (2010) 5.95

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet (2008) 5.80

Common inherited variation in mitochondrial genes is not enriched for associations with type 2 diabetes or related glycemic traits. PLoS Genet (2010) 5.79

Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. PLoS Comput Biol (2007) 3.37

A predictive model for transcriptional control of physiology in a free living cell. Cell (2007) 3.35

The evolution of hierarchical gene regulatory networks. Nat Rev Genet (2009) 2.62

Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc Natl Acad Sci U S A (2010) 2.61

eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol (2008) 2.45

On the utility of gene set methods in genomewide association studies of quantitative traits. Genet Epidemiol (2008) 2.12

Averaged gene expressions for regression. Biostatistics (2006) 2.03

Articles by these authors

(truncated to the top 100)

A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol (2005) 27.17

Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 20.59

Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science (2010) 18.45

Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol (2008) 15.90

A genomic regulatory network for development. Science (2002) 9.67

The program of androgen-responsive genes in neoplastic prostate epithelium. Proc Natl Acad Sci U S A (2002) 5.98

The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22

Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach. Proc Natl Acad Sci U S A (2002) 4.96

Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood. Nat Biotechnol (2008) 4.40

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol (2010) 4.32

PTEN-deficient intestinal stem cells initiate intestinal polyposis. Nat Genet (2007) 4.09

Rewiring of genetic networks in response to DNA damage. Science (2010) 4.03

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol Cell Proteomics (2002) 3.89

Systems medicine: the future of medical genomics and healthcare. Genome Med (2009) 3.85

Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res (2004) 3.46

A predictive model for transcriptional control of physiology in a free living cell. Cell (2007) 3.35

A data integration methodology for systems biology. Proc Natl Acad Sci U S A (2005) 2.93

A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A (2006) 2.89

Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods (2005) 2.87

Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A (2009) 2.76

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75

Extracellular microRNA: a new source of biomarkers. Mutat Res (2011) 2.55

Analysis of the human neurexin genes: alternative splicing and the generation of protein diversity. Genomics (2002) 2.54

Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc Natl Acad Sci U S A (2007) 2.38

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol (2002) 2.26

Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A (2003) 2.24

Hematopoietic stem cells contribute to the regeneration of renal tubules after renal ischemia-reperfusion injury in mice. J Am Soc Nephrol (2003) 2.12

The DNA sequence and analysis of human chromosome 14. Nature (2003) 2.02

A combined genomewide linkage scan of 1,233 families for prostate cancer-susceptibility genes conducted by the international consortium for prostate cancer genetics. Am J Hum Genet (2005) 1.96

Genetic effects on age-dependent onset and islet cell autoantibody markers in type 1 diabetes. Diabetes (2002) 1.89

The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis. BMC Genomics (2011) 1.79

Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Med (2011) 1.78

A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A (2005) 1.77

Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. Proc Natl Acad Sci U S A (2011) 1.76

Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res (2004) 1.74

Pooled genome linkage scan of aggressive prostate cancer: results from the International Consortium for Prostate Cancer Genetics. Hum Genet (2006) 1.70

Differential gene expression profiling of adult murine hematopoietic stem cells. Blood (2002) 1.69

A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med (2013) 1.69

Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One (2009) 1.68

Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. Immunity (2011) 1.66

Proteomic analysis identifies that 14-3-3zeta interacts with beta-catenin and facilitates its activation by Akt. Proc Natl Acad Sci U S A (2004) 1.66

Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet (2011) 1.58

Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C R Biol (2004) 1.58

Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics (2009) 1.55

Activated Notch4 inhibits angiogenesis: role of beta 1-integrin activation. Mol Cell Biol (2002) 1.52

Genetic mapping at 3-kilobase resolution reveals inositol 1,4,5-triphosphate receptor 3 as a risk factor for type 1 diabetes in Sweden. Am J Hum Genet (2006) 1.50

Analysis of the DNA sequence and duplication history of human chromosome 15. Nature (2006) 1.50

Genome-wide analysis of epigenetic silencing identifies BEX1 and BEX2 as candidate tumor suppressor genes in malignant glioma. Cancer Res (2006) 1.50

Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol Cell Proteomics (2006) 1.49

Kaviar: an accessible system for testing SNV novelty. Bioinformatics (2011) 1.47

Proteomic analysis of human prostasomes. Prostate (2003) 1.45

Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution. Med Hypotheses (2007) 1.39

Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma. PLoS One (2010) 1.39

Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res (2005) 1.39

Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol (2010) 1.38

Unusual gene order and organization of the sea urchin hox cluster. J Exp Zool B Mol Dev Evol (2006) 1.34

Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Genome Res (2003) 1.32

Silencing SOX2 induced mesenchymal-epithelial transition and its expression predicts liver and lymph node metastasis of CRC patients. PLoS One (2012) 1.31

Proteins associated with Cisplatin resistance in ovarian cancer cells identified by quantitative proteomic technology and integrated with mRNA expression levels. Mol Cell Proteomics (2005) 1.30

Sequence analysis of mouse vomeronasal receptor gene clusters reveals common promoter motifs and a history of recent expansion. Proc Natl Acad Sci U S A (2001) 1.26

Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol (2004) 1.25

ACGT-a comparative genomics tool. Bioinformatics (2003) 1.21

From functional genomics to systems biology: concepts and practices. C R Biol (2004) 1.20

Bridging the BMP and Wnt pathways by PI3 kinase/Akt and 14-3-3zeta. Cell Cycle (2005) 1.20

Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol (2013) 1.20

Proteomics analysis of the interactome of N-myc downstream regulated gene 1 and its interactions with the androgen response program in prostate cancer cells. Mol Cell Proteomics (2007) 1.20

Elevated expression of DKK1 is associated with cytoplasmic/nuclear beta-catenin accumulation and poor prognosis in hepatocellular carcinomas. J Hepatol (2009) 1.16

Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther (2009) 1.15

A third approach to gene prediction suggests thousands of additional human transcribed regions. PLoS Comput Biol (2006) 1.15

Proteomic analysis of an extreme halophilic archaeon, Halobacterium sp. NRC-1. Mol Cell Proteomics (2003) 1.15

Genomic scan of 254 hereditary prostate cancer families. Prostate (2003) 1.14

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. J Bacteriol (2003) 1.13

Long-range multilocus haplotype phasing of the MHC. Proc Natl Acad Sci U S A (2006) 1.12

Predictive, preventive, personalized and participatory medicine: back to the future. Genome Med (2010) 1.12

Low-pass sequencing for microbial comparative genomics. BMC Genomics (2004) 1.11

SRM targeted proteomics in search for biomarkers of HCV-induced progression of fibrosis to cirrhosis in HALT-C patients. Proteomics (2012) 1.11

Electrochemically programmed, spatially selective biofunctionalization of silicon wires. Langmuir (2004) 1.11

Pillars article: Transgenic mice that express a myelin basic protein-specific T cell receptor develop spontaneous autoimmunity. Cell. 1993. 72: 551-560. J Immunol (2013) 1.07

Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain. Proc Natl Acad Sci U S A (2013) 1.06

ERG upregulation and related ETS transcription factors in prostate cancer. Int J Oncol (2007) 1.05

Parallel microfluidic surface plasmon resonance imaging arrays. Lab Chip (2010) 1.04

Principal network analysis: identification of subnetworks representing major dynamics using gene expression data. Bioinformatics (2010) 1.03

Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics (2009) 1.03

Leroy Hood expounds the principles, practice and future of systems biology. Drug Discov Today (2003) 1.00

Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl (2009) 1.00

Label-free quantitative detection of tumor-derived exosomes through surface plasmon resonance imaging. Anal Chem (2014) 0.99

Increased expression of SIM2-s protein is a novel marker of aggressive prostate cancer. Clin Cancer Res (2007) 0.99

Quantitative proteomics analysis integrated with microarray data reveals that extracellular matrix proteins, catenins, and p53 binding protein 1 are important for chemotherapy response in ovarian cancers. OMICS (2009) 0.98

Gene expression profiles in prostate cancer: association with patient subgroups and tumour differentiation. Int J Oncol (2005) 0.98

A Review of Computational Tools in microRNA Discovery. Front Genet (2013) 0.98

A systems approach to rheumatoid arthritis. PLoS One (2012) 0.96

Quantitative serum proteomics from surface plasmon resonance imaging. Mol Cell Proteomics (2008) 0.96

Down-regulation of Shadoo in prion infections traces a pre-clinical event inversely related to PrP(Sc) accumulation. PLoS Pathog (2011) 0.96

Systems biology and the discovery of diagnostic biomarkers. Dis Markers (2010) 0.95

An enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution. BMC Evol Biol (2004) 0.93

Reverse engineering galactose regulation in yeast through model selection. Stat Appl Genet Mol Biol (2005) 0.92

Genomic analysis of the olfactory receptor region of the mouse and human T-cell receptor alpha/delta loci. Genome Res (2002) 0.92

The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases. Database (Oxford) (2009) 0.92

MODEVO: exploring modularity and evolution of protein interaction networks. Bioinformatics (2010) 0.92