Reverse engineering cellular networks.

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

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature (2012) 9.89

The transcriptional network for mesenchymal transformation of brain tumours. Nature (2009) 8.44

Transcriptome-based network analysis reveals a spectrum model of human macrophage activation. Immunity (2014) 3.94

Inferring regulatory networks from expression data using tree-based methods. PLoS One (2010) 3.37

Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy. Cancer Cell (2014) 2.60

The transcriptional coactivator TAZ regulates mesenchymal differentiation in malignant glioma. Genes Dev (2011) 2.48

A formal analysis of cytokine networks in chronic fatigue syndrome. Brain Behav Immun (2010) 1.95

Toward the dynamic interactome: it's about time. Brief Bioinform (2010) 1.91

Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biol (2008) 1.91

A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res (2011) 1.89

Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol (2009) 1.69

Transcriptional network analysis identifies BACH1 as a master regulator of breast cancer bone metastasis. J Biol Chem (2012) 1.58

Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PLoS Comput Biol (2012) 1.54

Inferring protein modulation from gene expression data using conditional mutual information. PLoS One (2014) 1.44

Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data. EURASIP J Bioinform Syst Biol (2009) 1.41

Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PLoS One (2014) 1.39

Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J R Soc Interface (2013) 1.38

Bagging statistical network inference from large-scale gene expression data. PLoS One (2012) 1.38

Network inference algorithms elucidate Nrf2 regulation of mouse lung oxidative stress. PLoS Comput Biol (2008) 1.38

Regulators of yeast endocytosis identified by systematic quantitative analysis. J Cell Biol (2009) 1.37

ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Rep (2014) 1.34

Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput (2009) 1.32

Systems biology. Conditional density-based analysis of T cell signaling in single-cell data. Science (2014) 1.28

ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer. Proc Natl Acad Sci U S A (2013) 1.26

Reverse engineering cellular networks with information theoretic methods. Cells (2013) 1.18

Biological network exploration with cytoscape 3. Curr Protoc Bioinformatics (2014) 1.14

A systems biology approach identifies molecular networks defining skeletal muscle abnormalities in chronic obstructive pulmonary disease. PLoS Comput Biol (2011) 1.13

Master regulators of FGFR2 signalling and breast cancer risk. Nat Commun (2013) 1.12

MIDER: network inference with mutual information distance and entropy reduction. PLoS One (2014) 1.07

Biochemical and statistical network models for systems biology. Curr Opin Biotechnol (2007) 1.07

Incorporating existing network information into gene network inference. PLoS One (2009) 1.04

Genetic and genomic analysis modeling of germline c-MYC overexpression and cancer susceptibility. BMC Genomics (2008) 0.97

CDH5 is specifically activated in glioblastoma stemlike cells and contributes to vasculogenic mimicry induced by hypoxia. Neuro Oncol (2013) 0.94

Applying systems biology methods to the study of human physiology in extreme environments. Extrem Physiol Med (2013) 0.94

Inferring nonlinear gene regulatory networks from gene expression data based on distance correlation. PLoS One (2014) 0.94

A cross-species transcriptomics approach to identify genes involved in leaf development. BMC Genomics (2008) 0.93

Using systems and structure biology tools to dissect cellular phenotypes. J Am Med Inform Assoc (2011) 0.92

Network-based functional enrichment. BMC Bioinformatics (2011) 0.91

Cytochrome P450 CYP78A9 is involved in Arabidopsis reproductive development. Plant Physiol (2013) 0.90

Modulation of gene expression regulated by the transcription factor NF-κB/RelA. J Biol Chem (2014) 0.90

A systems biology approach sheds new light on Escherichia coli acid resistance. Nucleic Acids Res (2011) 0.89

Genome-wide inference of regulatory networks in Streptomyces coelicolor. BMC Genomics (2010) 0.88

SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. BMC Genomics (2014) 0.88

Network completion using dynamic programming and least-squares fitting. ScientificWorldJournal (2012) 0.87

The Thermoanaerobacter glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria. PLoS Genet (2011) 0.86

A systems biology approach to transcription factor binding site prediction. PLoS One (2010) 0.85

NIMEFI: gene regulatory network inference using multiple ensemble feature importance algorithms. PLoS One (2014) 0.84

Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. BMC Bioinformatics (2009) 0.84

ZFP36L1 negatively regulates plasmacytoid differentiation of BCL1 cells by targeting BLIMP1 mRNA. PLoS One (2012) 0.83

Insights gained from the reverse engineering of gene networks in keloid fibroblasts. Theor Biol Med Model (2011) 0.83

Large differences in global transcriptional regulatory programs of normal and tumor colon cells. BMC Cancer (2014) 0.83

Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer. J Transl Med (2015) 0.83

Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics (2013) 0.82

Transcriptional mechanisms of cell fate decisions revealed by single cell expression profiling. Bioessays (2014) 0.82

Master regulators of infiltrate recruitment in autoimmune disease identified through network-based molecular deconvolution. Cell Syst (2015) 0.82

Post-transcriptional regulation of BCL2 mRNA by the RNA-binding protein ZFP36L1 in malignant B cells. PLoS One (2014) 0.82

Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells (2015) 0.81

Gene regulatory network inference using fused LASSO on multiple data sets. Sci Rep (2016) 0.81

ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks. BMC Plant Biol (2014) 0.81

ENNET: inferring large gene regulatory networks from expression data using gradient boosting. BMC Syst Biol (2013) 0.80

Microglia recapitulate a hematopoietic master regulator network in the aging human frontal cortex. Neurobiol Aging (2015) 0.80

JUNB is a key transcriptional modulator of macrophage activation. J Immunol (2014) 0.80

Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Front Plant Sci (2014) 0.80

How difficult is inference of mammalian causal gene regulatory networks? PLoS One (2014) 0.80

MicroRNA-mRNA interactions underlying colorectal cancer molecular subtypes. Nat Commun (2015) 0.80

Low-rank regularization for learning gene expression programs. PLoS One (2013) 0.80

Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle. BMC Genomics (2011) 0.80

Inferring gene regulatory networks by thermodynamic modeling. BMC Genomics (2008) 0.80

Proteome profiling outperforms transcriptome profiling for co-expression based gene function prediction. Mol Cell Proteomics (2016) 0.79

A computational procedure for identifying master regulator candidates: a case study on diabetes progression in Goto-Kakizaki rats. BMC Syst Biol (2012) 0.79

Identification of upstream regulators for prognostic expression signature genes in colorectal cancer. BMC Syst Biol (2013) 0.79

Reverse engineering the neuroblastoma regulatory network uncovers MAX as one of the master regulators of tumor progression. PLoS One (2013) 0.79

Gene expression prediction using low-rank matrix completion. BMC Bioinformatics (2016) 0.78

IPCA-CMI: an algorithm for inferring gene regulatory networks based on a combination of PCA-CMI and MIT score. PLoS One (2014) 0.78

Mining TCGA data using Boolean implications. PLoS One (2014) 0.78

Inference of Low and High-Grade Glioma Gene Regulatory Networks Delineates the Role of Rnd3 in Establishing Multiple Hallmarks of Cancer. PLoS Genet (2015) 0.78

ERBB3 is a marker of a ganglioneuroblastoma/ganglioneuroma-like expression profile in neuroblastic tumours. Mol Cancer (2013) 0.78

Seasonal immunoregulation in a naturally-occurring vertebrate. BMC Genomics (2016) 0.78

A systems approach to drug discovery in Alzheimer's disease. Neurotherapeutics (2015) 0.77

A Network Approach to Wound Healing. Adv Wound Care (New Rochelle) (2013) 0.77

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures. Cell Syst (2017) 0.76

Network completion for static gene expression data. Adv Bioinformatics (2014) 0.76

Evidence of dynamically dysregulated gene expression pathways in hyperresponsive B cells from African American lupus patients. PLoS One (2013) 0.76

Identification of Master Regulator Genes in Human Periodontitis. J Dent Res (2016) 0.76

IFI16 Expression Is Related to Selected Transcription Factors during B-Cell Differentiation. J Immunol Res (2015) 0.76

Differential expression of transcriptional regulatory units in the prefrontal cortex of patients with bipolar disorder: potential role of early growth response gene 3. Transl Psychiatry (2016) 0.76

Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data. J Comput Biol (2011) 0.76

CD11b(+)Ly6C(++)Ly6G(-) Cells with Suppressive Activity Towards T Cells Accumulate in Lungs of Influenza a Virus-Infected Mice. Eur J Microbiol Immunol (Bp) (2015) 0.76

Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis. Proteomics (2017) 0.76

Transcriptional regulatory mechanism of alcohol dehydrogenase 1-deficient mutant of rice for cell survival under complete submergence. Rice (N Y) (2016) 0.75

Genome-scale technology driven advances to research into normal and malignant haematopoiesis. Scientifica (Cairo) (2012) 0.75

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC Syst Biol (2014) 0.75

Changing expression of vertebrate immunity genes in an anthropogenic environment: a controlled experiment. BMC Evol Biol (2016) 0.75

Inferring Weighted Directed Association Network from Multivariate Time Series with a Synthetic Method of Partial Symbolic Transfer Entropy Spectrum and Granger Causality. PLoS One (2016) 0.75

Regulatory network reconstruction reveals genes with prognostic value for chronic lymphocytic leukemia. BMC Genomics (2015) 0.75

An NAD+-dependent transcriptional program governs self-renewal and radiation resistance in glioblastoma. Proc Natl Acad Sci U S A (2016) 0.75

Interactome-transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes. Sci Rep (2016) 0.75

Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem. BMC Bioinformatics (2013) 0.75

Correcting positional correlations in Affymetrix® genome chips. Sci Rep (2015) 0.75

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet (2010) 17.38

Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36

Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49

Rare variants create synthetic genome-wide associations. PLoS Biol (2010) 14.43

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature (2011) 13.23

Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16

Genotype, haplotype and copy-number variation in worldwide human populations. Nature (2008) 12.40

Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature (2009) 9.47

The transcriptional network for mesenchymal transformation of brain tumours. Nature (2009) 8.44

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol (2013) 7.97

Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature (2009) 7.37

The microRNA spectrum in 12 body fluids. Clin Chem (2010) 6.82

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc Natl Acad Sci U S A (2006) 6.80

A promoter-level mammalian expression atlas. Nature (2014) 6.25

An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell (2011) 5.75

Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA (2012) 5.16

The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell (2010) 4.71

Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. Am J Psychiatry (2011) 4.29

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res (2008) 4.22

Variants of DENND1B associated with asthma in children. N Engl J Med (2009) 4.18

Copy number variation at 1q21.1 associated with neuroblastoma. Nature (2009) 4.10

Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann N Y Acad Sci (2007) 3.89

Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet (2009) 3.82

Transcriptional analysis of the B cell germinal center reaction. Proc Natl Acad Sci U S A (2003) 3.45

Lessons from the DREAM2 Challenges. Ann N Y Acad Sci (2009) 3.44

Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet (2011) 3.43

A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet (2010) 3.42

Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes. PLoS Genet (2009) 3.42

Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 3.37

Ethics and scientific publication. Adv Physiol Educ (2005) 3.26

The landscape of recombination in African Americans. Nature (2011) 3.06

From disease association to risk assessment: an optimistic view from genome-wide association studies on type 1 diabetes. PLoS Genet (2009) 2.99

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol (2008) 2.99

Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Nat Genet (2009) 2.97

Information transduction capacity of noisy biochemical signaling networks. Science (2011) 2.95

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92

Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity. Nat Cell Biol (2013) 2.90

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol (2009) 2.79

Safety and efficacy of warfarin plus aspirin combination therapy for giant coronary artery aneurysm secondary to Kawasaki disease: a meta-analysis. Cardiology (2014) 2.64

Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics (2007) 2.63

Interleukin-17 signaling in inflammatory, Kupffer cells, and hepatic stellate cells exacerbates liver fibrosis in mice. Gastroenterology (2012) 2.58

Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics (2005) 2.56

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

Disease phenotype of a ferret CFTR-knockout model of cystic fibrosis. J Clin Invest (2010) 2.45

A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24. J Pediatr (2009) 2.44

LOXL1 mutations are associated with exfoliation syndrome in patients from the midwestern United States. Am J Ophthalmol (2007) 2.43

wANNOVAR: annotating genetic variants for personal genomes via the web. J Med Genet (2012) 2.43

Low fetuin-A levels are associated with cardiovascular death: Impact of variations in the gene encoding fetuin. Kidney Int (2005) 2.42

Photoselective vaporization with the green light laser vs transurethral resection of the prostate for treating benign prostate hyperplasia: a systematic review and meta-analysis. BJU Int (2012) 2.42

Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA (2010) 2.38

The role of obesity-associated loci identified in genome-wide association studies in the determination of pediatric BMI. Obesity (Silver Spring) (2009) 2.34

Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res (2013) 2.24

Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics (2008) 2.24

A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics (2007) 2.23

iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One (2008) 2.18

Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet (2010) 2.15

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res (2013) 2.12

Serum albumin, C-reactive protein, interleukin 6, and fetuin a as predictors of malnutrition, cardiovascular disease, and mortality in patients with ESRD. Am J Kidney Dis (2006) 2.09

The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain. Dev Cell (2009) 2.04

Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency. Cell Stem Cell (2013) 2.04

geWorkbench: an open source platform for integrative genomics. Bioinformatics (2010) 2.03

Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science (2012) 2.01

Gene-function wiki would let biologists pool worldwide resources. Nature (2006) 2.01

Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum Mutat (2011) 1.98

Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets. J Clin Invest (2007) 1.97

A model to predict antiviral treatment in HBeAg negative chronic hepatitis B with alanine aminotransferase≤2 upper limit of normal. Liver Int (2013) 1.97

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol (2014) 1.95

The TLX1 oncogene drives aneuploidy in T cell transformation. Nat Med (2010) 1.93

Identification of the human mature B cell miRNome. Immunity (2009) 1.82

Tracking CD40 signaling during germinal center development. Blood (2004) 1.81

Bioartificial sinus node constructed via in vivo gene transfer of an engineered pacemaker HCN Channel reduces the dependence on electronic pacemaker in a sick-sinus syndrome model. Circulation (2006) 1.70

Causes of alternative pathway dysregulation in dense deposit disease. Clin J Am Soc Nephrol (2012) 1.70

tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma. Proc Natl Acad Sci U S A (2013) 1.66

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc Natl Acad Sci U S A (2008) 1.65

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells. Blood (2009) 1.64

Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. Nat Genet (2011) 1.63

Towards patient-based cancer therapeutics. Nat Biotechnol (2010) 1.63

Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling. J Clin Invest (2003) 1.63

BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc Natl Acad Sci U S A (2009) 1.62

Gene expression networks in COPD: microRNA and mRNA regulation. Thorax (2011) 1.62

New routes to targeted therapy of intrahepatic cholangiocarcinomas revealed by next-generation sequencing. Oncologist (2014) 1.61

A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci. PLoS Genet (2011) 1.60

Mortality rates among prevalent hemodialysis patients in Beijing: a comparison with USRDS data. Nephrol Dial Transplant (2012) 1.59

Phenotype restricted genome-wide association study using a gene-centric approach identifies three low-risk neuroblastoma susceptibility Loci. PLoS Genet (2011) 1.57

A pilot study in non-human primates shows no adverse response to intravenous injection of quantum dots. Nat Nanotechnol (2012) 1.57