Published in Ann N Y Acad Sci on March 01, 2009
Wisdom of crowds for robust gene network inference. Nat Methods (2012) 6.91
Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A (2010) 5.41
Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One (2010) 4.94
Inferring regulatory networks from expression data using tree-based methods. PLoS One (2010) 3.37
Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 3.37
Critical assessment of automated flow cytometry data analysis techniques. Nat Methods (2013) 3.30
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Systematic analysis of challenge-driven improvements in molecular prognostic models for breast cancer. Sci Transl Med (2013) 2.34
Evaluation of methods for modeling transcription factor sequence specificity. Nat Biotechnol (2013) 2.34
Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data. PLoS One (2010) 1.93
Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal (2011) 1.83
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge. PLoS One (2010) 1.64
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Gene regulatory network reconstruction using Bayesian networks, the Dantzig Selector, the Lasso and their meta-analysis. PLoS One (2011) 1.08
Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge. PLoS One (2010) 1.08
Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res (2011) 1.08
A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks. Genomics (2010) 1.07
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Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods (2016) 1.04
Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics (2009) 1.04
Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks. PLoS One (2009) 1.01
Comparison of evolutionary algorithms in gene regulatory network model inference. BMC Bioinformatics (2010) 1.01
A linear model for transcription factor binding affinity prediction in protein binding microarrays. PLoS One (2011) 0.99
Reverse-engineering human regulatory networks. Wiley Interdiscip Rev Syst Biol Med (2012) 0.98
TRANSWESD: inferring cellular networks with transitive reduction. Bioinformatics (2010) 0.98
A top-performing algorithm for the DREAM3 gene expression prediction challenge. PLoS One (2010) 0.97
Analysis of flow cytometry data by matrix relevance learning vector quantization. PLoS One (2013) 0.96
Mapping functional transcription factor networks from gene expression data. Genome Res (2013) 0.94
Simulating systems genetics data with SysGenSIM. Bioinformatics (2011) 0.93
New methods for separating causes from effects in genomics data. BMC Genomics (2012) 0.92
Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy. PLoS One (2010) 0.91
Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. Front Cell Dev Biol (2014) 0.90
Leukemia prediction using sparse logistic regression. PLoS One (2013) 0.90
Ensemble inference and inferability of gene regulatory networks. PLoS One (2014) 0.90
Teamwork: improved eQTL mapping using combinations of machine learning methods. PLoS One (2012) 0.90
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Learning the structure of gene regulatory networks from time series gene expression data. BMC Genomics (2011) 0.84
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Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors. BMC Bioinformatics (2012) 0.83
An algebra-based method for inferring gene regulatory networks. BMC Syst Biol (2014) 0.83
Hub-centered gene network reconstruction using automatic relevance determination. PLoS One (2012) 0.83
Functional association networks as priors for gene regulatory network inference. Bioinformatics (2014) 0.82
An information-theoretic machine learning approach to expression QTL analysis. PLoS One (2013) 0.82
Reverse engineering validation using a benchmark synthetic gene circuit in human cells. ACS Synth Biol (2013) 0.81
Information theoretic approaches for inference of biological networks from continuous-valued data. BMC Syst Biol (2016) 0.80
CaSPIAN: a causal compressive sensing algorithm for discovering directed interactions in gene networks. PLoS One (2014) 0.80
Construction of gene regulatory networks using biclustering and Bayesian networks. Theor Biol Med Model (2011) 0.79
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. BMC Syst Biol (2014) 0.79
Inferring PDZ domain multi-mutant binding preferences from single-mutant data. PLoS One (2010) 0.78
De-novo learning of genome-scale regulatory networks in S. cerevisiae. PLoS One (2014) 0.78
The recurrent architecture of tumour initiation, progression and drug sensitivity. Nat Rev Cancer (2016) 0.78
An integrative approach to infer regulation programs in a transcription regulatory module network. J Biomed Biotechnol (2012) 0.78
RMaNI: Regulatory Module Network Inference framework. BMC Bioinformatics (2013) 0.77
DREAMTools: a Python package for scoring collaborative challenges. F1000Res (2015) 0.77
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun (2016) 0.76
TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. BMC Bioinformatics (2016) 0.76
Untangling statistical and biological models to understand network inference: the need for a genomics network ontology. Front Genet (2014) 0.76
Algorithms for modeling global and context-specific functional relationship networks. Brief Bioinform (2015) 0.76
Reverse engineering gene regulatory networks from measurement with missing values. EURASIP J Bioinform Syst Biol (2017) 0.75
Gene regulatory network inference and validation using relative change ratio analysis and time-delayed dynamic Bayesian network. EURASIP J Bioinform Syst Biol (2014) 0.75
Inferring Broad Regulatory Biology from Time Course Data: Have We Reached an Upper Bound under Constraints Typical of In Vivo Studies? PLoS One (2015) 0.75
Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast. Proc Natl Acad Sci U S A (2016) 0.75
DTW-MIC Coexpression Networks from Time-Course Data. PLoS One (2016) 0.75
Reconstruction of Gene Regulatory Networks based on Repairing Sparse Low-rank Matrices. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75
Plasma and serum metabolite association networks: comparability within and between studies using NMR and MS profiling. J Proteome Res (2017) 0.75
Genetic tests in major psychiatric disorders-integrating molecular medicine with clinical psychiatry-why is it so difficult? Transl Psychiatry (2017) 0.75
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics (2006) 14.49
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
The transcriptional network for mesenchymal transformation of brain tumours. Nature (2009) 8.44
Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature (2009) 7.37
Wisdom of crowds for robust gene network inference. Nat Methods (2012) 6.91
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
Revealing strengths and weaknesses of methods for gene network inference. Proc Natl Acad Sci U S A (2010) 5.41
The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell (2010) 4.71
Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference. Ann N Y Acad Sci (2007) 3.89
Reverse engineering cellular networks. Nat Protoc (2006) 3.67
Transcriptional analysis of the B cell germinal center reaction. Proc Natl Acad Sci U S A (2003) 3.45
Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature (2012) 3.37
A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas. Mol Syst Biol (2008) 2.99
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
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics (2007) 2.63
iTools: a framework for classification, categorization and integration of computational biology resources. PLoS One (2008) 2.18
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
geWorkbench: an open source platform for integrative genomics. Bioinformatics (2010) 2.03
Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets. J Clin Invest (2007) 1.97
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
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
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
Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL. Nat Med (2012) 1.56
Theory and limitations of genetic network inference from microarray data. Ann N Y Acad Sci (2007) 1.51
Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes. Blood (2011) 1.40
Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors. J Exp Med (2004) 1.37
A molecular signature predictive of indolent prostate cancer. Sci Transl Med (2013) 1.32
Master regulators used as breast cancer metastasis classifier. Pac Symp Biocomput (2009) 1.32
Gene expression analysis of angioimmunoblastic lymphoma indicates derivation from T follicular helper cells and vascular endothelial growth factor deregulation. Cancer Res (2007) 1.28
Verification of systems biology research in the age of collaborative competition. Nat Biotechnol (2011) 1.28
Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput (2009) 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
Motif-based construction of a functional map for mammalian olfactory receptors. Genomics (2003) 1.23
Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. Cancer Res (2012) 1.20
Improving breast cancer survival analysis through competition-based multidimensional modeling. PLoS Comput Biol (2013) 1.20
MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma. Nat Immunol (2013) 1.17
B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. Cancer Res (2012) 1.15
Rewiring makes the difference. Mol Syst Biol (2011) 1.13
A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature. Plant J (2009) 1.10
PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis. Plant J (2011) 1.07
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Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A (2007) 1.01
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The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland. Genes Dev (2014) 0.98
Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas. Haematologica (2008) 0.96
Pattern-based mining strategy to detect multi-locus association and gene x environment interaction. BMC Proc (2007) 0.93
Using systems and structure biology tools to dissect cellular phenotypes. J Am Med Inform Assoc (2011) 0.92
Genome-wide dissection of posttranscriptional and posttranslational interactions. Methods Mol Biol (2012) 0.92
Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation. J Cell Mol Med (2011) 0.89
Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats. Mol Neurodegener (2014) 0.87
Pharmacogenetics: ethical issues and policy options. Kennedy Inst Ethics J (2002) 0.86
Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling. Development (2011) 0.86
A systems biology approach to transcription factor binding site prediction. PLoS One (2010) 0.85
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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst (2015) 0.84
Survival factor NFIL3 restricts FOXO-induced gene expression in cancer. Genes Dev (2013) 0.83
BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters. Bioinformatics (2012) 0.83
Gene expression dynamics during germinal center transit in B cells. Ann N Y Acad Sci (2003) 0.83
Pooled shRNA screenings: computational analysis. Methods Mol Biol (2013) 0.82
Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency. Stem Cells (2015) 0.81
T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses. Genes Chromosomes Cancer (2011) 0.81
Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis. Proc Natl Acad Sci U S A (2012) 0.80
Report: workshop on mediastinal grey zone lymphoma. Eur J Haematol Suppl (2005) 0.80
Correlating measurements across samples improves accuracy of large-scale expression profile experiments. Genome Biol (2009) 0.80
CASTOR: clustering algorithm for sequence taxonomical organization and relationships. J Comput Biol (2003) 0.79
The challenges of systems biology. Preface. Ann N Y Acad Sci (2009) 0.79
Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor. Nat Commun (2013) 0.78
Management of complicated gallstones: results of an alternative approach to difficult cholecystectomies. Minim Invasive Ther Allied Technol (2010) 0.78
A systems approach to drug discovery in Alzheimer's disease. Neurotherapeutics (2015) 0.77
Direct ChIP-Seq significance analysis improves target prediction. BMC Genomics (2015) 0.75
Correction: Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information. PLoS One (2016) 0.75
New JBI emphasis on translational bioinformatics. J Biomed Inform (2009) 0.75
The use of superelastic suture clips in laparoscopic gastric banding. Minim Invasive Ther Allied Technol (2008) 0.75
Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue. J Comput Biol (2011) 0.75
Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue. J Comput Biol (2013) 0.75
Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks. Cell (2016) 0.75