Published in PLoS Comput Biol on October 11, 2012
Modeling molecular pathways of neuronal ischemia. Prog Mol Biol Transl Sci (2014) 0.77
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
Creating the gene ontology resource: design and implementation. Genome Res (2001) 55.73
Using GOstats to test gene lists for GO term association. Bioinformatics (2006) 12.58
Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res (2004) 9.99
Molecular signatures database (MSigDB) 3.0. Bioinformatics (2011) 8.08
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics (2002) 6.90
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol (2006) 5.22
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics (2010) 3.42
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Systemic lipopolysaccharide protects the brain from ischemic injury by reprogramming the response of the brain to stroke: a critical role for IRF3. J Neurosci (2009) 1.84
Toll-like receptor 9: a new target of ischemic preconditioning in the brain. J Cereb Blood Flow Metab (2008) 1.79
Toll-like receptor signaling in endogenous neuroprotection and stroke. Neuroscience (2008) 1.73
Modeling systems-level regulation of host immune responses. PLoS Comput Biol (2007) 1.56
Endotoxin preconditioning protects against the cytotoxic effects of TNFalpha after stroke: a novel role for TNFalpha in LPS-ischemic tolerance. J Cereb Blood Flow Metab (2007) 1.55
Comparing different ODE modelling approaches for gene regulatory networks. J Theor Biol (2009) 1.54
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. Genome Biol (2008) 1.54
Multiple preconditioning paradigms converge on interferon regulatory factor-dependent signaling to promote tolerance to ischemic brain injury. J Neurosci (2011) 1.35
LPS preconditioning redirects TLR signaling following stroke: TRIF-IRF3 plays a seminal role in mediating tolerance to ischemic injury. J Neuroinflammation (2011) 1.25
Neuroprotective effects of TNF binding protein in focal cerebral ischemia. Brain Res (1997) 1.17
Agent-based modeling of endotoxin-induced acute inflammatory response in human blood leukocytes. PLoS One (2010) 1.08
Controlling the response: predictive modeling of a highly central, pathogen-targeted core response module in macrophage activation. PLoS One (2011) 1.08
Inflammation and the emerging role of the toll-like receptor system in acute brain ischemia. Stroke (2008) 0.98
The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models. Conf Proc IEEE Eng Med Biol Soc (2009) 0.98
Toll-like receptor tolerance as a mechanism for neuroprotection. Transl Stroke Res (2010) 0.97
A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142. Mol Biosyst (2011) 0.93
Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data. Ann N Y Acad Sci (2007) 0.92
Derivation, identification and validation of a computational model of a novel synthetic regulatory network in yeast. J Math Biol (2010) 0.90
Representing bioinformatics causality. Brief Bioinform (2004) 0.90
Learning global models of transcriptional regulatory networks from data. Methods Mol Biol (2009) 0.90
It's all in the family: multiple Toll-like receptors offer promise as novel therapeutic targets for stroke neuroprotection. Future Neurol (2009) 0.86
Defining the players in higher-order networks: predictive modeling for reverse engineering functional influence networks. Pac Symp Biocomput (2011) 0.86
Using the gene ontology to enrich biological pathways. Int J Comput Biol Drug Des (2009) 0.83
Modeling gene regulation networks using ordinary differential equations. Methods Mol Biol (2012) 0.82
A systematic petri net approach for multiple-scale modeling and simulation of biochemical processes. Appl Biochem Biotechnol (2010) 0.77
Standards for microarray data. Science (2002) 4.11
Submission of microarray data to public repositories. PLoS Biol (2004) 3.83
Effect of ischaemic preconditioning on genomic response to cerebral ischaemia: similarity to neuroprotective strategies in hibernation and hypoxia-tolerant states. Lancet (2003) 3.36
Standards for microarray data: an open letter. Environ Health Perspect (2004) 3.15
The underlying principles of scientific publication. Bioinformatics (2002) 2.79
A cancer cell metalloprotease triad regulates the basement membrane transmigration program. Genes Dev (2006) 2.78
Mechanisms of ischemic brain damage. Neuropharmacology (2008) 2.40
Systemic lipopolysaccharide protects the brain from ischemic injury by reprogramming the response of the brain to stroke: a critical role for IRF3. J Neurosci (2009) 1.84
Endotoxin preconditioning prevents cellular inflammatory response during ischemic neuroprotection in mice. Stroke (2004) 1.79
Toll-like receptor 9: a new target of ischemic preconditioning in the brain. J Cereb Blood Flow Metab (2008) 1.79
The use of flow cytometry to evaluate temporal changes in inflammatory cells following focal cerebral ischemia in mice. Brain Res (2002) 1.77
Preconditioning reprograms the response to ischemic injury and primes the emergence of unique endogenous neuroprotective phenotypes: a speculative synthesis. Stroke (2007) 1.64
Endotoxin preconditioning protects against the cytotoxic effects of TNFalpha after stroke: a novel role for TNFalpha in LPS-ischemic tolerance. J Cereb Blood Flow Metab (2007) 1.55
Multiple preconditioning paradigms converge on interferon regulatory factor-dependent signaling to promote tolerance to ischemic brain injury. J Neurosci (2011) 1.35
Neuroprotection by osteopontin in stroke. J Cereb Blood Flow Metab (2005) 1.33
Solution structure of human von Willebrand factor studied using small angle neutron scattering. J Biol Chem (2006) 1.33
LPS preconditioning redirects TLR signaling following stroke: TRIF-IRF3 plays a seminal role in mediating tolerance to ischemic injury. J Neuroinflammation (2011) 1.25
Novel thyroxine derivatives, thyronamine and 3-iodothyronamine, induce transient hypothermia and marked neuroprotection against stroke injury. Stroke (2007) 1.23
Nasal administration of osteopontin peptide mimetics confers neuroprotection in stroke. J Cereb Blood Flow Metab (2008) 1.16
Effects of transgenic overproduction of CRH on anxiety-like behaviour. Eur J Neurosci (2002) 1.15
A new model of cortical stroke in the rhesus macaque. J Cereb Blood Flow Metab (2009) 1.13
Corticotropin-releasing factor-1 receptor involvement in behavioral neuroadaptation to ethanol: a urocortin1-independent mechanism. Proc Natl Acad Sci U S A (2008) 1.10
Proof of concept: pharmacological preconditioning with a Toll-like receptor agonist protects against cerebrovascular injury in a primate model of stroke. J Cereb Blood Flow Metab (2011) 1.10
CRF enhancement of GIRK channel-mediated transmission in dopamine neurons. Neuropsychopharmacology (2009) 1.07
An open letter on microarray data from the MGED Society. Microbiology (2004) 1.05
Genomics of preconditioning. Stroke (2004) 1.04
Poly-IC preconditioning protects against cerebral and renal ischemia-reperfusion injury. J Cereb Blood Flow Metab (2011) 1.03
Toll-like receptor 7 preconditioning induces robust neuroprotection against stroke by a novel type I interferon-mediated mechanism. Stroke (2012) 1.00
HER/ErbB receptor interactions and signaling patterns in human mammary epithelial cells. BMC Cell Biol (2009) 1.00
Inflammation and the emerging role of the toll-like receptor system in acute brain ischemia. Stroke (2008) 0.98
Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems. BMC Syst Biol (2011) 0.97
Potential of baboon endothelial progenitor cells for tissue engineered vascular grafts. J Biomed Mater Res A (2008) 0.97
Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context. Mol Biosyst (2010) 0.96
Corticotropin-releasing factor overexpression decreases ethanol drinking and increases sensitivity to the sedative effects of ethanol. Psychopharmacology (Berl) (2004) 0.94
Mice deficient in corticotropin-releasing factor receptor type 2 exhibit normal ethanol-associated behaviors. Alcohol Clin Exp Res (2005) 0.94
Toll-like receptors: novel pharmacological targets for the treatment of neurological diseases. Curr Opin Pharmacol (2007) 0.93
Biomechanics of P-selectin PSGL-1 bonds: shear threshold and integrin-independent cell adhesion. Biophys J (2005) 0.93
Wrestling with SUMO and bio-ontologies. Nat Biotechnol (2006) 0.92
Corticotropin-releasing factor-overexpressing mice exhibit reduced neuronal activation in the arcuate nucleus and food intake in response to fasting. Endocrinology (2008) 0.91
Poly-ICLC preconditioning protects the blood-brain barrier against ischemic injury in vitro through type I interferon signaling. J Neurochem (2012) 0.91
Corticotropin-releasing factor acting on corticotropin-releasing factor receptor type 1 is critical for binge alcohol drinking in mice. Alcohol Clin Exp Res (2011) 0.91
Reverse engineering adverse outcome pathways. Environ Toxicol Chem (2011) 0.90
Corticotropin-releasing hormone-related peptides and receptors: emergent regulators of cardiovascular adaptations to stress. Trends Cardiovasc Med (2002) 0.89
Steps to translate preconditioning from basic research to the clinic. Transl Stroke Res (2012) 0.88
Expression profiling identifies the CRH/CRH-R1 system as a modulator of neurovascular gene activity. J Cereb Blood Flow Metab (2007) 0.88
Localized alteration of microtubule polymerization in response to guidance cues. J Neurosci Res (2010) 0.86
Defining the players in higher-order networks: predictive modeling for reverse engineering functional influence networks. Pac Symp Biocomput (2011) 0.86
Reduced cerebral injury in CRH-R1 deficient mice after focal ischemia: a potential link to microglia and atrocytes that express CRH-R1. J Cereb Blood Flow Metab (2003) 0.86
It's all in the family: multiple Toll-like receptors offer promise as novel therapeutic targets for stroke neuroprotection. Future Neurol (2009) 0.86
Gene expression profiles highlight adaptive brain mechanisms in corticotropin releasing factor overexpressing mice. Brain Res Mol Brain Res (2004) 0.85
Identification and validation of Ifit1 as an important innate immune bottleneck. PLoS One (2012) 0.85
Fresh frozen plasma as a complement source. Lancet Oncol (2007) 0.85
Basic fibroblast growth factor regulates persistent ERK oscillations in premalignant but not malignant JB6 cells. J Invest Dermatol (2009) 0.85
Overproduction of corticotropin-releasing hormone blocks germinal center formation: role of corticosterone and impaired follicular dendritic cell networks. J Neuroimmunol (2004) 0.84
Using the gene ontology to enrich biological pathways. Int J Comput Biol Drug Des (2009) 0.83
Dissociation of corticotropin-releasing factor receptor subtype involvement in sensitivity to locomotor effects of methamphetamine and cocaine. Psychopharmacology (Berl) (2011) 0.83
Cell type-dependent gene transcription profile in a three-dimensional human skin tissue model exposed to low doses of ionizing radiation: implications for medical exposures. Environ Mol Mutagen (2012) 0.83
Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle. BMC Genomics (2014) 0.83
Ethanol concentration-dependent effects and the role of stress on ethanol drinking in corticotropin-releasing factor type 1 and double type 1 and 2 receptor knockout mice. Psychopharmacology (Berl) (2011) 0.82
TLR9 bone marrow chimeric mice define a role for cerebral TNF in neuroprotection induced by CpG preconditioning. J Cereb Blood Flow Metab (2012) 0.82
Matrix effects in biological mass spectrometry imaging: identification and compensation. Analyst (2014) 0.82
Activation of the CRF 2 receptor modulates skeletal muscle mass under physiological and pathological conditions. Am J Physiol Endocrinol Metab (2003) 0.82
Adenosine and stroke: maximizing the therapeutic potential of adenosine as a prophylactic and acute neuroprotectant. Curr Neuropharmacol (2009) 0.82
CRF receptor antagonist astressin-B reverses and prevents alopecia in CRF over-expressing mice. PLoS One (2011) 0.82
Bleeding in orthopaedic surgery: the role of blood transfusion and erythropoietin alpha. Acta Biomed (2010) 0.81
Plasma adiponectin levels are increased despite insulin resistance in corticotropin-releasing hormone transgenic mice, an animal model of Cushing syndrome. Endocr J (2009) 0.79
Toll-like receptors and ischemic brain injury. J Neuropathol Exp Neurol (2014) 0.78
Data standards for Omics data: the basis of data sharing and reuse. Methods Mol Biol (2011) 0.78
Working with GFP in the brain. Biotechniques (2003) 0.78
Corticotropin-releasing hormone (CRH) transgenic mice display hyperphagia with increased Agouti-related protein mRNA in the hypothalamic arcuate nucleus. Endocr J (2011) 0.78
ERK oscillation-dependent gene expression patterns and deregulation by stress response. Chem Res Toxicol (2014) 0.78
A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis. Bioinformatics (2002) 0.77
Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts. Int J Comput Biol Drug Des (2011) 0.77
Spatial aspects in biological system simulations. Methods Enzymol (2011) 0.77
Integrated analysis reveals that STAT3 is central to the crosstalk between HER/ErbB receptor signaling pathways in human mammary epithelial cells. Mol Biosyst (2014) 0.76
α-Lipoic acid and superoxide dismutase in the management of chronic neck pain: a prospective randomized study. Drugs R D (2014) 0.75
Gene network and pathway generation and analysis. Int J Comput Biol Drug Des (2011) 0.75
Integrated experimental and computational approach to understand the effects of heavy ion radiation on skin homeostasis. Integr Biol (Camb) (2013) 0.75
Designing a collaborative visual analytics tool for social and technological change prediction. IEEE Comput Graph Appl (2009) 0.75
Identification of a Small Molecule Activator for AphB, a LysR-Type Virulence Transcriptional Regulator in Vibrio cholerae. Biochemistry (2017) 0.75