Published in BMC Syst Biol on January 30, 2008
An integrative -omics approach to identify functional sub-networks in human colorectal cancer. PLoS Comput Biol (2010) 1.54
Subnetwork state functions define dysregulated subnetworks in cancer. J Comput Biol (2011) 1.21
Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases. BMC Syst Biol (2012) 0.99
Network biology methods integrating biological data for translational science. Brief Bioinform (2012) 0.99
Learning dysregulated pathways in cancers from differential variability analysis. Cancer Inform (2014) 0.94
Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction. PLoS Comput Biol (2010) 0.91
Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods. Biol Direct (2012) 0.88
Algorithmic and analytical methods in network biology. Wiley Interdiscip Rev Syst Biol Med (2010) 0.87
Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers. J Cell Mol Med (2015) 0.80
Synergy analysis reveals association between insulin signaling and desmoplakin expression in palmitate treated HepG2 cells. PLoS One (2011) 0.79
Inference of gene regulatory networks from genetic perturbations with linear regression model. PLoS One (2013) 0.78
Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol (2010) 0.78
Pre-clinical drug prioritization via prognosis-guided genetic interaction networks. PLoS One (2010) 0.78
Pathway analyses and understanding disease associations. Curr Genet Med Rep (2013) 0.76
Novel opportunities for computational biology and sociology in drug discovery. Trends Biotechnol (2009) 0.75
Discovering Pair-wise Synergies in Microarray Data. Sci Rep (2016) 0.75
Biomarker discovery using statistically significant gene sets. J Comput Biol (2011) 0.75
Feature ranking based on synergy networks to identify prognostic markers in DPT-1. EURASIP J Bioinform Syst Biol (2013) 0.75
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet (2000) 24.22
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
Inferring cellular networks using probabilistic graphical models. Science (2004) 9.91
Survival signalling by Akt and eIF4E in oncogenesis and cancer therapy. Nature (2004) 8.76
A module map showing conditional activity of expression modules in cancer. Nat Genet (2004) 8.57
Integrative molecular concept modeling of prostate cancer progression. Nat Genet (2006) 8.49
Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput (2000) 8.02
An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics (2004) 7.85
Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res (2001) 6.73
How to infer gene networks from expression profiles. Mol Syst Biol (2007) 5.79
alpha-Methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer. JAMA (2002) 5.07
Integrative analysis of the cancer transcriptome. Nat Genet (2005) 4.44
Expression profiling reveals hepsin overexpression in prostate cancer. Cancer Res (2001) 3.45
A role of the kinase mTOR in cellular transformation induced by the oncoproteins P3k and Akt. Proc Natl Acad Sci U S A (2001) 3.01
Mining for regulatory programs in the cancer transcriptome. Nat Genet (2005) 2.88
Frequent high-level expression of the immunotherapeutic target Ep-CAM in colon, stomach, prostate and lung cancers. Br J Cancer (2006) 2.45
Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks. Bioinformatics (2006) 1.95
Computational analysis of the synergy among multiple interacting genes. Mol Syst Biol (2007) 1.92
Prostate-specific membrane antigen: a novel folate hydrolase in human prostatic carcinoma cells. Clin Cancer Res (1996) 1.88
Ferritin and the response to oxidative stress. Biochem J (2001) 1.88
Loss-of-function of Nkx3.1 promotes increased oxidative damage in prostate carcinogenesis. Cancer Res (2005) 1.66
AGR2, an androgen-inducible secretory protein overexpressed in prostate cancer. Genes Chromosomes Cancer (2005) 1.58
Hypermethylation-associated Inactivation of the Cellular Retinol-Binding-Protein 1 Gene in Human Cancer. Cancer Res (2002) 1.45
Inference of disease-related molecular logic from systems-based microarray analysis. PLoS Comput Biol (2006) 1.33
Correspondence analysis of genes and tissue types and finding genetic links from microarray data. Genome Inform Ser Workshop Genome Inform (2000) 1.31
Computational inference of the molecular logic for synaptic connectivity in C. elegans. Bioinformatics (2006) 1.23
Cellular retinol-binding protein-I inhibits PI3K/Akt signaling through a retinoic acid receptor-dependent mechanism that regulates p85-p110 heterodimerization. Oncogene (2005) 1.19
ERG upregulation and related ETS transcription factors in prostate cancer. Int J Oncol (2007) 1.05
Protection of androgen-dependent human prostate cancer cells from oxidative stress-induced DNA damage by overexpression of clusterin and its modulation by androgen. Prostate (2004) 1.04
The translation elongation factor eEF1B plays a role in the oxidative stress response pathway. RNA Biol (2004) 1.04
Hydrogen peroxide stimulates proliferation and migration of human prostate cancer cells through activation of activator protein-1 and up-regulation of the heparin affin regulatory peptide gene. J Biol Chem (2005) 0.96
Elevated L-PGDS activity contributes to PMA-induced apoptosis concomitant with downregulation of PI3-K. Am J Physiol Cell Physiol (2002) 0.90
Oxidative stress upregulates ubiquitin proteasome pathway in retinal endothelial cells. Mol Vis (2006) 0.88
Inhibition of major histocompatibility complex class II gene transcription by nitric oxide and antioxidants. J Biol Chem (2002) 0.81
Stress and death: breaking up the c-Abl/14-3-3 complex in apoptosis. Nat Cell Biol (2005) 0.80
Receptor interacting protein kinase-3 determines cellular necrotic response to TNF-alpha. Cell (2009) 11.36
R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science (2003) 9.53
The BioGRID Interaction Database: 2011 update. Nucleic Acids Res (2010) 8.46
Mule/ARF-BP1, a BH3-only E3 ubiquitin ligase, catalyzes the polyubiquitination of Mcl-1 and regulates apoptosis. Cell (2005) 6.86
TNF-alpha induces two distinct caspase-8 activation pathways. Cell (2008) 6.81
Mixed lineage kinase domain-like protein mediates necrosis signaling downstream of RIP3 kinase. Cell (2012) 6.56
Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell (2005) 6.47
Elimination of Mcl-1 is required for the initiation of apoptosis following ultraviolet irradiation. Genes Dev (2003) 6.17
Cytochrome C-mediated apoptosis. Annu Rev Biochem (2004) 5.38
Specific ablation of the apoptotic functions of cytochrome C reveals a differential requirement for cytochrome C and Apaf-1 in apoptosis. Cell (2005) 5.37
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
Autocrine TNFalpha signaling renders human cancer cells susceptible to Smac-mimetic-induced apoptosis. Cancer Cell (2007) 5.09
Jaundice Constrain or Indication? Response. Radiology (2017) 5.07
A small molecule Smac mimic potentiates TRAIL- and TNFalpha-mediated cell death. Science (2004) 4.95
The mitochondrial phosphatase PGAM5 functions at the convergence point of multiple necrotic death pathways. Cell (2012) 4.37
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
Probing genetic overlap among complex human phenotypes. Proc Natl Acad Sci U S A (2007) 3.79
WormBase 2007. Nucleic Acids Res (2007) 3.69
Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proc Natl Acad Sci U S A (2004) 3.63
Distinctive roles of PHAP proteins and prothymosin-alpha in a death regulatory pathway. Science (2003) 3.59
Degradation of Mcl-1 by beta-TrCP mediates glycogen synthase kinase 3-induced tumor suppression and chemosensitization. Mol Cell Biol (2007) 3.23
Three-dimensional structure of the apoptosome: implications for assembly, procaspase-9 binding, and activation. Mol Cell (2002) 3.06
The ER UDPase ENTPD5 promotes protein N-glycosylation, the Warburg effect, and proliferation in the PTEN pathway. Cell (2010) 2.97
Indirect emissions from biofuels: how important? Science (2009) 2.71
Toll-like receptors activate programmed necrosis in macrophages through a receptor-interacting kinase-3-mediated pathway. Proc Natl Acad Sci U S A (2011) 2.64
Dietary flavonoids: effects on xenobiotic and carcinogen metabolism. Toxicol In Vitro (2005) 2.60
WormBase 2014: new views of curated biology. Nucleic Acids Res (2013) 2.39
How many people do you know?: Efficiently estimating personal network size. J Am Stat Assoc (2010) 2.37
The role of oxygen during fracture healing. Bone (2012) 2.21
Formation of apoptosome is initiated by cytochrome c-induced dATP hydrolysis and subsequent nucleotide exchange on Apaf-1. Proc Natl Acad Sci U S A (2005) 2.18
Nutrient starvation elicits an acute autophagic response mediated by Ulk1 dephosphorylation and its subsequent dissociation from AMPK. Proc Natl Acad Sci U S A (2011) 2.06
Development of a prognostic model for breast cancer survival in an open challenge environment. Sci Transl Med (2013) 1.90
Cytochrome P450 2E1 contributes to ethanol-induced fatty liver in mice. Hepatology (2008) 1.90
HIV/STD prevalence among men who have sex with men in Chengdu, China and associated risk factors for HIV infection. J Acquir Immune Defic Syndr (2010) 1.76
Cytokines in alcoholic liver disease. Arch Toxicol (2012) 1.74
Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network. Genome Res (2008) 1.71
Silica encapsulation of n-octadecane via sol-gel process: a novel microencapsulated phase-change material with enhanced thermal conductivity and performance. J Colloid Interface Sci (2009) 1.67
Backward Haplotype Transmission Association (BHTA) algorithm - a fast multiple-marker screening method. Hum Hered (2002) 1.63
Generation and characterization of Smac/DIABLO-deficient mice. Mol Cell Biol (2002) 1.61
Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1. BMC Med Genomics (2010) 1.57
A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. Bioinformatics (2004) 1.57
A structure of the human apoptosome at 12.8 A resolution provides insights into this cell death platform. Structure (2005) 1.53
Discovering interactions among BRCA1 and other candidate genes associated with sporadic breast cancer. Proc Natl Acad Sci U S A (2008) 1.50
Autophagy occurs upstream or parallel to the apoptosome during histolytic cell death. Development (2006) 1.50
Chronic alcohol-induced liver injury and oxidant stress are decreased in cytochrome P4502E1 knockout mice and restored in humanized cytochrome P4502E1 knock-in mice. Free Radic Biol Med (2010) 1.47
PHAPI, CAS, and Hsp70 promote apoptosome formation by preventing Apaf-1 aggregation and enhancing nucleotide exchange on Apaf-1. Mol Cell (2008) 1.44
Three-dimensional structure of a double apoptosome formed by the Drosophila Apaf-1 related killer. J Mol Biol (2005) 1.43
Overcoming cancer cell resistance to Smac mimetic induced apoptosis by modulating cIAP-2 expression. Proc Natl Acad Sci U S A (2010) 1.42
Structure of an apoptosome-procaspase-9 CARD complex. Structure (2010) 1.42
Interaction with Tap42 is required for the essential function of Sit4 and type 2A phosphatases. Mol Biol Cell (2003) 1.41
Osteopontin, an oxidant stress sensitive cytokine, up-regulates collagen-I via integrin α(V)β(3) engagement and PI3K/pAkt/NFκB signaling. Hepatology (2012) 1.40
The difference in superior adjacent segment pathology after lumbar posterolateral fusion by using 2 different pedicle screw insertion techniques in 9-year minimum follow-up. Spine (Phila Pa 1976) (2014) 1.40
A demonstration and findings of a statistical approach through reanalysis of inflammatory bowel disease data. Proc Natl Acad Sci U S A (2004) 1.40
Clinical application and evaluation of Sysmex XE-5000 analyser for detecting nucleated red blood cells in peripheral blood. Clin Lab (2014) 1.38
Inference of regulatory gene interactions from expression data using three-way mutual information. Ann N Y Acad Sci (2009) 1.37
MERTK receptor tyrosine kinase is a therapeutic target in melanoma. J Clin Invest (2013) 1.34
Inference of disease-related molecular logic from systems-based microarray analysis. PLoS Comput Biol (2006) 1.33
A molecular signature predictive of indolent prostate cancer. Sci Transl Med (2013) 1.32
Gene clustering based on clusterwide mutual information. J Comput Biol (2004) 1.30
Gene regulatory network reconstruction using conditional mutual information. EURASIP J Bioinform Syst Biol (2008) 1.30
Missing-value estimation using linear and non-linear regression with Bayesian gene selection. Bioinformatics (2003) 1.27
Automatic categorization of diverse experimental information in the bioscience literature. BMC Bioinformatics (2012) 1.27
Interaction-based feature selection and classification for high-dimensional biological data. Bioinformatics (2012) 1.26
Multiple roles for CCR2 during fracture healing. Dis Model Mech (2010) 1.26
Biomolecular events in cancer revealed by attractor metagenes. PLoS Comput Biol (2013) 1.26
Computational inference of the molecular logic for synaptic connectivity in C. elegans. Bioinformatics (2006) 1.23
Discovery of Novel Small Molecule Mer Kinase Inhibitors for the Treatment of Pediatric Acute Lymphoblastic Leukemia. ACS Med Chem Lett (2012) 1.22
Biochemical mechanisms of the RNA-induced silencing complex. Cell Res (2007) 1.22
Control of vesicle fusion by a tyrosine phosphatase. Nat Cell Biol (2004) 1.21
Wnt/beta-Catenin pathway in human glioma: expression pattern and clinical/prognostic correlations. Clin Exp Med (2010) 1.19
Diazonamide toxins reveal an unexpected function for ornithine delta-amino transferase in mitotic cell division. Proc Natl Acad Sci U S A (2007) 1.19
Quantitative modeling of coupled piezo-elastodynamic behavior of piezoelectric actuators bonded to an elastic medium for structural health monitoring: a review. Sensors (Basel) (2010) 1.18
Mitochondrial activation of apoptosis. Cell (2004) 1.17
A multi-cancer mesenchymal transition gene expression signature is associated with prolonged time to recurrence in glioblastoma. PLoS One (2012) 1.15
Customized multiwavelets for planetary gearbox fault detection based on vibration sensor signals. Sensors (Basel) (2013) 1.15
Binarization of microarray data on the basis of a mixture model. Mol Cancer Ther (2003) 1.15
Segregation in social networks based on acquaintanceship and trust. AJS (2011) 1.15
Small-molecule activation of the TRAIL receptor DR5 in human cancer cells. Nat Chem Biol (2012) 1.13
SMAC mimetic (JP1201) sensitizes non-small cell lung cancers to multiple chemotherapy agents in an IAP-dependent but TNF-α-independent manner. Cancer Res (2011) 1.13
AMPK and mTOR coordinate the regulation of Ulk1 and mammalian autophagy initiation. Autophagy (2011) 1.13
CYP2E1 enhances ethanol-induced lipid accumulation but impairs autophagy in HepG2 E47 cells. Biochem Biophys Res Commun (2010) 1.12
Therapeutic anticancer efficacy of a synthetic diazonamide analog in the absence of overt toxicity. Proc Natl Acad Sci U S A (2007) 1.12
Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. PLoS One (2013) 1.11
Lipopolysaccharide-induced liver injury in rats treated with the CYP2E1 inducer pyrazole. Am J Physiol Gastrointest Liver Physiol (2005) 1.11
Association screening for genes with multiple potentially rare variants: an inverse-probability weighted clustering approach. BMC Proc (2011) 1.10
Combinatorial photothermal and immuno cancer therapy using chitosan-coated hollow copper sulfide nanoparticles. ACS Nano (2014) 1.10
Amplitude of low-frequency oscillations in first-episode, treatment-naive patients with major depressive disorder: a resting-state functional MRI study. PLoS One (2012) 1.09
Remarkable performance of Ir1/FeO(x) single-atom catalyst in water gas shift reaction. J Am Chem Soc (2013) 1.09
Effects of rare earth elements on the growth of Cistanche deserticola cells and the production of phenylethanoid glycosides. J Biotechnol (2003) 1.09
Peli1 promotes microglia-mediated CNS inflammation by regulating Traf3 degradation. Nat Med (2013) 1.08
The interaction of Schwann cells with chitosan membranes and fibers in vitro. Biomaterials (2004) 1.07
Exogenous smac induces competence and permits caspase activation in sympathetic neurons. J Neurosci (2002) 1.07
Transcription activity hot spot, is it real or an artifact? BMC Proc (2007) 1.04
Differences in metabolite profile between blood plasma and serum. Anal Biochem (2010) 1.03
UNC1062, a new and potent Mer inhibitor. Eur J Med Chem (2013) 1.03
Effects of L-lactate and D-mannitol on gamma-hydroxybutyrate toxicokinetics and toxicodynamics in rats. Drug Metab Dispos (2008) 1.03
Endonuclease G is required for early embryogenesis and normal apoptosis in mice. Proc Natl Acad Sci U S A (2003) 1.02
The E3 ubiquitin ligase Mule acts through the ATM-p53 axis to maintain B lymphocyte homeostasis. J Exp Med (2012) 1.02