Gene Regulation and Systems Biology

A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity (Published on 18 Dec 2014)

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A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia (Published on 08 Dec 2014)

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Endothelin-1 but not Endothelial Nitric Oxide Synthase Gene Polymorphism is Associated with Sickle Cell Disease in Africa (Published on 25 May 2014)

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Species-Specific Regulation of t-PA and PAI-1 Gene Expression in Human and Rat Astrocytes (Published on 08 May 2014)

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Overfeeding Dairy Cattle During Late-Pregnancy Alters Hepatic PPARα-Regulated Pathways Including Hepatokines: Impact on Metabolism and Peripheral Insulin Sensitivity (Published on 03 Apr 2014)

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DNA Conformational Transitions Induced by Supercoiling Control Transcription in Chromatin (Published on 12 Mar 2014)

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Tissue-Specific Gene Expression and Regulation in Liver and Muscle Following Chronic Corticosteroid Administration (Published on 10 Mar 2014)

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Tetracycline Derivative Minocycline Inhibits Autophagy and Inflammation in Concanavalin-A-Activated Human Hepatoma Cells (Published on 04 Mar 2014)

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Discovery of Emphysema Relevant Molecular Networks from an A/J Mouse Inhalation Study Using Reverse Engineering and Forward Simulation (REFS™) (Published on 19 Feb 2014)

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Gene Expression and Gene Ontology Enrichment Analysis for H3K4me3 and H3K4me1 in Mouse Liver and Mouse Embryonic Stem Cell Using ChIP-Seq and RNA-Seq (Published on 20 Jan 2014)

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Central Role of the PPARγ Gene Network in Coordinating Beef Cattle Intramuscular Adipogenesis in Response to Weaning Age and Nutrition (Published on 08 Jan 2014)

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Innate Immunity Interactome Dynamics (Published on 06 Jan 2014)

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Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases (Published on 04 Nov 2013)

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CEBPG Exhibits Allele-Specific Expression in Human Bronchial Epithelial Cells (Published on 04 Jul 2013)

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Dietary Lipid During Late-Pregnancy and Early-Lactation to Manipulate Metabolic and Inflammatory Gene Network Expression in Dairy Cattle Liver with a Focus on PPARs (Published on 11 Jun 2013)

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Investigation of dmyc Promoter and Regulatory Regions (Published on 15 May 2013)

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Yin Yang 1 and Adipogenic Gene Network Expression in Longissimus Muscle of Beef Cattle in Response to Nutritional Management (Published on 16 Apr 2013)

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Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification (Published on 26 Mar 2013)

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A Comprehensive Profile of ChIP-Seq-Based STAT1 Target Genes Suggests the Complexity of STAT1-Mediated Gene Regulatory Mechanisms (Published on 26 Mar 2013)

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Global Consensus Theorem and Self-Organized Criticality: Unifying Principles for Understanding Self-Organization, Swarm Intelligence and Mechanisms of Carcinogenesis (Published on 20 Feb 2013)

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Implications of Systemic Dysfunction for the Etiology of Malignancy (Published on 06 Feb 2013)

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Extensive Ethnogenomic Diversity of Endothelial Nitric Oxide Synthase (eNOS) Polymorphisms (Published on 15 Jan 2013)

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Effects of High Fat Feeding on Liver Gene Expression in Diabetic Goto-Kakizaki Rats (Published on 28 Nov 2012)

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FOXO1 Up-Regulates Human L-selectin Expression Through Binding to a Consensus FOXO1 Motif (Published on 29 Oct 2012)

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A Next-Generation Sequencing Approach to Study the Transcriptomic Changes During the Differentiation of Physarum at the Single-Cell Level (Published on 01 Oct 2012)

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Ruminant Metabolic Systems Biology: Reconstruction and Integration of Transcriptome Dynamics Underlying Functional Responses of Tissues to Nutrition and Physiological Statea (Published on 25 Jun 2012)

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Binding Motifs in Bacterial Gene Promoters Modulate Transcriptional Effects of Global Regulators CRP and ArcA (Published on 30 May 2012)

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Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology (Published on 16 May 2012)

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Unique Sex-Based Approach Identifies Transcriptomic Biomarkers Associated with Non-Syndromic Craniosynostosis (Published on 16 May 2012)

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A Flexible and Qualitatively Stable Model for Cell Cycle Dynamics Including DNA Damage Effects (Published on 11 Apr 2012)

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Regulatory Mechanisms in Bone Following Mechanical Loading (Published on 17 Jan 2012)

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Identification of cis-Regulatory Elements in the dmyc Gene of Drosophila Melanogaster (Published on 21 Dec 2011)

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Alpha-Tocopherol Alters Transcription Activities that Modulates Tumor Necrosis Factor Alpha (TNF-a) Induced Inflammatory Response in Bovine Cells (Published on 05 Dec 2011)

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Biomolecular Self-Defense and Futility of High-Specificity Therapeutic Targeting (Published on 21 Nov 2011)

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Application of Structure Equation Modeling for Inferring a Serial Transcriptional Regulation in Yeast (Published on 10 Nov 2011)

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Developmental Regulation of Genes Encoding Universal Stress Proteins in Schistosoma mansoni (Published on 19 Sep 2011)

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Identification of New SRF Binding Sites in Genes Modulated by SRF Over-Expression in Mouse Hearts (Published on 12 Jul 2011)

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Critical Self-Organized Self-Sustained Oscillations in Large Regulatory Networks: Towards Understanding the Gene Expression Initiation (Published on 22 Mar 2011)

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Biology of the Mi-2/NuRD Complex in SLAC (Stemness, Longevity/Ageing, and Cancer) (Published on 27 Feb 2011)

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Molecular Cloning of the Genes Encoding the PR55/Bβ/δ Regulatory Subunits for PP-2A and Analysis of Their Functions in Regulating Development of Goldfish, Carassius auratus (Published on 20 Dec 2010)

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Identifying a Transcription Factor's Regulatory Targets from its Binding Targets (Published on 08 Dec 2010)

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Alpha-Tocopherol Modulates Transcriptional Activities that Affect Essential Biological Processes in Bovine Cells (Published on 22 Nov 2010)

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Overexpression of Colligin 2 in Glioma Vasculature is Associated with Overexpression of Heat Shock Factor 2 (Published on 20 Oct 2010)

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Omega-6 Fat Supplementation Alters Lipogenic Gene Expression in Bovine Subcutaneous Adipose Tissue (Published on 19 Oct 2010)

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HO1 mRNA and Protein do not Change in Parallel in Bronchial Biopsies of Patients After Long Term Exposure to Sulfur Mustard (Published on 01 Oct 2010)

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Fractal Topology of Gene Promoter Networks at Phase Transitions (Published on 28 Jul 2010)

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Do DNA Microarrays Tell the Story of Gene Expression? (Published on 29 Jun 2010)

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Model-Based Analysis of FGF23 Regulation in Chronic Kidney Disease (Published on 09 Jun 2010)

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GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase (Published on 24 May 2010)

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Inference of Cancer-specific Gene Regulatory Networks Using Soft Computing Rules (Published on 31 Mar 2010)

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Transcriptional Response Of E. coli Upon FimH-mediated Fimbrial Adhesion (Published on 24 Mar 2010)

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Microarray Data Analysis of Gene Expression Evolution (Published on 27 Nov 2009)

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Hereditary Inclusion Body Myopathy (HIBM2) (Published on 21 Oct 2009)

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Characteristics of Transcriptional Activity in Nonlinear Dynamics of Genetic Regulatory Networks (Published on 19 Oct 2009)

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Stochastic Spatio-Temporal Dynamic Model for Gene/Protein Interaction Network in Early Drosophila Development (Published on 19 Oct 2009)

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Evolution and Origin of HRS, a Protein Interacting with Merlin, the Neurofibromatosis 2 Gene Product (Published on 08 Oct 2009)

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Evaluation of the Role of FGF23 in Mineral Metabolism (Published on 03 Aug 2009)

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The Goldfish SG2NA Gene Encodes Two α-Type Regulatory Subunits for PP-2A and Displays Distinct Developmental Expression Pattern (Published on 21 Jul 2009)

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Application of Petri Nets in Bone Remodeling (Published on 06 Jul 2009)

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Letter to the Editor: Does Dicer Expression Affect shRNA Processing? (Published on 19 Jun 2009)

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Safety and in vivo Expression of a GNE-Transgene: A Novel Treatment Approach for Hereditary Inclusion Body Myopathy-2 (Published on 08 May 2009)

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Sigma Factors for Cyanobacterial Transcription (Published on 22 Apr 2009)

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An Effective Tri-Clustering Algorithm Combining Expression Data with Gene Regulation Information (Published on 15 Apr 2009)

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A Novel Function of Ethylene (Published on 07 Apr 2009)

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Post-Transcriptional Control of Chloroplast Gene Expression (Published on 12 Mar 2009)

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RNAi-Mediated Knockdown Showing Impaired Cell Survival in Drosophila Wing Imaginal Disc (Published on 19 Feb 2009)

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Patterns of Stochastic Behavior in Dynamically Unstable High-Dimensional Biochemical Networks (Published on 29 Jan 2009)

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The MAPK Signaling Cascade is a Central Hub in the Regulation of Cell Cycle, Apoptosis and Cytoskeleton Remodeling by Tripeptidyl-Peptidase II (Published on 24 Nov 2008)

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Systems Biology and Cancer Prevention: All Options on the Table (Published on 10 Oct 2008)

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Advances in Antisense Oligonucleotide Development for Target Identification, Validation, and as Novel Therapeutics (Published on 22 Sep 2008)

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Role of Cytokines During Epileptogenesis and in the Transition from the Interictal to the Ictal State in the Epileptic Mutant EL Mouse (Published on 27 Aug 2008)

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Molecular Mechanisms of Uterine Leiomyosarcomas: Involvement of Defect in LMP2 Expression (Published on 22 Jul 2008)

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Preclinical Assessment of wt GNE Gene Plasmid for Management of Hereditary Inclusion Body Myopathy 2 (HIBM2) (Published on 20 Jun 2008)

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Level of Expression of the Nonmutant Ferrochelatase Allele is a Determinant of Biochemical Phenotype in a Mouse Model of Erythropoietic Protoporphyria (Published on 29 May 2008)

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Gene Expression in Pre-MBT Embryos and Activation of Maternally-Inherited Program of Apoptosis to be Executed at around MBT as a Fail-Safe Mechanism in Xenopus Early Embryogenesis (Published on 29 May 2008)

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RNA Processing and mRNA Surveillance in Monogenic Diabetes (Published on 21 May 2008)

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Centrality Analysis Methods for Biological Networks and Their Application to Gene Regulatory Networks (Published on 15 May 2008)

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The Remarkable Mechanism of Prostaglandin E2 on Synaptic Plasticity (Published on 09 May 2008)

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Multi-Target Approaches in Colon Cancer Chemoprevention Based on Systems Biology of Tumor Cell-Signaling (Published on 02 May 2008)

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Pharmacodynamic/Pharmacogenomic Modeling of Insulin Resistance Genes in Rat Muscle After Methylprednisolone Treatment: Exploring Regulatory Signaling Cascades (Published on 23 Apr 2008)

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MicroRNAs Regulate Osteogenesis and Chondrogenesis of Mouse Bone Marrow Stromal Cells (Published on 22 Apr 2008)

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Association of Vascular Endothelial Growth Factor Polymorphisms with Asthma in Tunisian Children (Published on 10 Apr 2008)

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Calcitriol and TO-901317 Interact in Human Prostate Cancer LNCaP Cells (Published on 17 Mar 2008)

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Butyrate Induced Cell Cycle Arrest in Bovine Cells through Targeting Gene Expression Relevant to DNA Replication Apparatus (Published on 17 Mar 2008)

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Image Analysis and Data Normalization Procedures are Crucial for Microarray Analyses (Published on 17 Mar 2008)

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Comparison of Statistical Data Models for Identifying Differentially Expressed Genes Using a Generalized Likelihood Ratio Test (Published on 17 Mar 2008)

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Gene Regulation System of Vasopressin and Corticotoropin-Releasing Hormone (Published on 03 Mar 2008)

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TAK1 mRNA Expression in the Tumor Tissue of Locally Advanced Head and Neck Cancer Patients (Published on 14 Feb 2008)

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Pharmacodynamic Modeling of Acute and Chronic Effects of Methylprednisolone on Hepatic Urea Cycle Genes in Rats (Published on 14 Feb 2008)

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Genomic Loci Modulating the Retinal Transcriptome in Wound Healing (Published on 14 Feb 2008)

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Gene Expression Analysis of Biological Systems Driving an Organotypic Model of Endometrial Carcinogenesis and Chemoprevention (Published on 10 Feb 2008)

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Oxygen and Cell Fate Decisions (Published on 10 Feb 2008)

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Reconstructing a Network of Stress-Response Regulators via Dynamic System Modeling of Gene Regulation (Published on 10 Feb 2008)

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Gene Module Identification from Microarray Data Using Nonnegative Independent Component Analysis (Published on 15 Jan 2008)

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MicroRNA Expression in Alzheimer Blood Mononuclear Cells (Published on 20 Dec 2007)

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Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters (Published on 17 Dec 2007)

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Prostate Cancer Epigenetics: A Review on Gene Regulation (Published on 11 Dec 2007)

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Vectors Encoding Seven Oikosin Signal Peptides Transfected into CHO Cells Differ Greatly in Mediating Gaussia luciferase and Human Endostatin Production although mRNA Levels are Largely Unaffected (Published on 11 Dec 2007)

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Early Onset of Heat-Shock Response in Mouse Embryos Revealed by Quantification of Stress-Inducible hsp70i RNA (Published on 06 Dec 2007)

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New Insights into the Genetic Regulation of Plasmodium Falciparum Obtained by Bayesian Modeling (Published on 29 Nov 2007)

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Variability of DNA Microarray Gene Expression Profiles in Cultured Rat Primary Hepatocytes (Published on 18 Nov 2007)

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Current Status of Monocyte Differentiation-Inducing (MDI) Factors Derived from Human Fetal Membrane Chorion Cells Undergoing Apoptosis after Influenza Virus Infection (Published on 12 Nov 2007)

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Trichoderma Biocontrol: Signal Transduction Pathways Involved in Host Sensing and Mycoparasitism (Published on 08 Nov 2007)

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Proposed Regulation of Gene Expression by Glucose in Rodent Heart (Published on 05 Nov 2007)

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Enterobacterial Small Mobile Sequences Carry Open Reading Frames and are Found Intragenically—Evolutionary Implications for Formation of New Peptides (Published on 16 Oct 2007)

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Signaling Mechanisms of Endogenous Angiogenesis Inhibitors Derived from Type IV Collagen (Published on 14 Oct 2007)

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β1-Integrin Signaling is Essential for Lens Fiber Survival (Published on 12 Oct 2007)

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Nonlinear Dynamic Trans/Cis Regulatory Circuit for Gene Transcription via Microarray Data (Published on 12 Oct 2007)

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CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling (Published on 06 Oct 2007)

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Role of SP-1 in SDS-Induced Adipose Differentiation Related Protein Synthesis in Human Keratinocytes (Published on 04 Oct 2007)

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The Role and Regulation of Receptor-Like Kinases in Plant Defense (Published on 26 Sep 2007)

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The Effect of Aromatic Hydrocarbon Receptor on the Phenotype of the Hepa 1c1c7 Murine Hepatoma Cells in the Absence of Dioxin (Published on 18 Sep 2007)

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Computational Systems Biology in Cancer: Modeling Methods and Applications (Published on 17 Sep 2007)

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Insulin Sensitizing Pharmacology of Thiazolidinediones Correlates with Mitochondrial Gene Expression rather than Activation of PPARγ (Published on 17 Sep 2007)

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Role of Fetal Stem Cells in Maternal Tissue Regeneration (Published on 06 Sep 2007)

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Intensity Dependent Confidence Intervals on Microarray Measurements of Differentially Expressed Genes: A Case Study of the Effect of MK5, FKRP and TAF4 on the Transcriptome (Published on 17 Jul 2007)

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A Discussion Concerning the Inclusion of Variety Effect when Analysis of Variance is Used to Detect Differentially Expressed Genes (Published on 15 Jun 2007)

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Developing a Systems Biology Approach to Study Disease Progression Caused by Heterodera glycines in Glycine max (Published on 05 Jun 2007)

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Practical Lessons from Theoretical Models about the Somitogenesis (Published on 28 May 2007)

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Evaluation of Two Outlier-Detection-Based Methods for Detecting Tissue-Selective Genes from Microarray Data (Published on 01 May 2007)

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Systems Biology-Based Identification of Crosstalk between E2F Transcription Factors and the Fanconi Anemia Pathway (Published on 01 May 2007)

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