Please click on the systems biology references below to read the entire article. Check back occasionally as new systems biology articles will be posted.
- A framework to identify physiological responses in microarray based gene expression studies: selection and interpretation of biologically relevant genes
( Physiol Genomics (December 27, 2007). doi:10.1152/physiolgenomics.00167.2007 )
- Aberrant gene expression patterns in placentomes are associated with phenotypically normal and abnormal cattle cloned by somatic cell nuclear transfer
( Physiol Genomics (December 18, 2007). doi:10.1152/physiolgenomics.00223.2007 )
- Genome-wide gene expression profiling reveals renal genes regulated during metabolic acidosis
( Physiol Genomics, Dec 2007 )
- Dose response evaluation of gene expression profiles in the skin of K6/ODC mice exposed to sodium arsenite
( Toxicology and Applied Pharmacology Volume 227, Issue 3, 15 March 2008, Pages 400-416 )
- Transcriptional responses in thyroid tissues from rats treated with a tumorigenic and a non-tumorigenic triazole conazole fungicide
( Toxicology and Applied Pharmacology Volume 227, Issue 3, 15 March 2008, Pages 357-369 )
- Affymetrix and Illumina, a toxicogenomic based interplatform interplatform comparison
( Molecular Toxicology, Institute of Toxicology, Merck Serono Research, 64271 Darmstadt, Germany )
- The Genomic Landscapes of Human Breast and Colorectal Cancers
( Science 318, 1108 (2007) )
- Blood gene expression signatures predict exposure levels
( PNAS, November 13, 2007, vol. 104, no. 46, 18211–18216 )
- Host Gene Expression Profiling of Dengue Virus Infection in Cell Lines and Patients
( PLoS Neglected Tropical Diseases, 2007, Volume 1, Issue 2, e86 )
- Stem cell ageing: does it happen and can we intervene?
( Expert Reviews in Molecular Medicine, Vol. 9; Issue 31; November 2007 )
- Transcriptional networks in plasmacytoid dendritic cells stimulated with synthetic TLR 7 agonists
( BMC Immunology 2007, 8:26 )
- Fasting induces a biphasic adaptive metabolic response in murine small intestine
( BMC Genomics 2007, 8:361 )
- Chemogenomic Data Analysis: Prediction of Small-Molecule Targets and the Advent of Biological Fingerprints
( Combinatorial Chemistry & High Throughput Screening, 2007, 10, 719-731 )
- Acute Hepatotoxicity: A Predictive Model Based on Focused Illumina Microarrays
( Toxicological Sciences 99(1), 289-302 (2007) )
- Signature pathways identified from gene expression profiles in the human uterine cervix before and after spontaneous term parturition
( Am J Obstet Gynecol 2007;197:250.e1-250.e7 )
- Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
- Nutrigenomics: concepts and applications to pharmacogenomics and clinical medicine
( Pharmacogenomics. 8(4) 2007 )
- Overlapping gene expression profiles of model compounds provide opportunities for immunotoxicity screening.
( Toxicol. Appl. Pharmacol. (2007), doi:10.1016/j.taap.2007.08.026 )
- Seeding drug discovery: integrating telomerase cancer biology and cellular senescence to uncover new therapeutic opportunities in targeting cancer stem cells
( Drug Discovery Today, Volume 12, Numbers 15/16, August 2007 )
- DNA microarray analysis reveals a role for lysophosphatidic acid in the regulation of anti-inflammatory genes in MC3T3-E1 cells
( Bone 41 (2007) 833–841 )
- Transcriptional network governing the angiogenic switch in human pancreatic cancer
( PNAS, July 31, 2007, vol. 104, no. 31 )
- Telomerase redefined: Integrated regulation of hTR and hTERT for telomere maintenance and telomerase activity
( Biochimie (2007), doi:10.1016/j.biochi.2007.07.025 )
- Functional Network Analysis of the Transcriptomes of Mesenchymal Stem Cells Derived from Amniotic Fluid, Amniotic Membrane, Cord Blood, and Bone Marrow
( Stem Cells 2007;25;2511-2523 )
- Functional Network Analysis on the Transcriptomes of Mesenchymal Stem Cells Derived from Amniotic Fluid, Amniotic Membrane, Cord Blood, and Bone Marrow
( Stem Cells Express, June 7, 2007 )
- Toxicogenomics in the assessment of immunotoxicity
( Methods 41, 132-141, 2007 )
- Chemoinformatics: Theory, Practice, & Products
( Springer, 2007 )
- Lung response to Bordetella pertussis infection in mice identified by gene-expression profiling
( Immunogenetics, accepted )
- In vitro immunotoxicity of bis(tri-n-butyltin)oxide (TBTO) studied by toxicogenomics
( Toxicology 2007, accepted )
- Host transcription profiles upon primary Respiratory Syncytial Virus infection
( Journal of Virology, June 2007, p. 5958-5967 )
- Estrogenic Effects in the Immature Rat Uterus after Dietary Exposure to Ethinylestradiol and Zearalenone Using a Systems Biology Approach
( Toxicological Sciences 99(1), 303-314 (2007) )
- Quantitative proteomic analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer
( Mol Cell Proteomics 12 May 2007 )
- Huntington's disease: from experimental results to interaction networks, patho-pathway construction and disease hypothesis
( BMC Systems Biology 2007, 1(Suppl 1):P45 )
- Molecular Dissection of Hyperdiploid Multiple Myeloma by Gene Expression Profiling
( Cancer Res 2007; 67: (7). April 1, 2007 )
- Gene expression response of the rat small intestine following oral Salmonella infection
( Physiol Genomics. 2007 Mar 27 )
- Molecular Definition of Breast Tumor Heterogeneity
( Cancer Cell 11, 259-273, March 2007 )
- Networking genes with proteins: finding relations between proteomic and gene expression datasets using topology of the global protein interaction network
( University of Michigan Medical School )
- High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations
( BMC Genomics 2007, 8:28 doi:10.1186/1471-2164-8-28 )
- Proteomic Identification of Oxidatively Modified Golgi-Enzyme Glucuronyltransferase and Potential Consequences Related to the Modulation of Synaptic Plasticity in a Mouse Model of Alzheimer's Disease
( University of Southern California, Los Angeles, CA, USA )
- Radiation-induced protein release: A source of bystander signaling?
( Washington State University Tri-Cities and Pacific Northwest National Laboratory )
- Defining the Transcriptome of Accelerated and Replicatively Senescent Keratinocytes Reveals Links to Differentiation, Interferon Signaling, and Notch Related Pathways
( Journal of Cellular Biochemistry 98:394-408 (2006) )
- Gene Expression Profiling of Bis(tri-n-butyltin)oxide (TBTO)-Induced Immunotoxicity in Mice and Rats
( Journal of Immunotoxicology, 3:227-244, 2006 )
- Chronic quercetin exposure affects fatty acid catabolism in rat lung
( Cell. Mol. Life Sci. 63 (2006) 2847 - 2858. December 2006 )
- Mass Spectrometry-based Proteomic Studies of Human Anaplastic Large Cell Lymphoma
( Molecular & Cellular Proteomics 5:1787-1798, 2006 )
- Activin Modulates the Transcriptional Response of LβT2 Cells to Gonadotropin-Releasing Hormone and Alters Cellular Proliferation
( Molecular Endocrinology 20 (11) 2006 )
- Different Signaling Pathways in the Livers of Patients With Chronic Hepatitis B or Chronic Hepatitis C
( HEPATOLOGY, November 2006 )
- Gene expression profiles in anatomically and functionally distinct regions of the normal aged human brain
( Physiol Genomics. October 31, 2006 )
- Collaboration with GeneGo provides seamless access to compound databases, patents, literature and biological pathways
( Molecular Connection Vol 24 No 4 2006 )
- Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses
( Oncogenomics (2006), 1-12 )
- Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms
( Xenobiotica, Volume 36, Issue 10 & 11 October 2006 , pages 877 - 901 )
- Defective Ribosomal Protein Gene Expression Alters Transcription, Translation, Apoptosis, and Oncogenic Pathways in Diamond-Blackfan Anemia
( Stem Cell, 2006, 24, (9)2034-2044 )
- Evaluation of immunomodulation by Lactobacillus casei Shirota: immune function, autoimmunity and gene expression
( International Journal of Food Microbiology 112, 8-18, 2006 )
- Nicotinic modulation of gene expression in SH-SY5Y neuroblastoma cells
( Brain Research 1116 (2006) 39-49 )
- Gene Expression profiling of Waldenström&s Macroglobulinemia reveals a phenotype more similar to chronic lymphocytic leukemia than multiple myeloma
( Blood First Edition Paper, prepublished online June 27, 2006; DOI 10.1182/blood-2006-02-005488 )
- Gene Expression Profiling in Lung Tissues from Mice Exposed to Cigarette Smoke, Lipopolysaccharide, or Smoke Plus Lipopolysaccharide by Inhalation
( Inhalation Toxicology, 18:555-568, 2006 )
Poster
- High-protein and high-carbohydrate breakfasts differentially change the transcriptome of human blood cells
( Am J Clin Nutr 2006;84:1233-41 )
- Identification of interactive gene networks: A novel approach in gene array profiling of myometrial events during guinea pig pregnancy
( American Journal of Obstetrics and Gynecology (2006) 194, 1513-23 )
- Understanding Diabetes through Pathway Analysis
( Maggie Cam Genomics Core Laboratory NIDDK, NIH )
- Gene Expression Profiling in NF1 Knock-out Mice Suggests Link Between Neurofibromin, Kinesins, and Axonal Transport
( Barrow Neurological Institute )
- Microarray Platform Comparisons - Commentary on Barnes et al. (2005)
( Affymetrix White Paper, April 19, 2006 )
- Application of transcriptional and biological network analyses in mouse germ-cell transcriptomes
( Genomics, 2006 )
- Cognitive dysfunction in NF1 knock-out mice may result from altered vesicular trafficking of APP/DRD3 complex
( BMC Neuroscience 2006, 7:22 )
- Pathway Analyses of Chondrosarcoma
( Pathway Analysis for Target and Compound Evaluation San Francisco, CA )
- Data Mining for Gene Networks Relevant to Poor Prognosis in Lung Cancer Via Backward-Chaining Rule Induction
( Cancer Informatics. Libertas Academica )
- Gene Expression Alterations in the Cerebellum of Patients with Schizophrenia Revealed By DNA Microarray Analysis
( The University of New Mexico Health Sciences Center Department of Neurosciences )
- Biological Pathways at Your Fingertips
( iPath™ Quest Magazine, Vol.3, No.1, 77-81, 2006 )
- Comprehensive Network Analysis of Glaucoma Pathophisiology
( Mol. Sys. Biol. )
- Network analysis of human OMICs data: the toolkit and statistical evaluation
( Proc. Nattl. Acad. Sci. USA )
- Redox proteomic analysis of altered neuronal signaling in a PS1+APP mouse model of Alzheimer's disease
( J. Alzheimer Disease, in press )
- Systems level analysis of drug metabolism and its effects in human biology
( Bioinformatics. 2005, submitted )
- A Combined Approach to Drug Metabolism and Toxicity Assessment
( Drug Metabolism and Disposition 34:495-503, 2006 )
- Differential Protein Expression Profiling by iTRAQ-2DLC-MS/MS of Lung Cancer Cells Undergoing Epithelial-Mesenchymal Transition Reveals a Migratory/Invasive Phenotype
( Journal of Proteome Research )
- A Toolkit and Statistical Evaluation Method for Network Analysis of Human High Throughput Data
( FEBS Lett 2005, submitted )
- Reengineering the pharmaceutical industry by crash-testing molecules
( Drug Disc Today, Vol.10 Num. 17, September 2005 )
- MudPIT (Multidimensional Protein Identification Technology) for identification of post-translational protein modifications in complex biological mixtures
( In: Redox Proteomics: from Protein Modifications to Cellular Dysfunction and Diseases. Wiley Inter Science, in press )
- Altered protein expression following in utero exposure to arsenic
( Department of Cell Biology and Anatomy, and The Southwest Environmental Health Science Center, The University of Arizona, Tucson, AZ, and Department of Pharmacology, Toxicology, and Therapeutics, Kansas University Medical Center, Kansas City, KS )
- Using proteomics and network analysis to elucidate the consequences of synaptic protein oxidation in a PS1+AβPP mouse model of Alzheimer's disease
( Journal of Alzheimer's Disease, 7 (2005) 1-15 )
- Computational prediction of Human Drug Metabolism
( xpert Opinion. Drug Metab. Toxicol. (2005) )
- Use of the local lymph node assay in assessment of immune function
( Toxicology 211, 107-114, 2005 )
- Systems Biology; Applications in drug discovery
( In: Drug Discovery Handbook, Wiley, 2005 )
- Systems Level Network Analysis of OMICs Data
( Gen. Eng. News, 2005, 25, 1, 28-29 )
- Biological networks and analysis of experimental data in drug discovery
( Drug Discovery Today, DDT, Volume 10, Number 9, May 2005 )
- A Novel Method for Generation of Signature Networks as Biomarkers from Complex High Throughput Data
( Tox. Letters 158: 20-29, 2005 )
- Application of systems biology to absorption, distribution, metabolism, excretion and toxicity
( Trends in Pharmacological Sciences, Vol.26, No.4, 202-209, April 2005 )
- Techniques: Application of Systems Biology to Absorption, Distribution, Metabolism, Excretion and Toxicity
( TRENDS in Pharmacological Sciences Vol.26 No.4 April 2005 )
- A Novel Method for Visualizing Nuclear Hormone Receptor Networks Relevant to Drug Metabolism
( Drug Metabolism and Disposition, Vol.33, No.3 2005 )
- Identification Of Brain Ischemia-Induced Changes In Protein Profiles By Quantitative Proteomics
( LEGACY Health System )
- Comprehensive Computational Assessment of ADME Properties Using Mapping Techniques
( Current Drug Discovery Technologies, 2005, 2, 99-113 )
Mary E. Edgerton, a pathologist performing cancer research at MD Anderson and a long-term client, says “I have been using Metacore for many years in my research into pathways and networks that control aggressive behavior in cancers. I am currently using it to infer networks from analysis of gene expression array data for pathways in lung, brain, and breast cancer. I also use the curated pathways to formulate mathematical models of molecular networks that predict tumor behavior using multiscale modeling. Not only do I find the product to be very useful, but I also appreciate the responsiveness of the staff at Genego to my technical questions and suggestions.”