Systems Biology

2010

• The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
  ( Nat Biotechnol, 28: 827-838, 2010 )
  Gene expression data from microarrays are being applied to predict preclinical and clinical endpoints, but the reliability of these predictions has not been established. In the MAQC-II project, 36 independent ...
• Effective knowledge management in translational medicine
  ( Journal of Translational Medicine 2010, 8:68 )
  Background The growing consensus that most valuable data source for biomedical discoveries is derived from human samples is clearly reflected in the growing number of translational medicine and translational sciences ...
• Identification of the Eph receptor pathway as a novel target for eicosapentaenoic acid (EPA) modification of gene expression in human colon adenocarcinoma cells (HT-29)
  ( Nutrition & Metabolism 2010, 7:56 )
  Background The health benefits of polyunsaturated fatty acids (PUFAs), particularly those of the n-3 series are well documented. The mechanisms by which these effects are mediated are not fully clarified. ...
• Disruption of the clock components CLOCK and BMAL1 leads to hypoinsulinaemia and diabetes
  ( doi:10.1038/nature09253 )
  The molecular clock maintains energy constancy by producing circadian oscillations of rate-limiting enzymes involved in tissue metabolism across the day and night1–3. During periods of feeding, pancreatic islets secrete insulin ...
• Proteomic analysis of Nrf2 deficient transgenic mice reveals cellular defence and lipid metabolism as primary Nrf2-dependent pathways in the liver
  ( J Proteomics. 2010 Jun 16;73(8):1612-31 )
  The transcription factor Nrf2 regulates expression of multiple cellular defence proteins through the antioxidant response element (ARE). Nrf2-deficient mice (Nrf2(-/-)) are highly susceptible to xenobiotic-mediated toxicity, but the precise molecular ...
• Large-scale benchmark of Endeavour using MetaCore maps
  ( The Author (2010) )
  Summary: Endeavour is a tool that detects the most promising genes within large lists of candidates with respect to a biological process of interest and by combining several genomic data ...
• ‘‘Topological Significance’’ Analysis of Gene Expression and Proteomic Profiles from Prostate Cancer Cells Reveals Key Mechanisms of Androgen Response
  ( PLoS ONE 5(6): e10936. doi:10.1371/journal.pone.0010936 )
• Functional proteomics reveal the effect of Salvia miltiorrhiza aqueous extract against vascular atherosclerotic lesions
  ( Biochim Biophys Acta. 2010 Jun;1804(6):1310-21 )
  Salvia miltiorrhiza is a Chinese herb widely used for cardiovascular disorder regimens, yet little is known about the cellular mechanisms that contribute to attenuated growth of smooth muscle cells (SMCs) ...
• Integrative Genome Comparison of Primary and Metastatic Melanomas
  ( PLoS One. 2010; 5(5): e10770 )
  Abstract A cardinal feature of malignant melanoma is its metastatic propensity. An incomplete view of the genetic events driving metastatic progression has been a major barrier to rational development of ...
• Consistency of predictive signature genes and classifiers generated using different microarray platforms
  ( The Pharmacogenomics Journal (2010) 10, 247–257 )
  Microarray-based classifiers and associated signature genes generated from various platforms are abundantly reported in the literature; however, the utility of the classifiers and signature genes in cross-platform prediction applications remains ...
• Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes
  ( The Pharmacogenomics Journal (2010) 10, 310–323 )
  Gene expression signatures of toxicity and clinical response benefit both safety assessment and clinical practice; however, difficulties in connecting signature genes with the predicted end points have limited their application. ...
• Genomic indicators in the blood predict drug-induced liver injury
  ( The Pharmacogenomics Journal (2010) 10, 267–277 )
  Genomic biomarkers for the detection of drug-induced liver injury (DILI) from blood are urgently needed for monitoring drug safety. We used a unique data set as part of the Food ...
• A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data
  ( The Pharmacogenomics Journal (2010) 10, 278–291 )
  Batch effects are the systematic non-biological differences between batches (groups) of samples in microarray experiments due to various causes such as differences in sample preparation and hybridization protocols. Previous work ...
• Proteomics, bioinformatics and targeted gene expression analysis reveals up-regulation of cochlin and identifies other potential biomarkers in the mouse model for deafness in Usher syndrome type 1F
  ( Hum Mol Genet. 2010 Apr 15;19(8):1515-27 )
  Proteins and protein networks associated with cochlear pathogenesis in the Ames waltzer (av) mouse, a model for deafness in Usher syndrome 1F (USH1F), were identified. Cochlear protein from wild-type and ...
• Integrated network analysis of transcriptomic and proteomic data in psoriasis
  ( BMC Systems Biology 2010, 4:41 )
  Background Psoriasis is complex inflammatory skin pathology of autoimmune origin. Several cell types are perturbed in this pathology, and underlying signaling events are complex and still poorly understood. Results In ...
• Evidence of perturbations of cell cycle and DNA repair pathways as a consequence of human and murine NF1-haploinsufficiency
  ( BMC Genomics. 2010 Mar 22;11:194. )
  BACKGROUND: Neurofibromatosis type 1 (NF1) is a common monogenic tumor-predisposition disorder that arises secondary to mutations in the tumor suppressor gene NF1. Haploinsufficiency of NF1 fosters a permissive tumorigenic environment ...
• TCEAL7 Inhibition of c-Myc Activity in Alternative Lengthening of Telomeres Regulates hTERT Expression
  ( Neoplasia (2010) 12, 405–414 )
  Abstract Replicative senescence forms a major barrier to tumor progression. Cancer cells bypass this by using one of the two known telomere maintenance mechanisms: telomerase or the recombination-based alternative lengthening ...
• Molecular targets for diabetes mellitus-associated erectile dysfunction
  ( Mol Cell Proteomics. 2010 Mar;9(3):565-78 )
  Protein expression profiles in rat corporal smooth muscle tissue were compared between animal models of streptozotocin-induced diabetes mellitus (STZ-DM) and age-matched controls (AMCs) at 1 week and 2 months after ...
• Functional proteomic and structural insights into molecular targets related to the growth inhibitory effect of tanshinone IIA on HeLa cells
  ( Proteomics. 2010 Mar;10(5):914-29 )
  Certain antitumor agents have recently been extracted from the roots of Salvia miltiorrhiza Bunge. The diterpene derivative, tanshinone IIA, possesses cytotoxic activity against several human carcinoma cell lines. It also ...
• Change in amniotic fluid levels of multiple anti-angiogenic proteins before development of preeclampsia and intrauterine growth restriction
  ( J Clin Endocrinol Metab. 2010 Mar;95(3):1431-41 )
  Context: The cause of preeclampsia remains unknown. Excessive antiangiogenic proteins have been proposed to play a pathogenic role in preeclampsia. Objective: Our objective was to determine the differences in soluble ...
• Bimodal gene expression patterns in breast cancer
  ( BMC Genomics. 2010; 11(Suppl 1): S8. )
  We identified a set of genes with an unexpected bimodal distribution among breast cancer patients in multiple studies. The property of bimodality seems to be common, as these genes were ...
• Eight-plex iTRAQ analysis of variant metastatic human prostate cancer cells identifies candidate biomarkers of progression: An exploratory study.
  ( The Prostate )
  BACKGROUND: Due to the heterogeneity in the biological behaviour of prostate cancer, biomarkers that can reliably distinguish indolent from aggressive disease are urgently needed to inform treatment choices. METHODS: We ...
• Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder
  ( BMC Medical Genetics 2010, 11:14 )
• Impact of Cyclin B2 and Cell division cycle 2 on tubular hyperplasia in progressive chronic renal failure rats
  ( Am J Physiol Renal Physiol. 2010 Jan 13 )
  To clarify the specific molecular events of progressive tubular damage in chronic renal failure (CRF), we conducted microarray analyses using isolated proximal tubules from subtotally nephrectomized (Nx) rats as a ...
• Effect of training sample size and classification difficulty on the accuracy of genomic predictors
  ( Breast Cancer Research 2010, 12:R5 doi:10.1186/bcr2468 )
  Introduction: As part of the MicroArray Quality Control (MAQC)-II project, this analysis examines how the choice of univariate feature selection methods and classification algorithms may influence the performance of genomic ...
• Effect of training-sample size and classification difficulty on the accuracy of genomic predictors
  ( Breast Cancer Research 2010, 12:R5 )
• Telomerase upregulation is a postcrisis event during senescence bypass and immortalization of two Nijmegen breakage syndrome T cell cultures
  ( Aging Cell (2010) 9, pp220–235 )
  Our knowledge on immortalization and telomere biology is mainly based on genetically manipulated cells analyzed before and many population doublings post growth crisis. The general view is that growth crisis ...

2009

• Interactions between traditional Chinese medicines and Western therapeutics
  ( Current Opinion in Drug Discovery & Development 2010 13(1):50-65 )
  Traditional Chinese medicine (TCM) is a holistic approach to health that attempts to bring the body, mind and spirit into harmony. TCM is an essential part of the healthcare system ...
• Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals
  ( Toxicol Sci. 2009 Dec;112(2):311-21. )
• Systems Biology Modeling of the Radiation Sensitivity Network: A Biomarker Discovery Platform
  ( International Journal of Radiation Oncology, Biology, Physics (volume 75 issue 2 Pages 497-505) )
  Purpose: The discovery of effective biomarkers is a fundamental goal of molecular medicine. Developing a systems-biology understanding of radiosensitivity can enhance our ability of identifying radiation-specific biomarkers. Methods and Materials: ...
• MICRORNA PROFILING IN CANCER: A Bioinformatics Perspective
  ( Pan Stanford Publishing )
• A Gene Expression Model of Intrinsic Tumor Radiosensitivity: Prediction of Response and Prognosis after Chemoradiation
  ( International Journal of Radiation Oncology, Biology, Physics (volume 75 issue 2 Pages 489-496) )
  Purpose: Development of a radiosensitivity predictive assay is a central goal of radiation oncology. We reasoned a gene expression model could be developed to predict intrinsic radiosensitivity and treatment response ...
• Discrimination for genotoxic and non-genotoxic carcinogens by gene expression profiling in primary mouse hepatocytes improves with exposure time
  ( Toxicological Sciences, doi:10.1093/toxsci/kfp229 )
• Network and pathway analysis of compound-protein interactions
  ( Methods Mol Biol. 2009;575:225-47 )
  We describe an integrated system that brings together predictive chemical analyses based on compound structure, knowledge bases of chemogenomics data associating compounds to biological, pharmacological and toxicological properties, and a ...
• Identification of AhR-regulated genes involved in PAH-induced immunotoxicity using a highly-sensitive DNA chip, 3D-Gene Human Immunity & Metabolic Syndrome 9k
  ( Toxicol In Vitro. 2009 Sep 5. )
• A gene expression signature classifying telomerase and ALT immortalization reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT
  ( Oncogene (2009), 1–10 )
• Proteins that underlie neoplastic progression of ulcerative colitis
  ( Proteomics Clin. Appl. 2009, 3, 1326–1337 )
• Dynamic Telomerase Gene Suppression via Network Effects of GSK3 Inhibition
  ( PLoS ONE July 2009 | Volume 4 | Issue 7 | e6459 )
• Untangling the protein web
  ( NATURE|Vol 460|16 July 2009 )
• PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools
  ( Methods Mol Biol. 2009;563:123-40 )
• ArrayTrack: An FDA and Public Genomic Tool
  ( Methods Mol Biol. 2009;563:379-98 )
• Translational Research and Biomedical Informatics
  ( Methods Mol Biol. 2009;563:369-78 )
• MetaMiner (CF): a disease oriented bioinformatics analysis environment
  ( Methods Mol Biol. 2009;563:353-67 )
• MiRNAs: from biogenesis to networks
  ( Methods Mol Biol. 2009;563:303-52 )
• Pathway and Network Analysis with High-Density Allelic Association Data
  ( Methods Mol Biol. 2009;563:289-301 )
• High-throughput siRNA screening as a method of perturbation of biological systems and identification of targeted pathways coupled with compound screening
  ( Methods Mol Biol. 2009;563:275-87 )
• Solutions for complex, multi data type and multi tool analysis.  Principles and applications of using workflow and pipelining methods
  ( Methods Mol Biol. 2009;563:259-71 )
• Semantic Data Integration and Knowledge Management to Represent Biological Network Associations
  ( Methods Mol Biol. 2009;563:241-58 )
• Cytoscape: A community based framework for network modeling
  ( Methods Mol Biol. 2009;563:219-39 )
• Kinetic modeling as a tool to integrate multilevel dynamic experimental data
  ( Methods Mol Biol. 2009;563:197-218 )
• Functional analysis of OMICs data and small molecule compounds in an integrated “knowledge-based” platform
  ( Methods Mol Biol. 2009;563:177-96 )
• Discovering biological networks from diverse functional genomic data
  ( Methods Mol Biol. 2009;563:157-75 )
• Prioritizing Genes for Pathway Impact Using Network Analysis
  ( Methods Mol Biol. 2009;563:141-56 )
• Gene set enrichment analysis
  ( Methods Mol Biol. 2009;563:99-121 )
• Manual annotation of protein interactions
  ( Methods Mol Biol. 2009;563:75-95 )
• Relative Avidity, Specificity, Sensitivity of Transcription Factor-DNA Binding in Genome-Scale Experiments
  ( Methods Mol Biol. 2009;563:15-50 )
• Profiling Protein Interaction Networks with Functional Protein Microarrays
  ( Methods Mol Biol. 2009;563:63-74 )
• Curation of Inhibitor-Target data: Process and Impact on Pathway Analysis
  ( Methods Mol Biol. 2009;563:51-62 )
• Mining Protein-Protein Interactions from Published Literature using Linguamatics I2E
  ( Methods Mol Biol. 2009;563:3-13 )
• The Modern Library
  ( July 2009 Nature Biotechnology )
• A Strategy for Analyzing Gene–Nutrient Interactions in Type 2 Diabetes
  ( J Diabetes Sci Technol 2009;3(4):710-721 )
• Network analysis of human glaucomatous optic nerve head astrocytes
  ( BMC Medical Genomics 2009, 2:24 )
• Network Analysis of Primary Optic Nerves Astrocytes in Human Glaucoma
  ( BMC Medical Genomics )
• Discrimination of Tumorigenic Triazole Conazoles from Phenobarbital by Transcriptional Analyses of Mouse Liver Gene Expression
  ( Toxicol. Sci. Nesnow et al. )
• Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
  ( Genome Res. doi: 10.1101/gr.086546.108 )
• Identifying disease-specific genes based on their topological significance in protein networks
  ( BMC Systems Biology 2009, 3:36 )
• Pathway and network-based analysis of genome-wide association studies in multiple sclerosis
  ( Human Molecular Genetics, 2009, Vol. 18, No. 11 2078–2090 )
• Genetic similarity of chromosome 6 between patients receiving hematopoietic stem cell transplantation and HLA matched sibling donors
  ( Haematologica. 2009 April; 94(4): 528–535 )
  Background Matching for HLA genes located on chromosome 6 is required in hematopoietic stem cell transplantation to reduce the incidence of graft-versus-host disease. However, a considerable proportion of patients still ...
• Assessing the metabolic competence of sandwich-cultured mouse primary hepatocytes
  ( DMD Fast Forward. Published doi:10.1124/dmd.108.025775 )
• Molecular signatures of N-nitroso compounds in Caco-2 cells: implications for colon carcinogenesis
  ( Toxicol Sci. 2009 Feb 16 )
• Pathway analysis of senescence-associated miRNA targets reveals common processes to different senescence induction mechanisms
  ( Biochim. Biophys. Acta (2009), doi:10.1016/j.bbadis.2009.02.003 )
• LC/MS-Based Quantitative Proteomic Analysis of Paraffin-Embedded Archival Melanomas Reveals Potential Proteomic Biomarkers Associated with Metastasis
  ( PLoS ONE, Volume 4, Issue 2, e4430 )
• A Pathway-Based View of Human Diseases and Disease Relationships
  ( PLOS One, February 2009, Volume 4, Issue 2, e4346 )
• Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
  ( PLoS ONE, Volume 4, Issue 2, e4481 )
• MicroRNA deregulation and pathway alterations in nasopharyngeal carcinoma
  ( British Journal of Cancer (2009) 100, 1002 – 1011 )
• A systems biology approach to Down syndrome: Identification of Notch/Wnt dysregulation in a model of stem cells aging
  ( Biochim. Biophys. Acta (2009), doi:10.1016/j.bbadis.2009.01.015 )
• Multiplex immunoassay analysis of biomarkers in clinically accessible quantities of human aqueous humor
  ( Mol Vis. 2009;15:60-9 )
• Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis
  ( J. Chem. Inf. Model., Article ASAP )
• CYP2C9 polymorphisms: Considerations in NSAID therapy
  ( Current Opinion in Drug Discovery & Development 2009 12(1):108-114 )
• Protein networks and pathway analysis.
  ( Methods Mol Biol. 2009;563:v-vii. PMID: 19760825 )
• Investigation of potential antineoplastic activity of the anthelmintic drug mebendazole
  ( GeneGo, Inc. )
• Managing the Data Deluge
  ( Drug Discovery & Development )
• Immediate Upregulation of Proteins Belonging to Different Branches of the Apoptotic Cascade in the Retina after Optic Nerve Transection and Optic Nerve Crush
  ( Investigative Ophthalmology and Visual Science, January 2009, Vol. 50, No. 1 )
• Clustering and its application in multi-target prediction
  ( Current Opinion in Drug Discovery & Development 2009 12(1):98-107 )

2008

• Network analyses of differentially expressed proteins in amniotic fluid supernatant associated with abnormal human karyotypes
  ( Fertil Steril. 2008 Dec 22 )
• Transglutaminase 3 as a prognostic biomarker in esophageal cancer revealed by proteomics
  ( Int. J. Cancer: 124, 2106–2115 (2009) )
• Persistent fetal infection with bovine viral diarrhea virus differentially affects maternal blood cell signal transduction pathways
  ( PresS. Physiol Genomics doi:10.1152/physiolgenomics.90276.2008 )
• Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer
  ( AACR Publications Cancer Res 2008; 68: (22) )
• Differential microRNA expression between hepatitis B and hepatitis C leading disease progression to hepatocellular carcinoma
  ( DOI: 10.1002/hep.22749 )
• Short-term fatty acid intervention elicits differential gene expression responses in adipose tissue from lean and overweight men
  ( Published Online (doi:10.1007/s12263-008-0096-z) )
• A comprehensive functional analysis of tissue specificity of human gene expression
  ( BMC Biology 2008, 6:49 )
• Role of the molybdo-flavoenzyme, aldehyde oxidase homolog 2, in the biosynthesis of retinoic acid: generation and characterization of a knock-out mouse
  ( Mol. Cell. Biol. doi:10.1128/MCB.01385-08 )
• Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers
  ( PNAS, vol. 105, no. 42, 16224–16229 )
• Effect of γ-Synuclein Silencing on Apoptotic Pathways in Retinal Ganglion Cels
  ( J. Biol. Chem, 10.1074 )
• Establishment of Patient-Derived Non-Small Cell Lung Cancer Xenografts asModels for the Identification of Predictive Biomarkers
  ( Clin Cancer Res 2008;14(20) )
• Proteomic profiling of the effect of prostate-specific antigen on prostate cancer cells
  ( Prostate. 2008 Oct 1;68(14):1531-45 )
• Alteration of DBP levels in CSF of patients with MS by proteomics analysis
  ( Cell Mol Neurobiol. 2009 Mar;29(2):203-10. Epub 2008 Sep 19. )
• Cell type-specific DNA methylation patterns n the human breast
  ( PNAS vol. 105 no. 37 )
• Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
  ( Sciencexpress 10.1126 science.1164368 )
• An Integrated Genomic Analysis of Human Glioblastoma Multiforme
  ( Sciencexpress 10.1126 science.1164382 )
• Pathway Analysis for Drug Discovery: Computational Infrastructure and Applications
  ( ISBN: 978-0-470-10705-8 )
• Identification and functional analysis of SKA2 interaction with the glucocorticoid receptor
  ( Journal of Endocrinology (2008) 198, 499–509 )
• Interspliced transcription chimeras: Neglected pathological mechanism infiltrating gene accession queries?
  ( J Biomed Inform (2008), doi:10.1016/j.jbi.2008.11.002 )
• BMI-1 Promotes Ewing Sarcoma Tumorigenicity Independent of CDKN2A Repression
  ( Cancer Res 2008; 68: (16) )
• Systems biology approach to identification of biomarkers for metastatic progression in cancer
  ( BMC Bioinformatics 2008, 9(Suppl 9):S8 )
• Integrated Pathway Analysis of Rat Urine Metabolic Profiles and Kidney Transcriptomic Profiles To Elucidate the Systems Toxicology of Model Nephrotoxicants
  ( Chem Res Toxicol. 2008 Jul 26 )
• Modeling gene-by-environment interaction in comorbid depression with alcohol use disorders via an integrated bioinformatics approach
  ( BioData Mining 2008, 1:2 doi:10.1186/1756-0381-1-2 )
• Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomas
  ( Carcinogenesis vol.29 no.10 pp.1901–1910, 2008 )
• Type I Interferon: Potential Therapeutic Target for Psoriasis?
  ( PLoS ONE, Volume 3, Issue 7, e2737 )
• Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush
  ( Mol Vis. 2008 Jun 3;14:1050-63 )
• The Fibroblast Growth Factor–Inducible 14 Receptor Is Highly Expressed in HER2-Positive Breast Tumors and Regulates Breast Cancer Cell Invasive Capacity
  ( Mol Cancer Res 2008;6(5) )
• Fine-Tuning Compound Safety Assessments
  ( GEN Vol. 28, No. 6 )
• Proteomics Analysis Identifies Molecular Targets Related to Diabetes Mellitus Associated Bladder Dysfunction
  ( MCP Papers in Press. Published on March 12, 2008 as Manuscript M700563-MCP200 )
• Stochastic Resonance Reveals "Pilot Light" Expression in Mammalian Genes
  ( PLoS ONE, Volume 3, Issue 3, e1842 )
• Building pathway clusters from Random Forests classification using class votes
  ( BMC Bioinformatics. 2008 Feb 6;9:87 )
• Combined Computational Metabolite Prediction and Automated Structure-Based Analysis of Mass Spectrometric Data
  ( Toxicology Mechanisms and Methods, Volume 18, Issue 2 & 3, pages 243 - 250 )
• Characteristics of Genomic Signatures Derived Using Univariate Methods and Mechanistically Anchored Functional Descriptors for Predicting Drug- and Xenobiotic-Induced Nephrotoxicity
  ( Toxicology Mechanisms and Methods, Volume 18, Issue 2 & 3, pages 267 - 276 )
• In Silico Toxicological Screening of Natural Products
  ( Toxicology Mechanisms and Methods, Volume 18, Issue 2 & 3, pages 229 - 242 )
• Supplementation of healthy volunteers with nutritionally relevant amounts of selenium increases the expression of lymphocyte protein biosynthesis genes
  ( Am J Clin Nutr 2008;87:181–9 )
• Targeting Telomerase: Therapeutic Options for Cancer Treatment
  ( Springer-Verlag. P247 – 284, 2008. ISBN: 978-3-540-73708-7 )
• Recursive Partitioning Analysis of Anti-HIV Compounds
  ( Golden Helix )

2007

• 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 )
• 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 )
• 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 )
• 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
  ( Genome Biology 2007, 8:R200 )
  Additional data file section
• 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 on the Transcriptomes of Mesenchymal Stem Cells Derived from Amniotic Fluid, Amniotic Membrane, Cord Blood, and Bone Marrow
  ( Stem Cells Express, June 7, 2007 )
• 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 )
• 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 )
• Classification of metabolites with kernel-partial least squares (K-PLS)
  ( Drug Metab Dispos. 2007 Mar;35(3):325-7. Epub 2006 Dec 1. )
• 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 )
• Pathway mapping tools for analysis of high content data
  ( Methods Mol Biol. 2007;356:319-50 )

2006

• 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 )
• Different Signaling Pathways in the Livers of Patients With Chronic Hepatitis B or Chronic Hepatitis C
  ( HEPATOLOGY, November 2006 )
• Activin Modulates the Transcriptional Response of LβT2 Cells to Gonadotropin-Releasing Hormone and Alters Cellular Proliferation
  ( Molecular Endocrinology 20 (11) 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 )
• 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 )
• Identification of target genes in laryngeal squamous cell carcinoma by high-resolution copy number and gene expression microarray analyses
  ( Oncogenomics (2006), 1-12 )
• 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 )
• Effects of antipsychotic drugs on I(to), I (Na), I (sus), I (K1), and hERG: QT prolongation, structure activity relationship, and network analysis
  ( Pharm Res. 2006 Jun;23(6):1133-43. Epub 2006 May 25. )
• 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 )
• Data Mining for Gene Networks Relevant to Poor Prognosis in Lung Cancer Via Backward-Chaining Rule Induction
  ( Cancer Informatics. Libertas Academica )
• Pathway Analyses of Chondrosarcoma
  ( Pathway Analysis for Target and Compound Evaluation San Francisco, CA )
• 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 )
• Systems-ADME/Tox: resources and network approaches
  ( J Pharmacol Toxicol Methods. 2006 Jan-Feb;53(1):38-66. Epub 2005 Jul 27. )
• Biological Pathways at Your Fingertips
  ( iPath™ Quest Magazine, Vol.3, No.1, 77-81, 2006 )
• Comprehensive Network Analysis of Glaucoma Pathophisiology
  ( Mol. Sys. Biol. )
• Transcriptional profiles in liver from mice treated with hepatotumorigenic and nonhepatotumorigenic triazole conazole fungicides: Propiconazole, triadimefon, and myclobutanil
  ( Toxicol Pathol. 2006;34(7):863-78 )

2005

• 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
  ( Expert 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 )
• Techniques: Application of Systems Biology to Absorption, Distribution, Metabolism, Excretion and Toxicity
  ( TRENDS in Pharmacological Sciences Vol.26 No.4 April 2005 )
• Application of systems biology to absorption, distribution, metabolism, excretion and toxicity
  ( Trends in Pharmacological Sciences, Vol.26, No.4, 202-209, April 2005 )
• A Novel Method for Visualizing Nuclear Hormone Receptor Networks Relevant to Drug Metabolism
  ( Drug Metabolism and Disposition, Vol.33, No.3 2005 )
• Comprehensive Computational Assessment of ADME Properties Using Mapping Techniques
  ( Current Drug Discovery Technologies, 2005, 2, 99-113 )
• Identification Of Brain Ischemia-Induced Changes In Protein Profiles By Quantitative Proteomics
  ( LEGACY Health System )

2004

• Translation research: from accurate diagnosis to appropriate treatment
  ( Journal of Translational Medicine 2004, 2:35 )
• Quantitative Structure-metabolism Relationship Modeling of Metabolic N-dealkylation Reaction Rates
  ( Drug Metabolism and Disposition, DMD 32:1111-1120, 2004 )
• Kohonen Maps for Prediction of Binding to Human Cytochrome P450 3A4
  ( Drug Metabolism and Disposition, DMD 32:1183-1189, 2004 )
• Towards Global Proteomic Analysis in a PS1/APP Mouse Model of Alzheimer&s Disease
  ( University of Southern California, Los Angeles, CA, USA )
• Early Prediction of Drug Metabolism and Toxicity: Systems Biology Approach and Modeling
  ( Drug Discovery Today, DDT Vol.9, No.3, February 2004 )

2003

• PROTEOME-3D: An Interactive Bioinformatics Tool for Large-Scale Data Exploration and Knowledge Discovery
  ( Molecular & Cellular Proteomics 2:1164-1176, 2003 )
• Modeling of Human Cytochrome P450-Mediated Drug Metabolism Using Unsupervised Machine Learning Approach
  ( Journal of Medicinal Chemistry, 46: 3631-3643, 2003 )

2002

• So many targets, so many compounds, but so few resources
  ( Current Drug Discovery, December, pp. 17-22 )