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- Estrogen and retinoic acid antagonistically regulate several microRNA genes to control aerobic glycolysis in breast cancer cells. (Mol Biosyst. 2012 Oct 30;8(12):3242-53. doi: 10.1039/c2mb25298h)
In addition to estrogen receptor modulators, retinoic acid and other retinoids are promising agents to prevent breast cancer. Retinoic acid and estrogen exert antagonistic regulations on the transcription of coding genes and we evaluated here whether these two compounds…
- Cross-species transcriptomic analysis of mouse and rat lung exposed to chloroprene( Toxicol Sci. 2012 Nov 3 )
beta-chloroprene (2-chloro-1,3-butadiene), a monomer used in the production of neoprene elastomers, is of regulatory interest due to the production of multi-organ tumors in mouse and rat cancer bioassays. A significant ...
- Selective enrichment of newly synthesized proteins for quantitative secretome analysis( Nat Biotechnol. 2012 Oct 10;30(10):984-90 )
Secreted proteins constitute a large and biologically important subset of proteins that are involved in cellular communication, adhesion and migration. Yet secretomes are understudied because of technical limitations in the ...
- Whole-genome analysis informs breast cancer response to aromatase inhibition( Nature (2012) doi:10.1038/nature11143 )
To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, we studied pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant aromatase inhibitor therapy by ...
- Cross-species Comparisons of Transcriptomic Alterations in Human and Rat Primary Hepatocytes Exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin( Toxicol Sci. 2012 May;127(1):199-215 )
A toxicogenomics approach was used to qualitatively and quantitatively compare the gene expression changes in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Hepatocytes from five individual rats and ...
- An Integrated Proteomics and Metabolomics Approach for Defining Oncofetal Biomarkers in the Colorectal Cancer( Ann Surg 2012;255:720–730 )
Objective: The present study was designed to search for potential diagnostic biomarkers in the serum of colorectal cancer (CRC). Background: CRC is the third most common cancer worldwide, and its ...
- Age-Dependent Brain Gene Expression and Copy Number Anomalies in Autism Suggest Distinct Pathological Processes at Young Versus Mature Ages( PLoS Genet 8(3): e1002592. doi:10.1371/journal.pgen.1002592 )
Autism is a highly heritable neurodevelopmental disorder, yet the genetic underpinnings of the disorder are largely unknown. Aberrant brain overgrowth is a well-replicated observation in the autism literature; but association, ...
- Transcriptomics analysis of primary mouse thymocytes exposed to bis(tri-n-butyltin)dioxide (TBTO)( Toxicology 296 (2012) 37– 47 )
The biocide bis(tri-n-butyltin)oxide (TBTO) causes thymus atrophy in rodents and is toxic to many cell types of which thymocytes are the most sensitive. To obtain insight in the mechanisms of ...
- A Bivariate Genome-Wide Approach to Metabolic Syndrome( DOI: 10.2337/db10-1011 )
- Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics ( BMC Genomics 2012, 13:55 doi:10.1186/1471-2164-13-55 )
Background Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression ...
- Matrix metalloproteinase-12 deficiency ameliorates the clinical course and demyelination in Theiler's murine encephalomyelitis ( doi:10.1007/s00401-012-0942-3 )
Matrix metalloproteinases (MMPs) are a family of extracellular proteases involved in the pathogenesis of demyelinating diseases like multiple sclerosis (MS). The aim of the present study was to investigate whether ...
- Sodium arsenite dependent protein expression analysis on human embryonic carcinoma (NCCIT) cell line ( TOXICOLOGY LETTERS 207 (2): 149-158 10.1016 ) Due to their pluripotent nature, embryonic carcinoma (EC) cell lines are useful for the study of basic and applied aspects of medical therapeutics, disease management and environmental mutagenesis. We evaluated ...
- A model of early human embryonic stem cell differentiation reveals inter- and intracellular changes upon trophoblast specification. Stem Cellls & Development ( Stem Cells Dev. 2011 Oct 19 ) The molecular events leading to human embryonic stem cell (hESC) differentiation are the subject of considerable scrutiny. Here, we characterize an in vitro model that permits analysis of the earliest ...
- Effects of acute ethanol treatment on NCCIT cells and NCCIT cell-derived embryoid bodies (EBs) ( TOXICOLOGY IN VITRO Volume: 24 Issue: 6 Pages: 1696-1704 ) This study used human embryonic carcinoma (NCCIT) cells to evaluate genotoxicity and other effects of ethanol in earlier stages of cellular development. This undifferentiated pluripotent cell line has unlimited self-renewal ...
- Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells ( BMC Syst Biol. 2011 Aug 31;5:139. ) BACKGROUND:The integration of different ‘omics’ technologies has already been shown in several in vivo studies to offer a complementary insight into cellular responses to toxic challenges. Being interested in developing ...
- Dietary restriction of mice on a high-fat diet induces substrate efficiency and improves metabolic health ( J Mol Endocrinol. 2011;47(1):81-97 ) High energy intake and, specifically, high dietary fat intake challenge the mammalian metabolism and correlate with many metabolic disorders such as obesity and diabetes. However, dietary restriction (DR) is known ...
- Toward a comprehensive characterization of the phosphotyrosine proteome ( Cell Signal. 2011 Aug;23(8):1387-95. Epub 2011 Apr 5. ) Tyrosine phosphorylation (pTyr) regulates important cell functions and plays a key role in carcinogenesis. The purpose of this study was to perform a comprehensive study of the phosphotyrosine proteome. Immunoaffinity ...
- Effects of Simulated Microgravity on Expression Profile of MicroRNA in Human Lymphoblastoid Cells ( J. Biol. Chem. 2011 286: 32483-32490 ) This study explores the changes in expression of microRNA (miRNA) and related genes under simulated microgravity conditions. In comparison with static 1 × g, microgravity has been shown to alter ...
- Molecular Chaperones as a Common Set of Proteins That Regulate the Invasion Phenotype of Head and Neck Cancer ( Clin Cancer Res; 17(14); 4629-41. (C)2011AACR. ) Purpose: The goal of this study was to establish a common set of molecules that regulate cell invasion in head and neck cancer (HNC). Experimental Design: Five invasive sublines derived ...
- Glycemic index differences of high-fat diets modulate primarily lipid metabolism in murine ( Physiol Genomics. 2011 Aug 16;43(15):942-9 ) A low vs. high glycemic index of a high-fat (HF) diet (LGI and HGI, respectively) significantly retarded adverse health effects in adult male C57BL/6J mice, as shown recently (Van Schothorst ...
- Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs ( BMC SYSTEMS BIOLOGY, 5 1 10.1186/1752-0509-5-S1-S2 ) Background: Bi-directional gene pairs have received considerable attention for their prevalence in vertebrate genomes. However, their biological relevance and exact regulatory mechanism remain less understood. To study the inner properties ...
- Nuclear Outsourcing of RNA Interference Components to Human Mitochondria ( PLoS ONE 6(6): e20746 ) MicroRNAs (miRNAs) are small non-coding RNAs that associate with Argonaute proteins to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs ...
- The JAK2/STAT3 signaling pathway is required for growth of CD44 CD24- stem cell-like breast cancer cells in human tumors
( J Clin Invest doi:10.1172/JCI44745. )
Intratumor heterogeneity is a major clinical problem because tumor cell subtypes display variable sensitivity to therapeutics and may play different roles in progression. We previously characterized 2 cell populations in ...
- Gene expression analysis of precision-cut human liver slices indicates stable expression of ADME-Tox related genes ( Toxicol Appl Pharmacol. 2011 May 15;253(1):57-69 ) In the process of drug development it is of high importance to test the safety of new drugs with predictive value for human toxicity. A promising approach of toxicity testing ...
- Quantitative plasma proteome analysis reveals aberrant level of blood coagulation-related proteins in nasopharyngeal carcinoma ( JOURNAL OF PROTEOMICS 74 (5): 744-757 MAY 1 2011 ) Nasopharyngeal carcinoma (NPC), one of the most common cancers in Southeast Asia, is not easily diagnosed until advanced stages. To discover potential biomarkers for improving NPC diagnosis, we herein identified ...
- Retinal proteomic changes following unilateral optic nerve transection and early experimental glaucoma in non-human primate eyes ( Exp Eye Res. 2011 Jul;93(1):13-28. Epub 2011 Apr 23 ) In this work we compared proteomic changes in non-human primate (NHP) retinas at the onset of early experimental glaucoma (EEG) and 3 weeks after optic nerve transection (ONT), as a ...
- Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale
( Biology Direct 2011, 6:15 doi:10.1186/1745-6150-6-15 )
Background Pathway databases are becoming increasingly important and almost omnipresent in most types of biological and translational research. However, little is known about the quality and completeness of pathways stored ...
- A possible mechanism for hepatotoxicity induced by BIRB-796, an orally active p38 mitogen-activated protein kinase inhibitor ( J Appl Toxicol. 2011 Feb 16. doi: 10.1002/jat.1622. ) BIRB-796, a selective inhibitor of p38 mitogen-activated protein kinase, has entered clinical trials for the treatment of autoimmune diseases. Levels of alanine transaminase, a biomarker of hepatic toxicity in clinical ...
- Estrogen-dependent gene expression in the mouse ovary ( PLoS One. 2011 Feb 9;6(2):e14672. ) Estrogen (E) plays a pivotal role in regulating the female reproductive system, particularly the ovary. However, the number and type of ovarian genes influenced by estrogen remain to be fully ...
- The Genetic Landscape of the Childhood Cancer Medulloblastoma
( 10.1126/science.1198056 )
Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high-density microarrays and ...
- Reduction of CXCR3 in an in vitro Model of Continuous Asbestos Exposure on a Human T-cell Line, MT-2
( Am J Respir Cell Mol Biol. 2010 Dec 10 )
Since silicosis patients who are chronically exposed to silica particles develop not only pulmonary fibrosis, but also complications involving autoimmune diseases such as rheumatoid arthritis and systemic sclerosis, asbestos exposure ...
- Interactions between an inflammatory response to infection and protein trafficking pathways favor correction of defective protein trafficking in Cystic Fibrosis
( Bioinformation 5(6): 228-233 (2010) )
One unresolved issue in Cystic Fibrosis research is how functional loss of CFTR, a protein involved in chloride transport, results in chronic lung inflammation. Large scale experiments investigating protein or ...
- Altered antisense-to-sense transcript ratios in breast cancer
( PNAS doi: 10.1073/pnas.1010559107 )
Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in ...
- Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome
( BMC Cancer 2010, 10:506 )
Background Osteosarcoma (OSA) spontaneously arises in the appendicular skeleton of large breed dogs and shares many physiological and molecular biological characteristics with human OSA. The standard treatment for OSA in ...
- An "Omics" based survey of human colon cancer
( Mutation Research 693 (2010) 3–18 )
Despite an increased understanding of the molecular pathogenesis of colorectal cancer (CRC) during the past two decades, reliable and robust biomarkers to enable screening, surveillance, and primary prevention of this ...
- 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 ...
- 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. ...
- 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 ...
- 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 ...
- 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 ...
- 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 ...
- 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 ...
- 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 ...
- Effect of training-sample size and classification difficulty on the accuracy of genomic predictors
( Breast Cancer Research 2010, 12:R5 )
- 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 ...
- 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. )
- 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 ...
- 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: ...
- 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 )
- Curation of Inhibitor-Target data: Process and Impact on Pathway Analysis
( Methods Mol Biol. 2009;563:51-62 )
- 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 )
- PANTHER Pathway: an ontology-based pathway database coupled with data analysis tools
( Methods Mol Biol. 2009;563:123-40 )
- 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 )
- Mining Protein-Protein Interactions from Published Literature using Linguamatics I2E
( Methods Mol Biol. 2009;563:3-13 )
- 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 )
- 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 )
- Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
( PLoS ONE, Volume 4, Issue 2, e4481 )
- 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 )
- 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 )
- Protein networks and pathway analysis
( Methods Mol Biol. 2009;563:v-vii. PMID: 19760825 )
- Clustering and its application in multi-target prediction
( Current Opinion in Drug Discovery & Development 2009 12(1):98-107 )
- Investigation of potential antineoplastic activity of the anthelmintic drug mebendazole
( GeneGo, Inc. )
- 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 )
- CYP2C9 polymorphisms: Considerations in NSAID therapy
( Current Opinion in Drug Discovery & Development 2009 12(1):108-114 )
- Managing the Data Deluge
( Drug Discovery & Development )