R & Bioconductor - Manuals. R & Bioconductor Manual R Basics Introduction General Overview R ( is a comprehensive statistical environment and programming language for professional data analysis and graphical display.
The associated Bioconductor project provides many additional R packages for statistical data analysis in different life science areas, such as tools for microarray, next generation sequence and genome analysis. Scope of this Manual This R tutorial provides a condensed introduction into the usage of the R environment and its utilities for general data analysis and clustering. Format of this Manual A not always very easy to read, but practical copy & paste format has been chosen throughout this manual.
Computational Intelligence: Alexandru Floares: 9781620819012: Amazon.com. Home : Pathway Interaction Database. Dynamic Signaling Maps. Whole-Cell Computational Model of Mycoplasma genitalium: Overview. Description: The goal of this project was to develop the first detailed, "whole-cell" computational model of the entire life cycle of living organism, Mycoplasma genitalium.
The model describes the dynamics of every molecule over the entire life cycle and accounts for the specific function of every annotated gene product. We anticipate that whole-cell models will be critical for synthetic biology and personalized medicine. Please see the project website wholecell.stanford.edu and the Downloads page to explore the whole-cell knowledge base and simulations and obtain the model code. CellMiner - Home. Modeling stochasticity and robustness in gene regulatory networks. + Author Affiliations *To whom correspondence should be addressed.
Abstract Motivation: Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed interest in Boolean modeling techniques for gene regulatory networks (GRNs). However, due to their deterministic nature, it is often difficult to identify whether these modeling approaches are robust to the addition of stochastic noise that is widespread in gene regulatory processes.
A Novel Network Integrating a miRNA-203/SNAI1 Feedback Loop which Regulates Epithelial to Mesenchymal Transition. Background The majority of human cancer deaths are caused by metastasis.
The metastatic dissemination is initiated by the breakdown of epithelial cell homeostasis. During this phenomenon, referred to as epithelial to mesenchymal transition (EMT), cells change their genetic and trancriptomic program leading to phenotypic and functional alterations. The challenge of understanding this dynamic process resides in unraveling regulatory networks involving master transcription factors (e.g. SNAI1/2, ZEB1/2 and TWIST1) and microRNAs. GEO Accession viewer. Snail2 is an Essential Mediator of Twist1-Induced Epithelial Mesenchymal Transition and Metastasis. + Author Affiliations Corresponding Author: Jing Yang, Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0636.
Phone: 1-858-534-1994; Fax: 1-858-534-7390. E-mail: jingyang@ucsd.edu Abstract To metastasize, carcinoma cells must attenuate cell–cell adhesion to disseminate into distant organs. Introduction. BiocViews. Www.bioconductor.org/packages/release/bioc/vignettes/TDARACNE/inst/doc/TDARACNE.pdf. Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.
+ Author Affiliations *To whom correspondence should be addressed.
Received May 3, 2007. Revision received December 10, 2007. Accepted December 28, 2007. Abstract. Short time-series microarray analysis: methods and challenges. EmExome: Clinical Whole Exome Sequencing. Medical EmExome: Clinical Whole Exome Sequencing Medical EmExome: Clinical Exome Sequencing Four Medical EmExome Service Levels: *Includes analysis of one phenotype-specific NGS panel.
What is the Medical EmExome? The human exome is the complete coding (exonic) region of the genome. What options are available for Medical EmExome testing? How is the Medical EmExome performed? Medical EmExome analysis also includes mitochondrial genome sequencing. The Medical EmExome also features the EmExome Boost Option, which allows clinicians to choose an EGL gene panel relevant to the patient’s phenotype to ensure coverage of ALL exons and the detection of intragenic CNVs, at no additional cost. Reporting recommendations for tumor marker prognostic studies (REMARK): explanation and elaboration. Patients Item 2.
Describe the characteristics (for example, disease stage or co-morbidities) of the study patients, including their source and inclusion and exclusion criteria Examples. Colds and Cancer. Cancer Minute. This Week in the British Journal of Cancer. Is That How it Works? More and More Complex. Cancer Minute.
Sage Bionetworks Seattle. It's in the Mitochondria. Interolog Finder. BisoGenet. Differential dependency network analysis to identify condition-specific topological changes in biological networks. Computational Bioinformatics and Bioimaging Laboratory, Virginia Tech. CNSuite (Copy Number Suite) is a caBIGTM (cancer Biomedical Informatics Grid) analytical tool for gene copy number change analysis.
Analysis of Microarray Data - Matthias Dehmer, Frank Emmert-Streib. A Genomic Strategy to Elucidate Modules of Oncogenic Pathway Signaling Networks. Cancer systems biology: a network modeling perspective. + Author Affiliations *To whom correspondence should be addressed.
Tel: +1 617 252 1629; Fax: +1 617 258 0204; Email: lauffen@mit.edu Received August 19, 2009. Revision received October 17, 2009. Accepted October 18, 2009. Gene Networks and microRNAs Implicated in Aggressive Prostate Cancer. + Author Affiliations Requests for reprints: Liang Wang, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street Southwest, Rochester, MN 55905.
Integrative Network Biology: Graph Prototyping for Co-Expression Cancer Networks. Network-based analysis has been proven useful in biologically-oriented areas, e.g., to explore the dynamics and complexity of biological networks. Investigating a set of networks allows deriving general knowledge about the underlying topological and functional properties. The integrative analysis of networks typically combines networks from different studies that investigate the same or similar research questions. In order to perform an integrative analysis it is often necessary to compare the properties of matching edges across the data set.
This identification of common edges is often burdensome and computational intensive. Here, we present an approach that is different from inferring a new network based on common features. Figures. Swiss Scientists Program Mammalian Cells to Work As Logic Gates. A new biologic logic gate based on proteins can perform binary calculations, serving as the first "cellular calculator," researchers say. Various combinations of components can be arranged into circuit elements, leading to specific metabolic processes inside a cell. The setup can answer mathematical questions in a similar fashion to a computer. Foundation Medicine Announces First Genomic Profile for Patient Treatment. By Bio-IT World Staff May 30, 2012 | Foundation Medicine has announced the commercial launch of FoundationOne, the first pan-cancer, fully informative genomic profile designed to help oncologists expand their patients’ treatment options.
“The care of oncology patients is on the verge of being individualized,” CEO Michael Pellini told Bio-IT World’s Kevin Davies earlier this year (see, “Laying the Foundation for Next-Gen Cancer Diagnostics”). “The molecular make-up of each tumor is going to drive personalized medicine. Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes. Abstract Predicting the clinical outcome of cancer patients based on the expression of marker genes in their tumors has received increasing interest in the past decade.
Accurate predictors of outcome and response to therapy could be used to personalize and thereby improve therapy. However, state of the art methods used so far often found marker genes with limited prediction accuracy, limited reproducibility, and unclear biological relevance. To address this problem, we developed a novel computational approach to identify genes prognostic for outcome that couples gene expression measurements from primary tumor samples with a network of known relationships between the genes. Our approach ranks genes according to their prognostic relevance using both expression and network information in a manner similar to Google's PageRank. Ring My BEL: Selventa Releases Biological Expression Language. By Kevin Davies. Whole Genome Sequencing Sheds Light on Hepatitis Virus Integration in Cancer Genome. By Allison Proffitt May 29, 2012 | Researchers focusing on Asian cancers have used whole-genome sequencing to study the level of hepatitis B virus integration in the genomes of cancer patients and to discover three novel genes associated with recurrent hepatitis B virus integration in hepatocellular carcinoma.
Unitatea Executiva Pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii. Molecular Systems Biology. The Dream Project. Schrödinger equation. In quantum mechanics, the Schrödinger equation is a partial differential equation that describes how the quantum state of some physical system changes with time. Cancer Vaccines and Cancer Immunotherapy & Immunomodulation. Cancer Metabolomics. Keynote Speakers: Lewis C. Cancer Metabolomics: Elucidating the Biochemical Programs that Support Cancer Initiation and Progression. From Scientist to Entrepreneur. Organizers: David Anthony (21 Ventures, Inc.) and Monica Kerr (The New York Academy of Sciences)Presented by the Science Alliance Posted February 15, 2011 Overview.
ESCAPE. Metabolomics of human breast cancer: new approaches for tumor typing and biomarker discovery. Metabolomics: the final frontier? Characterization of global microRNA expression reveals oncogenic potential of miR-145 in metastatic colorectal cancer. Cell lines SW620, SW480, HCT116 and HT29 cell lines were obtained from the ATCC. Identification of a chrXq27.3 microRNA cluster associated with early relapse in advanced stage ovarian cancer patients. MicroRNA expression profiles classify human cancers : Article : Nature. Nature 435, 834-838 (9 June 2005) | doi:10.1038/nature03702; Received 2 February 2005; Accepted 5 May 2005 Jun Lu1,4,7, Gad Getz1,7, Eric A.
Miska2,7,8, Ezequiel Alvarez-Saavedra2, Justin Lamb1, David Peck1, Alejandro Sweet-Cordero3,4, Benjamin L. Ebert1,4, Raymond H. Mak1,4, Adolfo A. MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review - Iorio - 2012 - EMBO Molecular Medicine. 16 Free and Cheapest Online Storage Space to Backup Files. Microcosm Targets. ELIXIR. ArrayExpress Home. MiRBase. All Courses. Nova Science Publishers. Magazine Articles: Exploiting Gene-Expression Data.
Untitled. Systems biology and cancer stem cells - Price - 2007 - Journal of Cellular and Molecular Medicine. Identification of high-quality cancer prognostic markers and metastasis network modules : Nature Communications. Dynamic modeling and analysis of cancer cellular network motifs - Integrative Biology. The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. The context of gene expression regulation. Resveratrol ameliorates aging-related metabolic phenotypes by inhibiting cAMP phosphodiesterases. The Protein Structure Initiative: achievements and visions for the future. Telomeres in disease - F1000 Medicine Reports - F1000. Gene regulatory networks: a new conceptual framework to analyse breast cancer behaviour. Attractors and Democratic Dynamics.
Cell Stem Cell - Extreme Makeover: Converting One Cell into Another. The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation. Journal of Theoretical Biology - A model of sequential branching in hierarchical cell fate determination. Developmental Biology - Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Estimating developmental states of tumors and normal tissues using a linear time-ordered model.
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. Cancer Genome Characterization Initiative (CGCI) Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective. Characterizing regulatory path motifs in integrated networks using perturbational data. A scaling normalization method for differential expression analysis of RNA-seq data. Tracing the evolution of tissue identity with microRNAs. AACR: Genomics and the Progression of Cancer Metastasis. Berkeley course on Data Science, Spring 2012. 444862) New Layer of Genetic Information Discovered. Conditions of Use. Bladder: Urothelial carcinomas. Atlas of Genetics and Cytogenetics in Oncology and Haematology. ArrayExpress Archive. MicroRNA Expression Profiles Associated With Prognosis and Therapeutic Outcome in Colon Adenocarcinoma, January 30, 2008, Schetter et al. 299 (4): 425. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis 10.1016/j.ccr.2006.01.025 : Cancer Cell.
A MicroRNA Signature Associated with Prognosis and Progression in Chronic Lymphocytic Leukemia. GEO Accession viewer. MicroRNAs: Target Recognition and Regulatory Functions 10.1016/j.cell.2009.01.002 : Cell. Looking back at genomic medicine in 2011. MicroRNA Expression Profiles Associated With Prognosis and Therapeutic Outcome in Colon Adenocarcinoma, January 30, 2008, Schetter et al. 299 (4): 425. BGI Team Finds RNA Editing Is Common, May Affect MicroRNAs. Brain Computer Interface.