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My Biosoftware

My Biosoftware

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eteRNA - RNA Game Lets Players Help Find a Biological Prize By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines — new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science. the Das Lab Web BrowserFlash An RNA Aptamer Provides a Novel Approach for the Induction of Apoptosis by Targeting the HPV16 E7 Oncoprotein Abstract Background Human papillomavirus 16 (HPV16) is a high-risk DNA tumour virus, which is a major causative agent of cervical cancer. Cellular transformation is associated with deregulated expression of the E6 and E7 oncogenes. E7 has been shown to bind a number of cellular proteins, including the cell cycle control protein pRb.

Discovery of Protein–lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets Introduction Mammalian genomes encode thousands of long non-coding RNAs (lncRNAs) (Wang and Chang, 2011; Guttman and Rinn, 2012). lncRNAs play important roles in a variety of biological processes that have been implicated in regulating tumorigenesis through interaction with RNA-binding proteins (RBPs) (Konig et al., 2011; Wang and Chang, 2011; Guttman and Rinn, 2012; Ulitsky and Bartel, 2013). However, for the majority of lncRNAs, the mechanism underlying their interaction with RBPs remains unknown (Konig et al., 2011; Wang and Chang, 2011; Guttman and Rinn, 2012; Ulitsky and Bartel, 2013). The control and function of lncRNA are governed by the specificity of RBPs (Wang and Chang, 2011; Guttman and Rinn, 2012).

BRAGI 20091106 - A Protein Visualization and Modeling Program BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules.BRAGI enables you to view and explore the three-dimensional (3D) structure of any macromolecule. You can explore proteins, DNA, RNA, carbohydrates, and complexes, such as between transcriptional regulatory proteins and DNA, or enzymes and drugs. BRAGI Team Windows / Linux Citation BRAGI: linking and visualization of database information in a 3D viewer and modeling tool. Researchers develop RNA aptamers that inhibit HCV replication Published on June 3, 2013 at 12:46 AM Treatments against hepatitis C virus have only been partially successful. A major problem is that antivirals generate drug resistance. Now Seong-Wook Lee of Dankook University, Yongin, Republic of Korea and his collaborators have developed agents that bind to the business end of a critical protein, disabling it so successfully that no resistance has arisen.

getSharedSiteSession?rc=2&redirect= To view the full text, please login as a subscribed user or purchase a subscription. Click here to view the full text on ScienceDirect. Figure 1 CRISPR-Mediated Knockout of the Haunt Locus (A) Schematic diagram of ESC differentiation and RNA-seq analysis. (B) Heat map of FPKM values of lncRNAs enriched in ESCs and lineage-committed cells. PhenoFam - Gene Set Enrichment Analysis in the Protein Domain Context PhenoFam performs gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. The tool is designed to analyse complete sets of results from quantitative high-throughput studies (gene expression microarrays, functional RNAi screens, etc.) without prior pre-filtering or hits-selection steps. Frank Buchholz , Max Planck Institute of Molecular Cell Biology and Genetics. Web Browser

The Inhibition of Stat5 by a Peptide Aptamer Ligand Specific for the DNA Binding Domain Prevents Target Gene Transactivation and the Growth of Breast and Prostate Tumor Cells Open AccessThis article isfreely availablere-usable Article 1 Georg-Speyer-Haus, Institute for Biomedical Research, Frankfurt am Main 60596, Germany 2 Ganymed Pharmaceuticals AG, Mainz 55131, Germany 3 Boston Children's Hospital, Division of Hematology/Oncology, Boston MA 02115, USA 4 Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna 1090, Austria * Author to whom correspondence should be addressed. MicroRNA and Breast Cancer: Understanding Pathogenesis, Improving Management The advent of the microRNAs in the early 1990s has proven to be a tremendously significant development within the purview of gene regulation. They participate in the regulation of a broad assembly of processes vital to proper cell function and the perturbation of these pathways following alteration of miRNA expression is strongly believed to contribute to the pathogenesis of cancer. This review provides a comprehensive overview of the miRNAs that have to date been well-characterized in the context of human breast neoplasia.

Caryoscope 0.4.0 - View Gene Expression Data in Genome Caryoscope is an application for viewing gene expression data in a whole-genome context. Caryoscope has been used to “draw” microarray data onto a set of chromosomes so that changes in DNA copy number can identify regions of chromosome loss or duplication within the genome of tumor cells (Nat Genet. 1999 Sep;23(1):41-6). In addition, microarray data measuring mRNA expression levels can also be visualized in a genomic context using Caryoscope (PNAS 2002 Dec 10;99(25):16144-9). Data viewed with Caryscope need not be limited to microarray data — any type of numerical data that can be represented as a function of genomic position can be visualized using Caryoscope. Ihab A.B.

Development of a Multiplex Sandwich Aptamer Microarray for the Detection of VEGF165 and Thrombin Open AccessThis article isfreely availablere-usable Article 1 Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy 2 Veneto Nanotech S.C.p.A., Via S. Crispino 106, I -35129 Padova, Italy MicroRNA Silencing by DNA Methylation in Human Cancer: a Literature Analysis MicroRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate the expression of target mRNAs. MicroRNA genes themselves are regulated through epigenetic mechanisms, such as histone modifications and/or DNA methylation of CpG islands. Aberrant CpG island methylation patterns are frequently associated with cancer and thus researching DNA methylation of miRNA genes is a topic of increased research interest. Large quantities of available data from various studies are fragmented and incomplete; therefore, integration was performed. Data from 150 articles revealed 180 miRNA genes shown to be regulated via DNA methylation in 36 cancer types.

RLooM - RNA Loop Modeling RLooM is a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface.