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Category: Other topics, Gene expression
Roadmap Epigenomics Project allows: Epigenome
The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The Consortium leverages experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Registration not required.
Click here for more informationsPublished on 2012-04-13 04:45:47
The UC Santa Cruz Xena (Cancer Genomics Browser) is a suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It displays side-by-side heat maps of genomic data such as gene expression and copy number changes, and clinical data for a long list of cancer data sets, along with a feature that enables researchers to look for genomic variations that correlate with clinical outcomes. Registration not required.
Click here for more informationsPublished on 2012-04-12 10:02:38
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From Institute of Systems Biology
Category: Statistics miscellanea, Cancer research
Regulome Explorer is a set of tools that facilitates the integrative exploration of associations in clinical and molecular TCGA data by providing a wide-ranging view of connections between mutations, expression level changes, and clinical outcomes. The tools were developed by by the Institute for Systems Biology in Seattle, Washington, and MD Anderson Cancer Center at the University of Texas in Houston. Registration not required.
Click here for more informationsPublished on 2012-04-12 09:59:04
The Cancer Genome Atlas (TCGA) Data Portal provides a platform to retrieve information on somatic mutations, or other data types such as copy number, DNA methylation, and gene expression, for a number of tumor types. It contains clinical information, genomic characterization data, and high-throughput sequencing analysis of the tumor genomes.TCGA updates as soon as new data become available. Registration not required.
Click here for more informationsPublished on 2012-04-12 09:12:22
The International Cancer Genome Consortium (ICGC) Data Portal allows researchers to access mutation and expression data for specific genes, or to scroll through data sets collected so far on 24 types of cancers by project teams in 9 countries. It represents a good starting point to check for known mutations and other aberrations in a gene of interest. Registration not required.
Click here for more informationsPublished on 2012-04-12 09:03:50
The Genomics of Drug Sensitivity in Cancer project from Weelcome Trust is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. Participants are performing a large-scale drug screen incorporating detailed genomic and gene expression analyses to systematically identify drug response biomarkers. Registration not required.
Click here for more informationsPublished on 2012-04-12 08:56:29
It's a simple Excel spreadsheet from Jon Wittwer of Vertex42 for constructin box-plots by inputing single subject values. In addition the spreadsheet includes examples for generating a random number from a Normal distribution, for calculating cumulative probabilities and for shading a portion of the distribution. Registration not required.
Click here for more informationsPublished on 2012-04-10 10:23:54
It's a simple and well constructed Excel spreadsheet from Jon Wittwer of Vertex42 for graphing a Normal distribution curve by inputing either a mean & SD or single subject values. In addition the spreadsheet includes examples for generating a random number from a Normal distribution, for calculating cumulative probabilities and for shading a portion of the distribution. Registration not required.
Click here for more informationsPublished on 2012-04-10 10:14:10
The Broad-Novartis Cancer Cell Line Encyclopedia (CCLE) is an ongoing project from collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access analysis and visualization of DNA copy number, mRNA expression and mutation data for about 1000 cell lines. Registration required.
Click here for more informationsPublished on 2012-04-09 03:25:40
The server from MSKCC predicts the functional impact (high, medium, low, or neutral) of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. MutationAssessor looks at conservation across all the homologs of a protein and also it takes into account the conservation within just the closest homologs, which is called “specificity.” This gives the tool an advantage in predicting mutations that have a functional impact, particularly those that lead to a change in function rather than a loss or gain of function Registration not required.
Click here for more informationsPublished on 2012-03-19 11:28:46
The Common Fund's Human Microbiome Project (HMP) aims to characterize the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease. HMP includes the following initiatives Registration not required.
Click here for more informationsPublished on 2012-03-16 05:12:06
TargetScan (Whitehead Institute) predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA Registration not required.
Click here for more informationsPublished on 2012-03-09 12:39:31
The Vertebrate Genome Annotation (VEGA) genome browser is a central repository for high quality manual annotation of vertebrate finished genome sequence. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Registration not required.
Click here for more informationsPublished on 2012-03-02 12:12:28
LRG sequence format has been designed for the specific purpose of gene variant reporting. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for reporting variants. The data base provides a single-file record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants.
Click here for more informationsPublished on 2012-03-02 11:46:13
The HUGO Gene Nomenclature Committee (HGNC) has assigned unique gene symbols and names to over 33,000 human loci, of which around 19,000 are protein coding. http://genenames.org is a curated online repository of HGNC-approved gene nomenclature and associated resources including links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages. Registration not required.
Click here for more informationsPublished on 2012-03-02 11:13:08
The Participant Portal is the single-entry point for interactions with the research and innovation programmes of the European Commission. It offers you the possibility to use a great variety of services and tools that facilitate the monitoring and the management of your proposals and projects throughout their lifecycle. Registration required.
Click here for more informationsPublished on 2012-03-02 10:12:08
ESF is a strong international network of 75 research funding, performing organisations and academics. ESF offers a number of opportunities, scientific and non-scientific, and provides career opportunities that could progress in management and administrative science activities. Registration required.
Click here for more informationsPublished on 2012-03-02 10:06:18
The UCSC Genome Browser is an on-line genome browser hosted by the University of California, Santa Cruz (UCSC).[2] [3] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. Registration not required.
Click here for more informationsPublished on 2012-03-02 05:29:50
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. Registration not required.
Click here for more informationsPublished on 2012-02-29 12:12:49
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. Registration required.
Click here for more informationsPublished on 2012-02-29 12:01:55
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