Bioinformatics

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TCGA | TCGA Pan-Cancer Analysis TCGA | TCGA Pan-Cancer Analysis Genomic alterations in diverse cell types at different sites in the body give rise to hundreds of different forms of cancer, and the ways in which these changes result in tumors with different biology, pathology and treatment strategies are beginning to be characterized. The TCGA Research Network has catalogued aberrations in the DNA, chromatin and RNA of the genomes of thousands of tumors relative to matched normal cellular genomes and has analyzed their epigenetic and protein consequences. Here the Pan-Cancer initiative examines the similarities and differences among the genomic and cellular alterations found in the first dozen tumor types to be profiled by TCGA.
cell

English Communication for Scientists | Learn Science at Scitable
Mill Hill Essays | MRC National Institute for Medical Research, London
Chronic Myeloid Leukemia Spotlight : Spotlight : Leukemia
Public Library of Bioinformatics | focus on bioinformatics
PLoS articles

Biomarkers and Personalized Medicine Biomarkers and Personalized Medicine Excerpt from article: "The ARID1A/ARID1B association with survival time was discovered during a large-scale genomic analysis of the childhood cancer, which affects a set of neural crest cells destined to be part of the peripheral sympathetic nervous system. "These two genes function in a group of genes that seems to play an important role in neural cell behavior," Children's Hospital of Philadelphia pediatric oncologist Michael Hogarty, the study's co-senior author, said in a statement, "and we will now work to discover if this insight may open up new treatments for children with tumors having these mutations." Hogarty and the Johns Hopkins Kimmel Cancer Center's Victor Velculescu led a research group that relied on high-coverage genome sequencing, low-coverage genome sequencing, exome sequencing, and/or more targeted approaches to unearth genetic abnormalities ranging from point mutations to chromosomal changes in tumors from more than 70 children with neuroblastoma.
Next-generation sequencing technologies are revolutionising genomics and their effects are becoming increasingly widespread. Many tools and algorithms relevant to next-generation sequencing applications have been published in Bioinformatics, and so to celebrate this contribution we have gathered these together in this 'Bioinformatics for Next Generation Sequencing' virtual issue. This will be a living resource that we will continually update to include the very latest papers in this area to help researchers keep abreast of the latest developments. Editorial -Bioinformatics for Next Generation Sequencing Alex Bateman and John QuackenbushBioinformatics (2009) 25: 429 Full Text A Report on the 2009 SIG on Short Read Sequencing and Algorithms (Short-SIG)Michael Brudno et al.Bioinformatics (2009) 25: 2863–2864 Full Text Life Sciences & Mathematics & Physical Sciences | Bioinformatics | Next Generation Sequencing Life Sciences & Mathematics & Physical Sciences | Bioinformatics | Next Generation Sequencing
OpenHelix Blog OpenHelix Blog The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a tool that aims to help standardize and represent the key features of they systems biology and molecular interactions that we need to capture. NaviCell came to my attention as I was watching the tweets from the recent #isb2014 conference: The International Society for Biocuration conference. Suddenly a bunch of excited attendees started chatting about it: wow, navicell looks pretty awesome, using the Google-maps interface to zoom https://t.co/yClvCF3nQ0 #isb2014— Iddo Friedberg (@iddux) April 7, 2014
Ron Fredericks writes: Dr. Saptarshi Guha created an open-source interface between R and Hadoop called the R and Hadoop Integrated Processing Environment or RHIPE for short. LectureMaker was on the scene filming Saptarshi’s RHIPE presentation to the Bay Area’s useR Group, introduced by Michael E. Driscoll and hosted at Facebook’s Palo Alto office on March 9′th 2010. Special thanks to Jyotsna Paintal for helping me film the event. RHIPE: An Interface Between Hadoop and R for Large and Complex Data Analysis | LectureMaker, LLC RHIPE: An Interface Between Hadoop and R for Large and Complex Data Analysis | LectureMaker, LLC
Computational Biology Center We pursue basic and exploratory research at the interface of information technology and biology. Information technology plays a vital role in enabling new science and discovery in biology. Advances in high throughput and platform technologies in biology present an unprecedented challenge in scale, management, and analysis of biological data. Advances in computing architecture and scale are enabling simulations of complex biological processes at various organizational levels from atomic to cellular and beyond. Computational Biology Center
Web services for bioinformatics, Part 1 Web services for bioinformatics, Part 1 Web services for life sciences The IBM alphaWorks article on web services for life sciences is an example set of web services that offers standard bioinformatics applications and demonstrates the technology (See Resources). The project is written in Java and mainly acts as a wrapper around existing bioinformatics applications. It allows researchers to search through the web service and obtain output through XML documents and to view intermediate steps throughout the request. Bioinformatics research applications exist in various stages of completeness in many different languages. Furthermore, building a workflow from several different applications requires installing applications locally, copying input and output data by hand, and often modifying source code for adapting changes in output and input data format.
A growing collection of links to various TikZ and PGF resources. Various packages that extends or are built on top of TikZ and PGF. Beamer A LaTeX class for creating presentations. Written by the same author as PGF/TikZ. Bodegraph TikZ and PGF resources TikZ and PGF resources
Mathematics part 2 - Getting to grips with LaTeX - Andrew Roberts Mathematics part 2 - Getting to grips with LaTeX - Andrew Roberts by Andrew Roberts This tutorial builds on the basic foundations presented in the previous tutorial. If you often include a lot of maths in your documents, then you will probably find that you wish to have slightly more control over presentation issues. Some of the topics covered make writing equations more complex - but who said typesetting mathematics was easy?!
Bioinformatics Organization - Bioinformatics.Org Bioinformatics Organization - Bioinformatics.Org April 29-May 1, 2014 (ceremony on the 30th) Bio-IT World Conference & Expo, World Trade Center, Boston, MA, USA http://www.bio-itworldexpo.com/ Prof. Helen Berman of Rutgers University has been selected as the laureate of the 2014 Benjamin Franklin Award for Open Access in the Life Sciences! In the words of her nominators: Helen Berman (http://chem.rutgers.edu/berman_helen_m) was a champion for open access to scientific information at a time when the concept of data sharing was in its infancy. For nearly five-decades she has been committed to ensuring that the Protein Data Bank (PDB) archive has been a resource created by the community and for the community. As head of the Research Collaboratory for Structural Bioinformatics (RCSB), Helen became the Director of the PDB in 1998 and developed the RCSB PDB into a vital and key resource for biology and education (http://rcsb.org).
November 10: Provide an outline of your work, as well as a preliminary list of references; Develop your presentation skills. The format of the projects is quite flexible. Bioinformatics Projects List
.NET Bio .NET Bio is an open source library of common bioinformatics functions, intended to simplify the creation of life science applications. The core library implements a range of file parsers and formatters for common file types, connectors to commonly-used web services such as NCBI BLAST, and standard algorithms for the comparison and assembly of DNA, RNA and protein sequences. Sample tools and code snippets are also included. .NET Bio has been built with specific goals in mind:
bioinformatics journal list | nodalpoint.org
CHINESE WEBSITES

Courses

I write the Metabolic Melodies and Verses for the BB100, BB 350, BB 450/550 and BB 451/551 classes I teach at Oregon State University. You can download full recordings of my songs for free here. If you'd like to watch my lectures featuring these songs, you can select from collections of them HERE, HERE, and HERE. Kevin Ahern's Wildly Popular Metabolic Melodies
Schedule for BB 350 Ecampus (Note - this is the page for the ECAMPUS version of BB 350. The CLASSROOM version is different and should not be used by CLASSROOM students, nor should the ECAMPUS version be used by CLASSROOM students) The syllabus is required reading in this course. Download it HERE. BB 350 Oregon State University
Databases

Programming

Source Code for Biology and Medicine | All articles
tools

Online Lectures on Bioinformatics
Canadian Bioinformatics Workshops | Bioinformatics.ca - Canadian Bioinformatics Workshops (CBW)
MCL - a cluster algorithm for graphs