BOL: Related items

Cancer Dependency Map

Jit — Thu, 13 Feb 2020 04:38:47 -0600

The consequences of alterations in the DNA of cancer cells and subsequent vulnerabilities are not fully understood. This project aims to assign a dependency to every cancer cell in a patient which could be exploited to develop new therapies. This knowledge is foundational for precision cancer medicine.

Address of the bookmark: https://depmap.sanger.ac.uk/

List of cancer genomics research web resources !

biogeek — Wed, 27 Dec 2017 20:33:09 -0600

Major web resources for cancer genomics research

CGHub
https://cghub.ucsc.edu/
Comprehensive data repository; huge data size

EGA
https://www.ebi.ac.uk/ega/
Comprehensive data repository; huge data size

COSMIC
http://cancer.sanger.ac.uk
Largest somatic mutation database; genome sequencing paper curation

CPRG
http://www.broadinstitute.org/software/cprg
Interface for cancer program resources

GDAC
http://gdac.broadinstitute.org/
Data analysis; automatic pipelines; user-friendly reports

SNP500Cancer
http://snp500cancer.nci.nih.gov
Sequence and genotype verification of SNPs

canEvolve
www.canevolve.org/
Comprehensive analysis of tumor profile; Data from 90 studies involving more than 10,000 patients

MethyCancer
http://methycancer.psych.ac.cn
Relationship among DNA methylation, gene expression and cancer

SomamiR
http://compbio.uthsc.edu/SomamiR/
Correlation between somatic mutation and microRNA; genome-wide displaying

cBioPortal
http://www.cbioportal.org/public-portal/
Graphical summaries; gene alteration; processed data; visualization

UCSC Cancer Genomics Browser
https://genome-cancer.soe.ucsc.edu/
Clinical information; gene expression; copy number variation; visualization

CGWB
https://cgwb.nci.nih.gov/
Visualization; gene mutation and variation; automated analysis pipeline

GDSC
http://www.cancerrxgene.org
Drug sensitivity information; drug response information

canSAR
https://cansar.icr.ac.uk/
Multidisciplinary information; drug discovery

NONCODE
http://www.noncode.org/ ncRNAs;
lncRNAs; up-to-date and comprehensive resource

Liu Lab

Tue, 04 Feb 2020 06:27:02 -0600

Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

https://liulab-dfci.github.io/software/

methylKit

Jit — Fri, 03 Jun 2016 10:09:29 -0500

methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Address of the bookmark: https://github.com/al2na/methylKit

Sequencing Solutions to World Health

Rahul Agarwal — Thu, 29 Aug 2013 15:05:35 -0500

"New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine."

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

Two major breakthrough!!

Rahul Agarwal — Mon, 02 Sep 2013 10:18:11 -0500

"Scientists in Uruguay in colloboration with European partners sequenced the genome of the high-value Tannat grape, from which "the most healthy of red wines" are fermented.

A quick, $1 syphilis test in development by researchers from UNU-BIOLAC."

Source:

http://www.sciencedaily.com/releases/2013/09/130902101846.htm

http://www.eurekalert.org/pub_releases/2013-09/tca-ssg082613.php

Largest Genome Sequenced

Rahul Agarwal — Fri, 21 Mar 2014 13:57:19 -0500

The enormous size of the loblolly pine genome having 22 billion base pairs compared to only 3 billion in the human genome. In other words, it is seven times larger than a human’s and also the largest and the most complete conifer genome ever sequenced.

Related Paper:

http://genomebiology.com/2014/15/3/R59/abstract

Address of the bookmark: http://www.news.ucdavis.edu/search/news_detail.lasso?id=10859

New RNA Seq tool

Rahul Agarwal — Fri, 25 Apr 2014 10:59:04 -0500

"By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20–30 times faster than current methods without loss of accuracy."

Tool link:

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Address of the bookmark: http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.