PiNGO: a Cytoscape plugin to find candidate genes

http://www.ncbi.nlm.nih.gov/m/pubmed/21278188/?i=5&from=/23547033/related

The stem cell code in oral epithelial tissue

http://www.ncbi.nlm.nih.gov/m/pubmed/20599480/

FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data

http://bioinformatics.oxfordjournals.org/content/early/2013/04/24/bioinformatics.btt151.short?rss=1&buffer_share=c5ca4&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer%253A%252BSAGRudd%252Bon%252Btwitter

Genome Biology | Abstract | TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

http://genomebiology.com/2013/14/4/R36/abstract

The Long and Short of MicroRNA

http://www.cell.com/abstract/S0092-8674(13)00402-9?buffer_share=d1953&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer%253A%252BSAGRudd%252Bon%252Btwitter

Curr Protoc Bioinformatics. 2013 Mar;Chapter 8:Unit8.17. doi: 10.1002/0471250953.bi0817s41.

Using MEMo to Discover Mutual Exclusivity Modules in Cancer.

Ciriello G, Cerami E, Aksoy BA, Sander C, Schultz N.

Source

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York.

Abstract

Although individual tumors show surprisingly diverse genomic alterations, these events tend to occur in a limited number of pathways, and alterations that affect the same pathway tend to not co-occur in the same patient. While pathway analysis has been a powerful tool in cancer genomics, our knowledge of oncogenic pathway modules is incomplete. To systematically identify such modules, we have developed a novel method, Mutual Exclusivity Modules in Cancer (MEMo). The method searches and identifies modules characterized by three properties: (1) member genes are recurrently altered across a set of tumor samples; (2) member genes are known to or are likely to participate in the same biological process; and (3) alteration events within the modules are mutually exclusive. MEMo integrates multiple data types and maps genomic alterations to biological pathways. MEMo's mutual exclusivity uses a statistical model that preserves the number of alterations per gene and per sample. The MEMo software, source code and sample data sets are available for download at: http://cbio.mskcc.org/memo. Curr. Protoc. Bioinform. 41:8.17.1-8.17.12. © 2013 by John Wiley & Sons, Inc.

http://www.ncbi.nlm.nih.gov/pubmed/23504936

Gene-pair expression signatures reveal lineage control : Nature Methods : Nature Publishing Group

http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.2445.html

Deanna Church on the Reference Genome Past, Present and Future - Bio-IT World

http://www.bio-itworld.com/2013/4/22/church-on-reference-genomes-past-present-future.html

GRC38

( METAGENOMICS) FunFrame: functional gene ecological analysis pipeline

http://bioinformatics.oxfordjournals.org/content/29/9/1212.short?rss=1&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%253A+bioinformatics_today+%2528Bioinformatics%2529

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

http://bioinformatics.oxfordjournals.org/content/29/9/1210.short?rss=1&utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%253A+bioinformatics_today+%2528Bioinformatics%2529

QIIME Overview Tutorial: de novo OTU picking and diversity analyses

http://qiime.org/tutorials/tutorial.html

Metagenomic analysis.

VCF (Variant Call Format) version 4.1 | 1000 Genomes

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41

YOKOFAKUN: playing with BWA-MEM : my notebook

http://plindenbaum.blogspot.in/2013/04/playing-with-bwa-mem-my-notebook.html?utm_source=twitterfeed&utm_medium=twitter

Cancer genome-sequencing study design

http://www.nature.com/nrg/journal/v14/n5/full/nrg3445.html

A genomic view of mosaicism and human disease

http://www.nature.com/nrg/journal/v14/n5/full/nrg3424.html

TUMIR: an experimentally supported database of microRNA deregulation in various cancers

http://www.jclinbioinformatics.com/content/3/1/7/abstract

Isoform-level expression profiles provide better cancer signatures than gene-level expression profiles

http://genomemedicine.com/content/5/4/33/abstract

BMC Genomics | Abstract | Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting

http://www.biomedcentral.com/1471-2164/14/253/abstract

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas : Nature Genetics : Nature Publishing Group

http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.2611.html#affil-auth

Make your own cancer diagnostic test - 2011 FALL - Stanford Medicine Magazine - Stanford University School of Medicine

http://stanmed.stanford.edu/2011fall/article6.html

online variant calling - ScanV-Scanning Cancer Variants

http://siftdna.org/cancer/index.html

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas : Nature Genetics : Nature Publishing Group

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2611.html

Aristolochic acid: Chinese herbal remedy 'causes high rate of urinary tract cancer'

Another carcinogen.

http://www.dailymail.co.uk/health/article-2128656/Aristolochic-acid-Chinese-herbal-remedy-causes-high-rate-urinary-tract-cancer.html

Treating Cancer with Personalized Medicine | Highlight HEALTH

http://www.highlighthealth.com/healthcare/treating-cancer-with-personalized-medicine/

The FAM ( USP9X) Deubiquitylating Enzyme Localizes to Multiple Points of Protein Trafficking in Epithelia, where It Associates with E-cadherin and -catenin.

http://www.molbiolcell.org/content/15/4/1591.full.pdf


The FAM ( USP9X) Deubiquitylating Enzyme Localizes to Multiple Points of Protein Trafficking in Epithelia,  where It Associates with E-cadherin and -catenin.


USP9X is substrate-specific deubiquitylating enzyme highly expressed in epithelia where it interacts with its
substrate, beta -catenin.


In vivo depletion of USP9X in preimplantation mouse embryos, by addition of siRNA, resulted in a parallel decrease in beta -catenin.

It proves USP9X to be a member of Beta-catenin related pathway.

Cancer Genome Landscapes

http://www.sciencemag.org/content/339/6127/1546

Bert volelstein discusses about the core signalling pathways in human cancers.

Differential principal component analysis of ChIP-seq

http://www.pnas.org/content/early/2013/04/05/1204398110.short

Principal component analysis of chip-seq.

How to identify cancer drivers from tumor somatic mutations?

How to identify cancer drivers from tumor somatic mutations?

http://bg.upf.edu/blog/2012/07/how-to-identify-cancer-drivers-from-tumor-somatic-mutations/

Up, Up, and Array | The Scientist Magazine(R)

http://www.the-scientist.com/?articles.view/articleNo/34779/title/Up--Up--and-Array/

Biography of Todd golub.

Inspiring article.

Form and function : Nature News & Comment

http://www.nature.com/news/form-and-function-1.12580#/comment-56170

Stories on ENCODE coding and non-coding claims.

USP9x - Smad4 Interaction

http://www.cell.com/retrieve/pii/S0092867408014451

FAM/USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination.

Stephen Piccolo' group pointed out that loss of USP9x helps in the promotion of cancer progression through TGF-beta signalling.

http://www.pnas.org/content/109/10/3879.long#ref-23

Read the entire story on

Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing

by Todd Golub team.

Interesting Findings:

Somatic mutations found in  MYD88, CARD11, EZH2, and CREBBP genes with additional new drivers in MEF2B, MLL2,BTG1, GNA13, ACTB, P2RY8, PCLO, and TNFRSF14.