NAR database issue

http://m.nar.oxfordjournals.org/content/42/D1?etoc&utm_source=buffer&utm_campaign=Buffer&utm_content=buffer9beee&utm_medium=twitter

Reproducible copy number variation - CTC

http://www.ncbi.nlm.nih.gov/m/pubmed/24324171/?i=59&from=whole%20genome%20sequencing

Data analysis with Python — Practical Computing for Biologists

http://people.duke.edu/~ccc14/pcfb/analysis.html

Mining cancer methylomes: prospects and challenges

http://www.sciencedirect.com/science/article/pii/S0168952513001959

Wiggletool

http://m.bioinformatics.oxfordjournals.org/content/early/2013/12/18/bioinformatics.btt737.short?rss=1&utm_content=buffer21378&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

PLOS ONE: DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072614

Instant notes on Bioinformatics

http://davetang.org/wiki/tiki-index.php?page=Bioinformatics

GONOME: measuring correlations between GO terms and genomic positions

http://www.biomedcentral.com/1471-2105/7/94

Listening to silence and understanding - PubMed Mobile

http://www.ncbi.nlm.nih.gov/m/pubmed/11967553/

450k Chip Analysis Methylation Pipeline (ChAMP)

http://www.citeulike.org/user/neils/article/12832448?utm_source=twitterfeed&utm_medium=twitter

DGIdb - Mining the Druggable Genome

http://dgidb.genome.wustl.edu/

Platinum Genomes illumina whole genome sequence

http://www.illumina.com/platinumgenomes/

Genome Biology | Full text | Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue

http://genomebiology.com/2013/14/3/R24

Genome Biology | Full text | THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data

http://genomebiology.com/2013/14/7/R80

Genome Biology | Abstract | EXCAVATOR: detecting copy number variants from whole-exome sequencing data

http://genomebiology.com/2013/14/10/R120/abstract

Gene inactivation and its implications for annotation in the era of personal genomics

http://m.genesdev.cshlp.org/content/25/1/1.short

Network analysis of GWAS data

http://www.sciencedirect.com/science/article/pii/S0959437X13001354

Variant annotation AVIA - ABCC :: Upload Parameters for AVIA Analysis

http://avia.abcc.ncifcrf.gov/apps/site/sub_analysis/?id=3

GEMINI tutorial

http://quinlanlab.org/tutorials/cshl2013/gemini.html

Studies Reveal Extreme Diversity of Cancer Cells | Simons Foundation

https://www.simonsfoundation.org/quanta/20131113-tracking-the-evolution-of-cancer-cell-by-cell/

Human Somatic Variation: It’s Not Just for Cancer Anymore - Springer

http://link.springer.com/article/10.1007/s40142-013-0029-z

NonCode v4 database

http://m.nar.oxfordjournals.org/content/early/2013/11/26/nar.gkt1222.short?rss=1

Genome Medicine | Abstract | Efficiency of whole genome amplification of Single Circulating Tumor Cells enriched by CellSearch and sorted by FACS

http://genomemedicine.com/content/5/11/106/abstract

Fusion transcript comparison

http://link.springer.com/article/10.1186%2F1471-2105-14-S7-S2

A Lay Thesis: Maximum Likelihood Estimation - Notes, Bytes, Bases, and Plancks - Quora

Fantastic notes on MLE.

http://adarob.quora.com/A-Lay-Thesis-Maximum-Likelihood-Estimation

A Hopeful Monster: Free Resources I'd Gladly Have Paid For

http://ahopefulmonster.blogspot.com/2013/11/free-resources-id-gladly-have-paid-for.html

PLOS Computational Biology: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003326

RNA SEQ usadellab - Trimmomatic: A flexible read trimming tool for Illumina NGS data

http://www.usadellab.org/cms/?page=trimmomatic

Microsoft - Great Projects - Human Genome Project

http://greatprojectscampaign.com/human-genome-project.html

From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline - Current Protocols in Bioinformatics - Auwera - Wiley Online Library

http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1110s43/abstract;jsessionid=FF13D61431F1B7A0666A3D6C0B4173E1.f03t01

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

http://m.pnas.org/content/110/46/18602.abstract.html?etoc

Mosaic copy number variation in human genomes.

http://m.sciencemag.org/content/342/6158/632.short

Systematic evaluation of spliced alignment programs for RNA-seq data : Nature Methods : Nature Publishing Group

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2722.html

Exomiser - Wellcome Trust Sanger Institute

https://www.sanger.ac.uk/resources/databases/exomiser/query/

GTEx is throwing away 90% of their data | Bits of DNA

http://liorpachter.wordpress.com/2013/10/21/gtex/#comment-67

Cancer mutations: Genetic studies of tumors have not led to many drugs.

http://www.slate.com/articles/health_and_science/human_genome/2013/10/cancer_mutations_genetic_studies_of_tumors_have_not_led_to_many_drugs.html

BIOINFORMATICS Training portal | GOBLET

Good website

http://www.mygoblet.org/training-portal

Liquid Biopsies and Acquired Resistance CTC

http://biobits.org/liquid-biopsies.html

SAMtools - Primer / Tutorial

Complete protocol

http://biobits.org/samtools_primer.html

Non-uniform coverage of transcripts in RNA-Seq experiments | Bits of DNA

http://liorpachter.wordpress.com/2013/10/17/non-uniform-coverage-of-transcripts-in-rna-seq-experiments/

(RNA SEQ) Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

http://genomebiology.com/2013/14/7/R70

The mutational landscape of phosphorylation signaling in cancer : Scientific Reports : Nature Publishing Group

http://www.nature.com/srep/2013/131002/srep02651/full/srep02651.html

AJHG - Haplotype Estimation Using Sequencing Reads

http://www.cell.com/AJHG/abstract/S0002-9297(13)00415-1

Rare variants, disease, and population size

http://genomena.com/genomes-and-health/rare-variants-disease-and-population-size/

Cell - The Next-Generation Sequencing Revolution and Its Impact on Genomics

http://www.cell.com/abstract/S0092-8674(13)01141-0#MainText

Presentation : File formats for Next Generation Sequencing

http://plindenbaum.blogspot.in/2013/09/presentation-file-formats-for-next.html?utm_source=twitterfeed&utm_medium=twitter

The Mermaid's Tale: Genes for rare diseases

http://ecodevoevo.blogspot.com/2013/09/genes-for-rare-diseases.html?spref=tw

Transcriptome and genome sequencing uncovers functional variation in humans : Nature : Nature Publishing Group

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12531.html

*Seq | DIFFERNT TYPES OF NGS SEQUENCING METHODS

http://liorpachter.wordpress.com/seq/

GenomeRef: Tech Tip: The Pseudo-autosomal region of the reference assembly

http://genomeref.blogspot.in/2013/09/tech-tip-pseudo-autosomal-region-of.html

[RVCD] PLOS Genetics: Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis

http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003723

[RNA SEQ ] Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

http://genomebiology.com/2013/14/9/R95/abstract

Research papers on NGS algorithms

http://www2.informatik.hu-berlin.de/~hakenber/links/nextgen.html

my attempt at following every possible Best Practice in Bioinformatics | bioinfoblog.it

http://bioinfoblog.it/2013/09/my-attempt-at-following-every-possible-best-practice-in-bioinformatics/

Science | From AAAS

http://m.sciencemag.org/content/327/5964/425.abstract

Exome sequencing and the genetic basis of complex traits : Nature Genetics : Nature Publishing Group

http://www.nature.com/ng/journal/v44/n6/full/ng.2303.html#access

JCI - Atrial natriuretic peptide is negatively regulated by microRNA-425

http://www.jci.org/articles/view/67383/figure/2

3 UTR SNP regulated by mir425 ...

An evaluation of statistical approaches rare variant MANTRA

http://www.ncbi.nlm.nih.gov/m/pubmed/19810025/

Calculating Sample Size Estimates for R - PubMed Mobile

http://www.ncbi.nlm.nih.gov/m/pubmed/23961961/

For short reads, which aligners find all hits given certain edit distance threshold? - BioStar

http://www.biostars.org/p/63659/

Identification of transcription factor binding sites from ChIP-seq data at high-resolution

http://m.bioinformatics.oxfordjournals.org/content/early/2013/08/24/bioinformatics.btt470.abstract

Gene inactivation and its implications for annotation in the era of personal genomics

http://genesdev.cshlp.org/content/25/1/1.long

Take a color printout

Liebert Mobile

http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0283?utm_source=buffer&utm_campaign=Buffer&utm_content=bufferd3b50&utm_medium=twitter

The Effects of Non-Synonymous Single Nu - PubMed Mobile

http://www.ncbi.nlm.nih.gov/m/pubmed/23867278/

A method and server for predicting damaging missense mutations

http://www.nature.com/nmeth/journal/v7/n4/full/nmeth0410-248.html

BioNews - Cancer treatment should be based on gene 'fingerprints', says study

http://www.bionews.org.uk/page_294087.asp

A collection of both popular and lesser known biographies, autobiographies and histories of scientific figures and their discoveries. Focused primarily on biology and genetics. This is largely a collection of responses to a query on twitter.

https://gist.github.com/arq5x/6289306

[Mike Stratton Group] Signatures of mutational processes in human cancer : Nature : Nature Publishing Group

FYI

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12477.html

Charting a dynamic DNA methylation landscape of the human genome : Nature : Nature Publishing Group

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12433.html

Andrew Berls | Visualizing your bash history with d3.js

http://andrewberls.com/blog/post/visualizing-your-bash-history-with-d3js

Computational approaches to identify functional genetic variants in cancer genomes : Nature Methods : Nature Publishing Group

http://www.nature.com/nmeth/journal/v10/n8/pdf/nmeth.2562.pdf

PLOT Gallery · mbostock/d3 Wiki · GitHub

https://github.com/mbostock/d3/wiki/Gallery

Microbial Informatics and Experimentation | Full text | Beginner's guide to comparative bacterial genome analysis using next-generation sequence data

http://www.microbialinformaticsj.com/content/3/1/2

Evaluating cell lines as tumour models by comparison of genomic profiles : Nature Communications : Nature Publishing Group

http://www.nature.com/ncomms/2013/130709/ncomms3126/full/ncomms3126.html

The Exomes of the NCI-60 Panel: A Genomic Resource for Cancer Biology and Systems Pharmacology (EXOME DATA)

http://cancerres.aacrjournals.org/content/73/14/4372.abstract

Estimating and interpreting Fst: the impact of rare variants

http://genome.cshlp.org/content/early/2013/07/16/gr.154831.113.abstract.html?papetoc

A comparative analysis of algorithms for somatic SNV detection in cancer

http://bioinformatics.oxfordjournals.org/content/early/2013/07/13/bioinformatics.btt375.short?rss=1&utm_content=buffer2860e&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality : Nature Structural & Molecular Biology : Nature Publishing Group

http://www.nature.com/nsmb/journal/vaop/ncurrent/abs/nsmb.2640.html

Identifying driver mutations from sequencing data of heterogeneous tumors in the era of personalized genome sequencing

http://bib.oxfordjournals.org/content/early/2013/07/01/bib.bbt042.short?rss=1&utm_content=bufferd117e&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

BMC Genomics | Full text | Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers

http://www.biomedcentral.com/1471-2164/14/440?utm_content=buffer6ad6c&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

Trends in Genetics - Human housekeeping genes, revisited

http://www.cell.com/trends/genetics//retrieve/pii/S0168952513000899?_returnURL=http://linkinghub.elsevier.com/retrieve/pii/S0168952513000899?showall=true

Genome Biology | Abstract | Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

http://genomebiology.com/2013/14/7/R70/abstract

Sean Davis - R Tutorials

http://watson.nci.nih.gov/~sdavis/tutorials/

Identification of deleterious synonymous variants in human genomes

http://bioinformatics.oxfordjournals.org/content/early/2013/06/26/bioinformatics.btt308.short?rss=1&utm_content=buffera26e4&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

The Human Genome Contracts Again

http://bioinformatics.oxfordjournals.org/content/early/2013/06/22/bioinformatics.btt362.short?rss=1&utm_content=buffer094f0&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

The cancer genome in context: of mice and mutations | Cath Ennis

http://m.guardian.co.uk/science/occams-corner/2013/jun/25/cancer-genome-mice-mutations

What is sashimi_plot? — MISO 1.0 documentation

http://genes.mit.edu/burgelab/miso/docs/sashimi.html

GAT: a simulation framework for testing the association of genomic intervals

http://bioinformatics.oxfordjournals.org/content/early/2013/06/18/bioinformatics.btt343.abstract

[NGS] False Positives from Next-Gen Sequencing | MassGenomics

http://massgenomics.org/2013/06/ngs-false-positives.html

[NGS] BMC Bioinformatics | Abstract | Benchmarking short sequence mapping tools

http://www.biomedcentral.com/1471-2105/14/184/abstract

DMEAS: DNA Methylation Entropy Analysis Software

http://bioinformatics.oxfordjournals.org/content/early/2013/06/08/bioinformatics.btt332.short?rss=1

eXtasy: Variant Prioritization

http://homes.esat.kuleuven.be/~bioiuser/eXtasy/?utm_source=twitterfeed&utm_medium=twitter

BMC Genomics | Abstract | Web-based visual analysis for high-throughput genomics

http://www.biomedcentral.com/1471-2164/14/397/abstract

European Journal of Human Genetics - The Genome of the Netherlands: design, and project goals

http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2013118a.html

Exome Sequencing Scientific Publications

http://www.geuvadis.org/web/geuvadis/publications;jsessionid=46779B9D0BA3B4AE322A5654480608FD

PLOS ONE: A Novel Classification of Lung Cancer into Molecular Subtypes

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031906

The 1000 Genomes Project: paving the way for personalized genomic medicine, Personalized Medicine, Future Medicine

http://www.futuremedicine.com/doi/full/10.2217/pme.13.22

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data

http://nar.oxfordjournals.org/content/early/2013/05/21/nar.gkt372.short?rss=1

PLOS ONE: IMSA: Integrated Metagenomic Sequence Analysis for Identification of Exogenous Reads in a Host Genomic Background

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0064546

Cell-type, allelic and genetic signatures in the human pancreatic beta cell transcriptome

http://genome.cshlp.org/content/early/2013/05/28/gr.150706.112.abstract.html

The Genotype-Tissue Expression (GTEx) project : Nature Genetics : Nature Publishing Group

http://www.nature.com/ng/journal/v45/n6/full/ng.2653.html?WT.ec_id=NG-201306

SCAN: SNP and CNV Annotation Database

http://www.scandb.org/newinterface/about.html

SCAN is a large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations:

Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene).
Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene.

Orange Visual programming

http://orange.biolab.si/features/

Genetic Risks World Map

http://geneworld.stanford.edu/hgdp.html#

Molecular genetic testing and the future of clinical genomics : Nature Reviews Genetics : Nature Publishing Group

http://www.nature.com/nrg/journal/v14/n6/full/nrg3493.html

Exomiser - Wellcome Trust Sanger Institute

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

Bioinformatics Tools for Multiple Sequence Alignment | EBI

http://www.ebi.ac.uk/Tools/msa/

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer — NEJM

http://www.nejm.org/doi/full/10.1056/NEJMoa1213261

Trends in Genetics - Cryptic causation of human disease: reading between the (germ) lines

http://www.cell.com/trends/genetics/abstract/S0168-9525%2804%2900336-1

Somatic mutation involvement in different diseases.

BMC Bioinformatics | Abstract | CNV-TV: A robust method to discover copy number variation from short sequencing reads

http://www.biomedcentral.com/1471-2105/14/150/abstract?utm_content=buffer73da0&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

Clonal evolution, genomic drivers and effects of therapy in chronic lymphocytic leukemia

http://clincancerres.aacrjournals.org/content/early/2013/04/25/1078-0432.CCR-13-0138.abstract

DDBJ Read Annotation Pipeline

https://p.ddbj.nig.ac.jp/pipeline/Login.do

MiSeq SOP - mothur

http://www.mothur.org/wiki/MiSeq_SOP

A Report of the James Watson Lecture at Yale University

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447206/

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.