compgenome.org

CompGenome

Data Driven Discovery and Precise Medicine. Cancer Genomics using Next-Gen Sequencing Data. An open-source R program for downloading, processing and analyzing public TCGA data. A comprehensive depiction of genetic interactions in cancer by integrating TCGA data. [ BLOG. Recent Post: Zodiac (case 14). Integrative study on TCGA genomic data and TCIA radiological images for improved cancer research and treatment. A Bayesian method to reconstruct tumor phylogeny based on NGS Data. Congratulation to Lin Wei f...

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CompGenome | compgenome.org Reviews

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Data Driven Discovery and Precise Medicine. Cancer Genomics using Next-Gen Sequencing Data. An open-source R program for downloading, processing and analyzing public TCGA data. A comprehensive depiction of genetic interactions in cancer by integrating TCGA data. [ BLOG. Recent Post: Zodiac (case 14). Integrative study on TCGA genomic data and TCIA radiological images for improved cancer research and treatment. A Bayesian method to reconstruct tumor phylogeny based on NGS Data. Congratulation to Lin Wei f...

<META> KEYWORDS

1 big data cancer genomics

2 bayesian adaptive design

3 tcga assembler

4 zodiac

5 cancer radiogenomics

6 lochap

7 treeclone

8 bayclone2

9 nexgen df

10 people

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big data cancer genomics,bayesian adaptive design,tcga assembler,zodiac,cancer radiogenomics,lochap,treeclone,bayclone2,nexgen df,people,projects,research,news,welcome to compgenome,congratulations to nextgen df,yuan ji's lab,yuan ji,yitan zhu,lin wei

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CompGenome | compgenome.org Reviews

https://compgenome.org

Data Driven Discovery and Precise Medicine. Cancer Genomics using Next-Gen Sequencing Data. An open-source R program for downloading, processing and analyzing public TCGA data. A comprehensive depiction of genetic interactions in cancer by integrating TCGA data. [ BLOG. Recent Post: Zodiac (case 14). Integrative study on TCGA genomic data and TCIA radiological images for improved cancer research and treatment. A Bayesian method to reconstruct tumor phylogeny based on NGS Data. Congratulation to Lin Wei f...

INTERNAL PAGES

compgenome.org

1

ZODIAC

http://www.compgenome.org/TCGA/landing/show.html

In the result of Zodiac. Move and hover the mouse on the gene name to load the information of target gene from NCBI.

2

ZODIAC

http://www.compgenome.org/zodiac

Type in the query gene symbol / ID separated by space. Zodiac shows interactions between PALB2, BRCA1, and BRCA2. Zodiac interactions support ESR1-CCDC170 fusion in cancer. Zodiac reveals genetic interactions of cancer immunotherapy target gene. Zodiac shows interactions between SAA and S100A. Zodiac shows interactions between PYK2 and STAT3. Zodiac interactions support EML4-ALK fusion in cancer. Zodiac interactions support drug developing. Zodiac shows interactions between SPARC and VCAM1. You can "Zodi...

3

LocHap

http://www.compgenome.org/lochap

LocHap: Local-Haplotype Variant Calling Software. Subhajit Sengupta, Kamalakar Gulutoka, Yitan Zhu, Yuan Ji*. LocHap is currently licensed under the GPL version 3, LocHap may be distributed under GPL version 3. Sengupta, Subhajit, et al. "Ultra-fast local-haplotype variant calling using paired-end DNA-sequencing data reveals somatic mosaicism in tumor and normal blood samples." Nucleic acids research (2015): gkv953. Here is the pre-print. Of our Local Haplotype paper. Yuan Ji: koaeraser@gmail.com. We hav...

4

NextGen-DF

http://www.compgenome.org/NGDF

Recommended browsers as ordered: Firefox, Chrome and Safari. Do not use Internet Explorer. The NGDF tool can now be referenced as Yang, Wang and Ji, Contemporary Clinical Trials. 45 (2015) 426 434. Oct 12, 2015. Users will be allowed to set up simulation scenarios in three ways (Manually input, Batch input, Automatically input), under which the four designs (mTPI, 3 3, CRM, customized decision) can be performed to simulate trials separately. Of selection 2nd Track. Of treated 3rd Track. 45 (2015) 426 434.

5

BayClone2

http://www.compgenome.org/bayclone2

BayClone2: A Bayesian Sequence and Copy Number Caller for Subclones Using NGS Data. Juhee Lee, Peter Mueller, Subhajit Sengupta, Yuan Ji*. BayClone2 is currently licensed under the GPL version 3, BayClone2 may be distributed under GPL version 3. Juhee Lee: juheelee@soe.ucsc.edu. Subhajit Sengupta: subhajit06@gmail.com. Yuan Ji: koaeraser@gmail.com. Version 1.1 release - 12/25/2014. We now have a R package at CRAN repository ( http:/ cran.r-project.org/web/packages/BayClone2/index.html.

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health.bsd.uchicago.edu

Yuan Ji's Biostatistics and Bioinformatics Lab, Department ofHealth Studies

http://health.bsd.uchicago.edu/yji

Yuan Ji's Biostatistics and Bioinformatics Lab (BBL). Department of Public Health Sciences, The University of Chicago. Associate Professor (Part Time). Department of Public Health Sciences. The University of Chicago. 5841 South Maryland Ave MC 2000 Chicago, IL 60637. Yji@health.bsd.uchicago.edu. Director, Program of Computational Genomics and Medicine. Evanston, IL 60201. Feb 2014: Dissemination of big-data analytics Tools at our new website. Http:/ www.compgenome.org/.

compgenome.wordpress.com

November | 2014 | compgenome

https://compgenome.wordpress.com/2014/11

Zodiac (Case 14): IL1RAP — A NEW Marker for Alzheimer’s Disease and an OLD Fella for Cancer — Supports Negative Correlation between Alzheimer and Cancer! Zodiac (Case 13): Foxp3 — Why is it Potentially Nobel-Prize worthy. Zodiac (Case 12) — HER3: the little sister of HER2 and its potential role in liquid cancer. Zodiac (case 11): Are there similarities in genetic interactions between Cancer and Neurological Disorders? Zodiac (case 10): PTEN and MYC — Is there a middle man? Zodiac (Case 9): Zod…. Zodiac (...

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compgenome.org

CompGenome

Data Driven Discovery and Precise Medicine. Cancer Genomics using Next-Gen Sequencing Data. An open-source R program for downloading, processing and analyzing public TCGA data. A comprehensive depiction of genetic interactions in cancer by integrating TCGA data. [ BLOG. Recent Post: Zodiac (case 14). Integrative study on TCGA genomic data and TCIA radiological images for improved cancer research and treatment. A Bayesian method to reconstruct tumor phylogeny based on NGS Data. Congratulation to Lin Wei f...

compgenome.wordpress.com

compgenome | Computation Genomics Medicine

Zodiac (Case 14): IL1RAP — A NEW Marker for Alzheimer’s Disease and an OLD Fella for Cancer — Supports Negative Correlation between Alzheimer and Cancer! Zodiac (Case 13): Foxp3 — Why is it Potentially Nobel-Prize worthy. Zodiac (Case 12) — HER3: the little sister of HER2 and its potential role in liquid cancer. Zodiac (case 11): Are there similarities in genetic interactions between Cancer and Neurological Disorders? Zodiac (case 10): PTEN and MYC — Is there a middle man? Zodiac (Case 9): Zod…. Were fou...

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JBrowse

compgenomics.lab.uconn.edu

Home | Plant Computational Genomics Lab - Jill Wegrzyn

Department of Ecology and Evolutionary Biology. Plant Computational Genomics Lab – Jill Wegrzyn. We are recruiting MS and PhD students for Fall 2017. Apply here! January 5, 2016. Sugar pine genome in the news! The 31Gbp sugar pine genome, the largest sequenced to date, has been released to the public. December 21, 2015. USDA NIFA Proposal Funded! The USDA NIFA proposal led by Fikret Isik at NCSU will develop genotyping resources for loblolly pine and sugar pine to aid in genomic selection. July 9, 2015.

compgenomics.ucdavis.edu

CGP

UC Davis Genome Center.

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Amos Tanay's Group

Amos Tanay's Group. We are part of the Systems Biology community. At the Weizmann Institute. With affiliations to the Department of Computer Science and Applied Mathematics. And the Department of Biological Regulation. The group is involved in multiple efforts aimed at understanding the physical organization of chromosomes using Chromosome Conformation Capture (3C) and several of its high throughput implementations ( Hi-C. Published: DNA methylation turnover and epigenetic memory.