Moderator: Obi Griffith

gravatar for Obi Griffith
Obi Griffith18k
Reputation:
17,760
Status:
Trusted
Location:
Washington University, St Louis, USA
Website:
http://www.obigriffith...
Twitter:
obigriffith
Scholar ID:
Google Scholar Page
Last seen:
20 hours ago
Joined:
7 years, 9 months ago
Email:
o**********@gmail.com

I am an Assistant Professor of Medicine (Oncology) and Genetics at Washington University School of Medicine and Assistant Director at the McDonnell Genome Institute. I study cancer genomics, primarily through clinical statistics and bioinformatic analyses of next-generation sequence data such as whole genome (WGS), exome, and transcriptome (RNA-seq) data.

Posts by Obi Griffith

<prev • 420 results • page 1 of 42 • next >
2
votes
0
answers
368
views
0
answers
Job: Senior Scientist (Curator) - CIViC Editor at McDonnell Genome Institute (Washington University, St Louis USA)
... **Cancer Variant Curator (Senior Scientist)** - **[Apply Now!][9]** *McDonnell Genome Institute at Washington University in St Louis, MO, USA* The position’s primary task will be assisting in the editorial maintenance and evolution of the Clinical Interpretations of Variants in Cancer knowledgebas ...
civic cancer job genomics biocuration written 4 weeks ago by Obi Griffith18k
7
votes
2
answers
656
views
2
answers
Answer: A: Paternity Testing from WGS Trio
... It is definitely *possible* to assess paternity from whole genome sequence (WGS) data. Paternity can probably be established with as little as a few dozen or maybe hundreds of well-chosen single nucleotide polymorphisms (SNPs). If you have decent WGS data you can expect to genotype millions of SNPs. ...
written 14 months ago by Obi Griffith18k
2
votes
0
answers
51k
views
0
answers
Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... postimages.org has been having some issues with their hosting service (and business model for that matter). The domain name postimg.org was apparently locked by registry. They moved to postimg.cc. Once I updated the urls they returned. BioStars developers have been informed about this as I suspect i ...
written 18 months ago by Obi Griffith18k
0
votes
0
answers
51k
views
0
answers
Comment: C: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
... Still there for me. This sounds like a BioStars or system-specific issue? ...
written 19 months ago by Obi Griffith18k
5
votes
10
answers
53k
views
10
answers
Comment: C: Database Of Tumor Suppressors And/Or Oncogenes
... I feel like, right now, the best answer to this question is the Cancer Gene Census. They currently provide a TSV download of their complete list of 567 genes with nearly all being indicated as oncogene and/or tumor suppressor (TSG). ...
written 2.3 years ago by Obi Griffith18k
0
votes
0
answers
25k
views
0
answers
Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... Please note that the trainset_gcrma.txt and testset_gcrma.txt can change over time if using different versions of the custom CDF annotations. The clindetails.txt files should be static. I don't know why that command doesn't work. It seems like there are regularly issues with GEO services failing or ...
written 2.6 years ago by Obi Griffith18k
0
votes
3
answers
11k
views
3
answers
Comment: C: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random F
... This happens because over time the custom CDF files change so that hardcoded number to eliminate AFFX (control) probes becomes incorrect. It is then possible that some of these get included in the model. We added the alternative way to remove AFFX probes in some places but missed others and this lik ...
written 2.6 years ago by Obi Griffith18k
1
vote
3
answers
11k
views
3
answers
Comment: C: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random F
... @debitboro - welcome to Biostars. The predict function will only use predictor variables that exist in the (previously trained) model that is provided. Running most recently, I get 1247 predictors after filtering the training data down from 12264 total predictors. The RF model is trained on, and onl ...
written 2.6 years ago by Obi Griffith18k
0
votes
0
answers
25k
views
0
answers
Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... All of the files can be found here: https://github.com/obigriffith/biostar-tutorials/tree/master/MachineLearning. The file you are specifically looking for could be downloaded here: https://raw.githubusercontent.com/obigriffith/biostar-tutorials/master/MachineLearning/trainset_clindetails.txt ...
written 2.6 years ago by Obi Griffith18k
0
votes
0
answers
25k
views
0
answers
Comment: C: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
... The general principles are the same but this tutorial (part 1) is really focused on preparing a datafile from microarray data. You will want to use an alternative approach to create a file that is analogous to datafile="trainset_gcrma.txt". This would be a simple matrix of gene (or transcript or oth ...
written 2.6 years ago by Obi Griffith18k

Latest awards to Obi Griffith

Appreciated 3 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Appreciated 9 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 12 months ago, created a question with more than 1,000 views. For Bioinformatics Positions In Canada (Elsewhere)
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Scholar 14 months ago, created an answer that has been accepted. For A: How to download DNA sample files in dbGap?
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Appreciated 14 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Suggesting The Removal Of Post Closing
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Bioinformatics Positions In Canada (Elsewhere)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1507 users visited in the last hour