Moderator: Obi Griffith

gravatar for Obi Griffith
Obi Griffith16k
Reputation:
16,390
Status:
Trusted
Location:
Washington University, St Louis, USA
Website:
http://www.obigriffith...
Twitter:
obigriffith
Scholar ID:
Google Scholar Page
Last seen:
1 day, 8 hours ago
Joined:
6 years, 6 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 • 419 results • page 1 of 42 • next >
2
votes
1
answer
37k
views
1
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 3 months ago by Obi Griffith16k
0
votes
1
answer
37k
views
1
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 4 months ago by Obi Griffith16k
4
votes
9
answers
44k
views
9
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 12 months ago by Obi Griffith16k
0
votes
2
answers
21k
views
2
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 16 months ago by Obi Griffith16k
0
votes
3
answers
9.3k
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 16 months ago by Obi Griffith16k
1
vote
3
answers
9.3k
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 16 months ago by Obi Griffith16k
0
votes
2
answers
21k
views
2
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 16 months ago by Obi Griffith16k
0
votes
2
answers
21k
views
2
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 16 months ago by Obi Griffith16k
1
vote
2
answers
904
views
2
answers
Comment: C: Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS
... You are indeed correct that GC/AT content correlates with Alu elements. In general Alu elements seem to be correlated with more GC-rich regions, although it depends on the type/age of the Alu element (and is probably [more complicated][1] than that). Indeed the very top track in the IGV snapshot sho ...
written 18 months ago by Obi Griffith16k
2
votes
2
answers
904
views
2
answers
Comment: C: Uneven coverage correlated with Alu sequences (and discordant read pairs) in NGS
... Thanks for the comments! 1. I don't think this has to do with a general Alu repeat low complexity, low mapping quality issue. The reads in these peaks and both reads of the discordant pairs almost entirely have normal (very good) mapping qualities. In any case, if it just had to do with mapping is ...
written 18 months ago by Obi Griffith16k

Latest awards to Obi Griffith

Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Suggesting The Removal Of Post Closing
Popular Question 9 months ago, created a question with more than 1,000 views. For Bioinformatics Positions In Canada (Elsewhere)
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?
Scholar 10 months ago, created an answer that has been accepted. For A: What read lengths are produced by modern Illumina sequencers?
Popular Question 11 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Popular Question 11 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Popular Question 12 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Gold Standard 13 months ago, created a post with more than 25 bookmarks. For Analysing Microarray Data In Bioconductor
Great Question 14 months ago, created a question with more than 5,000 views. For Isaac Asimov Accurately Predicts Woes Of Bioinformatician
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How Has Bioinformatics Improved Over Time?
Appreciated 15 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Appreciated 17 months ago, created a post with more than 5 votes. For A: How Has Bioinformatics Improved Over Time?
Popular Question 17 months ago, created a question with more than 1,000 views. For Dgidb - Mining The Druggable Genome
Student 18 months ago, asked a question with at least 3 up-votes. For How Much Coverage Do We Need For An Rna-Seq Experiment?
Appreciated 19 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 21 months ago, created an answer with at least 3 up-votes. For A: How Has Bioinformatics Improved Over Time?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 978 users visited in the last hour