Malachi Griffith

The ITCR Training Network (ITN) itcrtraining.org develops training materials for informatics and research. We have a short survey ~3-9 min about your experience & preferences for learning as a researcher. Link: xiar7j-itn.shinyapps.io/itn_follow_up/

It will also be delivered in parallel using a distributed in-person model in Saskatoon. bioinformatics.ca/workshops-all/…

Excited to announce that we will be delivering a Canadian Bioinformatics Workshop (CBW) covering RNA-seq analysis and general bioinformatics this summer in Toronto. Hosted by Ontario Institute for Cancer Research (OICR). bioinformatics.ca/workshops-all/…

Excited to announce Splam is now published in @GenomeBiology! Splam, trained on thousands of splice junctions from GTEx, is your go-to tool for scoring splice junctions from alignment or annotation files. @elapertea @StevenSalzberg1 @alan_mayonnaise doi.org/10.1186/s13059…

TCR constant region not exactly constant: "For TRBC1, ...83%...contained TRBC1∗03, 2 carried (11%) TRBC1∗01, and only a single haplotype carried TRBC1∗02. Lastly, for TRBC2, we identified 6 alleles, including 4 novel alleles..." cell.com/cell-genomics/…

@aaronquinlan @UUtah Congratulations @aaronquinlan !

When I started grad school in 2004, I never could have imagined I would write the following sentence. I am honored and thrilled to be the Chairperson of Human Genetics @UUtah! I look forward to future excellence w/ current & new scientists in our amazing department. Stay tuned!

Our featured GCBR of the Week is CIViC, a community driven resource that improves the clinical interpretation of genetic variants in cancer. Click the link to find out more : bit.ly/4dqfpCO @genome_gov #globalbiodata #openscience

Applications are open for the Advanced Sequencing Technologies & Bioinformatics Analysis course @CSHL. This intense 2wk course will immerse you in genomics technologies and teach you the fundamental computational skills you need to analyze your own data. meetings.cshl.edu/courses.aspx?c…

What's the fastest antigen-specific TCR discovery method that's practical (publicly available validated kit, <$5k per antigen, arbitrary HLA alleles)? What's better than just doing peptide+PBMC culture followed by 5'GEX+VDJ scRNA-seq?

Anyone savvy CS x immunology x genomics looking for computational work?

I am delighted to announce that I will be opening my lab on July 1 at Washington University in St Louis within the Division of Oncology, Department of Medicine, & Section of Computational Biology! @WUDeptMedicine @WashUFWIM 1/4

If you are interested in this work, please consider applying here: wustl.wd1.myworkdayjobs.com/External?q=Fol… ! 4/4

A single-cell TCR-seq method for dogs suggests reannotation of some non-functional VJ genes and differentiates between diverse repertoires of healthy dogs and expanded repertoires in malignancies: nature.com/articles/s4200… @obigriffith @WUDeptMedicine @malachigriffith

Another opportunity that crossed my desk: external-nationwidechildrens.icims.com/jobs/49731/igm… These folks are doing really cool stuff.

Sharing this exciting opportunity for a colleague. careers.ucalgary.ca/jobs/14165302-…

So...is MALAT1 even a real thing? (it's so consistently the top hit in any expression analysis, I'm curious if any studies actually isolate its functionality rather than its pervasive correlation with *everything*)

@iskander Been wondering and joking about this since grad school. Like you, I have seen it in so many DE gene lists, collaborations, publications, etc. Seems like it could be explained by a technical artifact? (e.g. very sensitive to differences in degradation between conditions)?

Such as: cloud computing, command line unix, bioinformatics tool installation, understanding NGS file formats, expression and DE analysis, pathway analysis, batch correction, R, IGV, etc. Some lectures with background principles, but a heavy emphasis on hands-on application.

Registration is now open for CBW transcriptome and single cell transcriptome analysis workshops this summer in Toronto! bioinformatics.ca/workshops/curr…. @Bioinfodotca

Highly recommend to take these two courses together as a 5-day intensive crash course in transcriptome analysis. Along the way we aim to teach fundamental bioinformatics skills with broad applicability.