Scott Givan

Director of the #Bioinformatics and #Biostatistics Core (@varibbc) at the Van Andel Institute (@VAInstitute) #Genomics #Metagenomics

[Scott Givan @sgivan]

Vim After Bram: A Core Maintainer on How They’ve Kept It Going https://t.co/sEOhllfver

[Liz Tseng @Magdoll]

Use of Tomahto, a new targeted mass spec method, combined with @PacBio Kinnex full-length RNA data to to increase detection of isoforms that are turned into proteins - the first step into a personalized proteome. Great work from @GSheynkman lab! https://t.co/YdQFWjyhob

[Liz Tseng @Magdoll]

A nice review of long-read genome assemblers and its associated #bioinformatics terms

https://t.co/XbfaHGTMLv

[Rahul Satija @satijalab]

My overview talk from Single Cell Genomics Day 2024, covering our favorite new technologies and computational methods for the single-cell/spatial field, is now online at
https://t.co/SvdDLzFu0c

(thanks @ATCCagan for the live illustration!)

[Lior Pachter @lpachter]

Another paper on utility of polygenic risk scores: https://t.co/bZOYlJ0rhP

tl;dr: polygenic risk scores have no utility.

[Richard Sever @cshperspectives]

RIP Lubert Stryer - his Biochemistry was my first college textbook, a gift from the lab where I had a summer job

[Will Ratcliff @wc_ratcliff]

Time to ditch @BioRender? I had no idea they were claiming copyright to the figures we make with it, even after we pay for use of the service.

[Lior Pachter @lpachter]

It's been great to see the positive response of @satijalab & @fabian_theis to our preprint https://t.co/dKzVFb9z2y on Seurat & Scanpy, and their commitment to work to improve transparency of their tools. One immediate benefit will be better practice of PCA in genomics. 1/🧵

[Peter W. Laird (@peterwlaird.bsky.social) @peterwlaird]

Yesterday we lost our wonderful friend Ilya @ISB_Shmulevich. Ilya was an amazingly creative scientist and incredibly generous colleague. He displayed extraordinary courage in his battle against AML, while remaining upbeat and living life to its fullest. We will miss him dearly.

[Rahul Satija @satijalab]

As my lab develops Seurat, I wanted to share some thoughts on the important Seurat and scanpy package selection preprint from @Josephmrich/@lpachter 🧵

[Lior Pachter @lpachter]

Yes another analysis showing how poor t-SNE and UMAP are. Only 60% of the ten nearest neighbors are even among the 100 nearest neighbors in high dimension.

How many such demonstrations will it take to convince people to abandon these plots?

[Lior Pachter @lpachter]

This preprint is now published @PLOSCompBiol: https://t.co/mJlPu9u6t7

Thanks to many of you who provided suggestions / asked pertinent questions via this thread.

[𝕐 @nomad421]

Are you interested in performing splice-aware quantification of your #scrnaseq data, obtaining unspliced, spliced, and ambiguous UMI counts quickly & in <3GB of RAM? If so, check out the new manuscript by @DongzeHe, @CSoneson and me on #bioRxiv https://t.co/07iGAXn5xz. 1/🧵

[Van Andel Institute (VAI) @VAInstitute]

Research in review: 2022 was a year of growth, discovery and gratitude at Van Andel Institute, and we are looking forward to another year filled with the same bright hopes for the future of science, medicine and education. https://t.co/2R97oDtPQD

[Van Andel Institute (VAI) @VAInstitute]

Can parts of our bodies age faster than others? The answer is yes, and Van Andel Institute scientists @JamieEndicott, Paula Nolte, @shenhui1986 & @peterwlaird have developed a new way to measure exactly how. https://t.co/EZ79U72Myd

[Van Andel Institute (VAI) @VAInstitute]

Congratulations to Dr. Peter W. Laird (@peterwlaird) and Dr. Russell Jones (@DrRGJonesLab), who were named to the 2022 @Clarivate Highly Cited Researchers list! See more at https://t.co/2NLx9EC9IH

[Steve Inskeep @NPRinskeep]

Thank you for sharing this. That’s a big battery! Imagine what it’s like when you have to run to the drugstore to buy a fresh one.

[Peter W. Laird (@peterwlaird.bsky.social) @peterwlaird]

Our #epigenetics paper in Nature Communications is out with experimental evidence that DNA methylation loss in #aging and #cancer is caused by cell division. Congrats to @JamieEndicott, Paula Nolte, @shenhui1986 and @VAInstitute! https://t.co/Fr8Zd5e4qx

[Bioconductor @Bioconductor]

Bioconductor 3.16 is Released. Thanks to all developers and community members for contributing to the project! Please see the full release announcement: https://t.co/SqNN5UPe9S #Rstats @Bioconductor

[CockroachDB @CockroachDB]

Fun fact about @netflix: Their biggest #CockroachDB cluster is a 60-node, single-region cluster with 26.5 terabytes of data.

A closer look: https://t.co/6u1EzbnA9H