Vim After Bram: A Core Maintainer on How They’ve Kept It Going buff.ly/3QsQq8u
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Scott Givan
6.4K posts
Scott Givan
@sgivan
Director of the #Bioinformatics and #Biostatistics Core (@varibbc) at the Van Andel Institute (@VAInstitute) #Genomics #Metagenomics
Grand Rapids, MI Katılım Mayıs 2008
1.9K Takip Edilen762 Takipçiler
Scott Givan retweetledi
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! genomeweb.com/proteomics-pro…
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A nice review of long-read genome assemblers and its associated #bioinformatics terms
sciencedirect.com/science/articl…
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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
youtube.com/watch?v=eQ7wzm…
(thanks @ATCCagan for the live illustration!)
YouTube
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Scott Givan retweetledi
Another paper on utility of polygenic risk scores: nature.com/articles/s4146…
tl;dr: polygenic risk scores have no utility.
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RIP Lubert Stryer - his Biochemistry was my first college textbook, a gift from the lab where I had a summer job
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Scott Givan retweetledi
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.
Michael Baym@baym
@DaniBeckman @dava_keavney @nquinoneso Like, come tf on @BioRender biorender.com/academic-licen…
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It's been great to see the positive response of @satijalab & @fabian_theis to our preprint biorxiv.org/content/10.110… 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/🧵
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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.
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As my lab develops Seurat, I wanted to share some thoughts on the important Seurat and scanpy package selection preprint from @Josephmrich/@lpachter 🧵
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Scott Givan retweetledi
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?
Jan Lause 🟦 @janlause.bsky.social🦉@JanLause
tSNE/UMAP preserve neighbors in a "soft" sense: Yes, tSNE recalls only ~30% of neighbors exactly. But ~60-80% of the 10 nearest tSNE neighbors are among the 100 nearest true neighbors! So even if some tSNE neighbors are not next-door neighbors, most are "from the same block".
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This preprint is now published @PLOSCompBiol: journals.plos.org/ploscompbiol/a…
Thanks to many of you who provided suggestions / asked pertinent questions via this thread.
Lior Pachter@lpachter
It's time to stop making t-SNE & UMAP plots. In a new preprint w/ Tara Chari we show that while they display some correlation with the underlying high-dimension data, they don't preserve local or global structure & are misleading. They're also arbitrary.🧵biorxiv.org/content/10.110…
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Scott Givan retweetledi
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. vai.org/article/resear…
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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. vai.org/article/new-ce…
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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 vai.org/highly-cited-r…
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Scott Givan retweetledi
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.
insane trial balloon@KlompenGnome
@NPRinskeep @MorningEdition @NPR You mentioned this technology in the story. That's all the excuse I need to share this. 😅 The 4th largest battery in the world is in Ludington, Mich. (Also, a cool spot to visit) wzzm13.com wzzm13.com/article/news/l…
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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! nature.com/articles/s4146…
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Scott Givan retweetledi
Bioconductor 3.16 is Released. Thanks to all developers and community members for contributing to the project! Please see the full release announcement: bioconductor.org/news/bioc_3_16… #Rstats @Bioconductor
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Scott Givan retweetledi
Fun fact about @netflix: Their biggest #CockroachDB cluster is a 60-node, single-region cluster with 26.5 terabytes of data.
A closer look: cockroa.ch/3SI3buF
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