@sgivan

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

 Grand Rapids, MI
github.com/sgivan
Joined May 2008
  • Tweets6.4K
  • Following1.9K
  • Followers763
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Vim After Bram: A Core Maintainer on How They’ve Kept It Going buff.ly/3QsQq8u
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Scott Givan retweeted
Liz Tseng@Magdoll19 Apr 2024
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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Liz Tseng@Magdoll17 Apr 2024
A nice review of long-read genome assemblers and its associated #bioinformatics terms sciencedirect.com/science/ar…
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Rahul Satija@satijalab17 Apr 2024
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=eQ7wzmzW… (thanks @ATCCagan for the live illustration!)
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Lior Pachter@lpachter15 Apr 2024
Another paper on utility of polygenic risk scores: nature.com/articles/s41467-0… 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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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@baym13 Apr 2024
Replying to @DaniBeckman @nquinoneso
Like, come tf on @BioRender biorender.com/academic-licen…
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Lior Pachter@lpachter14 Apr 2024
It's been great to see the positive response of @satijalab & @fabian_theis to our preprint biorxiv.org/content/10.1101/… 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/🧵

The impact of package selection and versioning on single-cell RNA-seq analysis

Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including...

biorxiv.org
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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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Rahul Satija@satijalab12 Apr 2024
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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Lior Pachter@lpachter3 Apr 2024
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🦉@JanLause3 Apr 2024
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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Lior Pachter@lpachter17 Aug 2023
This preprint is now published @PLOSCompBiol: journals.plos.org/ploscompbi… Thanks to many of you who provided suggestions / asked pertinent questions via this thread.

The specious art of single-cell genomics

Dimensionality reduction is standard practice for filtering noise and identifying relevant features in large-scale data analyses. In biology, single-cell genomics studies typically begin with...

journals.plos.org
Lior Pachter@lpachter27 Aug 2021
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/10.1101/…
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𝕐@nomad4216 Jan 2023
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 bit.ly/3vJr0Ji. 1/🧵
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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/research-in-…

Research in review: A year of growth, discovery and gratitude – Van Andel Institute

Read about Research in review: A year of growth, discovery and gratitude on Van Andel Institute – Stay updated on the latest research and groundbreaking discoveries in science and health.

vai.org
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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-cellular…

New cellular ‘clock’ offers fresh way to measure age – Van Andel Institute

Read about New cellular ‘clock’ offers fresh way to measure age on Van Andel Institute – Stay updated on the latest research and groundbreaking discoveries in science and health.

vai.org
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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-researc…
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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.
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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/s41467-0…
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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… #Rstats @Bioconductor
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CockroachDB@CockroachDB2 Nov 2022
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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