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Lev Tsypin, PhD

@ltsyp.in

・Postdoc working on weirdo microalgae ・Bigger than any known bacterium ・Views represent trillions of little cells ・🌐 https://ltsyp.in ・🌈🦠🔬🌱🌏

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Lev Tsypin, PhD@ltsyp.in · last yr.

I started this work 10 years ago as an undergrad in a "Computing for Biologists" class, and now it's finally out in the world! I'm very proud for it to be my first contributing author paper. This work focuses on predicting and testing gene functions based on their co-expression, but there's more:

Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila

Abstract. Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bi

doi.org

Lev Tsypin, PhD@ltsyp.in · 2y ago

All of my old grievances and resentment toward faculty and administrators who asserted that science isn't political is bubbling to the surface.

Chenxin Li, PhD@chenxinli2.bsky.social · 2y ago

Had a great time talking to @atinygreencell.bsky.social abt my PhD work - small RNA transcriptome of rice gametes & zygotes. Please give his channel a follow. This podcast series of Sebastian is a great idea, and I found all previous episodes informative/inspirational. I hope mine is as well.

Sebastian S. Cocioba@atinygreencell.bsky.social · 2y ago

Tears In Rain Episode 6 is live!! I hung out with another favorite plant biologist of mine, @chenxinli2.bsky.social, where he regaled us with stories of his complex PhD project, pushing our understanding of the floral developmental transcriptome a bit further. Enjoy! www.youtube.com/watch?v=vWj4...

Lev Tsypin, PhD@ltsyp.in · 2y ago

Grad school interview season is starting, and Sebastian's collecting biology PhD stories that I wish I had heard when I was figuring out where I should go. 🧪 It was a pleasure to share my experience--if I can help anyone think through things, please send me a message!

Sebastian S. Cocioba@atinygreencell.bsky.social · 2y ago

Episode 4 of Tears In Rain is live!!! In this episode I hung out with Lev Tsypin (@ltsyp.in) and we talked about his adventures in microbiology during the pandemic and all the struggles that came with it. A nice dive into his project and lots of wisdom shared. Enjoy! youtu.be/ucSORPmTrl0

Lev Tsypin, PhD@ltsyp.in · 2y ago

It's now formatted more-or-less correctly!

Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila

Although an established model organism , Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datas...

doi.org

Lev Tsypin, PhD@ltsyp.in · 2y ago

My first last-author paper is out as a preprint! 🧪 "Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila" I wanted to wait til bioRxiv finished formatting it, but I couldn't! www.biorxiv.org/content/10.1...

Graphical abstract for my paper, showing a flowchart of how we consolidated microarray and RNA-seq gene expression data to generate informative co-expression clusters. The steps are: alignment to the newest genome model, gene filtering and quality control, expression normalization and averaging, clustering the high-dimensional dataset, performing parameter scans and computational negative controls, and building an interactive tool for data exploration.
Lev Tsypin, PhD@ltsyp.in · 2y ago

When a journal rejects your manuscript but recommends that you transfer it to a subsidiary, how do you decide whether to do it or send the paper somewhere else?

Elisabeth Bik@elisabethbik.bsky.social · 2y ago

Infamous paper that popularized unproven COVID-19 treatment finally retracted Study on hydroxychloroquine by Didier Raoult and colleagues gets pulled on ethical and scientific grounds @cathleenogrady.bsky.social reports. www.science.org/content/arti...

Infamous paper that popularized unproven COVID-19 treatment finally retracted

Study on hydroxychloroquine by Didier Raoult and colleagues gets pulled on ethical and scientific grounds

science.org

Lev Tsypin, PhD@ltsyp.in · 2y ago

My first last-author paper is out as a preprint! 🧪 "Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila" I wanted to wait til bioRxiv finished formatting it, but I couldn't! www.biorxiv.org/content/10.1...

Graphical abstract for my paper, showing a flowchart of how we consolidated microarray and RNA-seq gene expression data to generate informative co-expression clusters. The steps are: alignment to the newest genome model, gene filtering and quality control, expression normalization and averaging, clustering the high-dimensional dataset, performing parameter scans and computational negative controls, and building an interactive tool for data exploration.
Simon Fisher@profsimonfisher.bsky.social · 2y ago

In a @currentbiology.bsky.social paper earlier this year, led by @laurawesseldijk.bsky.social, we analysed Beethoven’s genome with a polygenic index related to musicality, as a way to communicate limits of genetic predictions at the individual level & the complexity of links between DNA & behaviour:

Notes from Beethoven’s genome

Wesseldijk et al. compare the genomic information collected from Ludwig van Beethoven with population-based datasets used to quantify musical achievement.

cell.com

Chanda Prescod-Weinstein 🌌@chanda.blacksky.app · 2y ago

This article, which contains not one critical commentator and reads like a press release, is a shocking dereliction of duty from one of our leading scientific publications 🧪 🔭

Keith Smith@drkeithsmith.bsky.social · 2y ago

Finance billionaire & private astronaut Jared Isaacman has been nominated as the next head of Nasa. How might he approach the job, and what challenges await him? Here’s the @science.org report 🧪🔭🚀 www.science.org/content/arti...

Lev Tsypin, PhD@ltsyp.in · 2y ago

In my circle, people are having important conversations about defending institutions, and I think that it's important to discuss more thoroughly how we define what we mean. Specifically, in the case of academia, I think the modern US university is at least three different things: