Simon Anders

94 posts

Simon Anders

@s_anders_m

Bioinformatics/Biostatistics Researcher @[email protected]

Heidelberg, Germany Katılım Temmuz 2016

137 Takip Edilen828 Takipçiler

Simon Anders retweetledi

Constantin Ahlmann-Eltze (@const-ae.bsky.social)@const_ae·21 Eyl

Great thread by Anshul, one of the pioneers of deep learning for biology, summarizing our preprint!

Anshul Kundaje@anshulkundaje

biorxiv.org/content/10.110… Nice benchmark of single cell "foundation models" (scGPT, scFoundation) and GEARS (a GNN model) further hyped as "virtual cell models" against linear baselines on perturbation prediction. Long-story short: they can't beat the linear baselines. 1/

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Simon Anders retweetledi

Constantin Ahlmann-Eltze (@const-ae.bsky.social)@const_ae·20 Eyl

This is the result of my brief postdoc with @s_anders_m in the last 6 months and grew out of an intriguing reviewer comment for the LEMUR paper with @wolfgangkhuber.

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Constantin Ahlmann-Eltze (@const-ae.bsky.social)@const_ae·20 Eyl

There's a lot of excitement about foundation models and their ability to learn biology 🧬💻 But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress. biorxiv.org/content/10.110…

Constantin Ahlmann-Eltze (@const-ae.bsky.social) tweet media

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Simon Anders@s_anders_m·23 Eyl

New preprint from our group:

Constantin Ahlmann-Eltze (@const-ae.bsky.social)@const_ae

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Simon Anders retweetledi

Martin-Villalba Lab@molneurolab·5 Eyl

🎉 Excited to share our latest study in @nature, showing that DNA🧬 #methylation is key to stemness in the adult #brain: nature.com/articles/s4158… A collaboration with @s_anders_m, driven by @LPMKremer and @SCerrizuela. #epigenetics #neuroscience #singlecell. Pre-print summary 🧵👇

Martin-Villalba Lab@molneurolab

We're excited to share our latest preprint where we use #singlecell #multiomics to show that stemness is encoded in the methylome of neural #stemcells (NSC) in the adult #brain 🐁🧠 #epigenetics #neuroscience #biorxiv_neursci 👉doi.org/10.1101/2022.0… 🧵1/9

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Nature Methods@naturemethods·31 Tem

And read the Research Briefing here: nature.com/articles/s4159…

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Nature Methods@naturemethods·31 Tem

.@LPMKremer, @molneurolab, @s_anders_m and colleagues introduce a data processing approach along with an easy-to-use software tool MethSCAn for scBS-seq data analysis. nature.com/articles/s4159…

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Simon Anders retweetledi

Martin-Villalba Lab@molneurolab·19 Eyl

We're so excited to share our latest work “Identification of astrocyte-driven pseudolineages reveals clinical stratification and therapeutic targets in #Glioblastoma” spearheaded by @OghuzhanKaya on the wet & @LCForst on the dry lab as a preprint @Biorxiv biorxiv.org/content/10.110…

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Simon Anders retweetledi

Nirmalya Kajuri@Kaju_Nut·3 Haz

Physicist Suvrat Raju shared this letter he sent to an editor of Nature Communications, declining to referee for them.

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Retraction Watch@RetractionWatch·13 Nis

“Is Science Self-Correcting? Evidence from 5 Recent Papers on the Effect of Replications on Citations.” replicationnetwork.com/2023/04/05/ree…

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Simon Anders retweetledi

Samuel Corless@sam_corless·16 Mar

Thanks chromatin community! We’ve been digging around in your repetitive DNA (>40,000 ChIP-seq samples) and have discovered a totally unexpected role for BRD4 and JQ1 at centromeres. Very happy to share our preprint. biorxiv.org/content/10.110…

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Simon Anders@s_anders_m·27 Şub

PhD and postdoc postions for computational biologists, in the labs of @s_anders_m (me) and @molneurolab (A. Martin-Villalba): Single-cell omics methods in neurobiology. dkfz.de/en/neurobiolog…

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Simon Anders@s_anders_m·27 Şub

Life science postdoc positions in Heidelberg: health-life-sciences.de/postdocs

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Simon Anders retweetledi

Martin-Villalba Lab@molneurolab·13 Eyl

@LPMKremer presenting our latest study on epigenetic features of adult neural stem cells at #TCESRC22 on Sicily 🌅, organized by @BrunetLab and @giacomo_cavalli.

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Simon Anders@s_anders_m·29 Tem

Proud to present this work by @LPMKremer, @SCerrizuela et al. from @molneurolab and our group:

Martin-Villalba Lab@molneurolab

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Simon Anders retweetledi

Felix Frauhammer@FelixFrauhammer·14 Haz

cellpypes - cell type pipes for R. Annotate scRNAseq data manually with simple rules:

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Simon Anders retweetledi

Dan Goodman@neuralreckoning·26 May

The current system of journals and peer review is not serving science. I have therefore resigned from all editorial roles and will no longer do pre-publication peer review. I explain why in this article and in the thread below. Please consider joining me. neural-reckoning.org/reviewing.html

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Simon Anders@s_anders_m·6 May

@mikelove @slavov_n @MorseCell anders-biostat.github.io/sleepwalk/

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Michael Love@mikelove·6 May

@slavov_n @MorseCell @s_anders_m had some software in this direction I believe

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Prof. Nikolai Slavov@slavov_n·5 May

Sometimes very large distances on tSNE / UMAP plots are quantitatively interpreted. Such interpretations are not meaningful. How do we communicate this more clearly? Shall we add a similarity distance scale to all such plots?

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Simon Anders@s_anders_m·14 Nis

Just started using @TrostNils's R package for plotting 3D scatter points (and more). It's very convenient, powerful and useful.

Nils Trost@TrostNils

babyplots - my tool for interactive 3D plots - is now available at bp.bleb.li! Available as a #JavaScript library, an #RStats package, a #PowerPoint add-in and as in interactive creator. Check out some examples: bp.bleb.li/viewer?p=E-WVj

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Keşfet

@Nature @LPMKremer @SCerrizuela @molneurolab @OghuzhanKaya @lcforst @biorxiv @BrunetLab