Ivan Berest

Bioinformatician Kopf lab @ETH_DBIOL | PhD @embl @zauggj group

[zack chiang @z_chiang]

7 years ago, I met a junior fellow named @JD_Buenrostro who blew me away with a vision of futuristic genomic technologies

Today, we (@ajaylabade31, @carolinecomenho) are excited to share our first steps into that future: Expansion in situ genome sequencing

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[Anna Mathioudaki @AnnaMathioudak1]

Check out our study linking T cell signatures with allo-HCT outcome in AML patients out in @BloodJournal🩸
Big thanks to everyone involved, especially to @muedequadrat and my PhD supervisors @zauggj @EMBL & C.Pabst @uniklinik_hd @MMPU_Heidelberg. 🧵(1/11)

https://t.co/SXrkQylu8I

[Christoph Schneider @ChSchneider_PhD]

Excited to share the lab’s newest work by Tilde Andersson & @XiaogangFeng on @biorxivpreprint

[Mark @Sanbomics]

RNAseq counting tools are not perfect. I simulated 240 GTEx samples to test multiple tools. Below I show the difference between actual and estimated counts for each simulated sample.

But, what is causing this? And will it affect differential expression? (1/7) #Bioinformatics

[Mikael Marttinen @MikaelMarttinen]

Happy to see the SUM-seq preprint out - our approach for scalable droplet-based single-cell ATAC+RNA (up to 1M cells, hundreds of samples)! 🧬

https://t.co/FYb0h1lQnV

[Jesse Engreitz @jengreitz]

An encyclopedia of enhancer-gene regulatory interactions in the human genome

https://t.co/lxzN7cQTGA

Very proud—4 years in the making, huge team effort.

This is a paper where the author list cannot convey everyone's incredible contributions.

My holiday highlights below:

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[Mitch Guttman @mitchguttman]

Gene expression involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. We developed ChIP-DIP – a method for simultaneous, genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. https://t.co/NEH92mQTGs

[Ilya Vorontsov @VorontsovIE]

The long-awaited update of HOCOMOCO, the database of transcription factor binding motifs, received a major update after 5 years of efforts, see https://t.co/jItL3x583a
and https://t.co/pLD2dnNaXp
/cc @halfacrocodile @ZinkevichA (1/15)

[Jonah Cool @JCoolScience]

Big News🚨: #CZCellxGene Discover Census launched today! https://t.co/GRjBDnKWS5

Built from >500 datasets, Census gives you efficient access to the largest aggregation of #SingleCell RNA data that’s immediately ready for analysis with harmonized labels for cell and gene metadata

[Aryan Kamal @AryanKamal_]

I am very happy to share my first PhD paper published in @MolSystBiol. Truly thankful to my incredible colleagues in @zauggj lab, specially @chrarnold84, @AnniqueC and @NilaServaas for their remarkable scientific insights.

[Treutlein lab @TreutleinLab]

Happy to announce #SCG2023! For the first time in the Swiss Alps! Exciting speakers! Website is up! Save-the-date: Registration opens May 2nd. https://t.co/2A2iwuHtbR @IdoAmitLab, AmosTanay, @slinnarsson, @sandberglab, @AlexandervanOu1, @MarioniLab AvivRegev @genentech, @ETH_en

[Andy Russell @AndyRusss]

Single-cell or spatial?

Our new technology - Slide-tags - allows both in the same experiment, enabling true single-cell multi-modal spatial genomics

➡️ https://t.co/i1m5T4bEme

[Ece Kartal @ps_ecekartal]

My village in malatya as all other cities is heavily damaged. We need your help for water, food, tent and all other essentials. I was visiting my family and still here. Please help us spread the word and make a donation. https://t.co/OiH4a8GUBe #DEPREMOLDU #turkeyearthquake2023

[Julia Joung @JuliaJoung]

Thrilled to share my primary PhD work: a Transcription Factor Atlas for understanding gene regulation and cell engineering @CellCellPress. We created a comprehensive TF ORF library and applied it to profile resulting expression changes. A thread 1/X https://t.co/PPcJ0HZEsW

[bioRxiv Bioinfo @biorxiv_bioinfo]

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks https://t.co/ntp58klcyd #biorxiv_bioinfo

[Rong Fan @RongFan8]

Here comes "spatial-ATAC-seq"!!! A wonderful collaboration between my lab at @YaleSEAS and @GoCasteloBranco at @karolinskainst

#epigenetics #spatialomics #spatialbiology

Spatial profiling of chromatin accessibility in mouse and human tissues | Nature https://t.co/7eSUb08IGN

[Vinay Kartha @vkartha88]

Excited to share some of my postdoc work surrounding the development of a computational framework to help derive gene regulatory networks, which we apply to determine drivers of immunogenic response in blood, officially out in @CellGenomics!

https://t.co/nYrCzNhJqn

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

New version of our comparison of transformations for single-cell data is on https://t.co/WvBINrR7lB 🥳🎉
We completely revised the paper. Across three benchmarks, we show that, despite its theoretical shortcomings, no transformation consistently outperforms log(y/s + 1) 🤯

[Min Dai @artofbiology]

Characterizing cis-regulatory elements using single-cell epigenomics | Review https://t.co/Jf6BNiwuk5

[Science Immunology @SciImmunology]

New research explores what happens to resident alveolar macrophages in the lungs of mice following influenza infection. @ETH_en @UZH_en

➡️ https://t.co/sJFlqkRlzz