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Reposted by Robin Andersson

xuening-he.bsky.social @xuening-he.bsky.social · Jun 26

Excited to share DeepCompARE + ISA - a lightweight deep learning model + efficient interpretation method, to uncover rules of TF cooperativity via genome-wide in silico motif ablations!

Preprint: www.biorxiv.org/content/10.1...
Github: github.com/anderssonlab...

Genome-wide rules of transcription factor cooperativity revealed through in silico binding site ablation

Transcription factor (TF) cooperativity plays a critical role in gene regulation. However, the underlying genomic rules remain unclear, calling for scalable methods to characterize the TF binding site...

www.biorxiv.org

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Robin Andersson @randersson.bsky.social · Jun 26

Latest from the lab! Led by @xuening-he.bsky.social, establishing a framework for interpretation of the motif syntax of regulatory elements and a quantitative model for transcription factor cooperativity. Plenty of cool stuff revealed, including TF redundancy and synergy, and their regulatory roles!

xuening-he.bsky.social @xuening-he.bsky.social · Jun 26

Excited to share DeepCompARE + ISA - a lightweight deep learning model + efficient interpretation method, to uncover rules of TF cooperativity via genome-wide in silico motif ablations!

Preprint: www.biorxiv.org/content/10.1...
Github: github.com/anderssonlab...

Genome-wide rules of transcription factor cooperativity revealed through in silico binding site ablation

Transcription factor (TF) cooperativity plays a critical role in gene regulation. However, the underlying genomic rules remain unclear, calling for scalable methods to characterize the TF binding site...

www.biorxiv.org

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Reposted by Robin Andersson

Denis Duboule @denisduboule.bsky.social · Mar 17

Symposium on ‘Enhancer Sequences’ at beautiful @collegedefrance.bsky.social in Paris, by April 11th. Open and free, no registration. Come to relax listening to facts #TherapeuticEffects #VillageGauloix Final programme below. Tell your friends! 🙏🤘

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Reposted by Robin Andersson

Robin Andersson @randersson.bsky.social · Feb 6

Job alert!

We are hiring a postdoc or PhD student focusing on
* developing computational methods to resolve gene regulation in single cells
* investigating the mechanisms and cell-type specific effects of genetic variants

PhD student: bsky.app/profile/jobr...

Postdoc: bsky.app/profile/jobr...

jobRxiv @jobrxiv.org · Feb 6

PhD student – Computational modeling of gene regulation in single cells #ScienceJobs #AcademicSky jobrxiv.org/job/univ...

PhD student - Computational modeling of gene regulation in single cells

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobrxiv.org

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Robin Andersson @randersson.bsky.social · Feb 6

Job alert!

We are hiring a postdoc or PhD student focusing on
* developing computational methods to resolve gene regulation in single cells
* investigating the mechanisms and cell-type specific effects of genetic variants

PhD student: bsky.app/profile/jobr...

Postdoc: bsky.app/profile/jobr...

jobRxiv @jobrxiv.org · Feb 6

PhD student – Computational modeling of gene regulation in single cells #ScienceJobs #AcademicSky jobrxiv.org/job/univ...

PhD student - Computational modeling of gene regulation in single cells

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobrxiv.org

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Reposted by Robin Andersson

Jeremy Faust, MD @jeremyfaust.bsky.social · Feb 1

BREAKING NEWS: CDC orders mass retraction and revision of submitted research across all science and medicine journals. Banned terms must be scrubbed.

Goes beyond MMWR +other CDC pubs. Applies to research already submitted to top medical journals.

Take a look.
open.substack.com/pub/insideme...

BREAKING NEWS: CDC orders mass retraction and revision of submitted research across all science and medicine journals. Banned terms must be scrubbed.

Any unpublished manuscript mentioning certain topics, including gender and "LGBT," must be pulled or revised.

open.substack.com

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Reposted by Robin Andersson

Rada-Iglesias Lab @radaiglesiaslab.bsky.social · Jan 31

Together with @smandrup.bsky.social and Minna Kaikkonen we are happy to announce the 3rd Edition of the EMBO Workshop on #Enhancers and #Enhanceropathies. This time we will meet during the beautiful Danish summer (June 16-21).

Book the dates and register soon!!!

meetings.embo.org/event/25-enh...

Enhancer Mechanics and Enhanceropathies

Join us for the highly anticipated third EMBO workshop on Enhancer Mechanics and Enhanceropathies! Building on the success of our previous meetings in Santander (2021) and Marseilles (2023), this eve…

meetings.embo.org

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Reposted by Robin Andersson

Yan Hu @yanhu97.bsky.social · Jan 23

Super excited to share our new study from the @jbuenrostro.bsky.social Lab in @nature.com! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning.
Paper: www.nature.com/articles/s41...

Multiscale footprints reveal the organization of cis-regulatory elements - Nature

We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.

www.nature.com

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Reposted by Robin Andersson

Yoav Gilad @ygilad.bsky.social · Jan 17

My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you could help spread the word, and I’d love to hear your thoughts and feedback. I hope people will find it useful.

It’s available on Amazon: tinyurl.com/mx2hewen

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Robin Andersson @randersson.bsky.social · Jan 17

This looks great! Just ordered.

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Reposted by Robin Andersson

Anshul Kundaje @anshulkundaje.bsky.social · Dec 25

Our ChromBPNet preprint out!

www.biorxiv.org/content/10.1...

Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/

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Reposted by Robin Andersson

Sebastian Bae @sebastianbae.bsky.social · Dec 22

We are pursuing the wrong applications for AI.

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Reposted by Robin Andersson

Bluesky @bsky.app · Dec 3

Scientists, academics, researchers: We’re excited to share that @altmetric.com is now tracking mentions of your research on Bluesky! 🧪

Altmetric @altmetric.com · Dec 3

There are already many articles for which there is more attention on Bluesky than on other comparable micro-blogging sites, meaning the academic community and the general public have clearly adopted Bluesky as one of its core places to disseminate and discuss new research.

A Place of Joy.

‘A place of joy’: why scientists are joining the rush to Bluesky
Researchers say the social-media platform — an alternative to X — offers more control over the content they see and the people they engage with.: https://www.nature.com/articles/d41586-024-03784-6

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Reposted by Robin Andersson

Duncan Sproul @sproullab.bsky.social · Nov 26

I'd suggest this starter pack for #epigenetics and #generegulation:
go.bsky.app/TKp9YAn
plus see the description for another 3!

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Reposted by Robin Andersson

Jesse Engreitz @jengreitz.bsky.social · Nov 25

Introducing scE2G: a new model to link enhancers to target genes using single-cell data.

Excited that scE2G will enable building enhancer maps in hundreds of cell types in the human body!

Wonderful collaboration with @randersson.bsky.social @613weilin.bsky.social @mayayayas.bsky.social

Thread👇

Wei-Lin Qiu @613weilin.bsky.social · Nov 25

Excited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks.

biorxiv.org/cgi/content/...

Read more below!

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Mapping enhancer-gene regulatory interactions from single-cell data

Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interac...

biorxiv.org

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Reposted by Robin Andersson

Jesse Engreitz @jengreitz.bsky.social · Nov 25

Our preprint:

Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart

Multiomic atlas + human genetics = new cell types, genes, and pathways that influence heart development and disease

www.medrxiv.org/content/10.1...

Thread 👇

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Reposted by Robin Andersson

Rosa Ma @rosaxma.bsky.social · Nov 25

What cell types drive congenital heart defects (CHD)?

Some new answers in our latest preprint, where we explored:
1). Key cell types contributing to CHD genetics
2). Impact of noncoding variants on CHD risk

https://www.medrxiv.org/content/10.1101/2024.11.20.24317557v1

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Robin Andersson @randersson.bsky.social · Nov 25

Check out some highlights of the work here bsky.app/profile/613w...

Wei-Lin Qiu @613weilin.bsky.social · Nov 25

Excited to share our latest preprint on scE2G – a new model to link enhancers to target genes using single-cell data – with state-of-the-art performance across multiple perturbation benchmarks.

biorxiv.org/cgi/content/...

Read more below!

1/12

Mapping enhancer-gene regulatory interactions from single-cell data

Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interac...

biorxiv.org

2

Robin Andersson @randersson.bsky.social · Nov 25

Check out our latest work, scE2G, for mapping the target genes of enhancers from single cell data! www.biorxiv.org/content/10.1...

Amazing work led by co-first authors @mayayayas.bsky.social and @613weilin.bsky.social in a great collaboration with @jengreitz.bsky.social's lab

See 🧵 by Wei-Lin ⬇️

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Reposted by Robin Andersson

Kaur Alasoo @kauralasoo.bsky.social · Nov 20

For an idea of how well fine mapping results replicate between biobanks, I would really recommend checking out this preprint from @masakanai.bsky.social
www.medrxiv.org/content/10.1...

Insights from complex trait fine-mapping across diverse populations

Despite the great success of genome-wide association studies (GWAS) in identifying genetic loci significantly associated with diseases, the vast majority of causal variants underlying disease-associat...

www.medrxiv.org

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Robin Andersson @randersson.bsky.social · Nov 16

Thanks! Glad you liked the talk. Feel free to share as you wish.

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Robin Andersson @randersson.bsky.social · Nov 14

Saturday morning: first session, second talk

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Robin Andersson @randersson.bsky.social · Nov 13

Looking forward to #cshldata24 meeting starting tonight!

I will present #scE2G, a highly accurate model for mapping enhancer-gene regulatory interactions from single cell data. The model was developed in close collaboration with @jengreitz.bsky.social lab.

Who else is attending the meeting?

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Robin Andersson @randersson.bsky.social · Nov 13

Seeing all the excitement from fellow scientists moving from X to here reminds me of academic Twitter 10 years ago. Let’s try out this platform!

I’m a computational genomicist focused on modeling gene regulation.

#firstpost #helloworld #introduction

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