Simone Procaccia

computational biologist | PhD student @furlonglab @embl | BSc @SapienzaRoma | MSc @UniTrento | formerly @IITalk
🇮🇹🏳️‍🌈

[Alan Murphy @Al_Murphy_]

New post w/@pkoo562: we test Enformer, Borzoi, NTv3 & AlphaGenome on K562 CRISPRi enhancers, extending Karollus 2023.
Performance has improved with newer seq2func models, but all still underpredict distal CREs. Distal perturbations remain an open problem!
https://t.co/EupR4X4cbg

[Bernardo Almeida @deAlmeida_BP]

🚀 Introducing Nucleotide Transformer v3 (NTv3)

Today, we are very excited to share our latest foundation model for biology - Nucleotide Transformer v3 (NTv3).

NTv3 is @instadeepai new multi-species genomics foundation model, designed for 1 Mb, single-nucleotide-resolution prediction, and for bridging representation learning, sequence-to-function modeling, and generative regulatory design within a single framework 🧬

This work was developed in close collaboration with @AlexanderStark8 , @volokuleshov , and @pkoo562 , and reflects several years of joint effort at the intersection of machine learning and regulatory genomics.

[Anshul Kundaje @anshulkundaje]

This is correct. High resolution temporal information will be critical to learn the causal chain of events in gene regulation especially in the presence of pervasive feedback loops & compensation mechanisms. Perturbations alone with arbitrary end points are insufficient.

[Yun S. Song @yun_s_song]

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
https://t.co/FTm3byYp67
(1/n)

[James Zou @james_y_zou]

⚡️Thrilled that #VirtualLab is published in @Nature! https://t.co/gAorOKKWy8

We created a team of AI agents to mirror my Stanford lab🤖. Led by a PI agent, the AI scientists ran their own group meetings and discovered effective binders to new CoVID variants that we validated.

The Virtual Lab is open source and can be applied to many problems! https://t.co/7RyG671EwB

👏Great job @KyleWSwanson John Pak, Wes Wu, Nash Bulaong @czbiohub @StanfordAILab @StanfordHAI

[Rongxin Fang, Ph.D. @RongxinFang]

Benchmarking computational methods for single cell ATAC-seq data. Check out SnapATAC2 - https://t.co/7FJ7U6Re6C

https://t.co/qIi0JQE19s

[Anshul Kundaje @anshulkundaje]

Great work from @lucapinello lab on a compact deep learning model that integrates sequence, DNase, H3k27ac (optionally HiC) to predict expression while learning long range effects of enhancers (against CRISPR FlowFISH expts) very well. 1/

https://t.co/6xzM0dZ8gc

[Politically Retro @political_retro]

Ferri d’Italia

#politicallyretro #fratelliditalia #capodanno #pozzolo #meme #pistola #delmastro

[Matteo Trovato @MatteTrovato23]

Seeking a cost-effective, scalable single-cell multiomic sequencing method? 🔍🧬 Meet SUM-seq: ATAC + RNA in single nuclei! Check the latest preprint from Noh and @zauggj groups @embl! Huge congrats to @sara_lobmor, @umut_yildiz12, @AnniqueC, @MikaelMarttinen, and all authors! 🎉

[The Journal of Immaterial Science @JImmatSci]

BREAKING NEWS
The 2023 #NobelPrize for Peace has been awarded to Marjorie Taylor Greene “for fostering harmony, unity and friendship between peoples in the USA". Her call for a "national divorce" has been universally received as the obvious solution to disunity in the USA.

[EMBL-EBI @emblebi]

President of @CamUniFemtech and active Bachata dancer 💃 @vlorenzi3 tells us about her fascinating PhD project to create a single-cell map of the developing human reproductive system.

https://t.co/xgQCm5GbA6

[Fascinating @fasc1nate]

Become ungovernable

[EMBL PhD Symposium @EMBLPhDSymp]

Submit your posters NOW! 🤩

Register as soon as possible and submit your abstract! We are very excited to have you all present your cool science, discuss it and network with other #PhD students

Don't miss the opportunity and submit it before the 25th of August

[antisense. @razoralign]

scover: Predicting the impact of sequence motifs on gene regulation using single-cell data https://t.co/jKpQsBeL0p

[Will Connell @wilstc]

💾🧬 Genomic foundation models have recently been a popular line of work in bio-ML. This research is further expansion of the transfer learning paradigm into biology. A few recent methods and thoughts 💾🧬

1) GPN
2) Nucleotide Transformer
3) DNA BERT 2
4) HyenaDNA

[EMBL Events @EMBLEvents]

2024 is a special year – it marks 50 years of @embl! 🥳 We've got a fantastic programme lined up for you: https://t.co/2WvLBMkbz3
Check out our 2024 EMBL Annual Poster and mark your calendars, because we're already thrilled to see you here for new events like the @EMBO | EMBL Symposium 'AI and biology' and classics such as #EESRNA 👏🏽

[Massimiliano Parente @parentetweet]

La carne coltivata non è sintetica. È come lo yogurt o la birra. Primo paese al mondo a prendere il Premio ignoranza chimica, e penalizzando la nostra ricerca e economia.

Ps: tra l’altro una molecola di vitamina C “sintetica” è identica a una molecola di vitamina C naturale. Studiate cazzo.

[Flora Vincent @vincentflora]

Somehow I’ve recently talked a lot about #imposteur #syndrome & surprised a few people saying I still had it. While making order in old boxes today this note from Nov 2010 came up, written right after Bsc degree. “I don’t know if I’m capable enough for a PhD”. 1/n

[Michael 英泉 Eisen @mbeisen]

Any p-value smaller than 1/# of atoms in universe is not an actual result - it is a problem with the hypothesis or model

[EMBL PhD Symposium @EMBLPhDSymp]

🥳REGISTRATION IS NOW OPEN!🥳

We have put together a lot of exciting topics and speakers for this year’s symposium
Register now and stay tuned to learn more about the speakers and some cool activities we have prepared
#PhD #EMBL #emblphdsymposium

https://t.co/3HaCybOIsc