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Joana Pereira @joanampereira.bsky.social · Jun 16

If you are at PASC25 this year, go listen to Reto talk about his master thesis work on rescaling GCsnap2. It was awesome to have Reto with us last year and collaborate so close with the @cflorina.bsky.social and @dmi-hpc.bsky.social to make our tool even more useful!

HPC Group @ Uni Basel @dmi-hpc.bsky.social · Jun 16

🎤 Excited to present our paper "Scalable Genomic Context Analysis with GCsnap2 on HPC Clusters" today at PASC25.
📍Room 6.0D13, FHNW Campus Brugg-Windisch
📅 17:00, June 16, 2025
📄 Check out the preprint: arxiv.org/abs/2505.02195

@joanampereira.bsky.social
@cflorina.bsky.social
@dmi.unibas.ch

An Autonomy Loop for Dynamic HPC Job Time Limit Adjustment

High Performance Computing (HPC) systems rely on fixed user-provided estimates of job time limits. These estimates are often inaccurate, resulting in inefficient resource use and the loss of unsaved w...

arxiv.org

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Reposted by Joana Pereira

PSB_Grenoble @psb-grenoble.bsky.social · May 27

🧬Great lineup of speakers!
@rommieamaro.bsky.social @jessicaandreani.bsky.social @gauravbhardwaj.bsky.social @bonomimax.bsky.social @rocovino.bsky.social @bioinfo.se Sergei Grudinin @magistratolab.bsky.social Christine Orengo @joanampereira.bsky.social Maya Topf, Sameer Velankar, Basile Wicky

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Reposted by Joana Pereira

Vojtech Spiwok @spiwokv.bsky.social · May 20

Joana Pereira @joanampereira.bsky.social on protein annotation by AI #ML4NGPVilnius

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Reposted by Joana Pereira

Gemma C. Atkinson @gemmaatkinson.bsky.social · May 19

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · May 17

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes https://www.biorxiv.org/content/10.1101/2025.05.14.653371v1

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Reposted by Joana Pereira

VIB.AI @vibai.bsky.social · May 6

VIB.AI's International PhD call is now open!
https://tinyurl.com/53nc9vnd

If you're interested in applying AI to biology, take a look at the PhD projects across our labs.

🗓️ Deadline: June 22nd

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Joana Pereira @joanampereira.bsky.social · Apr 26

Come join us in Leuven or Ghent 😎

VIB.AI @vibai.bsky.social · Apr 25

We are looking for additional Group Leaders to join the growing computational biology community at VIB.

If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!

https://vib.ai/en/opportunities#/job-description/110906

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Joana Pereira @joanampereira.bsky.social · Mar 27

So honoured and excited for being awarded a FWO Odysseus grant! This means, the Pereira lab will be hiring soon. Stay tuned 😃

VIB.AI @vibai.bsky.social · Mar 27

Congratulations to @joanampereira.bsky.social on being awarded a prestigious FWO Odysseus grant! 🙌

The grant will power the growth of her newly established lab at VIB.AI and the KU Leuven Department of Cellular and Molecular Medicine.

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Reposted by Joana Pereira

Biozentrum, University of Basel @biozentrum.unibas.ch · Mar 20

Apply now for our international Master of Science in Physics of Life @biozentrum.unibas.ch @unibasel.ch! Scholarships available.

More information: www.biozentrum.unibas.ch/education/de...

#Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland

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Reposted by Joana Pereira

Stein Aerts @steinaerts.bsky.social · Feb 28

Review alert - "Modelling and design of transcriptional enhancers" by Seppe and Vasilis 👇

Seppe De Winter @seppedewinter.bsky.social · Feb 28

We wrote a review article on modelling and design of transcriptional enhancers using sequence-to-function models.

From conventional machine learning methods to CNNs and using models as oracles/generative AI for synthetic enhancer design!

@natrevbioeng.bsky.social

www.nature.com/articles/s44...

Modelling and design of transcriptional enhancers - Nature Reviews Bioengineering

Enhancers are genomic elements critical for regulating gene expression. In this Review, the authors discuss how sequence-to-function models can be used to unravel the rules underlying enhancer activit...

www.nature.com

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Joana Pereira @joanampereira.bsky.social · Feb 28

Congratulations Santiago!! I am so happy for you and so much looking forward to see the fruits of your lab in Geneva 😃😃

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Joana Pereira @joanampereira.bsky.social · Feb 24

Hopefully a lot of cool science will come out of here for many many years 🌌 Let the journey begin 🚀🧑‍🚀👩‍🏫 @vibai.bsky.social @kuleuvenuniversity.bsky.social

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Joana Pereira @joanampereira.bsky.social · Dec 17

Oh yeah!! Congratulations 🍻🎉🥂🤓

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Reposted by Joana Pereira

Jerome Eberhardt @jeeberhardt.bsky.social · Dec 9

For future reference, this is the slide (without the bottom cropped) that should have been posted here. Boltz-1 and AF3 are actually performing similarly on the Chymase and Mpro datasets, and differ only on the Autotaxin dataset for still unknown reasons.

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Joana Pereira @joanampereira.bsky.social · Nov 25

Full house today for Bruno's talk today at our BC2 seminar series @biozentrum.bsky.social

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Reposted by Joana Pereira

VIB.AI @vibai.bsky.social · Nov 20

Full house and a filled schedule today. Some snapshots of the last session of the day, with talks by @benlehner.bsky.social, David Kelley and Tanja Kortemme. 📸 #VIBAIsymposium

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Reposted by Joana Pereira

VIB.AI @vibai.bsky.social · Nov 20

Fantastic start of the #VIBAIsymposium this morning with a welcome by our scientific director @steinaerts.bsky.social and talks by Julien Gagneur and @avsecz.bsky.social

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Reposted by Joana Pereira

VIB.AI @vibai.bsky.social · Nov 20

Good morning! Ready to welcome you at #VIBAIsymposium.

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Reposted by Joana Pereira

Eileen Furlong @eileen-furlong.bsky.social · Nov 18

My first post on Blue Sky - moving over !

For all post-docs out there - fantastic opportunity @EMBL. Independent group leader position: Core funding, state-of-the-art core facilities, access to fantastic Ph.D. students, and of course amazing colleagues. Please apply www.embl.org/jobs/positio...

EMBL Jobs

We offer a wide range of challenging scientific and non-scientific positions at all of our European locations and encourage applications from international candidates at all career levels.

www.embl.org

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Reposted by Joana Pereira

Renato Ostuni @ostunilab.bsky.social · Nov 17

With the deluge of new friends - if you are or know someone who is a looking for a position as computational scientist (any level) in #pancreaticcancer, #macrophages #spatialbiology #singlecell... we might have something for you. Will also consider wet lab ppl, send email if interested. pls repost!

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Reposted by Joana Pereira

Daniel Álvarez Salmoral @alvarezsalmoral.bsky.social · Nov 17

I haven’t come across this starter pack yet, so I made one! 👉 Check out the "Protein Prediction & Design" Starter Pack and join the conversation.

Think someone should be included? Tag them below! 👇

🧬🧶
go.bsky.app/C1oNcnj

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Reposted by Joana Pereira

Mackenzie Weygandt Mathis @trackingactions.bsky.social · Nov 16

I’m happy to support an AI Fellow at EPFL in my group! ⬇️

Aside from our applied #AI4Science work, we are excited to push on fundamental problems in #ML

Here is some recent fundamental work: arxiv.org/abs/2410.10744 & sslneurips23.github.io/paper_pdfs/p...

www.epfl.ch/research/fun...

EPFL AI Center Postdoctoral Fellowships

The EPFL AI Center Postdoctoral Fellowship call for proposals is now open with a deadline on 29 November 2024 (17:00 CET).Applications are encouraged from researchers at the postdoctoral level with a ...

www.epfl.ch

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Joana Pereira @joanampereira.bsky.social · Nov 16

This was way back when I was still using pipettes. I was helping a PhD student filling in a box of tips and when it was almost full, pushed it too hard and spilled them all on the floor 🙈

Joana Pereira @joanampereira.bsky.social · Nov 16

🚨The future Pereira lab is hiring!

We will start at @vibai.bsky.social in Feb 2025 and are looking for a postdoc to join our team 🤓

If you want to leverage AI and large networks to explore and understand the protein universe 🌌, check below!

*deadline: 21 Nov 2024*

jobs.vib.be/j/93314/post...

Postdoc in Protein Computational Biology / Structural Bioinformatics - VIB

Job description We are seeking a postdoc to join the Pereira Lab for an interdisciplinary project that integrates structural bioinformatics, protein evolution, complex network analysis, and deep learn...

jobs.vib.be

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Reposted by Joana Pereira

Gonzalo Parra @gonzaparra.bsky.social · Nov 19

We have a great list of already confirmed speakers and keynotes! Deadline for abstracts: December 15!
www.iscb.org/3dbioinfo202...

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Reposted by Joana Pereira

Gonzalo Parra @gonzaparra.bsky.social · Nov 19

Big announcement 📢🚨
The ISCB 3DSig together with the 3DBioinfo @ELIXIREurope community we are organising a joint conference in Barcelona March 19-21, 2025!
If you work in Structural Bioinformatics or Computational Biophysics communities register ASAP! Only 120 spots!
www.iscb.org/3dbioinfo202...

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