Joana Pereira
@joanampereira.bsky.social
Biochemist turned computational biologist and inner astronaut navigating the vastness of the protein universe using 💻. Group leader at @vibai.bsky.social and kuleuvenuniversity.bsky.social🇧🇪 Previously in🇨🇭🇩🇪🇵🇹
🌌 https://pereiralab.sites.vib.be
🌌 https://pereiralab.sites.vib.be
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!
🎤 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
📍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
June 16, 2025 at 9:55 AM
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!
Reposted by Joana Pereira
🧬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
@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
May 27, 2025 at 3:30 PM
🧬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
@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
Reposted by Joana Pereira
Joana Pereira @joanampereira.bsky.social on protein annotation by AI #ML4NGPVilnius
May 20, 2025 at 8:21 AM
Joana Pereira @joanampereira.bsky.social on protein annotation by AI #ML4NGPVilnius
Reposted by Joana Pereira
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
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
May 19, 2025 at 6:37 AM
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
Reposted by Joana Pereira
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
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
May 6, 2025 at 12:48 PM
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
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
Come join us in Leuven or Ghent 😎
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
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
April 26, 2025 at 11:04 AM
Come join us in Leuven or Ghent 😎
So honoured and excited for being awarded a FWO Odysseus grant! This means, the Pereira lab will be hiring soon. Stay tuned 😃
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.
The grant will power the growth of her newly established lab at VIB.AI and the KU Leuven Department of Cellular and Molecular Medicine.
March 27, 2025 at 1:36 PM
So honoured and excited for being awarded a FWO Odysseus grant! This means, the Pereira lab will be hiring soon. Stay tuned 😃
Reposted by Joana Pereira
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
More information: www.biozentrum.unibas.ch/education/de...
#Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland
March 20, 2025 at 8:10 AM
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
More information: www.biozentrum.unibas.ch/education/de...
#Master #Students #Research #Physics #Mathematics #ComputerScience #Engineering #Basel #Switzerland
Reposted by Joana Pereira
Review alert - "Modelling and design of transcriptional enhancers" by Seppe and Vasilis 👇
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...
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
February 28, 2025 at 4:53 PM
Review alert - "Modelling and design of transcriptional enhancers" by Seppe and Vasilis 👇
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
February 24, 2025 at 9:09 PM
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
Reposted by Joana Pereira
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.
December 9, 2024 at 3:38 PM
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.
Full house today for Bruno's talk today at our BC2 seminar series @biozentrum.bsky.social
November 25, 2024 at 3:15 PM
Full house today for Bruno's talk today at our BC2 seminar series @biozentrum.bsky.social
Reposted by Joana Pereira
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
November 20, 2024 at 4:54 PM
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
Reposted by Joana Pereira
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
November 20, 2024 at 10:45 AM
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
Reposted by Joana Pereira
Good morning! Ready to welcome you at #VIBAIsymposium.
November 20, 2024 at 7:31 AM
Good morning! Ready to welcome you at #VIBAIsymposium.
Reposted by Joana Pereira
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...
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
November 18, 2024 at 5:28 PM
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...
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...
Reposted by Joana Pereira
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!
November 17, 2024 at 3:17 PM
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!
Reposted by Joana Pereira
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
Think someone should be included? Tag them below! 👇
🧬🧶
go.bsky.app/C1oNcnj
November 17, 2024 at 8:58 AM
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
Think someone should be included? Tag them below! 👇
🧬🧶
go.bsky.app/C1oNcnj
Reposted by Joana Pereira
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...
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
November 16, 2024 at 5:44 PM
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...
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...
🚨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...
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
November 16, 2024 at 9:08 PM
🚨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...
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...
Reposted by Joana Pereira
We have a great list of already confirmed speakers and keynotes! Deadline for abstracts: December 15!
www.iscb.org/3dbioinfo202...
www.iscb.org/3dbioinfo202...
November 19, 2024 at 7:04 PM
We have a great list of already confirmed speakers and keynotes! Deadline for abstracts: December 15!
www.iscb.org/3dbioinfo202...
www.iscb.org/3dbioinfo202...
Reposted by Joana Pereira
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...
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...
November 19, 2024 at 7:04 PM
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...
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...
Reposted by Joana Pereira
We're thrilled to announce Joana Pereira will join VIB.AI as group leader!
Her pioneering research combines deep learning, network analysis, and bioinformatics to investigate protein diversity and evolution.
👉 vib.ai/en/news/joan...
Welcome aboard, Joana!
Her pioneering research combines deep learning, network analysis, and bioinformatics to investigate protein diversity and evolution.
👉 vib.ai/en/news/joan...
Welcome aboard, Joana!
Joana Pereira to join VIB.AI as new group leader
We are excited to announce the appointment of Dr. Joana Pereira as a new group leader at VIB.AI. Pereira’s research combines deep learning, network analysis, and bioinformatics to investigate the dive...
vib.ai
October 2, 2024 at 8:10 AM
We're thrilled to announce Joana Pereira will join VIB.AI as group leader!
Her pioneering research combines deep learning, network analysis, and bioinformatics to investigate protein diversity and evolution.
👉 vib.ai/en/news/joan...
Welcome aboard, Joana!
Her pioneering research combines deep learning, network analysis, and bioinformatics to investigate protein diversity and evolution.
👉 vib.ai/en/news/joan...
Welcome aboard, Joana!
Reposted by Joana Pereira
[Please repost] Looking for a PhD program that goes from molecules to ecosystems? Look no further, and apply to us! I'm offering two projects, on the 1001 Genomes Plus project and on investigating functional diversity in the plant immune system
www.phd.tuebingen.mpg.de/8387/detlef-...
www.phd.tuebingen.mpg.de/8387/detlef-...
December 7, 2023 at 3:19 PM
[Please repost] Looking for a PhD program that goes from molecules to ecosystems? Look no further, and apply to us! I'm offering two projects, on the 1001 Genomes Plus project and on investigating functional diversity in the plant immune system
www.phd.tuebingen.mpg.de/8387/detlef-...
www.phd.tuebingen.mpg.de/8387/detlef-...
Reposted by Joana Pereira
It is a great privilege and honor to be elected as new President of the SNSF Research Council. I’m very much looking forward to serving the Swiss scientific community in this new role in the coming years.
snf.ch/en/xgVKfkp88...
snf.ch/en/xgVKfkp88...
Torsten Schwede appointed as new President of the SNSF Research Council from 2025
Swiss National Science Foundation (SNSF)
snf.ch
December 8, 2023 at 12:20 PM
It is a great privilege and honor to be elected as new President of the SNSF Research Council. I’m very much looking forward to serving the Swiss scientific community in this new role in the coming years.
snf.ch/en/xgVKfkp88...
snf.ch/en/xgVKfkp88...