Philipp Schäfer

Computional biologist with background in biochem

[Sei Chang @sei_chang]

We're the BenchLifters 🏋️, building automated benchmarking for drug perturbation prediction at the #reagent hackathon.

24 hours, 8 people, one automated benchmarking agent for computational biology research. If agents are going to do science, someone has to spot their reps 💪

[Philipp Schäfer @psl_schaefer]

@MartinBJensen Thanks for putting this together!

[Saez-Rodriguez Group @saezlab]

Postdoc position in our group at @emblebi , analyzing single cell data to better understand and treat neurodegen diseases, collab with @AndrewBassett43 , @mo_lotfollahi, @bayraktar_lab M Strauss and others @OpenTargets . Deadline 20/07.

Please share🙏: https://t.co/AkQCHMIevR

[Philipp Schäfer @psl_schaefer]

@iskander @s_r_constantin What do you consider as independent validation?

[Saez-Rodriguez Group @saezlab]

We will be at the inaugural #ESSB conference this week in Berlin, presenting with @MariaCHeinz a talk on multi-modal whole brain tumor profiling, @psl_schaefer with @tanevski a poster on analyzing cross-condition/temporal spatial data [1/2]

[Kaessmann Lab @kaessmannlab]

#Postdoc or #PhD position jointly hosted in our lab and that of Alexander Sasse @LXandR_ to investigate the evolution of gene regulation at the single-cell level across primates/mammals using state-of-the-art deep learning approaches: https://t.co/PZk4OGgd5i Please RT!

[Saez-Rodriguez Group @saezlab]

📢 Introducing CORNETO: a unified, knowledge-driven framework for multi-sample network learning & modeling via constrained optimization, supporting a wide variety of network methods and prior knowledge

💻Code: https://t.co/OuM9Acrs9U
📜Paper: https://t.co/XFjEbKMAAL

🧵👇

[Saez-Rodriguez Group @saezlab]

This was a close collaboration with @schirmerlab, led by @Cels121 and our @PauBadiaM. Congrats to them and all the other co-authors: @roramirezf94, Patricia Sekol, @psl_schaefer, Christian J. Riedl, …

[Saez-Rodriguez Group @saezlab]

👉Consider joining us for a post-doc at @emblebi & @ASTRAZENECAUK as part of the EAZPOD program to study multicellular mechanisms associated with #cancer treatment resistance! #postdoc
https://t.co/Pfyp0P1fEf

[Saez-Rodriguez Group @saezlab]

📣 The much-revised manuscript of LIANA+, our all-in-one solution to study cell-cell communication from single-cell, spatial, and multi-omics technologies, is now published in @NatureCellBio https://t.co/KkHX3GVLn1

[Philipp Schäfer @psl_schaefer]

@Thom_Wolf @Max90325883

[Saez-Rodriguez Group @saezlab]

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭In collaboration with the Zhang lab @bcmhouston, we performed a comprehensive evaluation of kinase activity inference tools to help answer that question https://t.co/Em4cZbvcb7 🧵⬇️

[Jovan Tanevski @tanevski]

🚨 We are looking for a PhD student 🚨 to join the Tanevski Lab and @DenisSchapiro Lab at the Heidelberg University Hospital, working at the intersection of machine learning and spatial omics as part of the Translational Spatial Profiling Center. Please RT https://t.co/3bR3SUVjLO

[EMBL-EBI @emblebi]

We welcome Julio Saez-Rodriguez @JulioSaezRod as our new Head of Research!

Associate Director for EMBL-EBI Services Jo McEntyre @jomcentyre has been promoted to Deputy Director of EMBL-EBI & Rolf Apweiler is stepping back to Associate Director as he looks towards retirement.

[Saez-Rodriguez Group @saezlab]

Local heterogeneity of tissues can define their function and predict clinical outcomes. We introduce Kasumi 💻https://t.co/2xbfYuo39I to identify spatially localized neighborhoods of intra and intercellular relationships from spatial omics persistent across samples & conditions

[Saez-Rodriguez Group @saezlab]

1) Are you interested in computational approaches to study the immune system 🔎🦠by integrating single-cell + spatial multi-omics data with prior knowledge? Check our review 📖out now in @NatImmunol https://t.co/ilWxyshOLR 🧵

[Saez-Rodriguez Group @saezlab]

We are recruiting a PhD student on machine learning methods to analyze spatially resolved omics data in human disease within @ELLISforEurope #ELLISPhD programme

[Philipp Schäfer @psl_schaefer]

@yun_s_song @k_mikulik

[Saez-Rodriguez Group @saezlab]

📣 Introducing LIANA+: an all-in-one cell-cell communication (CCC) framework
🧬 Many tools exist, yet they use various syntaxes and are tailored for a specific purpose
LIANA+ harmonises and extends existing methods, enabling their synergistic applications https://t.co/FVwb3XS1ne

[Saez-Rodriguez Group @saezlab]

Integrating single-cell & spatial omics with different resolutions is key to understand tissue structure & function 🧬🔬 We had tackled this using multi-objective optimization - we just updated our paper and implemented an #rstats package https://t.co/JAU3FM0szn