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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 tinyurl.com/yc56axsv 🧵⬇️

Introducing *fullRankMatrix*, available on CRAN! Constantin Ahlmann-Eltze (@const-ae.bsky.social) and I developed this R package to construct full rank design matrices. Esp. relevant for binary matrices that contain linearly dependent columns. Use fullRankMatrix for accurate linear model interpretation! 📊 #rstats

Ever wondered how many amino acids you can mutate to alanine and AlphaFold2 still predicts same structure? 🤔For denovo design Top7 (1QYS), single-sequence mode, it's 60%. (1/2)

Our postdoc Iguaracy Pinheiro-de-Sousa Iguaracy Pinheiro-de-Sousa is using multiomics data to help develop better organoids and to understand how the heart🫀 and brain 🧠work at a molecular level. Collaboration and knowledge exchange are key in Iguaracy's work. ebi.ac.uk/about/news/per…

Matthias Matthias Mann Lab shows first joint proteome and RNA workflow in same cell - very exciting, and lots of promises to build multimodal atlases in nearer future!

We are happy to present SELPHI2.0 which uses the latest kinase specificity maps (PSSMs) and several other functional genomics and structural features to predict kinase-substrate associations. biorxiv.org/content/10.110…

BREAKING NEWS The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”

Wonderful time presenting at UW–Madison with Federico Marotta. Meeting talented scientists dedicated to driving #compbio towards a positive impact on society was truly inspiring. Many thanks to ISCB News for inviting us as the winning team of the PEGS DREAM Challenge to this great event!

PhosX is out! doi.org/10.1093/bioinf… Leveraging the latest kinase specificity maps from the recent monumental papers from the Cantley Lab Michael Yaffe Turk Lab and a rank sum statistic we created PhosX so now you can predict activities for near all kinases in your phosphodata :)

Kinases play a crucial role in many diseases, making them prime targets for therapeutic intervention. Enter PhosX, a new tool transforming the way researchers analyse and interpret kinase activity. Read the full article👇: academic.oup.com/bioinformatics… Alessandro Lussana 🇺🇦 Evangelia Petsalaki

Today marks the third consecutive year that Europe fails to act for what it's supposed to stand for. I have a good feeling about year four.

We present SELPHI 2.0 a machine learning model integrating >40 sequence, omics and structural features to predict kinase-substrate interactions between 420 kinases and 240K phosphosites and improve interpretation of phosphoproteomics data sciencedirect.com/science/articl…

Ever wondered which method to use to infer kinase activities from phosphoproteomics data? 💻💭Our revised comprehensive evaluation of kinase activity inference tools, done in collaboration with the Zhang lab BCMHouston, is now out Nature Communications 🔬 tinyurl.com/4twuc6z4

My group, Rahuman Sheriff biomodels and Ellie McDonagh Open Targets EMBL-EBI are looking for an enthusiastic postdoc with skills in modelling to create Digital Twins for rare disease (CZI-funded). Exciting opportunity at the forefront of network biology, multiomics, AI and DT