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"Analyzing causal relationships in proteomic profiles using CausalPath" STAR Protocols Ozgun Babur emekdemir Chris Sander aka cscbio Augustin Luna #proteomics #computationalbiology #cellsignaling #platelets star-protocols.cell.com/protocols/1199…

Help Biofactoid bridge related pathways and interactions from reactome IntAct at EBI BioGRID WikiPathways through contributions using our simple network editor thereby expanding Pathway Commons for pathway analysis. Details: elifesciences.org/articles/68292

Collaboration with Sjoerd van Hagen, Sander Rodenburg and Elena Garcia Lara The Hyve and Augustin Luna Augustin Luna - more to come as CPTAC enters its next phase. Go proteomics in cancer profiling!

Exploring causal relationships in proteomic profiles in Cytoscape using the CausalPath App f1000research.com/articles/11-45… #GSoC #networkbiology #dataviz #NRNB Ozgun Babur Alexander Pico F1000Research Jadavpur University #Cytoscape

REcurrent Features Leveraged for Combination Therapies (REFLECT) with 2K drug combinations matching co-alterations across 201 cohorts from 10K patients & 33 cancers; systematic comparison to screens from AstraZeneca National Cancer Institute ALMANAC Anil Korkut Cancer Discovery doi.org/10.1158/2159-8…

Introducing scPerturb, a collection of 44 single cell perturbation datasets with unified annotations available at scperturb.org (1/5)

BET inhibition induces vulnerability to MCL1 targeting through upregulation of fatty acid synthesis pathway in breast cancer dlvr.it/SYKwTZ

COVIDpro: Database for mining protein dysregulation in patients with COVID-19. Data for 3077 patients from 32 hospitals covering 14403 proteins. Done with Guomics colleagues. biorxiv.org/content/10.110… #coronavirus #COVID19 #preprint

Making biological pathway diagrams queryable like other data resources using Systems Biology Graphical Notation (#SBGN) diagrams and Neo4J by Adrien Rougny Irina Balaur Alexander Mazein at Luxembourg Centre for Systems Biomedicine HMS_SysBio SBGN

ImogiMap helps find interactions that are co-associated with a phenotype. Article use case: Relations between tumor-associated processes and immune regulation. Article: doi.org/10.1038/s42003… Web tool: bioinformatics.mdanderson.org/apps/imogimap Anil Korkut Chris Sander aka cscbio HMS_SysBio MD Anderson Cancer Center

New public drug screening resource made available from NCI & NCATS: 2,675 drugs in 183 cancer cell lines. 70% of the drug compounds are not in previous resources (e.g., Broad, Sanger, MDACC, etc). Article: pubmed.ncbi.nlm.nih.gov/37140427/ HMS_SysBio NCATS National Cancer Institute

Expression of 14403 proteins from 5434 MS analyses of clincial specimens from 3077 COVID-19 patients in 32 hospitals: COVIDpro (guomics.com/covidPro/). pubs.acs.org/doi/full/10.10…

cyjShiny R package allows network visualization in Shiny & R Markdown (github.com/cytoscape/cyjS…); it uses cytoscape.js graph library & provides converter functions from R (data.frame) to cytoscape.js. doi.org/10.1371/journa… #netbio #NRNB Chris Sander aka cscbio Alexander Pico

"scPerturb: harmonized single-cell perturbation data" is out now in Nature Methods!

It was a pleasure to be interviewed by Ana Castillo for my work on computational & network biology resources & methods to study cancer; with thoughts on careers in #bioinformatics shared with #BioinfoBridges of the ICSB student council

Submissions Call: Bio-Ontologies & Knowledge Representation (BOKR) COSI @ ISMB 2025 Liverpool UK July 20-24 Site bit.ly/4hO8dTh & ISMB bit.ly/40Vrqvy Topics New knowledge graphs/bases, and ontologies & their methods/applications Abstract Deadline: April 17

Advancing the search for biomarkers to combat triple-negative breast cancer with integrin inhibitors; study analyzed CRISPR and proteomics followed by experimental validation of hypotheses of pre-clinical model sensitivity bit.ly/4hUphqW

Anti-cancer effect of oxyphenisatin acetate in triple-negative breast cancer shown in patient-derived xenografts; TRPM4 as biomarker bit.ly/43gimEj

We review how to enhance deep learning architectures (convolutional & graph neural networks) with molecular interactions, gene sets, and ontological hierarchies to enhance accuracy & interpretability as part of predictive tasks bit.ly/4kwR7eN

Late-Breaking Poster Submissions Call: Bio-Ontologies & Knowledge Representation (BOKR) COSI @ ISMB 2025 Liverpool UK July 20-24 Site bit.ly/4hO8dTh & ISMB bit.ly/40Vrqvy Topics New knowledge graphs/bases and ontologies & methods/applications Deadline May 15