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

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

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

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

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

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

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

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

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…

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

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!

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

'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…

COVID19 Disease Map: Biology modeling and standards communities developing a repository of virus–host interaction mechanisms embopress.org/doi/full/10.15… Dr Anna Niarakis COMBINE COVID-19 Pathways @Reactome WikiPathways INDRA Labs FAIRDOM #CellDesigner Cytoscape Elsevier

TumorComparer a method & resource to guide experimental model choice; suitability of cell lines for 24 cancers assessed: cell.com/cell-reports-m… Rileen Sinha Chris Sander aka cscbio @sloan_kettering Harvard Medical School

Congrats Ozgun Babur emekdemir and team for this work and resource 👏👏👏 'Causal interactions from proteomic profiles: Molecular data meet pathway knowledge' cell.com/patterns/fullt… OHSUCompBio UMass Boston OHSU News Chris Sander aka cscbio Augustin Luna #cellsignaling #proteomics #compbio

Today our CellBox model is finally out in Cell Systems. Predicting dynamic cellular responses to extracellular pertubations is hard. We wanted to use deep neural network but they are limited by its black-box explainability. In this paper we introduced a hybrid approach... (1/3)

NCI-CellMinerCDB: Open Access Resource to Explore Pharmacogenomics in Patient-Derived Cancer Cell Lines. Paper: academic.oup.com/nar/advance-ar… Site: discover.nci.nih.gov/cellminercdb/ Vinodh Rajapakse Chris Sander aka cscbio NCI Center for Cancer Research Broad Institute MassGeneral News Wellcome Sanger Institute MD Anderson Cancer Center

AlignmentViewer: Web-based, high-performance multiple sequence alignment visualization & analysis; suitable for tens of thousands of sequences; Paper: f1000research.com/articles/9-213… Site/Code: alignmentviewer.org Christian Dallago Roc Reguant Chris Sander aka cscbio