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Happy to announce the release of Bioconductor pckgs dorothea (saezlab.github.io/dorothea) & CARNIVAL (saezlab.github.io/CARNIVAL/) + updated progeny (saezlab.github.io/progeny). This suite of packages enables mechanistic analysis of gene expression data.

Today we will talk on how we increased the resolution of #spatialtranscriptomics by making use of paired snRNAseq+scATACseq datasets and our functional transcriptomics tools. SPOILER ALERT: sneak peek on current efforts to model spatial interactions (intercell communication)

Congrats to Enio Gjerga Panuwat attila gabor et al! The paper describing CellNOpt 2.0 is now out in @OUPBioinfo academic.oup.com/bioinformatics…

Opportunity to attend AACR virtually for free, and among others the chance to hear Bence Szalai talk about the DREAMchallenges combo prediction challenge w. Michael Menden D Wang, J Guinney Sage Bionetworks Jonathan Dry + many others within the challenge community 10.1038/s41467-019-09799-2

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways biorxiv.org/cgi/content/sh… #biorxiv_sysbio

.Julio Saez-Rodriguez presents on Friday 'Extracting mechanistic insight from single-cell and spatial transcriptomics' #scRNA #visium and more, our tools DoRothEA,PROGENy, MISTy, CARNIVAL OmniPath saezlab.org/?#tools & applications to #heart & #kidney disease w. Rafael Kramann, MD PhD 👇

RNAseq data are widely used to extract knowledge from biology. You can extract intuitive mechanistic insights from it with our step by step guided transcriptutorial in R: github.com/saezlab/transc… 1/5

We are very happy to be part of PerMedCoE - coordinated by BSC-CNS AlfonsoValencia alfonsovalencia.bsky.social ; kick off today - we will work to facilitate the use of cell-level modeling (including our tools CellNOpt, CARNIVAL, etc. saezlab.org/?#tools) to analyze genomic data

f you are interested in (tissue) proteomics in the kidney, check this review of Markus Rinschen with our Julio Saez-Rodriguez (most holds for other organs too) nature.com/articles/s4158…

Today I have presented OmniPath at the #DiseaseMap Community Meeting. You can check the poster and video here disease-maps.org/DMCM2020posters OmniPath can help to build disease maps as the backbone. Feel free to contact for feedback to me or denes turei Julio Saez-Rodriguez KorcsmarosLab.

We are happy that our method COSMOS to infer causal links from multi-omics data and prior knowledge, as captured in the cover of Mol Syst Biol, is published embopress.org/doi/full/10.15…. See saezlab.github.io/COSMOS/ #bioinformatics #Kidneydisease #Cancer

No se puede creer. ¡Este penal no se puede creer! #CopaArgentinaEnTyCSports.

See our latest work introducing PHONEMeS-ILP, a new implementation of our method to reconstruct logic models of signaling networks from mass spectrometry phosphoproteomic data to build logical network models of signal perturbation flow lead by Enio Gjerga pubs.acs.org/doi/10.1021/ac…

The 2nd edition of our biennial "Software Tools and Resources" Special Issue is now published! pubs.acs.org/toc/jprobs/20/4 This issue provides an important overview of current efforts and immediate challenges in computational proteomics and metabolomics. Congrats to all authors!

Congrats Sara Zanivan and we are happy that our former Enio Gjerga could help a bit with the analysis 👇

The first contribution to my new lab :). Great work from Thiago Britto-Borges et.al.

Congrats to Julio Saez-Rodriguez :)

The publication for our new database TACOMA, led by Enio Gjerga, is now available. TACOMA contains multi-OMICs data from a time series experiment transverse aortic constriction (TAC) experiment, which induces pressure overload-induced cardiac hypertrophy in mice.

Christ is Risen ☦️✝️

Timeline cleanse.