Discovering the dynamic world of the EGFR-MAPK phosphoproteome. 🌐🔎

Feng, Sanford and colleagues #EMSLscience developed a multiplexed deep phosphoproteome profiling workflow unveiling 4500 protein sites exhibiting increased phosphorylation upon EGF stimulation.

Another great #preLight by Benjamin Maier 👉 https://prelights.biologists.com/highlights/a-phosphoproteomics-data-resource-for-systems-level-modeling-of-kinase-signaling-networks-v2/

#preprint # modelling #phosphoproteomics #signalling #bioinformatics #SystemsBiology

Now Neda Bagheri at U of Washington
https://www.bagherilab.com/

Emulating emergent spatio-temporal cell population dynamics with #machinelearning algorithms remains challenging

Population dynamics arise from autonomous #SingleCell decisions
e.g. in context of #cancer progression

Created tool called ARCADE = Agent-based Representation of Cells And Dynamic Environments
https://bagherilab.com/resources.php

But model is computationally expensive...
1/2

#ComputationalBiology
#SystemsBiology
#CSSingleCells23

Aviv Regev (Genentech)
https://www.gene.com/scientists/our-scientists/aviv-regev

From cell to perturbation atlases

Deciphering causal intra- and intercellular circuits

Using Perturb-seq
https://www.biorxiv.org/content/10.1101/2023.01.23.525198v1

#SystemsBiology
#CSSingleCells23
#GeneExpression

Now want to do multiple perturbations in one cell... do effects combine? Can do this with orig Perturb-seq, then categorize interactions

But the space of interactions is far bigger than the number of cells (in universe)

1/2

Excited to read! #CancerMetabolism #SystemsBiology #NotIntheGenes #cellscellscells

Weak supervision - Strong results! 💪

Smith and team introduce Perturbational Metric Learning (PeML) to extract biological relationships from noisy high-throughput perturbational datasets.

Team effort from preLighters Benjamin Dominik Maier & Anna Foix Romero – read their preLight! 👀

#preLight 👉 https://prelights.biologists.com/highlights/similarity-metric-learning-on-perturbational-datasets-improves-functional-identification-of-perturbations/

#bioinformatics #SystemsBiology #clustering #correlations #gsea #MachineLearning

"The immune system is a compelling and apt subject for a systems biology approach to research, as it is a distributed, multiagent system with emergent properties. It is a complex adaptive system (CAS), self-organized, and regulated by dynamical interactions of individual cells with a capacity to respond to environmental changes both collectively and individually"
#Immunology #SystemsBiology

https://www.cell.com/trends/immunology/fulltext/S1471-4906(23)00113-8

Evoluncheons weekly meetup (Week of 7 Aug 2023)

Some picks on papers and resources in #evolution-ey stuff I like from the past couple of weeks! Big backlog here since I was at a conference. #Systemsbiology, #genomic #epidemiology, #immunity, #cancer—something for everyone here: 1/n

I made this slide decades ago when I trying to understand why "human engineered" networks look like many of the networks (and other kinds of circuits) we find in nature...

#systemsbiology

Super excited to give invited talk at "Network Science for the #sustainabledevelopmentgoals" satellite @netsci2023 tomorrow, Tuesday July 11th at 14:55 (Horsaal 3). I will speak about our NIH-NLM funded work on #epilepsy and other #networkmedicine #socialmediamining #reducedinequality #goodhealthandwellbeing #genderequality #partnershipsforthegoals #netsci2023
https://sites.google.com/view/netsci4sdgs23/

And in case your are interested, giving a (4th!!) talk at the "The Statistical Inference for Network Models Satellite", tuesday July 11th at 12:10(Horsaal 4), on statistical and causal models of #dynamics in #automatanetworks models in #systemsbiology https://sinm.network/sinm2023/ #netsci2023

Are biological #complexnetworks near critical? Existing #systemsbiology models are not, as shown in our recent work with Jordan C Rozum, Reka Albert, Kyu Hyong Park, and Felipe Costa.
,
#Robustness of biomolecular #networks suggests functional modules far from the #edgeofchaos
https://www.biorxiv.org/content/10.1101/2023.06.30.547297v1

RT @: Last chance to apply for our #systemsbiology course where you'll learn about:

– #machinelearning
– #multiomics data integration
– functional inference
– network inference and signal propagation
– executable modelling

Applications close 9 July: https://ebi.ac.uk/training/events/systems-biology-large-datasets-biological-insight-1/…

New Institute! 📢 Together with Heidelberg University we just launched HI-TAC, the Helmholtz Institute for Translational AngioCardioScience. Located in Mannheim and Heidelberg, it will bring together vascular #biomedicine, #SystemsBiology, and #CardiacResearch:

Further reading: https://www.mdc-berlin.de/de/news/press/gefaesse-und-herz-als-kommunikationszentrale

I have a two publications to my name, mostly for being *attached* to the group that actually wrote and edited the papers. (I did write software based on some of the ideas in the paper, but they weren't originally my ideas.)

OK. Whatever. What I'm curious about is, I'm on #ResearchGate and, lately, I get pretty regular notifications of new #citations on one of these papers, about once a month. It's a total of 80 since September 2018. Is this typical?

It's not a bad paper: I think it's actually quite good. Still, it's not "groundbreaking"? It's about an approach to #SystemsBiology where we use computer simulation that integrates multiple models to validate our overall understanding of an organism. Is that what folks are into these days?

Anyway, I just want a hint, because I'm not likely to actually read all these papers that cite us, if this is, like, paper mill output or are other folks legitimately taking on the ideas and building on them.

We curated 18 new prefixes covering all international clinical trial registries appearing in the @WHO International Clinical Trials Registry Platform (https://trialsearch.who.int)

Read up here: https://bioregistry.io/collection/0000012

#bioinformatics #clinicalinformatics #systemsbiology #semanticweb #opendata #fairdata #fair

#introduction

Chemical engineer by training and profession. Spent my last working decade in the network and transport layers, plus security architecture. Retired now.

Never used the bird, ran from the faceplant and tightly constrain other social. Watched #Explore here for a bit and found interesting and welcoming positivity. Hoping to find a community to exchange and discuss ideas.

Fan of science fiction and original research in mammalian biology, microbiology and systems/network biology.

#biology #microbiology #systemsbiology #networkmedicine #ecoevo #pleiotropy #mechanisms #hiking #olympicweightlifting

Are high-content #cellmigration #imaging data reproducible? Staffan Strömblad et al find that the highest variability occurs between labs & the variance can be substantially reduced by batch effect removal ➡️ https://www.embopress.org/doi/full/10.15252/msb.202211490
#microscopy #reproducibility #SystemsBiology

04/2023 Issue ➡️http://bit.ly/3KTVT6m
metabolic microbial interactions, AI-assisted structural #proteomics, #signaltransduction, #proteome turnover rates tissues...
Cover (by Kyle Allison, EmoryUniversity): persister resuscitation dynamics #antibioticresistance #dynamics #QBio
#SystemsBiology

Why are biologists adopting #julialang #sciml? Performance, metaprogramming, and the development of new abstractions are improving software tools for #computationalbiology #systemsbiology #bioinformatics. Check out this new paper in Nature Methods!

https://www.nature.com/articles/s41592-023-01832-z

A modular #transposon-based platform for dynamically rewiring gene regulatory networks in bacteria ➡️ https://www.embopress.org/doi/full/10.15252/msb.202211398
from J Collins, Broad Institute, MIT
#functionalgenomics #SynBio #SyntheticBiology #SystemsBiology #GeneRegulatoryNetwork

Systems-level analyses in #Celegans show widespread transcriptional regulation of metabolic genes, coexpression of metabolic pathways & conditions of pathway activation/repression ➡️ https://www.embopress.org/doi/full/10.15252/msb.202211443
from Marian Walhout, University of Massachusetts Chan Medical School
#metabolism #metabolicnetwork #SystemsBiology #transcription