I am slow and lazy. So my project on writing the textbook on computational systems biology is moving at a snail's pace.
The book chapters are here on git: https://github.com/biplabbose/Systems_Biology_Textbook

Please use the materials in your course and give me feedback for improvements.

#SysBio #textbook #computationalbiology #qBio

Interesting opinion piece:

https://aps.org/publications/apsnews/202304/biological.cfm

#qBio #BiologicalPhysics #PhysicsOfBiology #TheoryOfLivingMatter

Interesting opinion piece:

https://aps.org/publications/apsnews/202304/biological.cfm

#qBio #BiologicalPhysics #PhysicsOfBiology #TheoryOfLivingMatter

RT @UriAlonWeizmann
Damage dynamics in individual E. coli cells as they age explains why identical cells die at different times.
Amazingly, damage follows a stochastic equation found also in mice. Aging may be universal in its fundamental dynamics. #qbio #aging
http://disq.us/t/4ftdprd

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

Bacterial #persister resuscitation is a drug-dependent & non-stochastic process. Persisters can partition into healthy &non-viable daughter cells to survive antibiotic treatment ➡️ http://bit.ly/3YlmzQV KR Allison @emoryuniversity #antibioticresistance #dynamics #QBio #SystemsBiology

A very useful cheat sheet if want to migrate to Julia but your brain is wired to Matlab:

https://cheatsheets.quantecon.org/

#matlab #julia #computing #coding #qbio

RT @StreichanS
Excited about quantitative #devbio - combining #syntheticmorphogenesis with theory? Join @IdseHeemskerk, Kinneret Keren, @MorphoLab_AS_AR, @viktri08, @XavierTrepat, @ZernickaGoetz, @StreichanS and more this summer in ☀️ Santa Barbara, CA in a hands-on course. #kitpqbio #qbio

RT @StreichanS
Excited about quantitative #devbio - combining #syntheticmorphogenesis with theory? Join @IdseHeemskerk, Kinneret Keren, @MorphoLab_AS_AR, @viktri08, @XavierTrepat, @ZernickaGoetz, @StreichanS and more this summer in ☀️ Santa Barbara, CA in a hands-on course. #kitpqbio #qbio

Excited about quantitative #devbio - combining #syntheticmorphogenesis with theory? Join @IdseHeemskerk, Kinneret Keren, @MorphoLab_AS_AR, @viktri08, @XavierTrepat, @ZernickaGoetz, @StreichanS and more this summer in ☀️ Santa Barbara, CA in a hands-on course. #kitpqbio #qbio.

Quantification of natural plasmid transfer rates reveals a tradeoff between conjugation and cell division that constrains plasmid evolution ➡️ http://bit.ly/3Xa9qd5
From Lingchong You's lab @dukeu #antibioticresistance #genetransfer #SystemsBiology #QBio

We hope that this study will be a useful resource for #ReproAging research and #TE Biology!
We also thank @param_p_singh@twitter.com, our🐠🧙‍♂️#AriAdler and talented #qbio and #mcb undergrad #AlanXu and #KatelynHsu for their help on this study! 9

RT lingchongyou: My lab (http://youlab.bio) is recruiting a postdoc to work on understanding and controlling microbiome dynamics. Further details about the position and the portal to submit applications can be found here: https://lnkd.in/gqej9kdc
Please RT. #qbio #synbio #microbiome #AMR

Hurray!

Eli Weinstein, @andrenguyen and myself got a contributed talk accepted at Winter Q-Bio! #winterqbio #qbio

Reach out if you'd like to hear about our work estimating the effects of mutations across the T cell receptor on epitope binding using observational data. The same sequence based methods generalize to a number of settings, including #antibodies.

#tcell #mutation #sequences #epitopes #epitopebinding #cdr #cdr3 #tcr #bcr

Anyone else headed to the conference in person?

Christmas gift for me- a nice science coffee table book.

#bookworm #qBio #theory #theoreticalbiology #science #sciencecommunication

Christmas gift for me- a nice science coffee table book.

#bookworm #qBio #theory #theoreticalbiology #science #sciencecommunication

12/2022 Issue ➡️ bit.ly/3V17ouv
#dynamics, #QBio, #CellSignalling, bacterial starvation responses, #microbiology, #Proteomics
On the cover -by TeamSciStories-: Coordination of MAPK &p53 dynamics (Eric Batchelor
UMN, Medical School)
#SystemsBiology

In single pancreatic cells responding to oxidative stress, JNK dynamics regulate an early trigger of cell death, #p53 controls late maintenance of cell cycle arrest &p38 controls a switch between JNK- and p53-dependent cell fate➡️ http://bit.ly/3UPf6YM E Batchelor (UMN Medical School) #QBio #cellfate #SystemsBiology

Here are a few jewels from this excellent article:

"At its core, statistics is about evaluating the uncertainty of estimates and how that uncertainty impacts inferences and decision making."

"Of course most of us receive some training in statistics, but it’s often so shallow it does more harm than good - a little knowledge can be dangerous if it obscures your own ignorance."

https://statsepi.substack.com/p/im-not-a-real-statistician-and-you

#math
#statistics
#qBio
#data
#dataanalysis

There are efforts to connect gene expression to cell morphology. But can we consider the mapping from the molecular space (gene expression) to morphological feature space to be Bijective? Possibly not. It could be non-injective also. Any thoughts?

#systemsbiology
#machinelearning
#qbio