An Introduction to Computational Systems Biology

by @karthikraman, Taylor & Francis, 2021

[Karthik Raman @karthikraman]

The paperback version is now out! https://t.co/rDgBWQnNwa

Do check the book out, and also the very nice companion website at https://t.co/vmWoLQOTw9

#systemsbiology #networks #teaching

[An Introduction to Computational Systems Biology @SysBioBook]

A nice example to add to the direct search algorithms in Chapter 6!

[Karthik Raman @karthikraman]

Just quoted this image last week in a talk on evolutionary algorithms 😀

[Karthik Raman @karthikraman]

Delighted to share our paper https://t.co/nGONdpl4fZ now out in @ISMEComms: Metabolic modelling to predict microbial interactions in deep sea extreme environment. Wonderful collaboration with @KarthikGeomicro, Zhichao Zhao & led by @dk_rusty @IBSE_IITM @rbc_dsai_iitm @iitmadras

[An Introduction to Computational Systems Biology @SysBioBook]

This can be a nice supplement to Chapter 11, for modelling microbial interactions/communities.

[Karthik Raman @karthikraman]

Our review is published in a special themed issue of the Journal of IISc: "Big Data for a Small World: A Review on Databases and Resources for Studying #Microbiomes" Thanks to Venkat from @NASAJPL for editing the issue, and my co-authors!

https://t.co/0BtiL5r0Ep

[Karthik Raman @karthikraman]

It's been a joyous ride working with Venkat, @RachitaKKumar and others on this exciting project, as we examine various kinds of interactions in the microbiome, including how various organisms support each other in such extreme environments. Video abstract: https://t.co/fqA3B7vst0

[Karthik Raman @karthikraman]

Delighted to share our publication https://t.co/hPGtcr1IqF in @MicrobiomeJ on the International @Space_Station #microbiome with our colleagues at @NASAJPL Venkat @Nitin_NJC and @Ceth_Parker. Ably led by @RachitaKKumar and Sanjaay @IBSE_IITM @rbc_dsai_iitm @iitmadras @iitmbt

[Karthik Raman @karthikraman]

Inspired by biological networks, where spare capacity & distributed robustness are ubiquitous, we propose a simple algorithm to identify optimal utilisation of spare capacity, establishing new connections between existing nodes, to achieve a significant increase in robustness

[Karthik Raman @karthikraman]

Our work on how dormant spare capacity can be exploited for attack tolerance in complex networks is now online @ Physica A: https://t.co/WTBUyrQEBX

Excellent work by Sai Saranga Das, who started this off as part of a course project! @iitmbt @iitmadras @rbc_dsai_iitm @IBSE_IITM

[ACS Synthetic Bio @ACSSynBio]

22 years after the first engineered genetic circuits, biology continues to confound designs. @karthikraman and colleagues @iitmadras #review progress made, including strategies, techniques, and achievements, and highlight gaps for future exploration.

https://t.co/vVr068L8Ku

[Karthik Raman @karthikraman]

Since https://t.co/H9vTNMIQZH is down, this is the next best thing to demo it to students... Any other suggestions???

https://t.co/nFHeP4OMSK

[Karthik Raman @karthikraman]

Our recent review in @ACSSynBio on Designing Biological Circuits: From Principles to Applications
is now out! https://t.co/WyiM7GydgH A very systematic mapping of literature, again resorting to a generalised morphological analysis. Thanks, Debomita and Raghu @iitmadras!

[Karthik Raman @karthikraman]

Delighted to share our recent paper on adaptation in biological networks, studied from a #systemstheory lense. Great work by Priyan Bhattacharya and thanks to Dr. Arun Tangirala from @Chemenggiitm: 50+ equations in the paper!😊😊
@iitmadras @IBSE_IITM @iitmbt @rbc_dsai_iitm

[An Introduction to Computational Systems Biology @SysBioBook]

This paper builds on the nice FSEOF method discussed in §10.3.1 - the tools is available from GitHub https://t.co/diMKpX8FHe

[Karthik Raman @karthikraman]

Our paper building on flux scanning (FSEOF), to predict metabolites that can be co-produced is now online https://t.co/iRfrmvZhZ4 -nice work by Lavanya Raajaraam @iitmbt @IBSE_IITM @rbc_dsai_iitm @iitmadras- Useful applications for #MetabolicEngineering #Biofuels @TheCOBRAToolbox

[Karthik Raman @karthikraman]

Glad to announce my @SWAYAMMHRD @nptelindia course on #Computational #SystemsBiology. Excited to offer it a fourth time—hoping to create a nice learning environment! Enrol@ https://t.co/aG81UKIw4V - This time, we have the textbook & its fully-featured companion site @SysBioBook!

[Harikrishnan R Namboothiri @HarikrishnanRN8]

@karthikraman @SWAYAMMHRD @nptelindia @SysBioBook This is an amazing course! Got to learn a lot of new concepts which were presented with lucid explanations.

[An Introduction to Computational Systems Biology @SysBioBook]

Very relevant for Chapter 11. Modelling Cellular Interactions #Microbiome #MicrobialCommunities #MetabolicNetworks #Networks

[Karthik Raman @karthikraman]

Very happy to share our latest work on community modelling: https://t.co/xkEw6FdjXg
Excellent work by Maziya Ibrahim @iitmbt @iitmadras @IBSE_IITM @rbc_dsai_iitm—CAMP (Co-culture/Community Analyses for Metabolite Production) can be very useful to pick communities for bioprocess!

[An Introduction to Computational Systems Biology @SysBioBook]

as also our @CRCPress Focus book: https://t.co/jiobKd2NPF
#SystemsBiology #Microbiome #modelling

[An Introduction to Computational Systems Biology @SysBioBook]

Chapter 11 will also be handy here: https://t.co/5W9LL6zaj8

[Karthik Raman @karthikraman]

Delighted to be doing this tutorial with @aarthiravikrish and Dinesh Kumar @IBSE_IITM @rbc_dsai_iitm @iitmbt @iitmadras - Join us to learn more about how metabolic modelling can be used to understand microbial interactions using #NetworkScience and @TheCOBRAToolbox! Thanks @iscb

[Karthik Raman @karthikraman]

Delighted to share the final published manuscript on NetGenes https://t.co/WeDUG3zKDW Thanks @senthamizhan__v
@ravi_iitm at @IBSE_IITM & @rbc_dsai_iitm & @iitmbt
@iitmadras

[Karthik Raman @karthikraman]

Delighted to be co-organising this workshop with @rsmsheriff from @emblebi and @IBSE_IITM @iitm — Reproducibility in #SystemsBiology is something that we're passionate about, along with @biomodels!

@reprobiomodels @aic_cphms