BØPosphere – June 2023 – Biowall Project

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Cell reports

Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome.

2023-06-06

PubMed:37285268; DOI:10.1016/j.celrep.2023.112619

Jongoh Shin¹, Kevin Rychel¹, Bernhard O Palsson²

Affiliations

Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.

Finally, all the genetic and molecular components of the network that drives competency in Vibrio natriegens has been revealed http://bit.ly/43PTQ9Z @DTUBiosustain @UCSDJacobs

2023-06-09

In Vibrio natriegens, a tale to unfold,
DNA competence, a story of old,
Novel iModulons, their functions arise,
Genetic symphony, under scientific skies,
Dancing with genes, their mysteries hold.

Repression of iron and translation’s domain,
A symphony muted, a deliberate refrain,
Yet activation blooms, in motility’s grace,
Polycations’ role, and ROS’s fervent chase,
Unveiling pathways, in phenotypic terrain.

With iModulons losses, competence fades,
A dance of genes, where mystery pervades,
Independent component analysis, as their guide,
Transcriptomic revelation, where secrets reside,
In Vibrio natriegens, insight cascades.

bioRxiv

Literate programming for iterative design-build-test-learn cycles in bioengineering

2023-06-19

DOI:10.1101/2023.06.18.545451

S. D. Petersen, L. Levassor, C. M. Pedersen, J. Madsen, L. G. Hansen, J. Zhang, A. K. Haidar, R. J. N. Frandsen, T. Weber, J. D. Keasling, N. Sonnenschein, M. K. Jensen

Affiliations

Technical University of Denmark

1/5 New collaborative pre-print on an #opensource #python-based platform integrating all elements of the iterative Design-Build-Test-Learrn cycle bioengineers are confronted with http://bit.ly/469i80H. The platform is compliant with #FAIR principles and available from #GitHub

2023-06-20

Dual-lab pre-print for all bioengineers interested to streamline their design-build-test-learn iterations. In this project http://bit.ly/469i80H we have developed a full-stacked #opensource #python-based computer-aided design and data analysis platform called

2023-06-19

Big day! Our pre-print on the open-source package teemi is finally out! Dive into our innovative use of literate protocols and teemi in the design-build-test-learn cycle. Excited to share our research with the #OpenScience community! Read more: http://bit.ly/469i80H #python

2023-06-20

In synthetic biology’s embrace,
Data-driven engineering sets the pace.
FAIR principles guide,
Genotype-phenotype’s tied,
Teemi platform aids in the chase!

With python and open-source in tow,
Teemi platform helps biosystems grow.
Designing and simulating,
Datasets integrating,
Predictive engineering’s the show.

Available on PyPi and GitHub’s sphere,
Teemi makes complex biosystems clear.
Literate programming’s aid,
Guidance and simulation displayed,
In the world of synthetic biology, it’s premier!

FBA-classic

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Bioinformatics (Oxford, England)

Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling.

2023-06-06

PubMed:37279743; DOI:10.1093/bioinformatics/btad367

Matthew L Jenior¹, Emma M Glass¹, Jason A Papin¹

Affiliations

Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States

Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling

2023-06-21

PLoS computational biology

Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses.

2023-06-16

PubMed:37327241; DOI:10.1371/journal.pcbi.1011232

Christopher J Skalnik¹, Sean Y Cheah¹, Mica Y Yang¹, Mattheus B Wolff¹, Ryan K Spangler¹, Lee Talman², Jerry H Morrison¹, Shayn M Peirce², Eran Agmon¹, Markus W Covert¹

Affiliations

Department of Bioengineering, Stanford University, Stanford, California, United States of America
Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America

bioinformatics/genomics

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bioRxiv

BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

2023-06-15

DOI:10.1101/2023.06.14.545018

M. Nuhamunada, O. S. Mohite, P. V. Phaneuf, B. Palsson, T. Weber

Affiliations

Technical University of Denmark

human-health

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Nature communications

Empowering drug off-target discovery with metabolic and structural analysis.

2023-06-09

PubMed:37296102; DOI:10.1038/s41467-023-38859-x

Sourav Chowdhury¹, Daniel C Zielinski², Christopher Dalldorf², Joao V Rodrigues¹, Bernhard O Palsson², Eugene I Shakhnovich³

Affiliations

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.

Systems-guided data integration workflow identifies off-target of a novel antibiotic: https://go.nature.com/3qFia0b @UCSDJacobs

2023-06-13

“This study demonstrates how established machine learning methods can be combined with mechanistic analyses to improve the resolution of drug target finding workflows for discovering off-targets of a metabolic inhibitor.”

physiology

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mSystems

Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains TCH1516 and LAC.

2023-06-13

PubMed:37310465; DOI:10.1128/msystems.00279-23

Ye Gao¹, Saugat Poudel², Yara Seif², Zeyang Shen², Bernhard O Palsson²

Affiliations

Department of Biological Sciences, University of California San Diego , La Jolla, California, USA
Department of Bioengineering, University of California San Diego , La Jolla, California, USA