highlight
bioRxiv : the preprint server for biology
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.
2023-02-21
PubMed:36865326; DOI:10.1101/2023.02.20.529291
Arjun Patel, Dominic McGrosso, Ying Hefner, Anaamika Campeau, Anand V Sastry, Svetlana Maurya, Kevin Rychel, David J Gonzalez, Bernhard O Palsson
Affiliations
Metabolic engineering
Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals.
2023-02-03
PubMed:36738854; DOI:10.1016/j.ymben.2023.01.012
Rebecca M Lennen1, Hyun Gyu Lim2, Kristian Jensen1, Elsayed T Mohammed1, Patrick V Phaneuf1, Myung Hyun Noh2, Sailesh Malla1, Rosa A Börner1, Ksenia Chekina1, Emre Özdemir1, Ida Bonde1, Anna Koza1, Jérôme Maury1, Lasse E Pedersen1, Lars Y Schöning1, Nikolaus Sonnenschein1, Bernhard O Palsson3, Alex T Nielsen1, Morten O A Sommer1, Markus J Herrgård4, Adam M Feist5
Affiliations
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr. #0412, La Jolla, CA, 92093-0412, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr. #0412, La Jolla, CA, 92093-0412, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; BioInnovation Institute, Ole Maaløes Vej 3, 2830, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Dr. #0412, La Jolla, CA, 92093-0412, USA.
FBA-classic
Communications biology
Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation.
2023-02-10
PubMed:36765199; DOI:10.1038/s42003-023-04540-8
Affiliations
- Department of Chemical Engineering, Queen’s University, Kingston, Canada
- Department of Computer Science, University of Tübingen, 72076, Tübingen, Germany
- Department of Chemical Engineering, Queen’s University, Kingston, Canada.
We’ve detected a paper from Communications Biology that cites a retracted paper post-retraction.
Citing paper: https://doi.org/10.1038/s42003-023-04540-8…
Retracted paper:
One of the most threatening hospital germs that can cause serious #infectiousdiseases is 𝘗𝘴𝘦𝘶𝘥𝘰𝘮𝘰𝘯𝘢𝘴 𝘢𝘦𝘳𝘶𝘨𝘪𝘯𝘰𝘴𝘢. Its now published, most comprehensive and accurate computer model to date should support fighting it – despite its antibiotic resistance.
metabolic-engineering
New biotechnology
Automating the design-build-test-learn cycle towards next-generation bacterial cell factories.
2023-02-01
PubMed:36736693; DOI:10.1016/j.nbt.2023.01.002
Affiliations
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens, Lyngby, Denmark.
Check the latest article by @NicolasGurdo, @Daniel__Volke & Douglas McCloskey on #automation of the #SynBio #DBTL cycle—the way forward to #bioproduction & #bioeconomy #OpenAccess @ElsevierConnect @LabNikel @DTUBiosustain
human-health
Lancet (London, England)
Cell-free fetal DNA for genetic evaluation in Copenhagen Pregnancy Loss Study (COPL): a prospective cohort study.
2023-02-02
PubMed:36739882; DOI:10.1016/S0140-6736(22)02610-1
Tanja Schlaikjær Hartwig1, Louise Ambye2, Jennifer R Gruhn3, Jesper Friis Petersen4, Tine Wrønding5, Letizia Amato6, Andrew Chi-Ho Chan3, Boyang Ji7, Maiken Hemme Bro-Jørgensen2, Lene Werge2, Mette Marie Babiel Schmidt Petersen5, Clara Brinkmann5, Julie Birch Petersen5, Morten Dunø8, Iben Bache8, Markus J Herrgård7, Finn Stener Jørgensen9, Eva R Hoffmann3, Henriette Svarre Nielsen10, COPL consortium
Affiliations
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Hvidovre Hospitals NIPT Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Hvidovre Hospitals NIPT Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Obstetrics and Gynaecology, Copenhagen University Hospital-North Zealand, Hillerød, Denmark; Department of Obstetrics and Gynaecology, Copenhagen University Hospital Herlev, Herlev, Denmark
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; BioInnovation Institute, Copenhagen, Denmark
- BioInnovation Institute, Copenhagen, Denmark
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
- Hvidovre Hospitals NIPT Center, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Fetal Medicine Unit, Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
AI
bioRxiv
Deep learning-based codon optimization with large-scale synonymous variant datasets enables generalized tunable protein expression
2023-02-12
DOI:10.1101/2023.02.11.528149
D. A. Constant, J. M. Gutierrez, A. V. Sastry, R. Viazzo, N. R. Smith, J. Hossain, D. A. Spencer, H. Carter, A. B. Ventura, M. T. M. Louie, C. Kohnert, R. Consbruck, J. Bennett, K. A. Crawford, J. M. Sutton, A. Morrison, A. K. Steiger, K. A. Jackson, J. T. Stanton, S. Abdulhaqq, G. Hannum, J. Meier, M. Weinstock, M. Gander
Affiliations
- Absci
First, we used #AI to optimize an antibody’s binding affinity and Naturalness score.
Then we used it to build novel antibodies.
Now we’ve turned AI towards codon optimization.
Read our latest preprint @biorxivpreprint
https://biorxiv.org/content/10.1101/2023.02.11.528149v1…
#AI #generativeAi