Academic lineage
- Jens Nielsen - PhD student
Author Correction: ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
- Madhusudhan Bysani, Rasmus Agren, Cajsa DavegÃ¥rdh, …, Per Unneberg, Karl Bacos, Charlotte Ling
- Sci Rep, 10.1038/s41598-020-58485-7
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
- Hao Wang, Simonas MarciÅ¡auskas, BenjamÃn J Sánchez, …, Rasmus Agren, Jens Nielsen, Eduard J Kerkhoven
- PLoS Comput Biol, 10.1371/journal.pcbi.1006541
Bioconda: sustainable and comprehensive software distribution for the life sciences
- Björn Grüning, Ryan Dale, Andreas Sjödin, …, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster
- Nat Methods, 10.1038/s41592-018-0046-7
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis
- Stepan Tymoshenko, Rebecca D Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis
- PLoS Comput Biol, 10.1371/journal.pcbi.1004261
Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease
- Adil Mardinoglu, Rasmus Agren, Caroline Kampf, Anna Asplund, Mathias Uhlen, Jens Nielsen
- Nat Commun, 10.1038/ncomms4083
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
- Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen
- PLoS Comput Biol, 10.1371/journal.pcbi.1002980
Integration of clinical data with a genome-scale metabolic model of the human adipocyte
- Adil Mardinoglu, Rasmus Agren, Caroline Kampf, …, Lena M Carlsson, Mathias Uhlen, Jens Nielsen
- Mol Syst Biol, 10.1038/msb.2013.5
A community-driven global reconstruction of human metabolism
- Ines Thiele, Neil Swainston, Ronan M T Fleming, …, Douglas B Kell, Pedro Mendes, Bernhard Ø Palsson
- Nat Biotechnol, 10.1038/nbt.2488
Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT
- Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
- PLoS Comput Biol, 10.1371/journal.pcbi.1002518
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
- Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen
- None, 10.1186/1752-0509-6-24
MEMOSys: Bioinformatics platform for genome-scale metabolic models
- Stephan Pabinger, Robert Rader, Rasmus Agren, Jens Nielsen, Zlatko Trajanoski
- None, 10.1186/1752-0509-5-20
Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
- Sergio Bordel, Rasmus Agren, Jens Nielsen
- PLoS Comput Biol, 10.1371/journal.pcbi.1000859