Jens Nielsen
Orcid: 0000-0002-8112-8449
According to our database1,
Jens Nielsen
authored at least 52 papers
between 2002 and 2023.
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Bibliography
2023
HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.
Briefings Bioinform., March, 2023
Nucleic Acids Res., January, 2023
2022
Coupling the time-warp algorithm with the graph-theoretical kinetic Monte Carlo framework for distributed simulations of heterogeneous catalysts.
Comput. Phys. Commun., 2022
2021
PLoS Comput. Biol., 2021
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism.
PLoS Comput. Biol., 2021
Nucleic Acids Res., 2021
Briefings Bioinform., 2021
2019
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.
BMC Syst. Biol., 2019
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model.
BMC Bioinform., 2019
2018
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.
PLoS Comput. Biol., 2018
Nucleic Acids Res., 2018
2017
Bioinform., 2017
2016
The development and use of a new methodology to reconstruct courses of admission and ambulatory care based on the Danish National Patient Registry.
Int. J. Medical Informatics, 2016
Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus.
BMC Syst. Biol., 2016
2015
Metabolic Needs and Capabilities of <i>Toxoplasma gondii </i> through Combined Computational and Experimental Analysis.
PLoS Comput. Biol., 2015
BMC Syst. Biol., 2015
Logical transformation of genome-scale metabolic models for gene level applications and analysis.
Bioinform., 2015
Database J. Biol. Databases Curation, 2015
Database J. Biol. Databases Curation, 2015
2014
Source Code Biol. Medicine, 2014
The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network.
Quant. Biol., 2014
Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue.
PLoS Comput. Biol., 2014
Nucleic Acids Res., 2014
Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae.
BMC Syst. Biol., 2014
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.
BMC Syst. Biol., 2014
Kiwi: a tool for integration and visualization of network topology and gene-set analysis.
BMC Bioinform., 2014
2013
Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress.
PLoS Comput. Biol., 2013
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for <i>Penicillium chrysogenum</i>.
PLoS Comput. Biol., 2013
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling.
BMC Syst. Biol., 2013
Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.
BMC Syst. Biol., 2013
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling.
BMC Syst. Biol., 2013
2012
Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT.
PLoS Comput. Biol., 2012
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials.
BMC Syst. Biol., 2012
2011
BMC Syst. Biol., 2011
Codon usage variability determines the correlation between proteome and transcriptome fold changes.
BMC Syst. Biol., 2011
2010
Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes.
PLoS Comput. Biol., 2010
BMC Syst. Biol., 2010
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.
BMC Syst. Biol., 2010
2009
BMC Syst. Biol., 2009
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae.
BMC Syst. Biol., 2009
2008
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks.
BMC Syst. Biol., 2008
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.
BMC Syst. Biol., 2008
Natural computation meta-heuristics for the in silico optimization of microbial strains.
BMC Bioinform., 2008
2007
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae.
BMC Syst. Biol., 2007
2006
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm.
Bioinform., 2006
2005
BMC Bioinform., 2005
2002