Jens Nielsen

According to our database1, Jens Nielsen authored at least 44 papers between 2002 and 2019.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.



In proceedings 
PhD thesis 




Coupling Cell Division to Metabolic Pathways Through Transcription.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

Performance of regression models as a function of experiment noise.
CoRR, 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

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.
PLoS Comput. Biol., 2018

TCSBN: a database of tissue and cancer specific biological networks.
Nucleic Acids Res., 2018

Systematic inference of functional phosphorylation events in yeast metabolism.
Bioinform., 2017

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

Metabolic Needs and Capabilities of <i>Toxoplasma gondii </i> through Combined Computational and Experimental Analysis.
PLoS Comput. Biol., 2015

Finding directionality and gene-disease predictions in disease associations.
BMC Syst. Biol., 2015

Logical transformation of genome-scale metabolic models for gene level applications and analysis.
Bioinform., 2015

Human metabolic atlas: an online resource for human metabolism.
Database J. Biol. Databases Curation, 2015

HCSD: the human cancer secretome database.
Database J. Biol. Databases Curation, 2015

A dedicated database system for handling multi-level data in systems biology.
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

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
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

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

FANTOM: Functional and taxonomic analysis of metagenomes.
BMC Bioinform., 2013

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

MEMOSys: Bioinformatics platform for genome-scale metabolic models.
BMC Syst. Biol., 2011

Codon usage variability determines the correlation between proteome and transcriptome fold changes.
BMC Syst. Biol., 2011

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes.
PLoS Comput. Biol., 2010

BioMet Toolbox: genome-wide analysis of metabolism.
Nucleic Acids Res., 2010

OptFlux: an open-source software platform for in silico metabolic engineering.
BMC Syst. Biol., 2010

Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.
BMC Syst. Biol., 2010

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.
BMC Syst. Biol., 2009

Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae.
BMC Syst. Biol., 2009

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

Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae.
BMC Syst. Biol., 2007

Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm.
Bioinform., 2006

Evolutionary programming as a platform for <i>in silico </i>metabolic engineering.
BMC Bioinform., 2005

Short trees in polygons.
Discret. Appl. Math., 2002