Jens Nielsen

According to our database, Jens Nielsen authored at least 52 papers between 2002 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.

Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven

Briefings Bioinform., March, 2023

GotEnzymes: an extensive database of enzyme parameter predictions.

Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen

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.

Srikanth Ravipati, Giannis D. Savva, Ilektra-Athanasia Christidi, Roland Guichard, Jens Nielsen, Romain Réocreux, Michail Stamatakis

Comput. Phys. Commun., 2022

2021

Machine learning-based investigation of the cancer protein secretory pathway.

Rasool Saghaleyni, Azam Sheikh Muhammad, Pramod Bangalore, Jens Nielsen, Jonathan L. Robinson

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.

Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijovic

PLoS Comput. Biol., 2021

Microbial community dynamics revisited.

Boyang Ji, Markus J. Herrgård, Jens Nielsen

Nat. Comput. Sci., 2021

iNetModels 2.0: an interactive visualization and database of multi-omics data.

Muhammad Arif, Cheng Zhang, Xiangyu Li, Cem Güngör, Bugra Çakmak, Metin Arslantürk, Abdellah Tebani, Berkay Özcan, Oguzhan Subas, Wenyu Zhou, Brian Piening, Hasan Turkez, Linn Fagerberg, Nathan Price, Leroy Hood, Michael Snyder, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu

Nucleic Acids Res., 2021

Addressing the heterogeneity in liver diseases using biological networks.

Simon Lam, Stephen Doran, Hatice Hilal Yuksel, Ozlem Altay, Hasan Turkez, Jens Nielsen, Jan Boren, Mathias Uhlen, Adil Mardinoglu

Briefings Bioinform., 2021

2019

Coupling Cell Division to Metabolic Pathways Through Transcription.

Petter Holland, Jens Nielsen, Thierry D. G. A. Mondeel, Matteo Barberis

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 3, 2019

Performance of regression models as a function of experiment noise.

Gang Li, Jan Zrimec, Boyang Ji, Jun Geng, Johan Larsbrink, Aleksej Zelezniak, Jens Nielsen, Martin K. M. Engqvist

CoRR, 2019

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.

Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen

BMC Syst. Biol., 2019

Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model.

Simonas Marcisauskas, Boyang Ji, Jens Nielsen

BMC Bioinform., 2019

2018

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.

Hao Wang, Simonas Marcisauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen, Eduard J. Kerkhoven

PLoS Comput. Biol., 2018

TCSBN: a database of tissue and cancer specific biological networks.

Sunjae Lee, Cheng Zhang, Muhammad Arif, Zhengtao Liu, Rui Benfeitas, Gholamreza Bidkhori, Sumit Deshmukh, Mohamed Al Shobky, Alen Lovric, Jan Boren, Jens Nielsen, Mathias Uhlen, Adil Mardinoglu

Nucleic Acids Res., 2018

2017

Systematic inference of functional phosphorylation events in yeast metabolism.

Yu Chen, Yonghong Wang, Jens Nielsen

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.

Sophie Gubbels, Kenn Schultz Nielsen, Jakob Sandegaard, Kåre Mølbak, Jens Nielsen

Int. J. Medical Informatics, 2016

Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus.

Andrea Doeschl-Wilson, Alison Wilson, Jens Nielsen, Hans Nauwynck, Alan L. Archibald, Tahar Ait-Ali

BMC Syst. Biol., 2016

2015

Metabolic Needs and Capabilities of <i>Toxoplasma gondii </i> through Combined Computational and Experimental Analysis.

Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis

PLoS Comput. Biol., 2015

Finding directionality and gene-disease predictions in disease associations.

Manuel Garcia-Albornoz, Jens Nielsen

BMC Syst. Biol., 2015

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

Cheng Zhang, Boyang Ji, Adil Mardinoglu, Jens Nielsen, Qiang Hua

Bioinform., 2015

Human metabolic atlas: an online resource for human metabolism.

Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen

Database J. Biol. Databases Curation, 2015

HCSD: the human cancer secretome database.

Amir Feizi, Amir Banaei-Esfahani, Jens Nielsen

Database J. Biol. Databases Curation, 2015

2014

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

Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson, Intawat Nookaew, Jens Nielsen

Source Code Biol. Medicine, 2014

The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network.

Guodong Liu, Antonio Marras, Jens Nielsen

Quant. Biol., 2014

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue.

Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen

PLoS Comput. Biol., 2014

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

Manuel Garcia-Albornoz, Subazini Thankaswamy-Kosalai, Avlant Nilsson, Leif Väremo, Intawat Nookaew, Jens Nielsen

Nucleic Acids Res., 2014

Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae.

Lifang Liu, Amir Feizi, Tobias Österlund, Carsten Hjort, Jens Nielsen

BMC Syst. Biol., 2014

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.

Ibrahim E. El-Semman, Fredrik H. Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir Hassan A. Soliman, Jens Nielsen

BMC Syst. Biol., 2014

Kiwi: a tool for integration and visualization of network topology and gene-set analysis.

Leif Väremo, Francesco Gatto, Jens Nielsen

BMC Bioinform., 2014

2013

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress.

Elzbieta Petelenz-Kurdziel, Clemens Kühn, Bodil Nordlander, Dagmara Klein, Kuk-Ki Hong, Therese Jacobson, Peter Dahl, Jörg Schaber, Jens Nielsen, Stefan Hohmann, Edda Klipp

PLoS Comput. Biol., 2013

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for <i>Penicillium chrysogenum</i>.

Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen

PLoS Comput. Biol., 2013

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling.

Tobias Österlund, Intawat Nookaew, Sergio Bordel, Jens Nielsen

BMC Syst. Biol., 2013

Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.

Pramote Chumnanpuen, Intawat Nookaew, Jens Nielsen

BMC Syst. Biol., 2013

Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling.

Sven E. F. Borgos, Sergio Bordel, Håvard Sletta, Helga Ertesvåg, Øyvind M. Jakobsen, Per Bruheim, Trond E. Ellingsen, Jens Nielsen, Svein Valla

BMC Syst. Biol., 2013

FANTOM: Functional and taxonomic analysis of metagenomes.

Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen

BMC Bioinform., 2013

2012

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., 2012

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

BMC Syst. Biol., 2012

2011

MEMOSys: Bioinformatics platform for genome-scale metabolic models.

Stephan Pabinger, Robert Rader, Rasmus Agren, Jens Nielsen, Zlatko Trajanoski

BMC Syst. Biol., 2011

Codon usage variability determines the correlation between proteome and transcriptome fold changes.

Roberto Olivares-Hernández, Sergio Bordel, Jens Nielsen

BMC Syst. Biol., 2011

2010

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes.

Sergio Bordel, Rasmus Agren, Jens Nielsen

PLoS Comput. Biol., 2010

BioMet Toolbox: genome-wide analysis of metabolism.

Marija Cvijovic, Roberto Olivares-Hernández, Rasmus Agren, Niklas Dahr, Wanwipa Vongsangnak, Intawat Nookaew, Kiran Raosaheb Patil, Jens Nielsen

Nucleic Acids Res., 2010

OptFlux: an open-source software platform for in silico metabolic engineering.

Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha

BMC Syst. Biol., 2010

Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.

Subir K. Nandy, Paula Jouhten, Jens Nielsen

BMC Syst. Biol., 2010

2009

Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.

Donatella Cimini, Kiran Raosaheb Patil, Chiara Schiraldi, Jens Nielsen

BMC Syst. Biol., 2009

Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae.

Tobias S. Christensen, Ana Oliveira, Jens Nielsen

BMC Syst. Biol., 2009

2008

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks.

Ana Oliveira, Kiran Raosaheb Patil, Jens Nielsen

BMC Syst. Biol., 2008

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.

Intawat Nookaew, Michael C. Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana

BMC Syst. Biol., 2008

Natural computation meta-heuristics for the in silico optimization of microbial strains.

Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha

BMC Bioinform., 2008

2007

Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae.

Tunahan Çakir, Betül Kirdar, Z. Ilsen Önsan, Kutlu Ö. Ülgen, Jens Nielsen

BMC Syst. Biol., 2007

2006

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

Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen

Bioinform., 2006

2005

Evolutionary programming as a platform for <i>in silico </i>metabolic engineering.

Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen

BMC Bioinform., 2005

2002

Short trees in polygons.

Pawel Winter, Martin Zachariasen, Jens Nielsen

Discret. Appl. Math., 2002