Jens Nielsen

52 papers Journal 51
YearRankTypeTitle / Venue / Authors
2023 J jnl
GotEnzymes: an extensive database of enzyme parameter predictions.
Nucleic Acids Res.
Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen
2023 J jnl
HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.
Briefings Bioinform.
Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
2022 J jnl
Coupling the time-warp algorithm with the graph-theoretical kinetic Monte Carlo framework for distributed simulations of heterogeneous catalysts.
Comput. Phys. Commun.
Srikanth Ravipati, Giannis D. Savva, Ilektra-Athanasia Christidi, Roland Guichard, Jens Nielsen, Romain Réocreux, Michail Stamatakis
2021 J jnl
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism.
PLoS Comput. Biol.
Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijovic
2021 J jnl
Addressing the heterogeneity in liver diseases using biological networks.
Briefings Bioinform.
Simon Lam, Stephen Doran, Hatice Hilal Yuksel, Ozlem Altay, Hasan Turkez, Jens Nielsen, Jan Boren, Mathias Uhlen, Adil Mardinoglu
2021 J jnl
Machine learning-based investigation of the cancer protein secretory pathway.
PLoS Comput. Biol.
Rasool Saghaleyni, Azam Sheikh Muhammad, Pramod Bangalore, Jens Nielsen, Jonathan L. Robinson
2021 J jnl
Microbial community dynamics revisited.
Nat. Comput. Sci.
Boyang Ji, Markus J. Herrgård, Jens Nielsen
2021 J jnl
iNetModels 2.0: an interactive visualization and database of multi-omics data.
Nucleic Acids Res.
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
2019 — ch.
Coupling Cell Division to Metabolic Pathways Through Transcription.
Encyclopedia of Bioinformatics and Computational Biology (3)
Petter Holland, Jens Nielsen, Thierry D. G. A. Mondeel, Matteo Barberis
2019 J jnl
Performance of regression models as a function of experiment noise.
CoRR
Gang Li, Jan Zrimec, Boyang Ji, Jun Geng, Johan Larsbrink, Aleksej Zelezniak, Jens Nielsen, Martin K. M. Engqvist
2019 J jnl
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model.
BMC Bioinform.
Simonas Marcisauskas, Boyang Ji, Jens Nielsen
2019 J jnl
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.
BMC Syst. Biol.
Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen
2018 J jnl
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.
PLoS Comput. Biol.
Hao Wang, Simonas Marcisauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen, Eduard J. Kerkhoven
2018 J jnl
TCSBN: a database of tissue and cancer specific biological networks.
Nucleic Acids Res.
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
2017 J jnl
Systematic inference of functional phosphorylation events in yeast metabolism.
Bioinform.
Yu Chen, Yonghong Wang, Jens Nielsen
2016 J jnl
Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus.
BMC Syst. Biol.
Andrea Doeschl-Wilson, Alison Wilson, Jens Nielsen, Hans Nauwynck, Alan L. Archibald, Tahar Ait-Ali
2016 J jnl
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
Sophie Gubbels, Kenn Schultz Nielsen, Jakob Sandegaard, Kåre Mølbak, Jens Nielsen
2015 J jnl
Finding directionality and gene-disease predictions in disease associations.
BMC Syst. Biol.
Manuel Garcia-Albornoz, Jens Nielsen
2015 J jnl
HCSD: the human cancer secretome database.
Database J. Biol. Databases Curation
Amir Feizi, Amir Banaei-Esfahani, Jens Nielsen
2015 J jnl
Human metabolic atlas: an online resource for human metabolism.
Database J. Biol. Databases Curation
Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
2015 J jnl
Logical transformation of genome-scale metabolic models for gene level applications and analysis.
Bioinform.
Cheng Zhang, Boyang Ji, Adil Mardinoglu, Jens Nielsen, Qiang Hua
2015 J jnl
Metabolic Needs and Capabilities of
PLoS Comput. Biol.
Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis
2014 J jnl
A dedicated database system for handling multi-level data in systems biology.
Source Code Biol. Medicine
Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson, Intawat Nookaew, Jens Nielsen
2014 J jnl
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Nucleic Acids Res.
Manuel Garcia-Albornoz, Subazini Thankaswamy-Kosalai, Avlant Nilsson, Leif Väremo, Intawat Nookaew, Jens Nielsen
2014 J jnl
Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae.
BMC Syst. Biol.
Lifang Liu, Amir Feizi, Tobias Österlund, Carsten Hjort, Jens Nielsen
2014 J jnl
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.
BMC Syst. Biol.
Ibrahim E. El-Semman, Fredrik H. Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir Hassan A. Soliman, Jens Nielsen
2014 J jnl
Kiwi: a tool for integration and visualization of network topology and gene-set analysis.
BMC Bioinform.
Leif Väremo, Francesco Gatto, Jens Nielsen
2014 J jnl
Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue.
PLoS Comput. Biol.
Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen
2014 J jnl
The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network.
Quant. Biol.
Guodong Liu, Antonio Marras, Jens Nielsen
2013 J jnl
FANTOM: Functional and taxonomic analysis of metagenomes.
BMC Bioinform.
Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen
2013 J jnl
Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast.
BMC Syst. Biol.
Pramote Chumnanpuen, Intawat Nookaew, Jens Nielsen
2013 J jnl
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling.
BMC Syst. Biol.
Tobias Österlund, Intawat Nookaew, Sergio Bordel, Jens Nielsen
2013 J jnl
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling.
BMC Syst. Biol.
Sven E. F. Borgos, Sergio Bordel, Håvard Sletta, Helga Ertesvåg, Øyvind M. Jakobsen, Per Bruheim, Trond E. Ellingsen, Jens Nielsen, Svein Valla
2013 J jnl
Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress.
PLoS Comput. Biol.
Elzbieta Petelenz-Kurdziel, Clemens Kühn, Bodil Nordlander, Dagmara Klein, Kuk-Ki Hong, Therese Jacobson, Peter Dahl, Jörg Schaber, Jens Nielsen, Stefan Hohmann, Edda Klipp
2013 J jnl
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for
PLoS Comput. Biol.
Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen
2012 J jnl
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials.
BMC Syst. Biol.
Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen
2012 J jnl
Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT.
PLoS Comput. Biol.
Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
2011 J jnl
Codon usage variability determines the correlation between proteome and transcriptome fold changes.
BMC Syst. Biol.
Roberto Olivares-Hernández, Sergio Bordel, Jens Nielsen
2011 J jnl
MEMOSys: Bioinformatics platform for genome-scale metabolic models.
BMC Syst. Biol.
Stephan Pabinger, Robert Rader, Rasmus Agren, Jens Nielsen, Zlatko Trajanoski
2010 J jnl
BioMet Toolbox: genome-wide analysis of metabolism.
Nucleic Acids Res.
Marija Cvijovic, Roberto Olivares-Hernández, Rasmus Agren, Niklas Dahr, Wanwipa Vongsangnak, Intawat Nookaew, Kiran Raosaheb Patil, Jens Nielsen
2010 J jnl
OptFlux: an open-source software platform for in silico metabolic engineering.
BMC Syst. Biol.
Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha
2010 J jnl
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation.
BMC Syst. Biol.
Subir K. Nandy, Paula Jouhten, Jens Nielsen
2010 J jnl
Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes.
PLoS Comput. Biol.
Sergio Bordel, Rasmus Agren, Jens Nielsen
2009 J jnl
Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3.
BMC Syst. Biol.
Donatella Cimini, Kiran Raosaheb Patil, Chiara Schiraldi, Jens Nielsen
2009 J jnl
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae.
BMC Syst. Biol.
Tobias S. Christensen, Ana Oliveira, Jens Nielsen
2008 J jnl
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks.
BMC Syst. Biol.
Ana Oliveira, Kiran Raosaheb Patil, Jens Nielsen
2008 J jnl
Natural computation meta-heuristics for the in silico optimization of microbial strains.
BMC Bioinform.
Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha
2008 J jnl
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism.
BMC Syst. Biol.
Intawat Nookaew, Michael C. Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana
2007 J jnl
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae.
BMC Syst. Biol.
Tunahan Çakir, Betül Kirdar, Z. Ilsen Önsan, Kutlu Ö. Ülgen, Jens Nielsen
2006 J jnl
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm.
Bioinform.
Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen
2005 J jnl
Evolutionary programming as a platform for
BMC Bioinform.
Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen
2002 J jnl
Short trees in polygons.
Discret. Appl. Math.
Pawel Winter, Martin Zachariasen, Jens Nielsen