Jens Nielsen

Publication Activity (10 Years)

Years Active: 2002-2023
Publications (10 Years): 16

Top Topics

High Throughput

Horizontal Gene Transfer

Modeling Framework

Top Venues

BMC Syst. Biol.

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

Le Yuan, Hongzhong Lu, Feiran Li, Jens Nielsen, Eduard J. Kerkhoven
HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer. Briefings Bioinform. 24 (2) (2023)
Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen
GotEnzymes: an extensive database of enzyme parameter predictions. Nucleic Acids Res. 51 (D1) (2023)
Srikanth Ravipati, Giannis D. Savva, Ilektra-Athanasia Christidi, Roland Guichard, Jens Nielsen, Romain Réocreux, Michail Stamatakis
Coupling the time-warp algorithm with the graph-theoretical kinetic Monte Carlo framework for distributed simulations of heterogeneous catalysts. Comput. Phys. Commun. 270 (2022)
Simon Lam, Stephen Doran, Hatice Hilal Yuksel, Ozlem Altay, Hasan Turkez, Jens Nielsen, Jan Boren, Mathias Uhlen, Adil Mardinoglu
Addressing the heterogeneity in liver diseases using biological networks. Briefings Bioinform. 22 (2) (2021)
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
iNetModels 2.0: an interactive visualization and database of multi-omics data. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
Rasool Saghaleyni, Azam Sheikh Muhammad, Pramod Bangalore, Jens Nielsen, Jonathan L. Robinson
Machine learning-based investigation of the cancer protein secretory pathway. PLoS Comput. Biol. 17 (4) (2021)
Boyang Ji, Markus J. Herrgård, Jens Nielsen
Microbial community dynamics revisited. Nat. Comput. Sci. 1 (10) (2021)
Linnea Österberg, Iván Domenzain, Julia Münch, Jens Nielsen, Stefan Hohmann, Marija Cvijovic
A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PLoS Comput. Biol. 17 (4) (2021)
Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven, Jens Nielsen
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. BMC Syst. Biol. 13 (1) (2019)
Simonas Marcisauskas, Boyang Ji, Jens Nielsen
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. BMC Bioinform. 20 (1) (2019)
Gang Li, Jan Zrimec, Boyang Ji, Jun Geng, Johan Larsbrink, Aleksej Zelezniak, Jens Nielsen, Martin K. M. Engqvist
Performance of regression models as a function of experiment noise. CoRR (2019)
Hao Wang, Simonas Marcisauskas, Benjamín J. Sánchez, Iván Domenzain, Daniel Hermansson, Rasmus Agren, Jens Nielsen, Eduard J. Kerkhoven
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Comput. Biol. 14 (10) (2018)
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
TCSBN: a database of tissue and cancer specific biological networks. Nucleic Acids Res. 46 (Database-Issue) (2018)
Yu Chen, Yonghong Wang, Jens Nielsen
Systematic inference of functional phosphorylation events in yeast metabolism. Bioinform. 33 (13) (2017)
Sophie Gubbels, Kenn Schultz Nielsen, Jakob Sandegaard, Kåre Mølbak, Jens Nielsen
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 95 (2016)
Andrea Doeschl-Wilson, Alison Wilson, Jens Nielsen, Hans Nauwynck, Alan L. Archibald, Tahar Ait-Ali
Combining laboratory and mathematical models to infer mechanisms underlying kinetic changes in macrophage susceptibility to an RNA virus. BMC Syst. Biol. 10 (2016)
Amir Feizi, Amir Banaei-Esfahani, Jens Nielsen
HCSD: the human cancer secretome database. Database J. Biol. Databases Curation 2015 (2015)
Manuel Garcia-Albornoz, Jens Nielsen
Finding directionality and gene-disease predictions in disease associations. BMC Syst. Biol. 9 (2015)
Cheng Zhang, Boyang Ji, Adil Mardinoglu, Jens Nielsen, Qiang Hua
Logical transformation of genome-scale metabolic models for gene level applications and analysis. Bioinform. 31 (14) (2015)
Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis
through Combined Computational and Experimental Analysis. PLoS Comput. Biol. 11 (5) (2015)
Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
Human metabolic atlas: an online resource for human metabolism. Database J. Biol. Databases Curation 2015 (2015)
Manuel Garcia-Albornoz, Subazini Thankaswamy-Kosalai, Avlant Nilsson, Leif Väremo, Intawat Nookaew, Jens Nielsen
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Guodong Liu, Antonio Marras, Jens Nielsen
The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network. Quant. Biol. 2 (1) (2014)
Ibrahim E. El-Semman, Fredrik H. Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir Hassan A. Soliman, Jens Nielsen
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. BMC Syst. Biol. 8 (2014)
Leif Väremo, Francesco Gatto, Jens Nielsen
Kiwi: a tool for integration and visualization of network topology and gene-set analysis. BMC Bioinform. 15 (2014)
Lifang Liu, Amir Feizi, Tobias Österlund, Carsten Hjort, Jens Nielsen
Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae. BMC Syst. Biol. 8 (2014)
Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson, Intawat Nookaew, Jens Nielsen
A dedicated database system for handling multi-level data in systems biology. Source Code Biol. Medicine 9 (2014)
Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen
Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue. PLoS Comput. Biol. 10 (7) (2014)
Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen
. PLoS Comput. Biol. 9 (3) (2013)
Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen
FANTOM: Functional and taxonomic analysis of metagenomes. BMC Bioinform. 14 (2013)
Sven E. F. Borgos, Sergio Bordel, Håvard Sletta, Helga Ertesvåg, Øyvind M. Jakobsen, Per Bruheim, Trond E. Ellingsen, Jens Nielsen, Svein Valla
Mapping global effects of the anti-sigma factor MucA in Pseudomonas fluorescens SBW25 through genome-scale metabolic modeling. BMC Syst. Biol. 7 (2013)
Tobias Österlund, Intawat Nookaew, Sergio Bordel, Jens Nielsen
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Syst. Biol. 7 (2013)
Elzbieta Petelenz-Kurdziel, Clemens Kühn, Bodil Nordlander, Dagmara Klein, Kuk-Ki Hong, Therese Jacobson, Peter Dahl, Jörg Schaber, Jens Nielsen, Stefan Hohmann, Edda Klipp
Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress. PLoS Comput. Biol. 9 (6) (2013)
Pramote Chumnanpuen, Intawat Nookaew, Jens Nielsen
Integrated analysis, transcriptome-lipidome, reveals the effects of INO-level (INO2 and INO4) on lipid metabolism in yeast. BMC Syst. Biol. 7 (S-3) (2013)
Luis Caspeta, Saeed Shoaie, Rasmus Agren, Intawat Nookaew, Jens Nielsen
Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst. Biol. 6 (2012)
Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT. PLoS Comput. Biol. 8 (5) (2012)
Roberto Olivares-Hernández, Sergio Bordel, Jens Nielsen
Codon usage variability determines the correlation between proteome and transcriptome fold changes. BMC Syst. Biol. 5 (2011)
Stephan Pabinger, Robert Rader, Rasmus Agren, Jens Nielsen, Zlatko Trajanoski
MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst. Biol. 5 (2011)
Sergio Bordel, Rasmus Agren, Jens Nielsen
Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes. PLoS Comput. Biol. 6 (7) (2010)
Isabel Rocha, Paulo Maia, Pedro Evangelista, Paulo Vilaça, Simão Soares, José P. Pinto, Jens Nielsen, Kiran Raosaheb Patil, Eugénio C. Ferreira, Miguel Rocha
OptFlux: an open-source software platform for in silico metabolic engineering. BMC Syst. Biol. 4 (2010)
Subir K. Nandy, Paula Jouhten, Jens Nielsen
Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation. BMC Syst. Biol. 4 (2010)
Marija Cvijovic, Roberto Olivares-Hernández, Rasmus Agren, Niklas Dahr, Wanwipa Vongsangnak, Intawat Nookaew, Kiran Raosaheb Patil, Jens Nielsen
BioMet Toolbox: genome-wide analysis of metabolism. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Tobias S. Christensen, Ana Oliveira, Jens Nielsen
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. BMC Syst. Biol. 3 (2009)
Donatella Cimini, Kiran Raosaheb Patil, Chiara Schiraldi, Jens Nielsen
Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3. BMC Syst. Biol. 3 (2009)
Intawat Nookaew, Michael C. Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst. Biol. 2 (2008)
Miguel Rocha, Paulo Maia, Rui Mendes, José P. Pinto, Eugénio C. Ferreira, Jens Nielsen, Kiran Raosaheb Patil, Isabel Rocha
Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinform. 9 (2008)
Ana Oliveira, Kiran Raosaheb Patil, Jens Nielsen
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst. Biol. 2 (2008)
Tunahan Çakir, Betül Kirdar, Z. Ilsen Önsan, Kutlu Ö. Ülgen, Jens Nielsen
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae. BMC Syst. Biol. 1 (2007)
Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm. Bioinform. 22 (1) (2006)
Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen
metabolic engineering. BMC Bioinform. 6 (2005)
Pawel Winter, Martin Zachariasen, Jens Nielsen
Short trees in polygons. Discret. Appl. Math. 118 (1-2) (2002)