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2020 – today
- 2023
[j50]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)- [j49]Feiran Li, Yu Chen, Mihail Anton, Jens Nielsen:
GotEnzymes: an extensive database of enzyme parameter predictions. Nucleic Acids Res. 51(D1): 583-586 (2023) - 2022
- [j48]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: 108148 (2022) - 2021
- [j47]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): 1751-1766 (2021) - [j46]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): 271-276 (2021) - [j45]Boyang Ji, Markus J. Herrgård, Jens Nielsen:
Microbial community dynamics revisited. Nat. Comput. Sci. 1(10): 640-641 (2021) - [j44]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) - [j43]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)
2010 – 2019
- 2019
- [j42]Simonas Marcisauskas, Boyang Ji, Jens Nielsen:
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. BMC Bioinform. 20(1): 551:1-551:9 (2019) - [j41]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): 4:1-4:9 (2019) - [r1]Petter Holland, Jens Nielsen, Thierry D. G. A. Mondeel, Matteo Barberis:
Coupling Cell Division to Metabolic Pathways Through Transcription. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 74-93 - [i1]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 abs/1912.08141 (2019) - 2018
- [j40]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): D595-D600 (2018) - [j39]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) - 2017
- [j38]Yu Chen, Yonghong Wang, Jens Nielsen:
Systematic inference of functional phosphorylation events in yeast metabolism. Bioinform. 33(13): 1995-2001 (2017) - 2016
- [j37]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: 101 (2016) - [j36]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: 49-59 (2016) - 2015
- [j35]Amir Feizi, Amir Banaei-Esfahani, Jens Nielsen:
HCSD: the human cancer secretome database. Database J. Biol. Databases Curation 2015 (2015) - [j34]Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen:
Human metabolic atlas: an online resource for human metabolism. Database J. Biol. Databases Curation 2015 (2015) - [j33]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): 2324-2331 (2015) - [j32]Manuel Garcia-Albornoz, Jens Nielsen:
Finding directionality and gene-disease predictions in disease associations. BMC Syst. Biol. 9: 35 (2015) - [j31]Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis:
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. PLoS Comput. Biol. 11(5) (2015) - 2014
- [j30]Leif Väremo, Francesco Gatto, Jens Nielsen:
Kiwi: a tool for integration and visualization of network topology and gene-set analysis. BMC Bioinform. 15: 408 (2014) - [j29]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: 41 (2014) - [j28]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: 73 (2014) - [j27]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): 175-181 (2014) - [j26]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) - [j25]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): 30-46 (2014) - [j24]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: 17 (2014) - 2013
- [j23]Kemal Sanli, Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen:
FANTOM: Functional and taxonomic analysis of metagenomes. BMC Bioinform. 14: 38 (2013) - [j22]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: 19 (2013) - [j21]Tobias Österlund, Intawat Nookaew, Sergio Bordel, Jens Nielsen:
Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Syst. Biol. 7: 36 (2013) - [j20]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): S7 (2013) - [j19]Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen:
The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum. PLoS Comput. Biol. 9(3) (2013) - [j18]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) - 2012
- [j17]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: 24 (2012) - [j16]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) - 2011
- [j15]Stephan Pabinger, Robert Rader, Rasmus Agren, Jens Nielsen, Zlatko Trajanoski:
MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst. Biol. 5: 20 (2011) - [j14]Roberto Olivares-Hernández, Sergio Bordel, Jens Nielsen:
Codon usage variability determines the correlation between proteome and transcriptome fold changes. BMC Syst. Biol. 5: 33 (2011) - 2010
- [j13]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: 45 (2010) - [j12]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: 68 (2010) - [j11]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): 144-149 (2010) - [j10]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)
2000 – 2009
- 2009
- [j9]Tobias S. Christensen, Ana Oliveira, Jens Nielsen:
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. BMC Syst. Biol. 3: 7 (2009) - [j8]Donatella Cimini, Kiran Raosaheb Patil, Chiara Schiraldi, Jens Nielsen:
Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3. BMC Syst. Biol. 3: 17 (2009) - 2008
- [j7]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) - [j6]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: 17 (2008) - [j5]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: 71 (2008) - 2007
- [j4]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: 18 (2007) - 2006
- [j3]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): 58-67 (2006) - 2005
- [j2]Kiran Raosaheb Patil, Isabel Rocha, Jochen Förster, Jens Nielsen:
Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinform. 6: 308 (2005) - 2002
- [j1]Pawel Winter, Martin Zachariasen, Jens Nielsen:
Short trees in polygons. Discret. Appl. Math. 118(1-2): 55-72 (2002)
Coauthor Index
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