Short trees in polygons. - Pawel Winter; Martin Zachariasen; Jens Nielsen (Discret. Appl. Math., 2002)

Evolutionary programming as a platform for in silico metabolic engineering. - Kiran Raosaheb Patil; Isabel Rocha; Jochen Förster; Jens Nielsen (BMC Bioinform., 2005)

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)

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)

Natural computation meta-heuristics for the in silico optimization of microbial strains. - Miguel Rocha 001; Paulo Maia; Rui Mendes 001; José P. Pinto; Eugénio C. Ferreira; Jens Nielsen; Kiran Raosaheb Patil; Isabel Rocha (BMC Bioinform., 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)

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)

Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. - Tobias S. Christensen; Ana Oliveira; Jens Nielsen (BMC Syst. Biol., 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 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)

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 001 (BMC Syst. 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)

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)

Codon usage variability determines the correlation between proteome and transcriptome fold changes. - Roberto Olivares-Hernández; Sergio Bordel; Jens Nielsen (BMC Syst. Biol., 2011)

MEMOSys: Bioinformatics platform for genome-scale metabolic models. - Stephan Pabinger; Robert Rader; Rasmus Agren; Jens Nielsen; Zlatko Trajanoski (BMC Syst. Biol., 2011)

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)

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)

FANTOM: Functional and taxonomic analysis of metagenomes. - Kemal Sanli; Fredrik H. Karlsson; Intawat Nookaew; Jens Nielsen (BMC Bioinform., 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)

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 condition-dependent regulation of metabolism in yeast through genome-scale modeling. - Tobias Österlund; Intawat Nookaew; Sergio Bordel; Jens Nielsen (BMC Syst. Biol., 2013)

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum. - Rasmus Agren; Liming Liu; Saeed Shoaie; Wanwipa Vongsangnak; Intawat Nookaew; Jens Nielsen (PLoS Comput. Biol., 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)

Kiwi: a tool for integration and visualization of network topology and gene-set analysis. - Leif Väremo; Francesco Gatto 001; Jens Nielsen (BMC Bioinform., 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)

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)

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)

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)

The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network. - Guodong Liu; Antonio Marras; Jens Nielsen (Quant. Biol., 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)

HCSD: the human cancer secretome database. - Amir Feizi; Amir Banaei-Esfahani; Jens Nielsen (Database J. Biol. Databases Curation, 2015)

Human metabolic atlas: an online resource for human metabolism. - Natapol Pornputtapong; Intawat Nookaew; Jens Nielsen (Database J. Biol. Databases Curation, 2015)

Logical transformation of genome-scale metabolic models for gene level applications and analysis. - Cheng Zhang 002; Boyang Ji; Adil Mardinoglu; Jens Nielsen; Qiang Hua (Bioinform., 2015)

Finding directionality and gene-disease predictions in disease associations. - Manuel Garcia-Albornoz; Jens Nielsen (BMC Syst. Biol., 2015)

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. - Stepan Tymoshenko; Rebecca D. Oppenheim; Rasmus Agren; Jens Nielsen; Dominique Soldati-Favre; Vassily Hatzimanikatis (PLoS Comput. Biol., 2015)

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)

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)

Systematic inference of functional phosphorylation events in yeast metabolism. - Yu Chen; Yonghong Wang; Jens Nielsen (Bioinform., 2017)

TCSBN: a database of tissue and cancer specific biological networks. - Sunjae Lee; Cheng Zhang 002; Muhammad Arif 007; Zhengtao Liu; Rui Benfeitas; Gholamreza Bidkhori; Sumit Deshmukh; Mohamed Al Shobky; Alen Lovric; Jan Boren; Jens Nielsen; Mathias Uhlen; et al. (Nucleic Acids Res., 2018)

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. - Hao Wang 078; Simonas Marcisauskas; Benjamín J. Sánchez; Iván Domenzain; Daniel Hermansson; Rasmus Agren; Jens Nielsen; Eduard J. Kerkhoven (PLoS Comput. Biol., 2018)

Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. - Simonas Marcisauskas; Boyang Ji; Jens Nielsen (BMC Bioinform., 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)

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)

Coupling Cell Division to Metabolic Pathways Through Transcription. - Petter Holland; Jens Nielsen; Thierry D. G. A. Mondeel; Matteo Barberis (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

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)

iNetModels 2.0: an interactive visualization and database of multi-omics data. - Muhammad Arif 007; Cheng Zhang 002; Xiangyu Li; Cem Güngör; Bugra Çakmak; Metin Arslantürk; Abdellah Tebani; Berkay Özcan; Oguzhan Subas; Wenyu Zhou; Brian Piening; Hasan Turkez; et al. (Nucleic Acids Res., 2021)

Microbial community dynamics revisited. - Boyang Ji; Markus J. Herrgård; Jens Nielsen (Nat. Comput. Sci., 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)

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)

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)

GotEnzymes: an extensive database of enzyme parameter predictions. - Feiran Li; Yu Chen; Mihail Anton; Jens Nielsen (Nucleic Acids Res., 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., 2023)