Nielsen, Jens

Tissue-based map of the human proteome

Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 15,286

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

Fagerberg, L., Hallström, B. M., Oksvold, P., Kampf, C., Djureinovic, D., Odeberg, J., Habuka, M., Tahmasebpoor, S., Danielsson, A., Edlund, K., et al. (2014) · Molecular & Cellular Proteomics

Bioinformatics and Genomic NetworksGene expression and cancer classification

Cited by 3,665

Gut metagenome in European women with normal, impaired and diabetic glucose control

Karlsson, F. H., Tremaroli, V., Nookaew, I., Bergström, G., Behre, C. J., Fagerberg, B., Nielsen, J., & Bäckhed, F. (2013) · Nature

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 3,115

Symptomatic atherosclerosis is associated with an altered gut metagenome

Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012) · Nature Communications

Gut microbiota and healthOral microbiology and periodontitis research

Cited by 1,371

Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network

Förster, J., Famili, I., Fu, P., Palsson, B. Ø., & Nielsen, J. (2003) · Genome Research

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 1,069

A community-driven global reconstruction of human metabolism

Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 1,019

Voluntary running suppresses tumor growth through epinephrine- and IL-6-dependent NK cell mobilization and redistribution

Pedersen, L., Idorn, M., Olofsson, G. H., Lauenborg, B., Nookaew, I., Hansen, R. H., Johannesen, H. H., Becker, J. C., Pedersen, K. S., Dethlefsen, C., et al. (2016) · Cell Metabolism

Cancer, Stress, Anesthesia, and Immune ResponseImmune Cell Function and Interaction

Cited by 888

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation

Tremaroli, V., Karlsson, F., Werling, M., Ståhlman, M., Kovatcheva-Datchary, P., Olbers, T., Fändriks, L., le Roux, C. W., Nielsen, J., & Bäckhed, F. (2015) · Cell Metabolism

Gut microbiota and healthBariatric Surgery and Outcomes

Cited by 757

An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains

van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heijnen, J. J., Hoare, M., Lange, H. C., et al. (2000) · Enzyme and Microbial Technology

Fungal and yeast genetics researchMicrobial Metabolic Engineering and Bioproduction

Cited by 598

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., et al. (2008) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 588

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., et al. (2020) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 509

The human secretome

Uhlén, M., Karlsson, M. J., Hober, A., Svensson, A.-S., Scheffel, J., Kotol, D., Zhong, W., Tebani, A., Strandberg, L., Edfors, F., et al. (2019) · Science Signaling

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 495

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

Li, F., Yuan, L., Lu, H., Li, G., Chen, Y., Engqvist, M. K. M., Kerkhoven, E. J., & Nielsen, J. (2022) · Nature Catalysis

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 466

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Sánchez, B. J., Zhang, C., Nilsson, A., Lahtvee, P., Kerkhoven, E. J., & Nielsen, J. (2017) · Molecular Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 466

An atlas of human metabolism

Robinson, J. L., Kocabaş, P., Wang, H., Cholley, P.-E., Cook, D., Nilsson, A., Anton, M., Ferreira, R., Domenzain, I., Billa, V., et al. (2020) · Science Signaling

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 442

The gut microbiota modulates host amino acid and glutathione metabolism in mice

Mardinoglu, A., Shoaie, S., Bergentall, M., Ghaffari, P., Zhang, C., Larsson, E., Bäckhed, F., & Nielsen, J. (2015) · Molecular Systems Biology

Gut microbiota and healthMicrobial Metabolic Engineering and Bioproduction

Cited by 383

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

Wang, H., Marcišauskas, S., Sánchez, B. J., Domenzain, I., Hermansson, D., Agren, R., Nielsen, J., & Kerkhoven, E. J. (2018) · PLOS Computational Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 381

Flux Distributions in Anaerobic, Glucose-Limited Continuous Cultures of Saccharomyces Cerevisiae

Nissen, T. L., Schulze, U., Nielsen, J., & Villadsen, J. (1997) · Microbiology

Microbial Metabolic Engineering and BioproductionFungal and yeast genetics research

Cited by 376

Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network

Famili, I., Förster, J., Nielsen, J., & Palsson, B. O. (2003) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 353

Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community

Blasche, S., Kim, Y., Mars, R. A. T., Machado, D., Maansson, M., Kafkia, E., Milanese, A., Zeller, G., Teusink, B., Nielsen, J., et al. (2021) · Nature Microbiology

Probiotics and Fermented FoodsGut microbiota and health

Cited by 328

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

Nookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlén, M., & Nielsen, J. (2012) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 309

Systems Biology of Metabolism

Nielsen, J. (2017) · Annual Review of Biochemistry

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 252

It Is All about MetabolicFluxes

Nielsen, J. (2003) · Journal of Bacteriology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 236

Microbiome-derived ethanol in nonalcoholic fatty liver disease

Meijnikman, A. S., Davids, M., Herrema, H., Aydin, O., Tremaroli, V., Rios-Morales, M., Levels, H., Bruin, S., de Brauw, M., Verheij, J., et al. (2022) · Nature Medicine

Gut microbiota and healthLiver Disease Diagnosis and Treatment

Cited by 215