Nielsen, Jens

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast

Lahtvee, P.-J., Sánchez, B. J., Smialowska, A., Kasvandik, S., Elsemman, I. E., Gatto, F., & Nielsen, J. (2017) · Cell Systems

RNA and protein synthesis mechanismsFungal and yeast genetics research

Cited by 193

Meta-analysis of the gut microbiota in predicting response to cancer immunotherapy in metastatic melanoma

Limeta, A., Ji, B., Levin, M., Gatto, F., & Nielsen, J. (2020) · JCI Insight

Gut microbiota and healthCancer Immunotherapy and Biomarkers

Cited by 185

Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes

Bordel, S., Agren, R., & Nielsen, J. (2010) · PLoS Computational Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 185

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

Zrimec, J., Börlin, C. S., Buric, F., Muhammad, A. S., Chen, R., Siewers, V., Verendel, V., Nielsen, J., Töpel, M., & Zelezniak, A. (2020) · Nature Communications

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 174

Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis

Hong, K.-K., Vongsangnak, W., Vemuri, G. N., & Nielsen, J. (2011) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionFungal and yeast genetics research

Cited by 161

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

Domenzain, I., Sánchez, B., Anton, M., Kerkhoven, E. J., Millán-Oropeza, A., Henry, C., Siewers, V., Morrissey, J. P., Sonnenschein, N., & Nielsen, J. (2021) · Nature Communications

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 158

Energy metabolism controls phenotypes by protein efficiency and allocation

Chen, Y., & Nielsen, J. (2019) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 156

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

Belda, E., Voland, L., Tremaroli, V., Falony, G., Adriouch, S., Assmann, K. E., Prifti, E., Aron-Wisnewsky, J., Debédat, J., Le Roy, T., et al. (2022) · Gut

Gut microbiota and healthBiotin and Related Studies

Cited by 140

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

Nilsson, A., & Nielsen, J. (2016) · Scientific Reports

Microbial Metabolic Engineering and BioproductionFungal and yeast genetics research

Cited by 137

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

Elsemman, I. E., Rodriguez Prado, A., Grigaitis, P., Garcia Albornoz, M., Harman, V., Holman, S. W., van Heerden, J., Bruggeman, F. J., Bisschops, M. M. M., Sonnenschein, N., et al. (2022) · Nature Communications

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 120

Impact of ‘ome’ analyses on inverse metabolic engineering

Bro, C., & Nielsen, J. (2004) · Metabolic Engineering

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 116

Current Status of COVID-19 Therapies and Drug Repositioning Applications

Altay, O., Mohammadi, E., Lam, S., Turkez, H., Boren, J., Nielsen, J., Uhlen, M., & Mardinoglu, A. (2020) · iScience

SARS-CoV-2 and COVID-19 ResearchCOVID-19 Clinical Research Studies

Cited by 98

Genome scale modeling of the protein secretory pathway reveals novel targets for improved recombinant protein production in yeast

Li, F., Chen, Y., Qi, Q., Wang, Y., Yuan, L., Huang, M., Elsemman, I. E., Feizi, A., Kerkhoven, E. J., & Nielsen, J. (2021) · Nature Communications

Microbial Metabolic Engineering and BioproductionFungal and yeast genetics research

Cited by 91

Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

Scalcinati, G., Otero, J. M., Vleet, J. R. H., Jeffries, T. W., Olsson, L., & Nielsen, J. (2012) · FEMS Yeast Research

Microbial Metabolic Engineering and BioproductionFungal and yeast genetics research

Cited by 89

Combined Metabolic Activators Accelerates Recovery in Mild‐to‐Moderate COVID‐19

Altay, O., Arif, M., Li, X., Yang, H., Aydın, M., Alkurt, G., Kim, W., Akyol, D., Zhang, C., Dinler‐Doganay, G., et al. (2021) · Advanced Science

COVID-19 Clinical Research StudiesLong-Term Effects of COVID-19

Cited by 88

Metabolic Models of Protein Allocation Call for the Kinetome

Nilsson, A., Nielsen, J., & Palsson, B. O. (2017) · Cell Systems

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 87

Combined metabolic activators improve cognitive functions in Alzheimer’s disease patients: a randomised, double-blinded, placebo-controlled phase-II trial

Yulug, B., Altay, O., Li, X., Hanoglu, L., Cankaya, S., Lam, S., Velioglu, H. A., Yang, H., Coskun, E., Idil, E., et al. (2023) · Translational Neurodegeneration

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 79

Genome scale models of yeast: towards standardized evaluation and consistent omic integration

Sánchez, B. J., & Nielsen, J. (2015) · Integrative Biology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 75

Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

Chen, Y., van Pelt‐KleinJan, E., van Olst, B., Douwenga, S., Boeren, S., Bachmann, H., Molenaar, D., Nielsen, J., & Teusink, B. (2021) · Molecular Systems Biology

Microbial Metabolic Engineering and BioproductionBacterial Genetics and Biotechnology

Cited by 73

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Li, G., Hu, Y., Zrimec, J., Luo, H., Wang, H., Zelezniak, A., Ji, B., & Nielsen, J. (2021) · Nature Communications

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 57

Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M., et al. (2015) · Molecular Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 57

Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer’s disease

Meng, L., Jin, H., Yulug, B., Altay, O., Li, X., Hanoglu, L., Cankaya, S., Coskun, E., Idil, E., Nogaylar, R., et al. (2024) · Alzheimer's Research & Therapy

Dementia and Cognitive Impairment ResearchAlzheimer's disease research and treatments

Cited by 49

Yeast optimizes metal utilization based on metabolic network and enzyme kinetics

Chen, Y., Li, F., Mao, J., Chen, Y., & Nielsen, J. (2021) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 46

Mathematical modeling of proteome constraints within metabolism

Chen, Y., & Nielsen, J. (2021) · Current Opinion in Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 44