Author: Jens Nielsen

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Preprints

Fine-tuning of coumaric acid synthesis to increase naringenin production in yeast

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Vaccine effectiveness after 1st and 2nd dose of the BNT162b2 mRNA Covid-19 Vaccine in long-term care facility residents and healthcare workers - a Danish cohort study

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  • Site-wide: 324
  • In epidemiology: 66
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  • Site-wide: 304
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  • Site-wide: 932

Vaccine effectiveness of the BNT162b2 mRNA COVID-19 vaccine against RT-PCR confirmed SARS-CoV-2 infections, hospitalisations and mortality in prioritised risk groups

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  • Site-wide: 1,044
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  • Site-wide: 5,394
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  • Site-wide: 12,366

Combined metabolic cofactor supplementation accelerates recovery in mild-to-moderate COVID-19

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  • Site-wide: 2,990
  • In infectious diseases: 756
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  • Site-wide: 4,997

The human secretome – the proteins secreted from human cells

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  • Site-wide: 4,710
  • In molecular biology: 99
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  • Site-wide: 10,868
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  • Site-wide: 9,769

Vaccine effectiveness when combining the ChAdOx1 vaccine as the first dose with an mRNA COVID-19 vaccine as the second dose

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  • Site-wide: 6,362
  • In epidemiology: 576
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  • Site-wide: 7,900
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Evolution from adherent to suspension – systems biology of HEK293 cell line development

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  • Site-wide: 6,694
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Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

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  • Site-wide: 8,900
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Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models

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  • Site-wide: 12,132
  • In bioengineering: 190
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Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

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  • Site-wide: 15,049
  • In bioinformatics: 1,610
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Deep learning based kcat prediction enables improved enzyme constrained model reconstruction

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  • Site-wide: 19,299
  • In systems biology: 599
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  • Site-wide: 3,072
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  • Site-wide: 2,037

iNetModels 2.0: an interactive visualization and database of multi-omics data

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  • Site-wide: 19,425
  • In bioinformatics: 2,105
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  • Site-wide: 63,387
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  • Site-wide: 25,587

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

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  • Site-wide: 21,098
  • In systems biology: 365
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  • Site-wide: 22,305
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  • Site-wide: 36,709

Genome-scale model of Rhodotorula toruloides metabolism

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  • Site-wide: 21,878
  • In systems biology: 424
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  • Site-wide: 28,813
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  • Site-wide: 23,787

Pan-cancer analysis of the metabolic reaction network

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  • Site-wide: 22,224
  • In cancer biology: 473
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Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae

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  • Site-wide: 22,463
  • In bioinformatics: 2,695
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  • Site-wide: 27,349
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  • Site-wide: 9,237

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

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  • Site-wide: 23,977
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Supervised generative design of regulatory DNA forgene expression control

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  • Site-wide: 25,767
  • In synthetic biology: 360
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  • Site-wide: 19,636
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Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

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  • Site-wide: 29,640
  • In systems biology: 843
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  • Site-wide: 8,037
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  • Site-wide: 3,558

The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism

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  • Site-wide: 38,307
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  • Site-wide: 22,625
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Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

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  • Site-wide: 46,517
  • In bioinformatics: 4,521
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  • Site-wide: 145,504
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  • Site-wide: 89,617

Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

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  • Site-wide: 57,952
  • In systems biology: 1,124
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  • Site-wide: 149,632
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Deciphering the tissue specificity of the protein secretory pathway in humans

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  • Site-wide: 60,280
  • In systems biology: 1,147
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  • Site-wide: 183,490
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  • Site-wide: 185,472

Discovery of functional alternatively spliced PKM transcripts in human cancers

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  • Site-wide: 61,396
  • In systems biology: 1,187
• Year to date:
  • Site-wide: 170,167
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  • Site-wide: 178,579

Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

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  • Site-wide: 64,021
  • In microbiology: 3,856
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  • Site-wide: 94,380
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  • Site-wide: 79,745

Fundamental Constraints In Synchronous Muscle Limit Superfast Motor Control In Vertebrates

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  • Site-wide: 67,813
  • In physiology: 359
• Year to date:
  • Site-wide: 137,939
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  • Site-wide: 165,734

SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

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  • Site-wide: 70,307
  • In systems biology: 1,395
• Year to date:
  • Site-wide: 156,232
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  • Site-wide: 150,148

Multi-omics analysis reveals the impact of microbiota on host metabolism in hepatic steatosis

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  • Site-wide: 74,711
  • In endocrinology: 73
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  • Site-wide: 22,610
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  • Site-wide: 27,243

Informing Pharmacokinetic Models with Physiological Data: Oral Population Modeling of L-Serine in Humans

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  • Site-wide: 76,106
  • In pharmacology and therapeutics: 88
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  • Site-wide: 115,724
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  • Site-wide: 180,062

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

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  • Site-wide: 77,120
  • In systems biology: 1,545
• Year to date:
  • Site-wide: 160,913
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  • Site-wide: 137,858

RMetD2: a tool for integration of relative transcriptomics data into Genome-scale metabolic models

• Downloaded 552 times
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  • Site-wide: 77,914
  • In bioinformatics: 7,135
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  • Site-wide: 82,027
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  • Site-wide: 88,028

Reconstruction and Analysis of a Kluyveromyces marxianus Genome-scale Metabolic Model

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  • Site-wide: 83,581
  • In systems biology: 1,744
• Year to date:
  • Site-wide: 128,173
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  • Site-wide: 115,889

Transcriptome analysis of EPO and GFP HEK293 Cell-lines Reveal Shifts in Energy and ER Capacity Support Improved Erythropoietin Production in HEK293F Cells

• Downloaded 485 times
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  • Site-wide: 90,663
  • In systems biology: 2,114
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  • Site-wide: 48,383
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  • Site-wide: 34,714

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

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  • Site-wide: 101,478
  • In systems biology: 2,031
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  • Site-wide: 183,388
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  • Site-wide: 161,905

Combined Metabolic Activators Reduces Liver Fat in Nonalcoholic Fatty Liver Disease Patients

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  • Site-wide: 102,944
  • In endocrinology: 106
• Year to date:
  • Site-wide: 36,687
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  • Site-wide: 36,185

Vaccine effectiveness against SARS-CoV-2 reinfection during periods of Alpha (B.1.1.7), Delta (B.1.617.2) or Omicron (B.1.1.529) dominance: A Danish nationwide study

• Downloaded 427 times
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  • Site-wide: 103,843
  • In epidemiology: None
• Year to date:
  • Site-wide: 6,321
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  • Site-wide: 803

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

• Downloaded 412 times
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  • Site-wide: 107,351
  • In systems biology: 2,591
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  • Site-wide: 24,780
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  • Site-wide: 16,267

Integrative functional analysis uncovers metabolic differences between Candida species

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  • Site-wide: 116,217
  • In systems biology: 2,489
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  • Site-wide: 67,812
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A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

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  • Site-wide: 122,381
  • In systems biology: 2,450
• Year to date:
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  • Site-wide: 128,157

Analytical Performance of a Standardized Kit for Mass Spectrometry-based Measurements of Human Glycosaminoglycans

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  • Site-wide: 124,011
  • In biochemistry: 3,879
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Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC

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  • Site-wide: 143,928
  • In systems biology: 2,880
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  • Site-wide: 68,365

Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast

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  • Site-wide: 145,906
  • In systems biology: 2,851
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  • Site-wide: 165,484
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  • Site-wide: 182,754

A Single Chromosome Strain of S. cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance.

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  • Site-wide: 149,399
  • In systems biology: 2,905
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  • Site-wide: 181,514

A network-based approach reveals the dysregulated transcriptional regulation in non-alcohol fatty liver disease

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  • Site-wide: 151,435
  • In systems biology: 3,016
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  • Site-wide: 93,018

Analysis of Normal Levels of Urine and Plasma Free Glycosaminoglycans in Adults

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  • Site-wide: 152,097
  • In biochemistry: 4,422
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  • Site-wide: 102,489

Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data

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  • Site-wide: 158,455
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  • Site-wide: 15,950
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Learning deep representations of enzyme thermal adaptation

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  • Site-wide: 158,433
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  • Site-wide: 15,957
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  • Site-wide: 18,132

Cellular limitation of enzymatic capacity explains glutamine addiction in cancers

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  • Site-wide: 165,163
  • In cancer biology: 5,167
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  • Site-wide: 60,138

Non-random organization of flux control mechanisms in yeast central metabolic pathways

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  • Site-wide: 165,904
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  • Site-wide: 102,468

Machine learning-based investigation of the cancer protein secretory pathway

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  • Site-wide: 172,977
  • In systems biology: 3,294
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  • Site-wide: 171,855
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  • Site-wide: 129,497

Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning

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  • Site-wide: 173,254
  • In systems biology: 3,502
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  • Site-wide: 24,112
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  • Site-wide: 53,150

Amino acid and nucleotide metabolism shape the selection of trophic levels in animals

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  • Site-wide: 176,676
  • In ecology: 5,969
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  • Site-wide: 108,357
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  • Site-wide: 82,896

Systems analysis of metabolic responses to a mixed meal test in an obese cohort reveals links between tissue metabolism and the gut microbiota

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  • Site-wide: 184,312
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• Year to date:
  • Site-wide: 41,429
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  • Site-wide: 20,533