Author: Jens Nielsen

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Preprints

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

• Downloaded 12,088 times
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  • Site-wide: 622
  • In epidemiology: 89
• Year to date:
  • Site-wide: 61
• Since beginning of last month:
  • Site-wide: 15

The human secretome – the proteins secreted from human cells

• Downloaded 2,950 times
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  • Site-wide: 4,273
  • In molecular biology: 94
• Year to date:
  • Site-wide: 9,726
• Since beginning of last month:
  • Site-wide: 10,486

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

• Downloaded 2,947 times
• Download rankings, all-time:
  • Site-wide: 4,280
  • In infectious diseases: 752
• Year to date:
  • Site-wide: 502
• Since beginning of last month:
  • Site-wide: 658

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

• Downloaded 2,120 times
• Download rankings, all-time:
  • Site-wide: 6,931
  • In systems biology: 124
• Year to date:
  • Site-wide: 29,362
• Since beginning of last month:
  • Site-wide: 31,731

Evolution from adherent to suspension – systems biology of HEK293 cell line development

• Downloaded 2,100 times
• Download rankings, all-time:
  • Site-wide: 7,026
  • In systems biology: 126
• Year to date:
  • Site-wide: 3,754
• Since beginning of last month:
  • Site-wide: 4,637

Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models

• Downloaded 1,708 times
• Download rankings, all-time:
  • Site-wide: 9,580
  • In bioengineering: 158
• Year to date:
  • Site-wide: 31,138
• Since beginning of last month:
  • Site-wide: 28,002

Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

• Downloaded 1,349 times
• Download rankings, all-time:
  • Site-wide: 13,567
  • In bioinformatics: 1,638
• Year to date:
  • Site-wide: 34,990
• Since beginning of last month:
  • Site-wide: 31,799

Pan-cancer analysis of the metabolic reaction network

• Downloaded 1,225 times
• Download rankings, all-time:
  • Site-wide: 15,735
  • In cancer biology: 343
• Year to date:
  • Site-wide: 93,600
• Since beginning of last month:
  • Site-wide: 92,889

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

• Downloaded 1,185 times
• Download rankings, all-time:
  • Site-wide: 16,501
  • In bioinformatics: 1,982
• Year to date:
  • Site-wide: 9,482
• Since beginning of last month:
  • Site-wide: 34,351

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

• Downloaded 1,153 times
• Download rankings, all-time:
  • Site-wide: 17,209
  • In systems biology: 343
• Year to date:
  • Site-wide: 55,822
• Since beginning of last month:
  • Site-wide: 67,827

Genome-scale model of Rhodotorula toruloides metabolism

• Downloaded 985 times
• Download rankings, all-time:
  • Site-wide: 21,622
  • In systems biology: 444
• Year to date:
  • Site-wide: 44,388
• Since beginning of last month:
  • Site-wide: 67,929

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae

• Downloaded 829 times
• Download rankings, all-time:
  • Site-wide: 27,661
  • In bioinformatics: 3,194
• Year to date:
  • Site-wide: 8,745
• Since beginning of last month:
  • Site-wide: 11,486

Addressing the pooled amplification paradox with unique molecular identifiers in single-cell RNA-seq

• Downloaded 700 times
• Download rankings, all-time:
  • Site-wide: 34,983
  • In bioinformatics: 3,898
• Year to date:
  • Site-wide: 43,392
• Since beginning of last month:
  • Site-wide: 57,420

Deciphering the tissue specificity of the protein secretory pathway in humans

• Downloaded 626 times
• Download rankings, all-time:
  • Site-wide: 40,504
  • In systems biology: 919
• Year to date:
  • Site-wide: 117,921
• Since beginning of last month:
  • Site-wide: 101,749

Discovery of functional alternatively spliced PKM transcripts in human cancers

• Downloaded 578 times
• Download rankings, all-time:
  • Site-wide: 44,764
  • In systems biology: 1,030
• Year to date:
  • Site-wide: 44,260
• Since beginning of last month:
  • Site-wide: 47,277

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

• Downloaded 578 times
• Download rankings, all-time:
  • Site-wide: 44,760
  • In systems biology: 1,029
• Year to date:
  • Site-wide: 112,125
• Since beginning of last month:
  • Site-wide: 130,612

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

• Downloaded 542 times
• Download rankings, all-time:
  • Site-wide: 48,462
  • In systems biology: 1,122
• Year to date:
  • Site-wide: 99,745
• Since beginning of last month:
  • Site-wide: 116,876

Fundamental Constraints In Synchronous Muscle Limit Superfast Motor Control In Vertebrates

• Downloaded 502 times
• Download rankings, all-time:
  • Site-wide: 53,016
  • In physiology: 302
• Year to date:
  • Site-wide: 80,124
• Since beginning of last month:
  • Site-wide: 85,548

Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

• Downloaded 477 times
• Download rankings, all-time:
  • Site-wide: 56,242
  • In microbiology: 3,627
• Year to date:
  • Site-wide: 39,080
• Since beginning of last month:
  • Site-wide: 20,365

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

• Downloaded 458 times
• Download rankings, all-time:
  • Site-wide: 58,765
  • In systems biology: 1,401
• Year to date:
  • Site-wide: 120,358
• Since beginning of last month:
  • Site-wide: 124,312

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

• Downloaded 454 times
• Download rankings, all-time:
  • Site-wide: 59,288
  • In systems biology: 1,412
• Year to date:
  • Site-wide: 15,492
• Since beginning of last month:
  • Site-wide: 12,483

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

• Downloaded 434 times
• Download rankings, all-time:
  • Site-wide: 61,965
  • In pharmacology and therapeutics: 60
• Year to date:
  • Site-wide: 41,879
• Since beginning of last month:
  • Site-wide: 32,624

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

• Downloaded 403 times
• Download rankings, all-time:
  • Site-wide: 66,843
  • In bioinformatics: 6,479
• Year to date:
  • Site-wide: 69,693
• Since beginning of last month:
  • Site-wide: 68,842

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

• Downloaded 371 times
• Download rankings, all-time:
  • Site-wide: 72,267
  • In systems biology: 1,729
• Year to date:
  • Site-wide: 126,106
• Since beginning of last month:
  • Site-wide: 129,615

The Reactobiome Unravels a New Paradigm in Human Gut Microbiome Metabolism

• Downloaded 342 times
• Download rankings, all-time:
  • Site-wide: 77,602
  • In systems biology: 1,844
• Year to date:
  • Site-wide: 5,703
• Since beginning of last month:
  • Site-wide: 12,842

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

• Downloaded 273 times
• Download rankings, all-time:
  • Site-wide: 91,696
  • In systems biology: 2,150
• Year to date:
  • Site-wide: 31,606
• Since beginning of last month:
  • Site-wide: 21,117

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

• Downloaded 224 times
• Download rankings, all-time:
  • Site-wide: 102,584
  • In systems biology: 2,367
• Year to date:
  • Site-wide: 40,078
• Since beginning of last month:
  • Site-wide: 28,790

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

• Downloaded 181 times
• Download rankings, all-time:
  • Site-wide: 112,155
  • In systems biology: 2,535
• Year to date:
  • Site-wide: 13,853
• Since beginning of last month:
  • Site-wide: 4,609

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

• Downloaded 170 times
• Download rankings, all-time:
  • Site-wide: 114,565
  • In systems biology: 2,579
• Year to date:
  • Site-wide: 84,284
• Since beginning of last month:
  • Site-wide: 83,222

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC

• Downloaded 170 times
• Download rankings, all-time:
  • Site-wide: 114,542
  • In systems biology: 2,581
• Year to date:
  • Site-wide: 104,885
• Since beginning of last month:
  • Site-wide: 108,294

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

• Downloaded 169 times
• Download rankings, all-time:
  • Site-wide: 114,728
  • In systems biology: 2,589
• Year to date:
  • Site-wide: 31,814
• Since beginning of last month:
  • Site-wide: 42,440

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

• Downloaded 146 times
• Download rankings, all-time:
  • Site-wide: 119,630
  • In biochemistry: 3,589
• Year to date:
  • Site-wide: 18,156
• Since beginning of last month:
  • Site-wide: 24,083

Machine learning-based investigation of the cancer protein secretory pathway

• Downloaded 124 times
• Download rankings, all-time:
  • Site-wide: 124,061
  • In systems biology: 2,718
• Year to date:
  • Site-wide: 94,287
• Since beginning of last month:
  • Site-wide: 89,530