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Author: Bernhard O. Palsson

Rankings

  • All-time downloads: 41,005 (rank: 4,945 )
  • Categories:
    • bioengineering: 1,287 (rank: 3,444 (tie) )
    • bioinformatics: 2,026 (rank: 8,788 (tie) )
    • biophysics: 1,804 (rank: 3,191 (tie) )
    • evolutionary biology: 379 (rank: 20,063 (tie) )
    • hematology: 370 (rank: 1,198 (tie) )
    • microbiology: 6,456 (rank: 2,696 )
    • molecular biology: 3,921 (rank: 1,185 )
    • systems biology: 24,762 (rank: 135 )

Downloads per author, site-wide

Preprints

The human secretome – the proteins secreted from human cells

molecular biology more details view paper
  • Downloaded 3,387 times
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    • Site-wide: 4,612
    • In molecular biology: 100
  • Year to date:
    • Site-wide: 10,011
  • Since beginning of last month:
    • Site-wide: 35,315

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

systems biology more details view paper
  • Downloaded 2,291 times
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    • Site-wide: 8,166
    • In systems biology: 130
  • Year to date:
    • Site-wide: 40,201
  • Since beginning of last month:
    • Site-wide: 108,035

Temperature-dependent estimation of Gibbs energies using an updated group contribution method

biophysics more details view paper
  • Downloaded 1,804 times
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    • Site-wide: 11,641
    • In biophysics: 246
  • Year to date:
    • Site-wide: 32,607
  • Since beginning of last month:
    • Site-wide: 124,653

Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion

systems biology more details view paper
  • Downloaded 1,754 times
  • Download rankings, all-time:
    • Site-wide: 12,114
    • In systems biology: 205
  • Year to date:
    • Site-wide: 77,629
  • Since beginning of last month:
    • Site-wide: 146,594

COBRAme: A Computational Framework for Models of Metabolism and Gene Expression

systems biology more details view paper
  • Downloaded 1,419 times
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    • Site-wide: 16,812
    • In systems biology: 298
  • Year to date:
    • Site-wide: 125,353
  • Since beginning of last month:
    • Site-wide: 139,423

Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments

systems biology more details view paper
  • Downloaded 1,340 times
  • Download rankings, all-time:
    • Site-wide: 18,327
    • In systems biology: 336
  • Year to date:
    • Site-wide: 85,905
  • Since beginning of last month:
    • Site-wide: 127,965

Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness

systems biology more details view paper
  • Downloaded 1,235 times
  • Download rankings, all-time:
    • Site-wide: 20,715
    • In systems biology: 386
  • Year to date:
    • Site-wide: 84,063
  • Since beginning of last month:
    • Site-wide: 96,274

Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production

microbiology more details view paper
  • Downloaded 1,166 times
  • Download rankings, all-time:
    • Site-wide: 22,616
    • In microbiology: 1,312
  • Year to date:
    • Site-wide: 39,000
  • Since beginning of last month:
    • Site-wide: 42,582

Enzyme promiscuity shapes evolutionary innovation and optimization

systems biology more details view paper
  • Downloaded 1,135 times
  • Download rankings, all-time:
    • Site-wide: 23,537
    • In systems biology: 445
  • Year to date:
    • Site-wide: 89,389
  • Since beginning of last month:
    • Site-wide: 91,505

Cellular responses to reactive oxygen species can be predicted on multiple biological scales from molecular mechanisms

systems biology more details view paper
  • Downloaded 1,126 times
  • Download rankings, all-time:
    • Site-wide: 23,829
    • In systems biology: 453
  • Year to date:
    • Site-wide: 76,711
  • Since beginning of last month:
    • Site-wide: 70,330

The y-ome defines the thirty-four percent of Escherichia coli genes that lack experimental evidence of function

systems biology more details view paper
  • Downloaded 1,105 times
  • Download rankings, all-time:
    • Site-wide: 24,563
    • In systems biology: 463
  • Year to date:
    • Site-wide: 111,651
  • Since beginning of last month:
    • Site-wide: 146,268

Escher-FBA: A web application for interactive flux balance analysis

bioengineering more details view paper
  • Downloaded 1,089 times
  • Download rankings, all-time:
    • Site-wide: 25,071
    • In bioengineering: 445
  • Year to date:
    • Site-wide: 91,743
  • Since beginning of last month:
    • Site-wide: 100,897

The Escherichia coli Transcriptome Mostly Consists of Independently Regulated Modules

systems biology more details view paper
  • Downloaded 1,020 times
  • Download rankings, all-time:
    • Site-wide: 27,709
    • In systems biology: 540
  • Year to date:
    • Site-wide: 100,826
  • Since beginning of last month:
    • Site-wide: 153,019

ssbio: A Python Framework for Structural Systems Biology

systems biology more details view paper
  • Downloaded 940 times
  • Download rankings, all-time:
    • Site-wide: 31,243
    • In systems biology: 621
  • Year to date:
    • Site-wide: 135,277
  • Since beginning of last month:
    • Site-wide: 145,841

BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

systems biology more details view paper
  • Downloaded 878 times
  • Download rankings, all-time:
    • Site-wide: 34,514
    • In systems biology: 698
  • Year to date:
    • Site-wide: 99,806
  • Since beginning of last month:
    • Site-wide: 117,082

Adaptive laboratory evolution of Escherichia coli under acid stress

microbiology more details view paper
  • Downloaded 850 times
  • Download rankings, all-time:
    • Site-wide: 36,131
    • In microbiology: 2,136
  • Year to date:
    • Site-wide: 66,312
  • Since beginning of last month:
    • Site-wide: 40,449

Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets

systems biology more details view paper
  • Downloaded 828 times
  • Download rankings, all-time:
    • Site-wide: 37,615
    • In systems biology: 770
  • Year to date:
    • Site-wide: 51,646
  • Since beginning of last month:
    • Site-wide: 51,302

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

systems biology more details view paper
  • Downloaded 784 times
  • Download rankings, all-time:
    • Site-wide: 40,609
    • In systems biology: 857
  • Year to date:
    • Site-wide: 14,886
  • Since beginning of last month:
    • Site-wide: 95,167

Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

systems biology more details view paper
  • Downloaded 706 times
  • Download rankings, all-time:
    • Site-wide: 47,146
    • In systems biology: 1,012
  • Year to date:
    • Site-wide: 140,785
  • Since beginning of last month:
    • Site-wide: 156,694

Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

systems biology more details view paper
  • Downloaded 647 times
  • Download rankings, all-time:
    • Site-wide: 53,119
    • In systems biology: 1,133
  • Year to date:
    • Site-wide: 133,628
  • Since beginning of last month:
    • Site-wide: 97,449

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

microbiology more details view paper
  • Downloaded 637 times
  • Download rankings, all-time:
    • Site-wide: 54,304
    • In microbiology: 3,348
  • Year to date:
    • Site-wide: 163,675
  • Since beginning of last month:
    • Site-wide: 158,557

Systems-level physiology of the human red blood cell is computed from metabolic and macromolecular mechanisms

systems biology more details view paper
  • Downloaded 633 times
  • Download rankings, all-time:
    • Site-wide: 54,713
    • In systems biology: 1,178
  • Year to date:
    • Site-wide: 48,708
  • Since beginning of last month:
    • Site-wide: 66,171

Laboratory evolution of multiple E. coli strains reveals unifying principles of adaptation but diversity in driving genotypes

systems biology more details view paper
  • Downloaded 601 times
  • Download rankings, all-time:
    • Site-wide: 58,478
    • In systems biology: 1,275
  • Year to date:
    • Site-wide: 67,774
  • Since beginning of last month:
    • Site-wide: 84,441

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

systems biology more details view paper
  • Downloaded 598 times
  • Download rankings, all-time:
    • Site-wide: 58,847
    • In systems biology: 1,285
  • Year to date:
    • Site-wide: 61,633
  • Since beginning of last month:
    • Site-wide: 61,970

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

microbiology more details view paper
  • Downloaded 570 times
  • Download rankings, all-time:
    • Site-wide: 62,409
    • In microbiology: 3,934
  • Year to date:
    • Site-wide: 153,413
  • Since beginning of last month:
    • Site-wide: 163,562

Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism

systems biology more details view paper
  • Downloaded 545 times
  • Download rankings, all-time:
    • Site-wide: 66,070
    • In systems biology: 1,465
  • Year to date:
    • Site-wide: 159,280
  • Since beginning of last month:
    • Site-wide: 144,548

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

microbiology more details view paper
  • Downloaded 539 times
  • Download rankings, all-time:
    • Site-wide: 66,892
    • In microbiology: 4,291
  • Year to date:
    • Site-wide: 153,568
  • Since beginning of last month:
    • Site-wide: 154,260

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions

molecular biology more details view paper
  • Downloaded 534 times
  • Download rankings, all-time:
    • Site-wide: 67,699
    • In molecular biology: 1,937
  • Year to date:
    • Site-wide: 162,759
  • Since beginning of last month:
    • Site-wide: 154,029

Impact of insertion sequences on convergent evolution of Shigella species

microbiology more details view paper
  • Downloaded 464 times
  • Download rankings, all-time:
    • Site-wide: 79,300
    • In microbiology: 5,244
  • Year to date:
    • Site-wide: 160,477
  • Since beginning of last month:
    • Site-wide: 160,944

ALEdb 1.0: A Database of Mutations from Adaptive Laboratory Evolution

bioinformatics more details view paper
  • Downloaded 437 times
  • Download rankings, all-time:
    • Site-wide: 84,560
    • In bioinformatics: 7,602
  • Year to date:
    • Site-wide: 153,325
  • Since beginning of last month:
    • Site-wide: 151,971

Characterizing the response of Acinetobacter baumannii ATCC 17978 to azithromycin in multiple in vitro growth conditions

microbiology more details view paper
  • Downloaded 433 times
  • Download rankings, all-time:
    • Site-wide: 85,303
    • In microbiology: 5,707
  • Year to date:
    • Site-wide: 44,105
  • Since beginning of last month:
    • Site-wide: 59,283

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

systems biology more details view paper
  • Downloaded 433 times
  • Download rankings, all-time:
    • Site-wide: 85,332
    • In systems biology: 1,898
  • Year to date:
    • Site-wide: 120,569
  • Since beginning of last month:
    • Site-wide: 136,543

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

systems biology more details view paper
  • Downloaded 426 times
  • Download rankings, all-time:
    • Site-wide: 86,775
    • In systems biology: 1,922
  • Year to date:
    • Site-wide: 153,855
  • Since beginning of last month:
    • Site-wide: 155,690

PRECISE 2.0: an expanded high-quality RNA-seq compendium for Escherichia coli K-12 reveals high-resolution transcriptional regulatory structure

bioinformatics more details view paper
  • Downloaded 417 times
  • Download rankings, all-time:
    • Site-wide: 88,704
    • In bioinformatics: 7,863
  • Year to date:
    • Site-wide: 21,066
  • Since beginning of last month:
    • Site-wide: 12,875

Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators and role in key physiological responses

microbiology more details view paper
  • Downloaded 414 times
  • Download rankings, all-time:
    • Site-wide: 89,225
    • In microbiology: 6,025
  • Year to date:
    • Site-wide: 154,445
  • Since beginning of last month:
    • Site-wide: 150,658

Functional pathways for metabolic network-based data analysis: the MetPath algorithm

systems biology more details view paper
  • Downloaded 397 times
  • Download rankings, all-time:
    • Site-wide: 92,955
    • In systems biology: 2,050
  • Year to date:
    • Site-wide: 140,656
  • Since beginning of last month:
    • Site-wide: 117,104

Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics

evolutionary biology more details view paper
  • Downloaded 379 times
  • Download rankings, all-time:
    • Site-wide: 97,025
    • In evolutionary biology: 4,856
  • Year to date:
    • Site-wide: 152,289
  • Since beginning of last month:
    • Site-wide: 149,069

Matrix factorization recovers consistent regulatory signals from disparate datasets

bioinformatics more details view paper
  • Downloaded 377 times
  • Download rankings, all-time:
    • Site-wide: 97,429
    • In bioinformatics: 8,402
  • Year to date:
    • Site-wide: 99,052
  • Since beginning of last month:
    • Site-wide: 84,891

Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens

microbiology more details view paper
  • Downloaded 377 times
  • Download rankings, all-time:
    • Site-wide: 97,435
    • In microbiology: 6,709
  • Year to date:
    • Site-wide: 110,543
  • Since beginning of last month:
    • Site-wide: 148,449

Blood donor exposome and impact of common drugs on red blood cell metabolism

hematology more details view paper
  • Downloaded 370 times
  • Download rankings, all-time:
    • Site-wide: 99,002
    • In hematology: 94
  • Year to date:
    • Site-wide: 102,680
  • Since beginning of last month:
    • Site-wide: 137,940

Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance

systems biology more details view paper
  • Downloaded 369 times
  • Download rankings, all-time:
    • Site-wide: 99,195
    • In systems biology: 2,183
  • Year to date:
    • Site-wide: 102,006
  • Since beginning of last month:
    • Site-wide: 97,253

DynamicME: Dynamic simulation and refinement of integrated models of metabolism and protein expression

systems biology more details view paper
  • Downloaded 369 times
  • Download rankings, all-time:
    • Site-wide: 99,160
    • In systems biology: 2,186
  • Year to date:
    • Site-wide: 164,540
  • Since beginning of last month:
    • Site-wide: 163,393

Regulatory perturbations of ribosome allocation optimize the growth proteome with a trade-off in adaptation capacity

systems biology more details view paper
  • Downloaded 362 times
  • Download rankings, all-time:
    • Site-wide: 100,854
    • In systems biology: 2,211
  • Year to date:
    • Site-wide: 26,139
  • Since beginning of last month:
    • Site-wide: 61,440

Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in Escherichia coli pgi knockout evolutions

systems biology more details view paper
  • Downloaded 353 times
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    • Site-wide: 103,015
    • In systems biology: 2,251
  • Year to date:
    • Site-wide: 151,140
  • Since beginning of last month:
    • Site-wide: 160,621

Optimal dimensionality selection for independent component analysis of transcriptomic data

bioinformatics more details view paper
  • Downloaded 315 times
  • Download rankings, all-time:
    • Site-wide: 112,577
    • In bioinformatics: 9,329
  • Year to date:
    • Site-wide: 31,913
  • Since beginning of last month:
    • Site-wide: 41,164

Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains

microbiology more details view paper
  • Downloaded 311 times
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    • Site-wide: 113,481
    • In microbiology: 8,036
  • Year to date:
    • Site-wide: 32,565
  • Since beginning of last month:
    • Site-wide: 52,308

Growth adaptation of gnd and sdhCB Escherichia coli deletion strains diverges from a similar initial perturbation of the transcriptome

systems biology more details view paper
  • Downloaded 301 times
  • Download rankings, all-time:
    • Site-wide: 116,183
    • In systems biology: 2,519
  • Year to date:
    • Site-wide: 156,777
  • Since beginning of last month:
    • Site-wide: 146,542

Catalytic potential and disturbance rejection of glycolytic kinases in the human red blood cell

systems biology more details view paper
  • Downloaded 298 times
  • Download rankings, all-time:
    • Site-wide: 116,997
    • In systems biology: 2,534
  • Year to date:
    • Site-wide: 153,700
  • Since beginning of last month:
    • Site-wide: 154,329

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

systems biology more details view paper
  • Downloaded 293 times
  • Download rankings, all-time:
    • Site-wide: 118,285
    • In systems biology: 2,568
  • Year to date:
    • Site-wide: 122,085
  • Since beginning of last month:
    • Site-wide: 155,423

Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media

microbiology more details view paper
  • Downloaded 277 times
  • Download rankings, all-time:
    • Site-wide: 122,401
    • In microbiology: 8,821
  • Year to date:
    • Site-wide: 72,548
  • Since beginning of last month:
    • Site-wide: 119,360

Elucidation of regulatory modes for five two-component systems in Escherichia coli reveals novel relationships

systems biology more details view paper
  • Downloaded 274 times
  • Download rankings, all-time:
    • Site-wide: 123,197
    • In systems biology: 2,674
  • Year to date:
    • Site-wide: 112,701
  • Since beginning of last month:
    • Site-wide: 123,571

The quantitative metabolome is shaped by abiotic constraints

systems biology more details view paper
  • Downloaded 273 times
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    • Site-wide: 123,538
    • In systems biology: 2,677
  • Year to date:
    • Site-wide: 96,977
  • Since beginning of last month:
    • Site-wide: 110,587

Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo

systems biology more details view paper
  • Downloaded 272 times
  • Download rankings, all-time:
    • Site-wide: 123,792
    • In systems biology: 2,679
  • Year to date:
    • Site-wide: 39,159
  • Since beginning of last month:
    • Site-wide: 35,838

Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

bioinformatics more details view paper
  • Downloaded 268 times
  • Download rankings, all-time:
    • Site-wide: 124,992
    • In bioinformatics: 10,044
  • Year to date:
    • Site-wide: 40,058
  • Since beginning of last month:
    • Site-wide: 29,254

Machine learning of all Mycobacterium Tuberculosis H37Rv RNA-seq data reveals complex interplay between metabolism, stress response, and infection

systems biology more details view paper
  • Downloaded 258 times
  • Download rankings, all-time:
    • Site-wide: 127,566
    • In systems biology: 2,733
  • Year to date:
    • Site-wide: 41,979
  • Since beginning of last month:
    • Site-wide: 17,441

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus

microbiology more details view paper
  • Downloaded 254 times
  • Download rankings, all-time:
    • Site-wide: 128,712
    • In microbiology: 9,350
  • Year to date:
    • Site-wide: 128,682
  • Since beginning of last month:
    • Site-wide: 122,897

Reconstruction of Fur pan-regulon uncovers the complexity and diversity of transcriptional regulation in E. coli

systems biology more details view paper
  • Downloaded 242 times
  • Download rankings, all-time:
    • Site-wide: 131,759
    • In systems biology: 2,808
  • Year to date:
    • Site-wide: 115,619
  • Since beginning of last month:
    • Site-wide: 89,199

Machine Learning of Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

bioinformatics more details view paper
  • Downloaded 212 times
  • Download rankings, all-time:
    • Site-wide: 139,329
    • In bioinformatics: 10,866
  • Year to date:
    • Site-wide: 54,118
  • Since beginning of last month:
    • Site-wide: 31,678

Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

bioengineering more details view paper
  • Downloaded 198 times
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    • Site-wide: 142,762
    • In bioengineering: 2,906
  • Year to date:
    • Site-wide: 58,667
  • Since beginning of last month:
    • Site-wide: 118,344

Machine learning uncovers a data-driven transcriptional regulatory network for the Crenarchaeal thermoacidophile Sulfolobus acidocaldarius

systems biology more details view paper
  • Downloaded 167 times
  • Download rankings, all-time:
    • Site-wide: 149,608
    • In systems biology: 3,105
  • Year to date:
    • Site-wide: 71,478
  • Since beginning of last month:
    • Site-wide: 88,754

Profiling the effect of nafcillin on HA-MRSA D592 using bacteriological and physiological media

microbiology more details view paper
  • Downloaded 164 times
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    • Site-wide: 150,264
    • In microbiology: 11,319
  • Year to date:
    • Site-wide: 152,753
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    • Site-wide: 147,269

Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism

systems biology more details view paper
  • Downloaded 90 times
  • Download rankings, all-time:
    • Site-wide: 161,156
    • In systems biology: 3,289
  • Year to date:
    • Site-wide: 122,502
  • Since beginning of last month:
    • Site-wide: 19,956

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