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Author: Yang-Yu Liu

Rankings

  • All-time downloads: 30,494 (rank: 9,087 )
  • Categories:
    • bioinformatics: 10,391 (rank: 1,179 )
    • ecology: 5,957 (rank: 336 )
    • evolutionary biology: 708 (rank: 14,639 (tie) )
    • gastroenterology: 751 (rank: 910 (tie) )
    • genomics: 335 (rank: 53,552 (tie) )
    • microbiology: 7,971 (rank: 2,797 )
    • neurology: 250 (rank: 9,816 (tie) )
    • neuroscience: 336 (rank: 85,124 (tie) )
    • systems biology: 2,081 (rank: 2,866 )

Downloads per author, site-wide

Preprints

Association Rule Mining of the Human Gut Microbiome

microbiology more details view paper

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Link Prediction through Deep Generative Model

bioinformatics more details view paper
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    • Site-wide: 3,215
    • In bioinformatics: 224
  • Year to date:
    • Site-wide: 127,474
  • Since beginning of last month:
    • Site-wide: 44,244

Deciphering Functional Redundancy in the Human Microbiome

microbiology more details view paper
  • Downloaded 2,361 times
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    • Site-wide: 10,126
    • In microbiology: 584
  • Year to date:
    • Site-wide: 170,915
  • Since beginning of last month:
    • Site-wide: 72,875

Controlling complex microbial communities: a network-based approach

microbiology more details view paper
  • Downloaded 2,246 times
  • Download rankings, all-time:
    • Site-wide: 10,935
    • In microbiology: 626
  • Year to date:
    • Site-wide: 119,083
  • Since beginning of last month:
    • Site-wide: 72,826

Mapping the ecological networks of microbial communities

ecology more details view paper
  • Downloaded 1,497 times
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    • Site-wide: 20,401
    • In ecology: 273
  • Year to date:
    • Site-wide: 200,528
  • Since beginning of last month:
    • Site-wide: 175,346

On the Stability Landscape of the Human Gut Microbiome: Implications for Microbiome-based Therapies

ecology more details view paper
  • Downloaded 1,306 times
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    • Site-wide: 25,354
    • In ecology: 386
  • Year to date:
    • Site-wide: 128,338
  • Since beginning of last month:
    • Site-wide: 59,611

Challenges in Benchmarking Metagenomic Profilers

bioinformatics more details view paper
  • Downloaded 1,303 times
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    • Site-wide: 25,465
    • In bioinformatics: 2,655
  • Year to date:
    • Site-wide: 104,367
  • Since beginning of last month:
    • Site-wide: 145,824

Revealing complex ecological dynamics via symbolic regression

bioinformatics more details view paper
  • Downloaded 1,249 times
  • Download rankings, all-time:
    • Site-wide: 27,210
    • In bioinformatics: 2,823
  • Year to date:
    • Site-wide: 203,786
  • Since beginning of last month:
    • Site-wide: 201,240

Predicting microbiome compositions from species assemblages through deep learning.

microbiology more details view paper
  • Downloaded 973 times
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    • Site-wide: 40,007
    • In microbiology: 2,294
  • Year to date:
    • Site-wide: 20,176
  • Since beginning of last month:
    • Site-wide: 149,749

Ecological dynamics of the gut microbiome in response to dietary fiber

ecology more details view paper
  • Downloaded 919 times
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    • Site-wide: 43,676
    • In ecology: 1,278
  • Year to date:
    • Site-wide: 7,559
  • Since beginning of last month:
    • Site-wide: 6,606

A Novel Clustering Method for Patient Stratification

bioinformatics more details view paper
  • Downloaded 895 times
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    • Site-wide: 45,466
    • In bioinformatics: 4,514
  • Year to date:
    • Site-wide: 119,625
  • Since beginning of last month:
    • Site-wide: 66,302

Pitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data

bioinformatics more details view paper
  • Downloaded 892 times
  • Download rankings, all-time:
    • Site-wide: 45,699
    • In bioinformatics: 4,613
  • Year to date:
    • Site-wide: 113,789
  • Since beginning of last month:
    • Site-wide: 58,234

Integrating Gut Microbiota and Host Immune Markers for Highly Accurate Diagnosis of Clostridioides difficile Infection

gastroenterology more details view paper
  • Downloaded 783 times
  • Download rankings, all-time:
    • Site-wide: 55,656
    • In gastroenterology: 60
  • Year to date:
    • Site-wide: 83,374
  • Since beginning of last month:
    • Site-wide: 54,625

Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities

evolutionary biology more details view paper
  • Downloaded 744 times
  • Download rankings, all-time:
    • Site-wide: 59,855
    • In evolutionary biology: 2,635
  • Year to date:
    • Site-wide: 106,891
  • Since beginning of last month:
    • Site-wide: 66,096

Identifying sensor species to predict critical transitions in complex ecosystems

ecology more details view paper
  • Downloaded 679 times
  • Download rankings, all-time:
    • Site-wide: 68,314
    • In ecology: 1,532
  • Year to date:
    • Site-wide: 167,506
  • Since beginning of last month:
    • Site-wide: 118,618

StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

bioinformatics more details view paper
  • Downloaded 664 times
  • Download rankings, all-time:
    • Site-wide: 70,337
    • In bioinformatics: 7,132
  • Year to date:
    • Site-wide: 6,746
  • Since beginning of last month:
    • Site-wide: 32,110

Nutritional Redundancy in Human Diet

systems biology more details view paper
  • Downloaded 612 times
  • Download rankings, all-time:
    • Site-wide: 78,453
    • In systems biology: 1,661
  • Year to date:
    • Site-wide: 34,421
  • Since beginning of last month:
    • Site-wide: 81,615

Dissimilarity-Overlap Analysis of Replicate Enrichment Communities

ecology more details view paper
  • Downloaded 608 times
  • Download rankings, all-time:
    • Site-wide: 78,961
    • In ecology: 1,806
  • Year to date:
    • Site-wide: 156,065
  • Since beginning of last month:
    • Site-wide: 181,627

Overcome Competitive Exclusion in Ecosystems

ecology more details view paper
  • Downloaded 587 times
  • Download rankings, all-time:
    • Site-wide: 82,654
    • In ecology: 1,922
  • Year to date:
    • Site-wide: 181,348
  • Since beginning of last month:
    • Site-wide: 175,401

Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes

systems biology more details view paper
  • Downloaded 573 times
  • Download rankings, all-time:
    • Site-wide: 85,099
    • In systems biology: 1,683
  • Year to date:
    • Site-wide: 208,864
  • Since beginning of last month:
    • Site-wide: 172,627

Assessment of community efforts to advance computational prediction of protein-protein interactions

systems biology more details view paper
  • Downloaded 503 times
  • Download rankings, all-time:
    • Site-wide: 99,374
    • In systems biology: 2,159
  • Year to date:
    • Site-wide: 31,321
  • Since beginning of last month:
    • Site-wide: 56,988

Gut Microbiota predicts Healthy Late-life Aging in Male Mice

microbiology more details view paper
  • Downloaded 480 times
  • Download rankings, all-time:
    • Site-wide: 104,863
    • In microbiology: 6,701
  • Year to date:
    • Site-wide: 105,404
  • Since beginning of last month:
    • Site-wide: 188,350

Characterizing scaling laws in gut microbial dynamics from time series data: caution is warranted

microbiology more details view paper
  • Downloaded 445 times
  • Download rankings, all-time:
    • Site-wide: 113,093
    • In microbiology: 7,466
  • Year to date:
    • Site-wide: 54,724
  • Since beginning of last month:
    • Site-wide: 151,354

Establishment and Resilience of Transplanted Gut Microbiota in Aged Mice

microbiology more details view paper
  • Downloaded 429 times
  • Download rankings, all-time:
    • Site-wide: 117,268
    • In microbiology: 7,752
  • Year to date:
    • Site-wide: 103,612
  • Since beginning of last month:
    • Site-wide: 149,934

The impact of colonization history on the composition of ecological systems

ecology more details view paper
  • Downloaded 425 times
  • Download rankings, all-time:
    • Site-wide: 118,183
    • In ecology: 3,157
  • Year to date:
    • Site-wide: 193,444
  • Since beginning of last month:
    • Site-wide: 123,383

Origins of Scaling Laws in Microbial Dynamics

microbiology more details view paper
  • Downloaded 395 times
  • Download rankings, all-time:
    • Site-wide: 126,282
    • In microbiology: 8,890
  • Year to date:
    • Site-wide: 77,226
  • Since beginning of last month:
    • Site-wide: 111,160

Dissecting the Role of the Human Microbiome in COVID-19 via Metagenome-assembled Genomes

microbiology more details view paper
  • Downloaded 394 times
  • Download rankings, all-time:
    • Site-wide: 126,569
    • In microbiology: 8,729
  • Year to date:
    • Site-wide: 16,057
  • Since beginning of last month:
    • Site-wide: None

Higher-order interaction of brain microstructural and functional connectome

neuroscience more details view paper
  • Downloaded 359 times
  • Download rankings, all-time:
    • Site-wide: 136,754
    • In neuroscience: 19,832
  • Year to date:
    • Site-wide: 67,624
  • Since beginning of last month:
    • Site-wide: 149,550

Peripheral blood microbial signatures in COPD

genomics more details view paper
  • Downloaded 357 times
  • Download rankings, all-time:
    • Site-wide: 137,405
    • In genomics: 7,272
  • Year to date:
    • Site-wide: 158,923
  • Since beginning of last month:
    • Site-wide: 142,844

Revealing Protein-Level Functional Redundancy in the Human Gut Microbiome using Ultra-deep Metaproteomics

systems biology more details view paper
  • Downloaded 346 times
  • Download rankings, all-time:
    • Site-wide: 140,619
    • In systems biology: 2,899
  • Year to date:
    • Site-wide: 83,257
  • Since beginning of last month:
    • Site-wide: 47,173

Predicting metabolomic profiles from microbial composition through neural ordinary differential equations

microbiology more details view paper
  • Downloaded 326 times
  • Download rankings, all-time:
    • Site-wide: 146,839
    • In microbiology: 13,061
  • Year to date:
    • Site-wide: 21,723
  • Since beginning of last month:
    • Site-wide: 21,016

A Computational Method to Dissect Colonization Resistance of the Gut Microbiota against Pathogens

bioinformatics more details view paper
  • Downloaded 315 times
  • Download rankings, all-time:
    • Site-wide: 149,998
    • In bioinformatics: 11,948
  • Year to date:
    • Site-wide: 22,901
  • Since beginning of last month:
    • Site-wide: 94,222

Teasing out Missing Reactions in Genome-scale Metabolic Networks through Deep Learning

bioinformatics more details view paper
  • Downloaded 300 times
  • Download rankings, all-time:
    • Site-wide: 154,433
    • In bioinformatics: 14,017
  • Year to date:
    • Site-wide: 24,734
  • Since beginning of last month:
    • Site-wide: 7,574

Identifying the critical time window for the association of the early-life gut microbiome and metabolome with childhood neurodevelopment

neurology more details view paper
  • Downloaded 289 times
  • Download rankings, all-time:
    • Site-wide: 157,599
    • In neurology: 960
  • Year to date:
    • Site-wide: 26,372
  • Since beginning of last month:
    • Site-wide: 83,472

Impact of temporal pH fluctuations on the coexistence of nasal bacteria

ecology more details view paper
  • Downloaded 271 times
  • Download rankings, all-time:
    • Site-wide: 162,945
    • In ecology: 5,124
  • Year to date:
    • Site-wide: 190,230
  • Since beginning of last month:
    • Site-wide: 160,507

Gut feelings: Associations of emotions and emotion regulation with the gut microbiome in women

microbiology more details view paper
  • Downloaded 235 times
  • Download rankings, all-time:
    • Site-wide: 172,898
    • In microbiology: 13,574
  • Year to date:
    • Site-wide: 35,838
  • Since beginning of last month:
    • Site-wide: 35,134

A Statistical Physics Approach for Disease Module Detection

systems biology more details view paper
  • Downloaded 226 times
  • Download rankings, all-time:
    • Site-wide: 175,278
    • In systems biology: 3,485
  • Year to date:
    • Site-wide: 37,971
  • Since beginning of last month:
    • Site-wide: 43,417

Ecological Dynamics Imposes Fundamental Challenges in Microbial Source Tracking

microbiology more details view paper
  • Downloaded 137 times
  • Download rankings, all-time:
    • Site-wide: 194,778
    • In microbiology: 14,626
  • Year to date:
    • Site-wide: 70,788
  • Since beginning of last month:
    • Site-wide: 189,469

Pairing Metagenomics and Metaproteomics to Pinpoint Ecological Niches and Metabolic Essentiality of Microbial Communities

ecology more details view paper
  • Downloaded 68 times
  • Download rankings, all-time:
    • Site-wide: 205,756
    • In ecology: None
  • Year to date:
    • Site-wide: 132,089
  • Since beginning of last month:
    • Site-wide: 10,086

Eliminate false positives in metagenomic profiling based on type IIB restriction sites

bioinformatics more details view paper
  • Downloaded 67 times
  • Download rankings, all-time:
    • Site-wide: 205,942
    • In bioinformatics: None
  • Year to date:
    • Site-wide: 134,299
  • Since beginning of last month:
    • Site-wide: 10,217

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