Author: Xin Gao

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Preprints

Deep learning in bioinformatics: introduction, application, and perspective in big data era

• Downloaded 7,027 times
• Download rankings, all-time:
  • Site-wide: 1,962
  • In bioinformatics: 114
• Year to date:
  • Site-wide: 7,433
• Since beginning of last month:
  • Site-wide: 9,050

ClusterMap: Comparing analyses across multiple Single Cell RNA-Seq profiles

• Downloaded 6,055 times
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  • Site-wide: 2,399
  • In bioinformatics: 156
• Year to date:
  • Site-wide: 25,787
• Since beginning of last month:
  • Site-wide: 24,220

PGCN: Disease gene prioritization by disease and gene embedding through graph convolutional neural networks

• Downloaded 4,500 times
• Download rankings, all-time:
  • Site-wide: 3,584
  • In bioinformatics: 287
• Year to date:
  • Site-wide: 8,279
• Since beginning of last month:
  • Site-wide: 7,736

Role of 1’-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication

• Downloaded 2,307 times
• Download rankings, all-time:
  • Site-wide: 9,327
  • In biophysics: 170
• Year to date:
  • Site-wide: 36,424
• Since beginning of last month:
  • Site-wide: 26,244

Machine learning with biomedical ontologies

• Downloaded 1,844 times
• Download rankings, all-time:
  • Site-wide: 12,970
  • In bioinformatics: 1,371
• Year to date:
  • Site-wide: 31,957
• Since beginning of last month:
  • Site-wide: 42,048

DeepSimulator: a deep simulator for Nanopore sequencing

• Downloaded 1,524 times
• Download rankings, all-time:
  • Site-wide: 17,269
  • In bioinformatics: 1,820
• Year to date:
  • Site-wide: 114,002
• Since beginning of last month:
  • Site-wide: 164,392

An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing

• Downloaded 1,360 times
• Download rankings, all-time:
  • Site-wide: 20,558
  • In bioinformatics: 2,181
• Year to date:
  • Site-wide: 113,946
• Since beginning of last month:
  • Site-wide: 119,069

Analysis of the effects of related fingerprints on molecular similarity using an eigenvalue entropy approach

• Downloaded 1,167 times
• Download rankings, all-time:
  • Site-wide: 26,012
  • In bioinformatics: 2,930
• Year to date:
  • Site-wide: 30,340
• Since beginning of last month:
  • Site-wide: 36,217

Atypical B cells are a normal component of immune responses to vaccination and infection in humans

• Downloaded 1,075 times
• Download rankings, all-time:
  • Site-wide: 29,525
  • In immunology: 1,040
• Year to date:
  • Site-wide: 39,421
• Since beginning of last month:
  • Site-wide: 49,132

Integrative Clinical and Molecular Characterization of Translocation Renal Cell Carcinoma

• Downloaded 1,029 times
• Download rankings, all-time:
  • Site-wide: 31,361
  • In cancer biology: 772
• Year to date:
  • Site-wide: 39,790
• Since beginning of last month:
  • Site-wide: 114,692

PureseqTM: efficient and accurate prediction of transmembrane topology from amino acid sequence only

• Downloaded 986 times
• Download rankings, all-time:
  • Site-wide: 33,465
  • In bioinformatics: 3,546
• Year to date:
  • Site-wide: 67,200
• Since beginning of last month:
  • Site-wide: 119,277

NERO: A Biomedical Named-entity (Recognition) Ontology with a Large, Annotated Corpus Reveals Meaningful Associations Through Text Embedding

• Downloaded 953 times
• Download rankings, all-time:
  • Site-wide: 35,215
  • In systems biology: 663
• Year to date:
  • Site-wide: 58,892
• Since beginning of last month:
  • Site-wide: 148,158

PointSite: a point cloud segmentation tool for identication of protein ligand binding atoms

• Downloaded 920 times
• Download rankings, all-time:
  • Site-wide: 37,076
  • In bioinformatics: 3,853
• Year to date:
  • Site-wide: 54,960
• Since beginning of last month:
  • Site-wide: 66,722

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing

• Downloaded 910 times
• Download rankings, all-time:
  • Site-wide: 37,687
  • In bioinformatics: 3,893
• Year to date:
  • Site-wide: 108,953
• Since beginning of last month:
  • Site-wide: 93,387

Reduced graphene oxide membrane as supporting film for high-resolution cryo-EM

• Downloaded 715 times
• Download rankings, all-time:
  • Site-wide: 53,324
  • In biophysics: 1,715
• Year to date:
  • Site-wide: 79,198
• Since beginning of last month:
  • Site-wide: 111,868

SupportNet: a novel incremental learning framework through deep learning and support data

• Downloaded 655 times
• Download rankings, all-time:
  • Site-wide: 60,237
  • In bioinformatics: 5,567
• Year to date:
  • Site-wide: 184,282
• Since beginning of last month:
  • Site-wide: 183,516

Integrative Molecular Characterization of Sarcomatoid and Rhabdoid Renal Cell Carcinoma Reveals Determinants of Poor Prognosis and Response to Immune Checkpoint Inhibitors

• Downloaded 652 times
• Download rankings, all-time:
  • Site-wide: 60,560
  • In cancer biology: 1,659
• Year to date:
  • Site-wide: 152,665
• Since beginning of last month:
  • Site-wide: 117,060

Computational Model for Simulating Drug-Induced Arrhythmia Sensitivity of Human iPSC-derived Cardiomyocytes

• Downloaded 583 times
• Download rankings, all-time:
  • Site-wide: 69,842
  • In physiology: 396
• Year to date:
  • Site-wide: 175,176
• Since beginning of last month:
  • Site-wide: 132,913

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data

• Downloaded 545 times
• Download rankings, all-time:
  • Site-wide: 75,838
  • In bioinformatics: 6,783
• Year to date:
  • Site-wide: 143,672
• Since beginning of last month:
  • Site-wide: 168,773

Avid binding by B cells to the Plasmodium circumsporozoite protein repeat suppresses responses to protective subdominant epitopes

• Downloaded 531 times
• Download rankings, all-time:
  • Site-wide: 78,196
  • In immunology: 2,358
• Year to date:
  • Site-wide: 93,662
• Since beginning of last month:
  • Site-wide: 117,534

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

• Downloaded 498 times
• Download rankings, all-time:
  • Site-wide: 84,355
  • In bioinformatics: 7,403
• Year to date:
  • Site-wide: 142,422
• Since beginning of last month:
  • Site-wide: 103,395

Modeling the IL-2-Teff-Treg system in Systemic Lupus Erythematosus patients: possible mechanism and treatment strategies

• Downloaded 482 times
• Download rankings, all-time:
  • Site-wide: 87,456
  • In systems biology: 1,961
• Year to date:
  • Site-wide: 48,780
• Since beginning of last month:
  • Site-wide: 22,030

Serum metabolite profiles are associated with the presence of advanced liver fibrosis in Chinese patients with chronic hepatitis B viral infection

• Downloaded 458 times
• Download rankings, all-time:
  • Site-wide: 92,423
  • In gastroenterology: 96
• Year to date:
  • Site-wide: 165,836
• Since beginning of last month:
  • Site-wide: 171,862

HiC-LDNet: A general and robust deep learning framework for accurate chromatin loop detection in genome-wide contact maps

• Downloaded 425 times
• Download rankings, all-time:
  • Site-wide: 99,784
  • In bioinformatics: 11,179
• Year to date:
  • Site-wide: 4,626
• Since beginning of last month:
  • Site-wide: 7,802

Automatic identification of small molecules that promote cell conversion and reprogramming

• Downloaded 419 times
• Download rankings, all-time:
  • Site-wide: 101,338
  • In bioinformatics: 8,427
• Year to date:
  • Site-wide: 145,440
• Since beginning of last month:
  • Site-wide: 108,799

Identifying Novel Targets by using Drug-binding Site Signature: A Case Study of Kinase Inhibitors

• Downloaded 412 times
• Download rankings, all-time:
  • Site-wide: 103,011
  • In bioinformatics: 8,498
• Year to date:
  • Site-wide: 161,249
• Since beginning of last month:
  • Site-wide: 173,155

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning

• Downloaded 407 times
• Download rankings, all-time:
  • Site-wide: 104,190
  • In bioinformatics: 8,758
• Year to date:
  • Site-wide: 101,347
• Since beginning of last month:
  • Site-wide: 157,692

An RNA-seq quantification method for analysis of transcriptional aberrations

• Downloaded 362 times
• Download rankings, all-time:
  • Site-wide: 115,613
  • In bioinformatics: 9,292
• Year to date:
  • Site-wide: 160,696
• Since beginning of last month:
  • Site-wide: 138,696

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

• Downloaded 356 times
• Download rankings, all-time:
  • Site-wide: 117,112
  • In bioinformatics: 9,436
• Year to date:
  • Site-wide: 134,094
• Since beginning of last month:
  • Site-wide: 127,650

Self-normalizing learning on biomedical ontologies using a deep Siamese neural network

• Downloaded 314 times
• Download rankings, all-time:
  • Site-wide: 128,821
  • In bioinformatics: 9,970
• Year to date:
  • Site-wide: 153,176
• Since beginning of last month:
  • Site-wide: 172,254

Stable maintenance of a hidden switch as a way to increase the gene expression stability

• Downloaded 307 times
• Download rankings, all-time:
  • Site-wide: 130,695
  • In evolutionary biology: 6,079
• Year to date:
  • Site-wide: 130,815
• Since beginning of last month:
  • Site-wide: 154,619

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

• Downloaded 260 times
• Download rankings, all-time:
  • Site-wide: 144,728
  • In systems biology: 2,880
• Year to date:
  • Site-wide: 161,795
• Since beginning of last month:
  • Site-wide: 184,917

Group Similarity Constraint Functional Brain Network Estimation for Mild Congititive Impairment Classification

• Downloaded 223 times
• Download rankings, all-time:
  • Site-wide: 155,192
  • In bioinformatics: 11,527
• Year to date:
  • Site-wide: 170,019
• Since beginning of last month:
  • Site-wide: 132,447

DeeReCT-TSS: A novel meta-learning-based method annotates TSS in multiple cell types based on DNA sequences and RNA-seq data

• Downloaded 202 times
• Download rankings, all-time:
  • Site-wide: 160,842
  • In bioinformatics: 12,137
• Year to date:
  • Site-wide: 72,122
• Since beginning of last month:
  • Site-wide: 68,914