Jun Yu

Affiliations:
  • Chinese Academy of Sciences, Beijing Institute of Genomics, China
  • Zhejiang University, James D. Watson Institute of Genome Sciences, China (former)


According to our database1, Jun Yu authored at least 68 papers between 2004 and 2023.

Collaborative distances:

Timeline

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Bibliography

2023
Draft Genome of White-blotched River Stingray Provides Novel Clues for Niche Adaptation and Skeleton Formation.
Genom. Proteom. Bioinform., June, 2023

2022
Position-Defined CpG Islands Provide Complete Co-methylation Indexing for Human Genes.
Proceedings of the Intelligent Computing Theories and Application, 2022

2021
2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

CpG-island-based annotation and analysis of human housekeeping genes.
Briefings Bioinform., 2021

Roles of host small RNAs in the evolution and host tropism of coronaviruses.
Briefings Bioinform., 2021

2020
CGIDLA: Developing the Web Server for CpG Island Related Density and LAUPs (Lineage-Associated Underrepresented Permutations) Study.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2.
Genom. Proteom. Bioinform., 2020

Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.
Genom. Proteom. Bioinform., 2020

Genome Assembly and Pathway Analysis of Edible Mushroom <i>Agrocybe cylindracea</i>.
Genom. Proteom. Bioinform., 2020

Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in <i>Saccharina japonica</i>.
Genom. Proteom. Bioinform., 2020

The Elements of Data Sharing.
Genom. Proteom. Bioinform., 2020

2019
In Memory of Vladimir B. Bajic (1952-2019).
Genom. Proteom. Bioinform., 2019

Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients.
Genom. Proteom. Bioinform., 2019

2018
REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results.
J. Comput. Biol., 2018

A <i>Scientist Guerilla Fighter</i> in the Frontiers of Bioinformatics - In Memory of Bailin Hao.
Genom. Proteom. Bioinform., 2018

Rice Genomics: over the Past Two Decades and into the Future.
Genom. Proteom. Bioinform., 2018

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
Genom. Proteom. Bioinform., 2018

Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA).
Bioinform., 2018

2017
A Step Forward in Precision Medicine on "One Belt One Road".
Genom. Proteom. Bioinform., 2017

A Piece of History that Cannot Be Missed for Precision Medicine.
Genom. Proteom. Bioinform., 2017

ISVASE: identification of sequence variant associated with splicing event using RNA-seq data.
BMC Bioinform., 2017

MTD: a mammalian transcriptomic database to explore gene expression and regulation.
Briefings Bioinform., 2017

2016
Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences?
Genom. Proteom. Bioinform., 2016

Precision Medicine: What Challenges Are We Facing?
Genom. Proteom. Bioinform., 2016

2015
Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs.
Nucleic Acids Res., 2015

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.
Nucleic Acids Res., 2015

Biological Databases for Human Research.
Genom. Proteom. Bioinform., 2015

A Brief Review of Software Tools for Pangenomics.
Genom. Proteom. Bioinform., 2015

2014
RiceWiki: a wiki-based database for community curation of rice genes.
Nucleic Acids Res., 2014

Adolescent Mouse Takes on An Active Transcriptomic Expression During Postnatal Cerebral Development.
Genom. Proteom. Bioinform., 2014

Ribogenomics: the Science and Knowledge of RNA.
Genom. Proteom. Bioinform., 2014

A Comprehensive Transcriptomic Analysis of Infant and Adult Mouse Ovary.
Genom. Proteom. Bioinform., 2014

Human Pharyngeal Microbiome May Play A Protective Role in Respiratory Tract Infections.
Genom. Proteom. Bioinform., 2014

Genome sequencing of high-penicillin producing industrial strain of Penicillium chrysogenum.
BMC Genom., 2014

PanGP: A tool for quickly analyzing bacterial pan-genome profile.
Bioinform., 2014

2013
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology.
Nucleic Acids Res., 2013

Does the Genetic Code Have A Eukaryotic Origin?
Genom. Proteom. Bioinform., 2013

MeRIP-PF: An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data.
Genom. Proteom. Bioinform., 2013

2012
The Pendulum Model for Genome Compositional Dynamics: from the Four Nucleotides to the Twenty Amino Acids.
Genom. Proteom. Bioinform., 2012

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition.
Genom. Proteom. Bioinform., 2012

An RNA-seq-based Gene Expression Profiling of Radiation-induced Tumorigenic Mammary Epithelial Cells.
Genom. Proteom. Bioinform., 2012

Comparative Analyses of H3K4 and H3K27 Trimethylations Between the Mouse Cerebrum and Testis.
Genom. Proteom. Bioinform., 2012

The Association Between H3K4me3 and Antisense Transcription.
Genom. Proteom. Bioinform., 2012

The Transcript-centric Mutations in Human Genomes.
Genom. Proteom. Bioinform., 2012

Distinct Contributions of Replication and Transcription to Mutation Rate Variation of Human Genomes.
Genom. Proteom. Bioinform., 2012

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.
BMC Bioinform., 2012

PGAP: pan-genomes analysis pipeline.
Bioinform., 2012

BAsplice: Bi-direction alignment for detecting splice junctions.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

2011
On the Organizational Dynamics of the Genetic Code.
Genom. Proteom. Bioinform., 2011

BIGpre: A Quality Assessment Package for Next-Generation Sequencing Data.
Genom. Proteom. Bioinform., 2011

2010
KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies.
Genom. Proteom. Bioinform., 2010

Evolutionary Transients in the Rice Transcriptome.
Genom. Proteom. Bioinform., 2010

Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae.
Genom. Proteom. Bioinform., 2010

The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome.
Genom. Proteom. Bioinform., 2010

Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans.
Genom. Proteom. Bioinform., 2010

2009
Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees.
Genom. Proteom. Bioinform., 2009

How Do Variable Substitution Rates Influence Ka and Ks Calculations?
Genom. Proteom. Bioinform., 2009

A Brief Review on the Mechanisms of miRNA Regulation.
Genom. Proteom. Bioinform., 2009

2008
Phylogenetic Analysis of Brine Shrimp (Artemia) in China Using DNA Barcoding.
Genom. Proteom. Bioinform., 2008

2007
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.
Nucleic Acids Res., 2007

A Scenario on the Stepwise Evolution of the Genetic Code.
Genom. Proteom. Bioinform., 2007

2006
Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits.
Genom. Proteom. Bioinform., 2006

Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates.
Genom. Proteom. Bioinform., 2006

KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging.
Genom. Proteom. Bioinform., 2006

2005
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun.
PLoS Comput. Biol., 2005

SilkDB: a knowledgebase for silkworm biology and genomics.
Nucleic Acids Res., 2005

ChickVD: a sequence variation database for the chicken genome.
Nucleic Acids Res., 2005

2004
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics.
Nucleic Acids Res., 2004


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