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List of works by Fangqing Zhao

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

scientific article

A new pheromone trail-based genetic algorithm for comparative genome assembly

scientific article

A novel codon-based de Bruijn graph algorithm for gene construction from unassembled transcriptomes.

scientific article

Accurate quantification of circular RNAs identifies extensive circular isoform switching events

scientific article published on 03 January 2020

An Extremely Streamlined Macronuclear Genome in the Free-Living Protozoan Fabrea salina

scientific article published on 01 April 2022

Ancestry of the Australian termitivorous numbat.

scientific article published on 21 February 2013

Argonaute proteins from human gastrointestinal bacteria catalyze DNA-guided cleavage of single- and double-stranded DNA at 37 °C

scientific article published on 30 July 2019

Bioinformatics Commons: The Cornerstone of Life and Health Sciences

article

CIRI: an efficient and unbiased algorithm for de novo circular RNA identification.

scientific article

Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8<sup>+/-</sup> mouse model of ASD-like behavior

scientific article published on 03 March 2022

Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains

scientific article

Characterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer cell line by deep sequencing

scientific article

Circular RNA identification based on multiple seed matching.

scientific article published on 28 February 2017

Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus

scientific article published on 21 October 2011

Combinational biosynthesis of a fluorescent cyanobacterial holo-alpha-phycocyanin in Escherichia coli by using one expression vector.

scientific article published in July 2007

Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus.

scientific article published on 8 August 2006

Comparison of envelope-related genes in unicellular and filamentous cyanobacteria.

scientific article published on January 2007

Complete Khoisan and Bantu genomes from southern Africa

scientific article

Complete mitochondrial genome of Membranipora grandicella (Bryozoa: Cheilostomatida) determined with next-generation sequencing: The first representative of the suborder Malacostegina ⬇️

scientific article published on March 30, 2012

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

scientific article published on 31 August 2012

Comprehensive identification of internal structure and alternative splicing events in circular RNAs

scientific article published on 28 June 2016

Computational Strategies for Exploring Circular RNAs.

scientific article published on 12 January 2018

Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals

scientific article published on 15 June 2016

Detection and Reconstruction of Circular RNAs from Transcriptomic Data

scientific article published in January 2018

Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer

scientific article

Deterministic transition of enterotypes shapes the infant gut microbiome at an early age

scientific article published on 24 August 2021

Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus

article by Jinfeng Wang et al published September 2018 in Gut

Dysbiosis signature of fecal microbiota in colorectal cancer patients

scientific article

Evidence of extensive homologous recombination in the core genome of rickettsia

scientific article published on 25 May 2009

Evolutionary analysis of phycobiliproteins: implications for their structural and functional relationships

scientific article published on 7 July 2006

Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals

scientific article published on 01 March 2019

Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing

scientific article published on 10 June 2022

Extensive lysine acetylation occurs in evolutionarily conserved metabolic pathways and parasite-specific functions during Plasmodium falciparum intraerythrocytic development

scientific article published on 12 July 2013

FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.

scientific article

Genetic basis for the establishment of endosymbiosis in Paramecium

scientific article published on 15 January 2019

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

scientific article

Genome-wide identification and divergent transcriptional expression of StAR-related lipid transfer (START) genes in teleosts.

scientific article published on 13 February 2013

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria

scientific article

Gut microbiota dysbiosis contributes to the development of hypertension.

scientific article published on February 2017

HTQC: a fast quality control toolkit for Illumina sequencing data

scientific article

Lineage-specific domain fusion in the evolution of purine nucleotide cyclases in cyanobacteria.

scientific article published on 13 June 2008

MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution

scientific article

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

scientific article

MetaSort untangles metagenome assembly by reducing microbial community complexity

scientific article (publication date: 23 January 2017)

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

scientific article

Metagenomic profile of the bacterial communities associated with Ixodes ricinus ticks

scientific article

Nodeomics: pathogen detection in vertebrate lymph nodes using meta-transcriptomics

scientific article

PGA4genomics for comparative genome assembly based on genetic algorithm optimization

scientific article published on 30 June 2009

Phage-bacteria interaction network in human oral microbiome.

scientific article

Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti

scientific article published on 15 June 2018

PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families

scientific article published on 12 March 2008

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

scientific article

Population genomics reveals speciation and introgression between Brown Norway rats and their sibling species.

scientific article published on 8 May 2017

Precision Medicine: What Challenges Are We Facing?

scientific article published on 12 October 2016

Prioritization and functional assessment of noncoding variants associated with complex diseases.

scientific article published on 11 July 2018

Reconstruction of full-length circular RNAs enables isoform-level quantification

scientific article published on 19 January 2019

RiboFR-Seq: a novel approach to linking 16S rRNA amplicon profiles to metagenomes

scientific article

Saccharina genomes provide novel insight into kelp biology

scientific article

Sequencing and genetic variation of multidrug resistance plasmids in Klebsiella pneumoniae

scientific article

Sequencing the nuclear genome of the extinct woolly mammoth

scientific article

Single-cell metagenomics: challenges and applications.

scientific article published on 25 April 2018

Small RNA transcriptome investigation based on next-generation sequencing technology.

scientific article published on 31 August 2011

TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization

scientific article published on 17 November 2014

The Value and Significance of Metagenomics of Marine Environments. Preface

scientific article

The combination of direct and paired link graphs can boost repetitive genome assembly

scientific article

The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes.

scientific article published on 5 March 2009

The first metagenome of activated sludge from full-scale anaerobic/anoxic/oxic (A2O) nitrogen and phosphorus removal reactor using Illumina sequencing.

scientific article published on 30 June 2015

The first mitochondrial genome from Mysida (Crustacea: Malacostraca) reveals an unusual gene arrangement

article

The hidden genomic diversity of ciliated protists revealed by single-cell genome sequencing

scientific article published on 14 December 2021

The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota

scientific article published on 01 November 2020

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

scientific article published in February 2009

The repertoire and evolution of ATP-binding cassette systems in Synechococcus and Prochlorococcus

scientific article published on 16 September 2009

Tracing the accumulation of in vivo human oral microbiota elucidates microbial community dynamics at the gateway to the GI tract

scientific article published on 20 June 2019

Translocation of vaginal microbiota is involved in impairment and protection of uterine health

scientific article published on 07 July 2021

Visualization of circular RNAs and their internal splicing events from transcriptomic data

scientific article published on 17 January 2020

Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity

scientific article published on 21 June 2016

cTFbase: a database for comparative genomics of transcription factors in cyanobacteria

scientific article

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data

scientific article published in January 2019

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

scientific article

inGAP: an integrated next-generation genome analysis pipeline

scientific article (publication date: 2010)

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