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List of works by Gane Ka-Shu Wong

10KP: A phylodiverse genome sequencing plan.

scientific article

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

scientific article

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering.

scientific article published in July 2019

A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China

scientific article published on June 2007

A cross-species alignment tool (CAT)

scientific article

A draft sequence for the genome of the domesticated silkworm (Bombyx mori).

scientific article

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

scientific article

A genome triplication associated with early diversification of the core eudicots

scientific article (publication date: 26 January 2012)

A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

scientific article published on 16 December 2008

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

scientific article

A population threshold for functional polymorphisms

scientific article

A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity

scientific article

Algal ancestor of land plants was preadapted for symbiosis

scientific article

All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins

scientific article

An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages

scientific article published on 02 March 2020

Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data

scholarly article by Vitor Hugo Maia et al published July 2014 in International Journal of Plant Sciences

Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

scientific article published on 13 March 2020

Apparition of the NAC Transcription Factors Predates the Emergence of Land Plants

article

Assembly of high-resolution restriction maps based on multiple complete digests of a redundant set of overlapping clones

scientific article published in May 1996

Author Correction: The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

scientific article published on 16 July 2020

BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

scientific article

Branched evolution and genomic intratumor heterogeneity in the pathogenesis of cutaneous T-cell lymphoma

scientific article published on 01 June 2020

Cerebrospinal Fluid in a Small Cohort of Patients with Multiple Sclerosis Was Generally Free of Microbial DNA.

scientific article published on January 2016

Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes

scientific article published on 7 July 2016

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

scientific article

ChickVD: a sequence variation database for the chicken genome

scientific article

Clonotypic heterogeneity in cutaneous T-cell lymphoma (mycosis fungoides) revealed by comprehensive whole-exome sequencing

scientific article published on 01 April 2019

Comparing the whole-genome-shotgun and map-based sequences of the rice genome

article by Jun Yu et al published August 2006 in Trends in Plant Science

Compositional gradients in Gramineae genes

scientific article

Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids

scientific article

Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage.

scientific article

Cyclotide discovery in Gentianales revisited--identification and characterization of cyclic cystine-knot peptides and their phylogenetic distribution in Rubiaceae plants

scientific article published on September 2013

Data access for the 1,000 Plants (1KP) project

scientific article

De novo assembly of a haplotype-resolved human genome.

scientific article

Disorder and the Superfluid Transition in LiquidHe4

scientific article published in Physical Review Letters

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

scientific article

Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass

scientific article published on 19 February 2019

Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology

scientific article

Editorial: Betaretrovirus in biliary epithelia of patients with autoimmune and cryptogenic liver disease - authors' reply

scientific article

Effect of Oral Capsule- vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection: A Randomized Clinical Trial

scientific article published in November 2017

Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells

scientific article published on June 2015

Enhanced Detection of Cancer Biomarkers in Blood-Borne Extracellular Vesicles Using Nanodroplets and Focused Ultrasound

scientific article published on 28 October 2016

Erratum: Corrigendum: Independent optical excitation of distinct neural populations

scholarly article published in Nature Methods

Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes

scientific article

Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants

scientific article

Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land

article

Evolution of fruit development genes in flowering plants

scientific article

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues ⬇️

scientific article published on 29 June 2017

Evolution. Response to Comment on "A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity".

scientific article published on February 2015

Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program

scientific article published on 04 April 2017

Evolutionary transients in the rice transcriptome

scientific article published on December 2010

Extending the Time Domain of Neuronal Silencing with Cryptophyte Anion Channelrhodopsins

scientific article published on 01 May 2018

Fecal Microbial Transplant After Ileocolic Resection Reduces Ileitis but Restores Colitis in IL-10-/- Mice

scholarly article by Troy Perry et al published July 2015 in Inflammatory Bowel Diseases

Fern genomes elucidate land plant evolution and cyanobacterial symbioses

article

Frequent proviral integration of the human betaretrovirus in biliary epithelium of patients with autoimmune and idiopathic liver disease

scientific article

Functional and topological diversity of LOV domain photoreceptors

scientific article published on 29 February 2016

Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae

scientific article published on 19 July 2019

Gamma-Retrovirus Integration Marks Cell Type-Specific Cancer Genes: A Novel Profiling Tool in Cancer Genomics

scientific article

Gene conversion in the rice genome.

scientific article

Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance. ⬇️

scientific article

Genetic variation at the tumour virus B locus in commercial and laboratory chicken populations assessed by a medium-throughput or a high-throughput assay.

scientific article

Genome biology: the second modern synthesis

scientific article

Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds.

scientific article

Genomes of early-diverging streptophyte algae shed light on plant terrestrialization

scientific article published on 16 December 2019

Gα and regulator of G-protein signaling (RGS) protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants.

scientific article published on 16 September 2016

High rate of chimeric gene origination by retroposition in plant genomes

scientific article published on 7 July 2006

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

scientific article (publication date: 6 May 2014)

Host immunoglobulin G selectively identifies pathobionts in pediatric inflammatory bowel diseases

scientific article published on 03 January 2019

Human Fetal Astrocytes Infected with Zika Virus Exhibit Delayed Apoptosis and Resistance to Interferon: Implications for Persistence

article

Identification and characterization of insect-specific proteins by genome data analysis

scientific article (publication date: 4 April 2007)

Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis.

scientific article published on 20 February 2018

Identification of hepatotropic viruses from plasma using deep sequencing: a next generation diagnostic tool

scientific article

Impact of sequencing depth and technology on de novo RNA-Seq assembly

scientific article published on 23 July 2019

Independent optical excitation of distinct neural populations

scientific article

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

scientific article

Intellectual property. Publication rights in the era of open data release policies

scientific article

Is "junk" DNA mostly intron DNA?

scientific article

Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify.

scientific article published on 30 October 2017

KaKs_Calculator: calculating Ka and Ks through model selection and model averaging

scientific article

Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients.

scientific article published on 29 April 2008

Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales

scientific article

Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria

scientific article

Metagenomics and the case of the deadly hamster

scientific article published in August 2008

Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants

scientific article published on 10 October 2016

Minimal introns are not "junk".

scientific article published on August 2002

Modeling the Colchicum autumnale Tubulin and a Comparison of Its Interaction with Colchicine to Human Tubulin

scientific article

Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin.

scientific article published on 26 July 2012

Most of the human genome is transcribed.

scientific article

Mucosal Barrier Depletion and Loss of Bacterial Diversity are Primary Abnormalities in Paediatric Ulcerative Colitis

scientific article published on 9 December 2015

Multiple polyploidy events in the early radiation of nodulating and nonnodulating legumes

scientific article

Multiple-complete-digest restriction fragment mapping: generating sequence-ready maps for large-scale DNA sequencing

scientific article published on May 1997

Natural selection and repeated patterns of molecular evolution following allopatric divergence

scientific article published on 02 August 2019

Neutral evolution of ‘non-coding’ complementary DNAs

scientific article published in Nature

Next-generation sequencing and bioinformatic approaches to detect and analyze influenza virus in ferrets

scientific article published on 15 April 2014

Novel mutations involving βI-, βIIA-, or βIVB-tubulin isotypes with functional resemblance to βIII-tubulin in breast cancer.

scientific article published on 9 December 2016

Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae

scientific article

Occurrence, structure, and evolution of nitric oxide synthase-like proteins in the plant kingdom

scientific article published on March 2016

Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution

scientific article published on 08 December 2019

Origin and evolution of new exons in rodents

scientific article

Origin and evolution of the nuclear auxin response system.

scientific article published on 27 March 2018

Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor

scientific article published on 27 September 2014

Paralogous radiations of PIN proteins with multiple origins of noncanonical PIN structure

scientific article

Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics.

scientific article

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

scientific article published in Science

Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants

scientific article

Phylotranscriptomic analysis of the origin and early diversification of land plants

scientific article

Phytochrome diversity in green plants and the origin of canonical plant phytochromes

scientific article published on 28 July 2015

Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing

scientific article

Plastid phylogenomic analysis of green plants: A billion years of evolutionary history

article

RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications

scientific article published on 18 June 2015

ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

scientific article

RePS: a sequence assembler that masks exact repeats identified from the shotgun data

scientific article

Recurrent loss of sex is associated with accumulation of deleterious mutations in Oenothera

scientific article published on 21 December 2014

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

scientific article

Sampling SNPs

article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants

scientific article published on 18 December 2019

Shared origins of a key enzyme during the evolution of C4 and CAM metabolism

scientific article

SilkDB: a knowledgebase for silkworm biology and genomics

scientific article

Skin colonization by circulating neoplastic clones in cutaneous T-cell lymphoma

scientific article published on 01 October 2019

Superfluid critical behavior in the presence of a dilute correlated impurity

scientific article published on 01 August 1993

Superfluid critical behavior infilled4porous media

scientific article published in Physical Review Letters

Terpene Biosynthesis in Red Algae Is Catalyzed by Microbial Type But Not Typical Plant Terpene Synthases

article

The DNA sequence, annotation and analysis of human chromosome 3

scientific article (publication date: 27 April 2006)

The Evolution of HD2 Proteins in Green Plants.

scientific article

The Expanding Family of Natural Anion Channelrhodopsins Reveals Large Variations in Kinetics, Conductance, and Spectral Sensitivity

scientific article published on 3 March 2017

The Genomes of Oryza sativa: a history of duplications

scientific article

The Origin and Evolution of the Plant Cell Surface: Algal Integrin-Associated Proteins and a New Family of Integrin-Like Cytoskeleton-ECM Linker Proteins

scientific article

The P. patens chromosome-scale assembly reveals moss genome structure and evolution. ⬇️

scientific article

The complete genomic sequence of 424,015 bp at the centromeric end of the HLA class I region: gene content and polymorphism

scientific article

The diploid genome sequence of an Asian individual

scientific article

The evolutionary history of ferns inferred from 25 low-copy nuclear genes

scientific article

The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants

scientific article published on 22 June 2020

The genome of flax ( Linum usitatissimum ) assembled de novo from short shotgun sequence reads

scientific article

The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family

scientific article

The origin and evolution of phototropins

scientific article published on 12 August 2015

The sequence and de novo assembly of the giant panda genome

scientific article

Transcriptome-mining for single-copy nuclear markers in ferns

scientific article

TreeFam: a curated database of phylogenetic trees of animal gene families

scientific article

Vertebrate gene predictions and the problem of large genes

scientific article

Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) - Insights from transcriptome sequences

scientific article

Wild soybean roots depend on specific transcription factors and oxidation reduction related genesin response to alkaline stress

scientific article

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