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List of works by Wen-Hsiung Li

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

scientific article

A general tendency for conservation of protein length across eukaryotic kingdoms

scientific article

A highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5

scientific article

A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection

scientific article published on 29 March 2007

A new measure of the robustness of biochemical networks

scientific article published on 24 February 2005

A note on the arrival probability, first arrival time and age of a mutant gene in a finite population

scientific article published on May 1, 1976

A novel puf-A gene predicted from evolutionary analysis is involved in the development of eyes and primordial germ-cells

scientific article

A simple method using PyrosequencingTM to identify de novo SNPs in pooled DNA samples

scientific article

A simulation study on Nei and Li's model for estimating DNA divergence from restriction enzyme maps ⬇️

scientific article published on January 1, 1981

A study of the phylogeny of Brassica rapa, B. nigra, Raphanus sativus, and their related genera using noncoding regions of chloroplast DNA.

scientific article

A systematic approach to detecting transcription factors in response to environmental stresses

scientific article

A thermo- and toxin-tolerant kefir yeast for biorefinery and biofuel production

article

Accumulation of mutations in sexual and asexual populations

scientific article published on 01 April 1987

Adverse interactions between micro-RNAs and target genes from different species

scientific article

Allelic Variation in the Squirrel Monkey X-Linked Color Vision Gene: Biogeographical and Behavioral Correlates

article

Alternatively and constitutively spliced exons are subject to different evolutionary forces

scientific article

Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination

scientific article

Antroquinonol from ethanolic extract of mycelium of Antrodia cinnamomea protects hepatic cells from ethanol-induced oxidative stress through Nrf-2 activation. ⬇️

scientific article

Are GC-rich isochores vanishing in mammals?

scientific article published on 5 August 2006

Assembler for de novo assembly of large genomes

scientific article published on 21 August 2013

Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production

scientific article

Assembling the Setaria italica L. Beauv. genome into nine chromosomes and insights into regions affecting growth and drought tolerance

scientific article

Characterizing regulatory and functional differentiation between maize mesophyll and bundle sheath cells by transcriptomic analysis

scientific article

Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum

scientific article published in July 2002

Classification of protein functional surfaces using structural characteristics

scientific article

Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes

scholarly article

Comparative Genomics and Evolutionary Genetics of Yeast Carbon Metabolism

article

Comparative analysis of the receptor-like kinase family in Arabidopsis and rice

scientific article published on 22 April 2004

Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data

scientific article

Computational Reconstruction of Transcriptional Regulatory Modules of the Yeast Cell Cycle

Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle

scientific article

Construction of linear invariants in phylogenetic inference ⬇️

scientific article published on May 1, 1992

Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast

scientific article

Coordinated histone modifications are associated with gene expression variation within and between species

scientific article

CpG island density and its correlations with genomic features in mammalian genomes

scientific article published on 13 May 2008

DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes

scientific article published in January 2012

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

scientific article published in April 2004

Detection of gene duplications and block duplications in eukaryotic genomes

scientific article

Development of cellulosic ethanol production process via co-culturing of artificial cellulosomal Bacillus and kefir yeast

Developmental constraint on gene duplicability in fruit flies and nematodes

scientific article published in October 2004

Different age distribution patterns of human, nematode, and Arabidopsis duplicate genes

scientific article published in November 2004

Discovering gapped binding sites of yeast transcription factors

scholarly article

Distribution of nucleotide differences between two randomly chosen cistrons in a subdivided population: The finite island model

article

Divergence in the spatial pattern of gene expression between human duplicate genes

scientific article

Down-Regulation of Cytokinin Oxidase 2 Expression Increases Tiller Number and Improves Rice Yield

scientific article published on 7 December 2015

Drift variances of heterozygosity and genetic distance in transient states

scientific article published on 01 June 1975

Duplicate genes increase gene expression diversity within and between species

scientific article published on 2 May 2004

Dynamic association rules for gene expression data analysis

scientific article

Dynamic modeling of cis-regulatory circuits and gene expression prediction via cross-gene identification

scientific article

ETOPE: Evolutionary test of predicted exons

scientific article

Effect of changes in population size on the correlation between mutation rate and heterozygosity ⬇️

scientific article published on April 12, 1979

Effects of GC content and mutational pressure on the lengths of exons and coding sequences

scientific article

Electrophoretic identity of proteins in a finite population and genetic distance between taxa

scientific article published on 01 October 1976

Erratum: correction: Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum

scientific article published in Nature

Establishment of the metabolite profile for an Antrodia cinnamomea health food product and investigation of its chemoprevention activity

scientific article published on 30 August 2013

Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution ⬇️

scientific article published on May 26, 1998

Evidence from opsin genes rejects nocturnality in ancestral primates

scientific article published on 28 September 2005

Evolution of 5' untranslated region length and gene expression reprogramming in yeasts

scientific article

Evolution of protein inhibitors of serine proteinases: Positive Darwinian selection or compositional effects?

article

Evolution of the hominoid semenogelin genes, the major proteins of ejaculated semen

scientific article (publication date: September 2003)

Evolution of the yeast protein interaction network

scientific article published on 13 October 2003

Evolutionary approach to predicting the binding site residues of a protein from its primary sequence

scientific article

Evolutionary conservation of histone modifications in mammals

scientific article

Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts

scientific article

Expression divergence between duplicate genes

scientific article

Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors

scientific article

External factors accelerate expression divergence between duplicate genes

scientific article

Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution

scientific article published on 11 November 2015

Fast evolution of core promoters in primate genomes

scientific article

Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes

scientific article

Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses

scientific article (publication date: 17 August 2011)

Functional compensation by duplicated genes in mouse

scientific article published on 25 September 2009

Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana

scientific article published on 24 August 2010

Functional evolution of cardiac microRNAs in heart development and functions

scientific article published on 24 July 2014

GS-Aligner: a novel tool for aligning genomic sequences using bit-level operations

scientific article published on 30 May 2003

Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus

scientific article

Gene Expression Evolves Faster in Narrowly Than in Broadly Expressed Mammalian Genes

article

Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes

scientific article

Gene essentiality, gene duplicability and protein connectivity in human and mouse

scientific article published on 21 May 2007

Gene family size conservation is a good indicator of evolutionary rates

scientific article

Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes

scientific article (publication date: February 2008)

Genetically distinct coelacanth population off the northern Tanzanian coast

scientific article (publication date: November 2011)

Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks

scientific article published on 01 May 2022

Genome-wide patterns of genetic variation in two domestic chickens

scientific article

Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development

scientific article

Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms

scientific article

Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. coli

scientific article published in December 2004

Higher rates of amino acid substitution in rodents than in humans

scientific article (publication date: September 1992)

Historical profiling of maize duplicate genes sheds light on the evolution of C4 photosynthesis in grasses

scientific article published on 27 August 2012

How strong is the mutagenicity of recombination in mammals?

scientific article published on 20 October 2004

Human SNPs reveal no evidence of frequent positive selection

scientific article

Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development

scientific article

Human adaptive evolution at Myostatin (GDF8), a regulator of muscle growth

scientific article published on 10 October 2006

Human polymorphism at microRNAs and microRNA target sites

scholarly article

Human-specific insertions and deletions inferred from mammalian genome sequences

scientific article

Identification of protein functional surfaces by the concept of a split pocket

scientific article published in September 2009

Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts

scientific article published on January 2013

Identifying gene regulatory modules of heat shock response in yeast

scientific article

Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data

scientific article

Improved variance estimators for one- and two-parameter models of nucleotide substitution

scientific article published on 10 May 2008

Increasing MicroRNA target prediction confidence by the relative R(2) method

scientific article published on 20 May 2009

Insights into the regulation of C4 leaf development from comparative transcriptomic analysis

scientific article published on 29 January 2016

Integrating RNA-seq and ChIP-seq data to characterize long non-coding RNAs in Drosophila melanogaster

scientific article

Integrating an algal β-carotene hydroxylase gene into a designed carotenoid-biosynthesis pathway increases carotenoid production in yeast

scientific article published on 3 December 2014

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

scientific article

Large numbers of vertebrates began rapid population decline in the late 19th century

scientific article

Lowly expressed human microRNA genes evolve rapidly

scientific article published on 19 March 2009

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast

scientific article published on 30 May 2007

Maize and millet transcription factors annotated using comparative genomic and transcriptomic data

scientific article

Mammalian housekeeping genes evolve more slowly than tissue-specific genes

scientific article published on 31 October 2003

Mathematical properties of some measures of evolutionary distance

scientific article published on 8 December 2006

Metabolite profiles for Antrodia cinnamomea fruiting bodies harvested at different culture ages and from different wood substrates

scientific article

Method for identifying transcription factor binding sites in yeast

scientific article published on 27 April 2006

MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues

scientific article

MicroRNA regulation of human protein protein interaction network

scientific article published on 24 July 2007

MicroRNA-like small RNAs prediction in the development of Antrodia cinnamomea

scientific article

Mixed culture fermentation from lignocellulosic materials using thermophilic lignocellulose-degrading anaerobes

article

Molecular Evolution of Recombination Hotspots and Highly Recombining Pseudoautosomal Regions in Hominoids

scientific article published on 09 February 2005

Molecular Systematics of Pikas (Genus Ochotona) Inferred from Mitochondrial DNA Sequences

scholarly article by Ning Yu et al published July 2000 in Molecular Phylogenetics and Evolution

Molecular evolution meets the genomics revolution

scientific article

Molecular evolution of bat color vision genes.

scientific article

Molecular evolution of ubiquitin genes ⬇️

scientific article published on November 1, 1987

Multidimensional scaling for large genomic data sets

scientific article

Natural selection on cis and trans regulation in yeasts

scientific article

Necessary and sufficient conditions for the existence of certain quadratic invariants under a phylogenetic tree ⬇️

scientific article published on July 1, 1991

Necessary and sufficient conditions for the existence of linear invariants in phylogenetic inference

scientific article published on March 1, 1992

News and views: the chimpanzee and us.

scientific article published in September 2005

Non-random association between electromorphs and inversion chromosomes in finite populations

scientific article published on 01 February 1980

Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications

Nucleotide diversity in gorillas

scientific article

Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations

scientific article

Omics Applications to Biofuel Research

Organismal complexity, protein complexity, and gene duplicability

scientific article (publication date: 23 December 2003)

Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes

scientific article published on 12 February 2004

Overlapping genes in the human and mouse genomes

scientific article

PGASO: A synthetic biology tool for engineering a cellulolytic yeast

scientific article

PSC: protein surface classification

scientific article

Parallel evolution between aromatase and androgen receptor in the animal kingdom

scientific article

Patterns of Gene Deletion following Genome Duplication in Yeast

article

Patterns of Gene Duplication in Saccharomyces cerevisiae and Caenorhabditis elegans

article

Patterns of expansion and expression divergence in the plant polygalacturonase gene family

scientific article published on January 2006

Patterns of internal gene duplication in the course of metazoan evolution

scientific article published on 15 March 2007

Patterns of nucleotide substitution in pseudogenes and functional genes

article

Phosphorylated and nonphosphorylated serine and threonine residues evolve at different rates in mammals

scientific article

Positional distribution of transcription factor binding sites in Arabidopsis thaliana

scientific article

Prediction of human miRNAs using tissue-selective motifs in 3' UTRs

scientific article

Prediction of splice sites with dependency graphs and their expanded bayesian networks

scientific article published on 16 September 2004

Primary structure of Beijing duck apolipoprotein A-1

scientific article published on 01 October 1993

Probability of identical monomorphism in related species

article

Proportion of solvent-exposed amino acids in a protein and rate of protein evolution.

scientific article

Protein Function, Connectivity, and Duplicability in Yeast

scientific article published on 24 August 2005

Protein complexity, gene duplicability and gene dispensability in the yeast genome

scientific article published on 14 September 2006

Protein under-wrapping causes dosage sensitivity and decreases gene duplicability

scientific article

RNA landscape of evolution for optimal exon and intron discrimination

scholarly article

Radical amino acid change versus positive selection in the evolution of viral envelope proteins

scientific article published on 24 August 2006

Rate of protein evolution versus fitness effect of gene deletion

scientific article published on 2 April 2003

Rates of synonymous substitution in plant nuclear genes

article by Kenneth H. Wolfe et al published September 1989 in Journal of Molecular Evolution

Recombination has little effect on the rate of sequence divergence in pseudoautosomal boundary 1 among humans and great apes

scientific article

Regulatory Differences in Natal Down Development between Altricial Zebra Finch and Precocial Chicken.

scientific article

Regulatory Divergence among Beta-Keratin Genes during Bird Evolution

scientific article

Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion

scientific article published on 9 March 2006

Role of duplicate genes in genetic robustness against null mutations

scientific article (publication date: 2 January 2003)

Role of positive selection in the retention of duplicate genes in mammalian genomes

scholarly article

Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast

scientific article published on 23 June 2008

Roles of trans and cis variation in yeast intraspecies evolution of gene expression

scientific article published on 31 July 2009

Sequence, structure, receptor-binding domains and internal repeats of human apolipoprotein B-100

scientific article published in Nature

Signalling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer

scientific article published on 26 August 2011

Signatures of domain shuffling in the human genome

scientific article published on November 2002

Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution

scholarly article

SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns

scientific article published on 30 April 2009

Statistical Tests of DNA Phylogenies

scholarly article by Wen-Hsiung Li & Andrey Zharkikh published March 1995 in Systematic Biology

Statistical methods for identifying yeast cell cycle transcription factors

scientific article

Statistical models for studying DNA sequence evolution

Strong male-driven evolution of DNA sequences in humans and apes

scientific article (publication date: 11 April 2002)

Sulfate activation enzymes: phylogeny and association with pyrophosphatase

scientific article

Systematic identification of yeast cell cycle transcription factors using multiple data sources

scientific article

Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiae identifies mutants with improved heterologous exocellulase activity and host secretion

scientific article (publication date: 3 September 2013)

The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study

scientific article

The biochemical phylogeny of guinea-pigs and gundis, and the paraphyly of the order Rodentia ⬇️

scientific article published on April 1, 1992

The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis

scientific article

The evolution of aerobic fermentation in Schizosaccharomyces pombe was associated with regulatory reprogramming but not nucleosome reorganization

scientific article

The genetic basis of evolutionary change in gene expression levels

scientific article

The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses

scientific article

The influence of adjacent nucleotides on the pattern of nucleotide substitution in mitochondrial introns of angiosperms

scientific article published in July 2002

The molecular clock ticks regularly in muroid rodents and hamsters

scientific article published on November 1, 1992

The nonsynonymous/synonymous substitution rate ratio versus the radical/conservative replacement rate ratio in the evolution of mammalian genes

scientific article published on 25 July 2007

The prognostic significance of RUNX2 and miR-10a/10b and their inter-relationship in breast cancer

scientific article

The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate

scientific article

The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation

scientific article

The transient distribution of allele frequencies under mutation pressure

scientific article published on 01 December 1976

Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives

scientific article

Total number of individuals affected by deleterious mutant genes in a finite population ⬇️

scientific article published on January 1, 1975

Transcription factor families have much higher expansion rates in plants than in animals

scientific article published in September 2005

Transcriptional profiling of adult Drosophila antennae by high-throughput sequencing

scientific article published in 2013

Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors

scientific article published on 27 April 2015

Transcriptomes of mouse olfactory epithelium reveal sexual differences in odorant detection

scientific article

Transcriptomic analyses of regenerating adult feathers in chicken

scientific article

Uncovering MicroRNA Regulatory Hubs that Modulate Plasma Cell Differentiation

scientific article published on 11 December 2015

Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing

scientific article

Unexpected Conservation of the X-Linked Color Vision Gene in Nocturnal Prosimians: Evidence from Two Bush Babies ⬇️

scientific article published on December 1, 1997

Variance of genetic distance and correlation of heterozygosity between populations under the pressure of stepwise mutation

Whole genome transcriptome polymorphisms in Arabidopsis thaliana

scientific article

fPOP: footprinting functional pockets of proteins by comparative spatial patterns

scientific article

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