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List of works by Shin-Han Shiu

A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis.

scientific article published on 19 November 2015

A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana

scientific article

A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches

scientific article published in December 2004

A large complement of the predicted Arabidopsis ARM repeat proteins are members of the U-box E3 ubiquitin ligase family

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 model-based approach for identifying functional intergenic transcribed regions and non-coding RNAs.

scientific article published on 15 March 2018

A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads

scientific article published on 20 April 2016

A rare case of plastid protein-coding gene duplication in the chloroplast genome of Euglena archaeoplastidiata (Euglenophyta).

scientific article

Alternative splicing of a multi-drug transporter from Pseudoperonospora cubensis generates an RXLR effector protein that elicits a rapid cell death

scientific article

Anatomical and transcriptional dynamics of maize embryonic leaves during seed germination

scientific article

Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes

scientific article published on 10 November 2014

Benchmarking Parametric and Machine Learning Models for Genomic Prediction of Complex Traits

scientific article published on 05 November 2019

Benchmarking algorithms for genomic prediction of complex traits

CLUMPED CHLOROPLASTS 1 is required for plastid separation in Arabidopsis

scientific article published on 24 October 2011

COST1 regulates autophagy to control plant drought tolerance

scientific article published on 13 March 2020

Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism

scientific article

Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis

scientific article

Characteristics of Plant Essential Genes Allow for within- and between-Species Prediction of Lethal Mutant Phenotypes

scientific article published on 18 August 2015

Characterization of genes involved in cytokinin signaling and metabolism from rice

scientific article published on March 2012

Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity

scientific article published on 24 September 2019

Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana

scientific article

Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana

scientific article

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

scientific article published on 22 April 2004

Comparative transcriptomics method to infer gene coexpression networks and its applications to maize and rice leaf transcriptomes

article

Comparative transcriptomics of three Poaceae species reveals patterns of gene expression evolution

article

Consequences of Whole-Genome Triplication as Revealed by Comparative Genomic Analyses of the Wild Radish Raphanus raphanistrum and Three Other Brassicaceae Species

scientific article

Contrasting transcriptional responses to Fusarium virguliforme colonization in symptomatic and asymptomatic hosts

scientific article published on 01 April 2021

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast

scientific article published on 20 August 2015

Correction: Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779

scientific article published on 23 May 2017

Correction: Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays

scientific article

Defining Functional Genic Regions in the Human Genome through Integration of Biochemical, Evolutionary, and Genetic Evidence

scientific article published on 6 April 2017

Determinants of nucleosome positioning and their influence on plant gene expression

scientific article published on 10 June 2015

Diversity, classification and function of the plant protein kinase superfamily ⬇️

scientific article published on September 19, 2012

Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families

scientific article published on 10 August 2016

Epigenomic programming contributes to the genomic drift evolution of the F-Box protein superfamily in Arabidopsis

scientific article published on 30 September 2013

Evolution of Gene Duplication in Plants

scientific article

Evolution of Plant Genomes

article

Evolution of stress-regulated gene expression in duplicate genes of Arabidopsis thaliana

scientific article (publication date: July 2009)

Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice

scientific article

Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae

scientific article published on 20 August 2019

Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes

scientific article published on 25 March 2009

Evolutionary relationships and functional diversity of plant sulfate transporters

scientific article published on January 2011

Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis

scientific article published in June 2003

Expression and regulatory asymmetry of retained Arabidopsis thaliana transcription factor genes derived from whole genome duplication

article

Factors Influencing Gene Family Size Variation Among Related Species in a Plant Family, Solanaceae

scientific article published on 01 October 2018

Factors influencing gene family size variation among related species in a plant family

Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 35.

scientific article published on 26 April 2007

Gene expression shifts during perithecium development in Gibberella zeae (anamorph Fusarium graminearum), with particular emphasis on ion transport proteins

scientific article published on 8 May 2007

Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779

scientific article

Genomic transition to pathogenicity in chytrid fungi

scientific article

Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays

scientific article

High‐throughput measurement of plant fitness traits with an object detection method using Faster R‐CNN

scientific article published in 2022

Identification of important regions for ethylene binding and signaling in the transmembrane domain of the ETR1 ethylene receptor of Arabidopsis

scientific article published in 2006

Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli

scientific article published on 20 August 2008

Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

scientific article published on 13 February 2020

Large-scale, lineage-specific expansion of a bric-a-brac/tramtrack/broad complex ubiquitin-ligase gene family in rice

scientific article published on 24 August 2007

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations

scientific article published on 4 December 2013

Maize ANT1 modulates vascular development, chloroplast development, photosynthesis, and plant growth

scientific article published on 19 August 2020

Modeling temporal and hormonal regulation of plant transcriptional response to wounding

scientific article published on 01 February 2022

Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana

scientific article published on 23 June 2015

Molecular identification and characterization of the tomato flagellin receptor LeFLS2, an orthologue of Arabidopsis FLS2 exhibiting characteristically different perception specificities.

scientific article published on 25 May 2007

Multifunctional arm repeat domains in plants

scientific article published on January 2006

Nomenclature for two-component signaling elements of rice

scientific article published in February 2007

Opening the Black Box: Interpretable Machine Learning for Geneticists

scientific article published on 17 April 2020

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

scientific article published on 12 February 2004

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

scientific article published on January 2006

Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift

scientific article

Predictive Models of Genetic Redundancy in Arabidopsis thaliana

scientific article published on 01 July 2021

Predictive Models of Spatial Transcriptional Response to High Salinity.

scientific article published on 3 April 2017

Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii

scientific article

Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots

scientific article published on 14 January 2020

Recovery from N Deprivation Is a Transcriptionally and Functionally Distinct State in Chlamydomonas

scientific article

Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato

scientific article published on 09 May 2018

Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains.

scientific article

Robust predictions of specialized metabolism genes through machine learning

article published in the Proceedings of the National Academy of Sciences of the United States of America

Robust predictions of specialized metabolism genes through machine learning

article

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

scholarly article

The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis

scientific article

The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis.

scientific article published on 18 May 2015

The causes and molecular consequences of polyploidy in flowering plants

scientific article

The functional role of pack-MULEs in rice inferred from purifying selection and expression profile

scientific article published in 2009

The next generation of microarray research: applications in evolutionary and ecological genomics.

scientific article published on 8 November 2006

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

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

scientific article published in September 2005

Transcriptional coordination of physiological responses in Nannochloropsis oceanica CCMP1779 under light/dark cycles

scientific article published on 27 July 2015

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

scientific article published on 27 April 2015

Transcriptome-Based Prediction of Complex Traits in Maize

scientific article published on 22 October 2019

Transcriptome-based prediction of complex traits in maize

Two-component signaling elements and histidyl-aspartyl phosphorelays

scientific article published on 14 July 2008

Two-component systems and their co-option for eukaryotic signal transduction

scientific article

Utility and Limitations of Using Gene Expression Data to Identify Functional Associations

scientific article

Within- and cross-species predictions of plant specialized metabolism genes using transfer learning

scientific article published on 30 July 2020

sORF finder: a program package to identify small open reading frames with high coding potential

scientific article published on 14 December 2009

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