Shin-Han Shiu

发表

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

T. Boller, S. Shiu, G. Felix, 2007, Plant Molecular Biology.

Optimizing the use of gene expression data to predict plant metabolic pathway memberships

Melissa D. Lehti-Shiu, Cornelius S. Barry, S. Shiu, 2020, bioRxiv.

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

Cheng Peng, Shin-Han Shiu, Sahra Uygun, 2016, PLoS Comput. Biol..

Expansion of the Receptor-Like Kinase/Pelle Gene Family and Receptor-Like Proteins in Arabidopsis1[w]

S. Shiu, A. Bleecker, Shin-han Shiu, 2003, Plant Physiology.

Evolution of Gene Duplication in Plants1[OPEN]

Shin-Han Shiu, Nicholas Panchy, Melissa D. Lehti-Shiu, 2016, Plant Physiology.

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

David E. Hufnagel, Alisandra K. Denton, S. Shiu, 2015, BMC Genomics.

The causes and molecular consequences of polyploidy in flowering plants

S. Shiu, G. Moghe, Shin-han Shiu, 2014, Annals of the New York Academy of Sciences.

Diversity, classification and function of the plant protein kinase superfamily

Shin-Han Shiu, Melissa D. Lehti-Shiu, S. Shiu, 2012, Philosophical Transactions of the Royal Society B: Biological Sciences.

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

J. Bennetzen, A. Salamov, S. Sugano, 2008, Science.

Plant Receptor-Like Kinase Gene Family: Diversity, Function, and Signaling

S. Shiu, A. Bleecker, Shin-han Shiu, 2001, Science's STKE.

Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases

S. Shiu, A. Bleecker, Shin-han Shiu, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Cis-Regulatory Code for Predicting Plant Cell-Type Transcriptional Response to High Salinity1[OPEN]

Christina B. Azodi, S. Shiu, S. Uygun, 2019, Plant Physiology.

Predicting cell-cycle expressed genes identifies canonical and non-canonical regulators of time-specific expression in Saccharomyces cerevisiae

S. Shiu, J. P. Lloyd, Nicholas Panchy, 2018, bioRxiv.

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

M. Thomashow, Kelian Sun, S. Shiu, 2011, Proceedings of the National Academy of Sciences.

High throughput measurement of Arabidopsis thaliana fitness traits using deep learning

Melissa D. Lehti-Shiu, S. Shiu, P. Krysan, 2021, bioRxiv.

The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

Christina B. Azodi, S. Shiu, J. P. Lloyd, 2020, bioRxiv.

COST1 regulates autophagy to control plant drought tolerance

S. Shiu, Bei Li, Hongxia Zhang, 2020, Proceedings of the National Academy of Sciences.

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

S. Shiu, J. P. Lloyd, Nicholas Panchy, 2020, BMC Genomics.

Changes in Transcript Abundance in Chlamydomonas reinhardtii following Nitrogen Deprivation Predict Diversion of Metabolism1[W][OA]

Shin-Han Shiu, Astrid Vieler, Yair Shachar-Hill, 2010, Plant Physiology.

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN]

Carolyn J. Lawrence-Dill, David E. Hufnagel, M. Yandell, 2013, Plant Physiology.

Two-Component Systems and Their Co-Option for Eukaryotic Signal Transduction

Judith P. Armitage, Shin-Han Shiu, G. Eric Schaller, 2011, Current Biology.

Characterization of Genes Involved in Cytokinin Signaling and Metabolism from Rice1[W][OA]

Shin-Han Shiu, Yu-Chang Tsai, S. Shiu, 2012, Plant Physiology.

Two-Component Signaling Elements and Histidyl-Aspartyl Phosphorelays†

Shin-Han Shiu, S. Shiu, J. Kieber, 2008, The arabidopsis book.

Transcription Factor Families Have Much Higher Expansion Rates in Plants than in Animals1

Wen-Hsiung Li, S. Shiu, M. Shih, 2005, Plant Physiology.

Characteristics and Significance of Intergenic Polyadenylated RNA Transcription in Arabidopsis1[W][OA]

Melissa D. Lehti-Shiu, S. Shiu, J. Bailey-Serres, 2012, Plant Physiology.

Characteristics and Signi fi cance of Intergenic Polyadenylated RNA Transcription in Arabidopsis 1 [ W ] [ OA ]

Melissa D. Lehti-Shiu, S. Shiu, J. Bailey-Serres, 2012 .

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN]

Jikai Lei, Yanni Sun, Mark Yandell, 2014, Plant Physiology.

Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift

S. Shiu, R. Vierstra, C. Zou, 2011, PloS one.

Evolution of research topics and paradigms in plant sciences

Melissa D. Lehti-Shiu, Shin-Han Shiu, 2023, bioRxiv.

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

Melissa D. Lehti-Shiu, S. Shiu, Nicholas Panchy, 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.

Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle Genes1[W][OA]

Melissa D. Lehti-Shiu, Kousuke Hanada, S. Shiu, 2009, Plant Physiology.

Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice

Klaus F. X. Mayer, Wen-Hsiung Li, W. Karłowski, 2004, The Plant Cell Online.

Origin, Diversity, Expansion History, and Functional Evolution of the Plant Receptor-Like Kinase/ Pelle Family

Melissa D. Lehti-Shiu, S. Shiu, C. Zou, 2012 .

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

J. Bennetzen, A. Salamov, Y. van de Peer, 2008, Science.

Predictive Models of Spatial Transcriptional Response to High Salinity1[OPEN]

Christina B. Azodi, Alexander E. Seddon, S. Uygun, 2017, Plant Physiology.

Cis-regulatory code of spatial stress response 1 2 Corresponding

Christina B. Azodi, S. Shiu, Alexander E. Seddon, 2017 .

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

E. M. Farré, S. Shiu, Guangxi Wu, 2015, The Plant journal : for cell and molecular biology.

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli1[W][OA]

Melissa D. Lehti-Shiu, K. Shinozaki, Kousuke Hanada, 2008, Plant Physiology.

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

Colleen J. Doherty, M. Thomashow, S. Shiu, 2011, Journal of experimental botany.

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

Xun Gu, C Robin Buell, Shin-Han Shiu, 2010, BMC Evolutionary Biology.

Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana

Melissa D. Lehti-Shiu, M. Thomashow, S. Shiu, 2009, PLoS genetics.

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

Melissa D. Lehti-Shiu, S. Shiu, Nicholas Panchy, 2018, bioRxiv.

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

Wen-Hsiung Li, S. Shiu, S. Patterson, 2006, Genome Biology.

Temporal regulation of cold transcriptional response in switchgrass

S. Shiu, Peipei Wang, T. Ranaweera, 2022, bioRxiv.

Evolutionary analysis of the LORELEI gene family in angiosperms reveals regulatory subfunctionalization

C. Zipfel, Thomas A. DeFalco, M. Beilstein, 2020, bioRxiv.

Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice1[C][W][OA]

Melissa D. Lehti-Shiu, F. Thibaud-Nissen, S. Shiu, 2009, Plant Physiology.

Modeling temporal and hormonal regulation of plant transcriptional response to wounding

Christina B. Azodi, E. Grotewold, S. Shiu, 2021, The Plant cell.

Modeling gene regulation in response to wounding: temporal variations, hormonal variations, and specialized metabolism pathways induced by wounding

E. Grotewold, S. Shiu, Y. Lee, 2020, bioRxiv.

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

S. Shiu, R. Davidson, Haining Lin, 2012, The Plant journal : for cell and molecular biology.

on Gene Duplication Evolution of Gene Duplication in Plants 1 [ OPEN ]

Melissa D. Lehti-Shiu, S. Shiu, Nicholas Panchy, 2016 .

Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling

Amogh P. Jalihal, S. Shiu, Allen H Hubbard, 2021, Frontiers in Plant Science.

A G-Box-Like Motif Is Necessary for Transcriptional Regulation by Circadian Pseudo-Response Regulators in Arabidopsis1[OPEN]

E. M. Farré, S. Shiu, Ming-Jung Liu, 2015, Plant Physiology.

Genome Analysis Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase / Pelle Genes 1 [ W ] [ OA ]

Melissa D. Lehti-Shiu, Kousuke Hanada, S. Shiu, 2009 .

Evolutionary History and Stress Regulation of Plant Receptor-Like Kinase/Pelle Genes

Melissa D. Lehti-Shiu, Kousuke Hanada, S. Shiu, 2009 .

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

Wen-Hsiung Li, S. Shiu, Shin-han Shiu, 2004, Molecular biology and evolution.

Selection-Enriched Genomic Loci (SEGL) Reveals Genetic Loci for Environmental Adaptation and Photosynthetic Productivity in Chlamydomonas reinhardtii

J. Weissman, S. Shiu, P. Neofotis, 2021, bioRxiv.

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

J. Borevitz, S. Shiu, Shin-han Shiu, 2008, Heredity.

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

Christina B. Azodi, S. Shiu, K. Childs, 2019, Scientific Reports.

Evolutionary characteristics of intergenic transcribed regions indicate widespread noisy transcription in the Poaceae

Christina B. Azodi, S. Shiu, K. Childs, 2018, bioRxiv.

Opening the Black Box: Interpretable Machine Learning for Geneticists.

Christina B. Azodi, Jiliang Tang, S. Shiu, 2020, Trends in genetics : TIG.

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

S. Shiu, R. Vierstra, J. Gagne, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice[W]

Kousuke Hanada, S. Shiu, R. Vierstra, 2007, The Plant Cell Online.

Defining the functional significance of intergenic transcribed regions

S. Shiu, Z. Tsai, J. P. Lloyd, 2017, bioRxiv.

Defining functional intergenic transcribed regions based on heterogeneous features of phenotype genes and pseudogenes

S. Shiu, Z. Tsai, J. P. Lloyd, 2017 .

Co-expression signatures of combinatorial gene regulation

E. Grotewold, Arjun Krishnan, S. Shiu, 2020, bioRxiv.

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

Hsin-Hung Lin, S. Shiu, Shu-Hsing Wu, 2019, Proceedings of the National Academy of Sciences.

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

David E. Hufnagel, Haibao Tang, C. Town, 2014, Plant Cell.

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

Rebecca L. Roston, Sanjaya, K. Niyogi, 2017, PLoS genetics.

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

Rebecca L. Roston, Sanjaya, K. Niyogi, 2012, PLoS genetics.

Robust predictions of specialized metabolism genes through machine learning

Shin-Han Shiu, Peipei Wang, John P. Lloyd, 2018, Proceedings of the National Academy of Sciences.

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

S. Opiyo, Runmao Lin, S. Shiu, 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 35.

Shin-Han Shiu, S. Shiu, D. Bevan, 2007, Phytochemistry.

Transcriptome-Based Prediction of Complex Traits in Maize[OPEN]

Christina B. Azodi, G. de los Campos, S. Shiu, 2019, Plant Cell.

Putative cis-Regulatory Elements Predict Iron Deficiency Responses in Arabidopsis Roots1[OPEN]

Christina B. Azodi, S. Shiu, P. Bauer, 2019, Plant Physiology.

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

Matthew D. Schultz, Robert J. Schmitz, J. Pool, 2013, Proceedings of the National Academy of Sciences.

A Large Complement of the Predicted Arabidopsis ARM Repeat Proteins Are Members of the U-Box E3 Ubiquitin Ligase Family1[w]

S. Shiu, Y. Mudgil, D. Goring, 2004, Plant Physiology.

EVIDENCE FOR A LARGE-SCALE , LINEAGE-SPECIFIC EXPANSION OF A BRIC-A-BRAC / TRAMTRACK / BROAD COMPLEX ( BTB ) UBIQUITIN-LIGASE GENE SUBFAMILY IN MONOCOTS . Running Title : BTB Ubiquitin-Protein Ligases in Rice By

Kousuke Hanada, S. Shiu, R. Vierstra, 2007 .

Evolutionary Relationships and Functional Diversity of Plant Sulfate Transporters

S. Shiu, Hideki Takahashi, M. Hawkesford, 2011, Front. Plant Sci..

The Impact of the Branched-Chain Ketoacid Dehydrogenase Complex on Amino Acid Homeostasis in Arabidopsis1[OPEN]

R. Last, Cheng Peng, S. Uygun, 2015, Plant Physiology.

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

S. Shiu, B. Day, Huan Chen, 2020, The Plant cell.

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

Hsin-Hung Lin, Shu-Hsing Wu, A. C. Shih, 2015, Proceedings of the National Academy of Sciences.

Elevated auxin biosynthesis and transport underlie high vein density in C4 leaves

S. Shiu, Shu-Hsing Wu, Wen-Hsiung Li, 2017, Proceedings of the National Academy of Sciences.

Multifunctional arm repeat domains in plants.

S. Shiu, D. Goring, M. Samuel, 2006, International review of cytology.

Identification of Important Regions for Ethylene Binding and Signaling in the Transmembrane Domain of the ETR1 Ethylene Receptor of Arabidopsis[W][OA]

J. Esch, S. Shiu, Caren Chang, 2006, The Plant Cell Online.

Identiﬁcation of Important Regions for Ethylene Binding and Signaling in the Transmembrane Domain of the ETR1 Ethylene Receptor of Arabidopsis

S. Shiu, Caren Chang, B. Binder, 2006 .

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN]

Carolyn J. Lawrence-Dill, David E. Hufnagel, M. Yandell, 2013, Plant Physiology.

Evolution and diversification of the ACT-like domain associated with plant basic helix–loop–helix transcription factors

E. Grotewold, Y. Lee, Shin-Han Shiu, 2023, Proceedings of the National Academy of Sciences of the United States of America.

Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells

S. Shiu, Wen-Hsiung Li, M. Lu, 2022, Proceedings of the National Academy of Sciences of the United States of America.

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.

Wen-Hsiung Li, J. Borevitz, Kousuke Hanada, 2007, Genome research.

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

K. Shinozaki, Kousuke Hanada, Tetsuro Toyoda, 2010, Bioinform..

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

S. Shiu, Z. Tsai, J. P. Lloyd, 2017, Molecular biology and evolution.

Determinants of nucleosome positioning and their influence on plant gene expression

G. Howe, S. Shiu, I. Major, 2015, Genome research.

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

Huai-Kuang Tsai, Zing Tsung-Yeh Tsai, Shin-Han Shiu, 2015, PLoS Comput. Biol..

The SEEL motif and members of the MYB-related REVEILLE transcription factor family are important for the expression of LORELEI in the synergid cells of the Arabidopsis female gametophyte

Alexander E. Seddon, S. Smith, S. Uygun, 2021, Plant Reproduction.

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

Justin O. Borevitz, J. Borevitz, Xu Zhang, 2008, PLoS genetics.

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

M. Yandell, G. Howe, Michael Campbell, 2018, Plant Cell.

Regulatory divergence in wound-responsive gene expression in domesticated and wild tomato

M. Yandell, G. Howe, Michael Campbell, 2017, bioRxiv.

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

Christina B. Azodi, G. de los Campos, S. Shiu, 2019, G3: Genes, Genomes, Genetics.

Benchmarking algorithms for genomic prediction of complex traits

Mark Roantree, Gustavo de los Campos, Andrew McCarren, 2019, bioRxiv.

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

S. Shiu, R. Last, F. Brandizzi, 2020, bioRxiv.

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

Melissa D. Lehti-Shiu, Cornelius S. Barry, S. Shiu, 2020, bioRxiv.