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Shin Han Shiu
Michigan State University
91Publications
43H-index
7,413Citations
Publications 91
Newest
Published on Mar 13, 2019in BMC Evolutionary Biology 3.04
Nicholas Panchy7
Estimated H-index: 7
(UT: University of Tennessee),
Christina B. Azodi2
Estimated H-index: 2
(MSU: Michigan State University)
+ 2 AuthorsShin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
Background Transcription factors (TFs) play a key role in regulating plant development and response to environmental stimuli. While most genes revert to single copy after whole genome duplication (WGD) event, transcription factors are retained at a significantly higher rate. Little is known about how TF duplicates have diverged in their expression and regulation, the answer to which may contribute to a better understanding of the elevated retention rate among TFs.
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Published on Apr 20, 2019in bioRxiv
Christina B. Azodi2
Estimated H-index: 2
(MSU: Michigan State University),
Andrew McCarren3
Estimated H-index: 3
(DCU: Dublin City University)
+ 2 AuthorsShin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
The usefulness of Genomic Prediction (GP) in crop and livestock breeding programs has led to efforts to develop new and improved GP approaches including non-linear algorithm, such as artificial neural networks (ANN) (i.e. deep learning) and gradient tree boosting. However, the performance of these algorithms has not been compared in a systematic manner using a wide range of GP datasets and models. Using data of 18 traits across six plant species with different marker densities and training popul...
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Published on Apr 9, 2019in bioRxiv
Birte Schwarz (HHU: University of Düsseldorf), Christina B. Azodi2
Estimated H-index: 2
(MSU: Michigan State University)
+ 1 AuthorsPetra Bauer28
Estimated H-index: 28
(HHU: University of Düsseldorf)
Abstract Iron (Fe) is a key cofactor in many cellular redox processes, including respiration and photosynthesis. Plant Fe deficiency (-Fe) activates a complex regulatory network which coordinates root Fe uptake and distribution to sink tissues, while avoiding over-accumulation of Fe and other metals to toxic levels. In Arabidopsis ( Arabidopsis thaliana ), FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR), a bHLH transcription factor (TF), is required for up-regulation of root Fe acquisi...
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Published on Mar 24, 2019in bioRxiv
Christina B. Azodi2
Estimated H-index: 2
(MSU: Michigan State University),
Jeremy Pardo3
Estimated H-index: 3
(MSU: Michigan State University)
+ 2 AuthorsShin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
The ability to predict traits from genome-wide sequence information (Genomic Prediction, GP), has improved our understanding of the genetic basis of complex traits and transformed breeding practices. Transcriptome data may also be useful for GP. However, it remains unclear how well transcript levels can predict traits, particularly when traits are scored at different development stages. Using maize genetic markers and transcript levels from seedlings to predict mature plant traits, we found tran...
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Yao-Ming Chang5
Estimated H-index: 5
(AS: Academia Sinica),
Hsin-Hung Lin9
Estimated H-index: 9
(AS: Academia Sinica)
+ 12 AuthorsJinn-Jy Lin5
Estimated H-index: 5
(AS: Academia Sinica)
Time-series transcriptomes of a biological process obtained under different conditions are useful for identifying the regulators of the process and their regulatory networks. However, such data are 3D (gene expression, time, and condition), and there is currently no method that can deal with their full complexity. Here, we developed a method that avoids time-point alignment and normalization between conditions. We applied it to analyze time-series transcriptomes of developing maize leaves under ...
1 Citations Source Cite
Published on Nov 15, 2018in bioRxiv
John P. Lloyd3
Estimated H-index: 3
(UM: University of Michigan),
Megan J. Bowman2
Estimated H-index: 2
(MSU: Michigan State University)
+ 4 AuthorsShin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
Extensive transcriptional activity occurring in unannotated, intergenic regions of genomes has raised the question whether intergenic transcription represents the activity of novel genes or noisy expression. To address this, we evaluated cross-species and post-duplication sequence and expression conservation of intergenic transcribed regions (ITRs) in four Poaceae species. Most ITR sequences are species-specific. Those found across species tend to be more divergent in expression and have more re...
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Published on Nov 8, 2018in bioRxiv
Sahra Uygun5
Estimated H-index: 5
(MSU: Michigan State University),
Christina B. Azodi2
Estimated H-index: 2
(MSU: Michigan State University),
Shin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
Multicellular organisms have diverse cell types with distinct roles in development and responses to the environment. At the transcriptional level, the differences in environmental response between cell types are due to differences in regulatory programs. In plants, although cell-type environmental responses have been examined, details on how these responses are regulated remain spotty. Here, we identify a set of putative cis-regulatory elements (pCREs) enriched in the promoters of genes responsi...
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Published on Oct 1, 2018in Genome Biology and Evolution 3.73
Peipei Wang2
Estimated H-index: 2
(MSU: Michigan State University),
Bethany M. Moore1
Estimated H-index: 1
(MSU: Michigan State University)
+ 3 AuthorsShin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
2 Citations Source Cite
Published on Aug 7, 2018in bioRxiv
Nicholas Panchy7
Estimated H-index: 7
(UT: University of Tennessee),
John P. Lloyd3
Estimated H-index: 3
(UM: University of Michigan),
Shin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
The collection all TFs, target genes and their interactions in an organism form a gene regulatory network (GRN), which underly complex patterns of transcription even in unicellular species. However, identifying which interactions regulate expression in a specific temporal context remains a challenging task. With multiple experimental and computational approaches to characterize GRNs, we predicted general and phase-specific cell-cycle expression in Saccharomyces cerevisiae using four regulatory d...
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Published on Jan 1, 2018in The Plant Cell 8.63
Ming-Jung Liu3
Estimated H-index: 3
(AS: Academia Sinica),
Koichi Sugimoto3
Estimated H-index: 3
(MSU: Michigan State University)
+ 5 AuthorsShin Han Shiu43
Estimated H-index: 43
(MSU: Michigan State University)
The evolution of transcriptional regulatory mechanisms is central to how stress response and tolerance differ between species. However, it remains largely unknown how divergence in cis-regulatory sites and, subsequently, transcription factor (TF) binding specificity contribute to stress-responsive expression divergence, particularly between wild and domesticated spe-cies. By profiling wound-responsive gene transcriptomes in wild Solanum pennellii and do-mesticated S. lycopersicum, we found exten...
3 Citations Source Cite
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