Upendra Kumar Devisetty
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View article: A bioinformatic ecological risk assessment framework for externally applied dsRNA-based biopesticides
A bioinformatic ecological risk assessment framework for externally applied dsRNA-based biopesticides Open
Double-stranded RNA (dsRNA)-based biopesticides are a promising new method of pest management. These biopesticides leverage the endogenous RNA interference (RNAi) pathway to selectively regulate expression of key genes involved in growth a…
View article: In Silico Analysis of Potential Off-Target Effects of a Next-Generation dsRNA Acaricide for Varroa Mites (Varroa destructor) and Lack of Effect on a Bee-Associated Arthropod
In Silico Analysis of Potential Off-Target Effects of a Next-Generation dsRNA Acaricide for Varroa Mites (Varroa destructor) and Lack of Effect on a Bee-Associated Arthropod Open
Double-stranded RNA (dsRNA) biopesticides offer the potential for highly targeted pest control with minimal off-target impacts. Varroa mites (Varroa destructor) are an important pest of honey bees (Apis mellifera) that are primarily manage…
View article: CyVerse: Cyberinfrastructure for open science
CyVerse: Cyberinfrastructure for open science Open
CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud c…
View article: CyVerse: Cyberinfrastructure for Open Science
CyVerse: Cyberinfrastructure for Open Science Open
CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud c…
View article: Retrograde Induction of phyB Orchestrates Ethylene-Auxin Hierarchy to Regulate Growth
Retrograde Induction of phyB Orchestrates Ethylene-Auxin Hierarchy to Regulate Growth Open
Exquisitely regulated plastid-to-nucleus communication by retrograde signaling pathways is essential for fine-tuning of responses to the prevailing environmental conditions. The plastidial retrograde signaling metabolite methylerythritol c…
View article: Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (<i>Populus tremuloides</i>)
Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (<i>Populus tremuloides</i>) Open
Populus tremuloides is the widest‐ranging tree species in North America and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome‐wide SNPs (34,796…
View article: Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate growth
Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate growth Open
Exquisitely regulated plastid-to-nucleus communication by retrograde signaling pathways is essential for fine-tuning of responses to the prevailing environmental conditions. The plastidial retrograde signaling metabolite methylerythritol c…
View article: Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data
Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data Open
Next-generation RNA-sequencing is an incredibly powerful means of generating a snapshot of the transcriptomic state within a cell, tissue, or whole organism. As the questions addressed by RNA-sequencing (RNA-seq) become both more complex a…
View article: RIL_v1.5_mapping_UN.csv.gz
RIL_v1.5_mapping_UN.csv.gz Open
Gene expression values for Brassica rapa
View article: RIL_v1.5_mapping_UN.csv.gz
RIL_v1.5_mapping_UN.csv.gz Open
Gene expression values for Brassica rapa
View article: The role of a class <scp>III</scp> gibberellin 2‐oxidase in tomato internode elongation
The role of a class <span>III</span> gibberellin 2‐oxidase in tomato internode elongation Open
Summary A network of environmental inputs and internal signaling controls plant growth, development and organ elongation. In particular, the growth‐promoting hormone gibberellin ( GA ) has been shown to play a significant role in organ elo…
View article: Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance
Network Analysis Reveals a Role for Salicylic Acid Pathway Components in Shade Avoidance Open
Plants have sophisticated mechanisms for sensing neighbor shade. To maximize their ability to compete for light, plants respond to shade through enhanced elongation and physiological changes. The shade avoidance response affects many diffe…
View article: Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen ( <i>Populus tremuloides</i> )
Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen ( <i>Populus tremuloides</i> ) Open
Populus tremuloides is the widest-ranging tree species in North America, and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,79…
View article: Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (<i>Populus tremuloides</i>)
Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (<i>Populus tremuloides</i>) Open
Populus tremuloides is the widest-ranging tree species in North America, and an ecologically important component of mesic forest ecosystems displaced by the Pleistocene glaciations. Using phylogeographic analyses of genome-wide SNPs (34,79…
View article: Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common <i>Brassica rapa</i> Mapping Population
Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common <i>Brassica rapa</i> Mapping Population Open
Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived f…
View article: Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs
Evolinc: A Tool for the Identification and Evolutionary Comparison of Long Intergenic Non-coding RNAs Open
Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, cover…
View article: Leveraging CyVerse Resources for <em>De Novo</em> Comparative Transcriptomics of Underserved (Non-model) Organisms
Leveraging CyVerse Resources for <em>De Novo</em> Comparative Transcriptomics of Underserved (Non-model) Organisms Open
This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative transcriptomics. It also serves as a primer for biologists to develop data scientist computation…
View article: The Divergence of Flowering Time Modulated by FT/TFL1 Is Independent to Their Interaction and Binding Activities
The Divergence of Flowering Time Modulated by FT/TFL1 Is Independent to Their Interaction and Binding Activities Open
FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) proteins share highly conserved amino acid residues but they play opposite regulatory roles in promoting and repressing the flowering response, respectively. Previous substitution models a…
View article: Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis
Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis Open
Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, cover…
View article: Bringing your tools to CyVerse Discovery Environment using Docker
Bringing your tools to CyVerse Discovery Environment using Docker Open
Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and d…
View article: Bringing your tools to CyVerse Discovery Environment using Docker
Bringing your tools to CyVerse Discovery Environment using Docker Open
Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and d…
View article: Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common<i>Brassica rapa</i>mapping population
Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common<i>Brassica rapa</i>mapping population Open
Brassica rapa is a model species for agronomic, ecological, evolutionary and translational studies. Here we describe high-density SNP discovery and genetic map construction for a Brassica rapa recombinant inbred line (RIL) population deriv…
View article: A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants
A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants Open
Transcriptomic analyses from across eukaryotes indicate that most of the genome is transcribed at some point in the developmental trajectory of an organism. One class of these transcripts is termed long intergenic noncoding RNAs (lincRNAs)…
View article: Bringing your tools to CyVerse Discovery Environment using Docker
Bringing your tools to CyVerse Discovery Environment using Docker Open
Docker has become a very popular container-based virtualization platform for software distribution that has revolutionized the way in which scientific software and software dependencies (software stacks) can be packaged, distributed, and d…