Publications

Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate growth

Published in Plant Physiology, 2020

Recommended citation: Jishan Jiang, Yanmei Xiao, Hao Chen, Wei Hu, Liping Zeng, Haiyan Ke, Franck Anicet Ditengou, Upendra Kumar Devisetty, Klaus Palme, Julin N. Maloof, Katayoon Dehesh. (2020). Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate growth. Plant Physiology, DOI: https://doi.org/10.1104/pp.20.00090. http://upendrak.github.io/files/paper22.pdf

Genotyping‐by‐sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides)

Published in Ecology and Evolution, 2020

Recommended citation: Steven H. Strauss Justin C. Bagley, Neander M. Heming, Eliécer E. Gutiérrez, Upendra K. Devisetty, Karen E. Mock, Andrew J. Eckert. (2020). Ecology and Evolution, https://doi.org/10.1002/ece3.6214. http://upendrak.github.io/files/paper21.pdf

Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data

Published in Frontiers in Genetics, 2020

Recommended citation: Peri Sateesh, Roberts Sarah, Kreko Isabella R., McHan Lauren B., Naron Alexandra, Ram Archana, Murphy Rebecca L., Lyons Eric, Gregory Brian D., Devisetty Upendra K., Nelson Andrew D. L. (2020). Read Mapping and Transcript Assembly: A Scalable and High-Throughput Workflow for the Processing and Analysis of Ribonucleic Acid Sequencing Data. Front. Genet., 24 January 2020 | https://doi.org/10.3389/fgene.2019.01361 http://upendrak.github.io/files/paper20.pdf

RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification

Published in BMC Genomics, 2019

Recommended citation: Arslan, M., Devisetty, U.K., Porsch, M. et al. RNA-Seq analysis of soft rush (Juncus effusus): transcriptome sequencing, de novo assembly, annotation, and polymorphism identification. BMC Genomics 20, 489 (2019). https://doi.org/10.1186/s12864-019-5886-8 http://upendrak.github.io/files/paper19.pdf

Network analysis reveals a role for salicylic acid pathway components in shade avoidance

Published in Plant Physiology, 2018

Recommended citation: Kazunari Nozue, Upendra Kumar Devisetty, Saradadevi Lekkala, Patricia Mueller-Moulé, Aurélie Bak, Clare L. Casteel, Julin N. Maloof. (2018). Network analysis reveals a role for salicylic acid pathway components in shade avoidance. Plant Physiology Dec 2018, 178 (4) 1720-1732; DOI: 10.1104/pp.18.00920 http://upendrak.github.io/files/paper17.pdf

The role of a class III gibberellin 2‐oxidase in tomato internode elongation

Published in The Plant Journal, 2018

Recommended citation: Amanda Schrager‐Lavelle, Natalie N. Gath, Upendra K. Devisetty, Esther Carrera, Isabel López‐Díaz, Miguel A. Blázquez, Julin N. Maloof (2018). The role of a class III gibberellin 2‐oxidase in tomato internode elongation. The Plant Journal, https://doi.org/10.1111/tpj.14145. http://upendrak.github.io/files/paper18.pdf

Improved RNA‐seq Workflows Using CyVerse Cyberinfrastructure

Published in CURRENT PROTOCOLS, 2018

Recommended citation: Chougule, K. M., Wang, L., Stein, J. C., Wang, X., Devisetty, U. K., Klein, R. R., & Ware, D. (2018). Improved RNA‐seq workflows using cyverse cyberinfrastructure. Current Protocols in Bioinformatics, 63, e53. doi: 10.1002/cpbi.53. http://upendrak.github.io/files/paper16.pdf

Bioconda: sustainable and comprehensive software distribution for the life sciences

Published in Nature Methods, 2018

Recommended citation: Johannes Köster Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Upendra Kumar Devisetty. “Bioconda: sustainable and comprehensive software distribution for the life sciences.” (2018). http://upendrak.github.io/files/paper15.pdf

MAKER as a Service: Moving HPC applications to Jetstream Cloud

Published in IEEE International Conference on Cloud Engineering, 2018

Recommended citation: Hazekamp, Nicholas L., Upendra K Devisetty, Nirav Merchant and Douglas Thain. “MAKER as a Service: Moving HPC applications to Jetstream Cloud.” (2018). http://upendrak.github.io/files/paper14.pdf

Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common Brassica rapa mapping population

Published in G3, 2017

Recommended citation: RJ Cody Markelz, Michael F Covington, Marcus T Brock, Upendra K Devisetty, Daniel J Kliebenstein, Cynthia Weinig, Julin N Maloof (2017). "Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common Brassica rapa mapping population" G3. 1(13). http://upendrak.github.io/files/paper13.pdf

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

Published in JOVE, 2017

Recommended citation: Blake Joyce, Asher K Haug-Baltzell, Jonathan P Hulvey, Fiona McCarthy, Upendra Kumar Devisetty, Eric Lyons (2017). "Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms" JOVE. 1(12). http://upendrak.github.io/files/paper12.pdf

The divergence of flowering time modulated by FT/TFL1 is independent to their interaction and binding activities

Published in Frontiers in Plant science, 2017

Recommended citation: Wang, Z, R. Yang, U. Devisetty, J. Maloof, Y. Zuo, J. Li, Y. Shen, J. Zhao, M. Bao and G. Ning (2016). "The divergence of flowering time modulated by FT/TFL1 is independent to their interaction and binding activities" Frontiers in Plant science. 1(11). http://upendrak.github.io/files/paper11.pdf

Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis

Published in Frontiers in Genetics, 2017

* These authors contributed equally to this manuscript

Recommended citation: Andrew D. Nelson*, Upendra K. Devisetty*, Kyle Palos, Asher K. Haug-Baltzell, Eric Lyons, Mark A. Beilstein (2017). "Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis" Frontiers in Genetics. 1(10). http://upendrak.github.io/files/paper10.pdf

Bringing your tools to CyVerse Discovery Environment using Docker

Published in F1000, 2016

Recommended citation: Upendra Kumar Devisetty, Kathleen Kennedy, Paul Sarando, Nirav Merchant, Eric Lyons (2016). "Bringing your tools to CyVerse Discovery Environment using Docker" F1000. 1(8). http://upendrak.github.io/files/paper8.pdf

A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants

Published in G3, 2016

Recommended citation: Andrew D. L. Nelson, Evan S. Forsythe, Upendra K. Devisetty, David S. Clausen, Asher K. Haug-Batzell, Ari M. R. Meldrum,* Michael R. Frank, Eric Lyons, and Mark A. Beilstein (2016). "A Genomic Analysis of Factors Driving lincRNA Diversification: Lessons from Plants" G3. 1(9). http://upendrak.github.io/files/paper9.pdf

Genetic architecture, biochemical underpinnings, and ecological impact of floral UV patterning

Published in Molecular Ecology, 2016

Recommended citation: Marcus T. Brock, Lauren K. Lucas, Nicholas A. Anderson, Matthew J . Rubin, R. J. Cody Markelez, Michael F. Covington, Upendra K. Devisetty, Clint Chappel,‡ Julin N. Maloof and Cynthia Weing (2015). "Genetic architecture, biochemical underpinnings, and ecological impact of floral UV patterning" Molecular Ecology. 1(7). http://upendrak.github.io/files/paper7.pdf

Modeling leaf development enables quantitative trait mapping mapping of novel loci and reveals independent genetic modules for leaf size and shape in Brassica rapa

Published in New Phytology, 2015

Recommended citation: Robert L. Baker, Wen Fung Leong, Marcus T. Brock, Robert C. Markelz, Mike Covington, Upendra K. Devisetty, Julin Maloof, Stephen Welch, and Cynthia Weinig (2015). "Modeling leaf development enables quantitative trait mapping mapping of novel loci and reveals independent genetic modules for leaf size and shape in Brassica rapa" New Phytology. 1(6). http://upendrak.github.io/files/paper6.pdf

Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling

Published in PLOS GENETICS, 2015

Recommended citation: Kazunari Nozue, An Tat, Upendra Kumar Devisetty, Matt Robinson, Maxwell Mumbach, Yasunori Ichihashi, Saradadevi Lekkala, and Julin N. Maloof (2015). "Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling" PLOS GENETICS. 1(5). http://upendrak.github.io/files/paper5.pdf

Polymorphism identification and improved genome annotation of Brassica rapa through deep RNA sequencing

Published in G3, 2014

Recommended citation: Upendra Kumar Devisetty, Mike Covington, An V. Tat and Julin N. Maloof (2014). "Using deep RNA-Seq for polymorphism detection and improving genome annotation of Brassica rapa " G3. 1(4). http://upendrak.github.io/files/paper4.pdf

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

Published in PNAS, 2013

Recommended citation: Daniel Koenig, José M. Jiménez-Gómez, Seisuke Kimura, Daniel Fulop, Daniel H. Chitwood, Lauren R. Headland, Ravi Kumar, Michael F. Covington, Upendra Kumar Devisetty, An V. Tat, Takayuki Tohge, Anthony Bolger, Korbinian Schneeberger, Stephan Ossowski, Christa Lanz, Guangyan Xiongi, Mallorie Taylor-Teeples, Siobhan M. Bradya,j, Markus Pauly, Detlef Weigel, Björn Usadel, Alisdair R. Fernie, Jie Peng, Neelima R. Sinha, and Julin N. Maloof (2015). "Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato" PNAS. 1(3). http://upendrak.github.io/files/paper3.pdf

Accurate timekeeping is controlled by a cycling activator in Arabidopsis

Published in eLIFE, 2013

Recommended citation: Polly Yingshan Hsu, Upendra K Devisetty, Stacey L Harmer (2013). "Accurate timekeeping is controlled by a cycling activator in Arabidopsis" eLIFE. 1(2). http://upendrak.github.io/files/paper2.pdf

The RAD51 and DMC1 homoeologous genes of bread wheat: cloning, molecular characterization and expression analysis

Published in BMC Research Notes, 2010

Recommended citation: Upendra Kumar Devisetty, Katie Mayes and Sean Mayes (2010). "The RAD51 and DMC1 homoeologous genes of bread wheat: cloning, molecular characterization and expression analysis" BMC Research Notes. 1(1). http://upendrak.github.io/files/paper1.pdf